Viewport Size Code:
Login | Create New Account
picture

  MENU

About | Classical Genetics | Timelines | What's New | What's Hot

About | Classical Genetics | Timelines | What's New | What's Hot

icon

Bibliography Options Menu

icon
QUERY RUN:
HITS:
PAGE OPTIONS:
Hide Abstracts   |   Hide Additional Links
NOTE:
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Ecological Informatics

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.

More About:  ESP | OUR CONTENT | THIS WEBSITE | WHAT'S NEW | WHAT'S HOT

ESP: PubMed Auto Bibliography 25 Oct 2021 at 01:42 Created: 

Ecological Informatics

Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are National Science Foundation Datanet projects, DataONE and Data Conservancy.

Created with PubMed® Query: "ecology OR ecological" and ("data management" or informatics) NOT "assays for monitoring autophagy" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

-->

RevDate: 2021-10-22
CmpDate: 2021-10-22

Jansson S, Malmqvist E, Mlacha Y, et al (2021)

Real-time dispersal of malaria vectors in rural Africa monitored with lidar.

PloS one, 16(3):e0247803.

Lack of tools for detailed, real-time observation of mosquito behavior with high spatio-temporal resolution limits progress towards improved malaria vector control. We deployed a high-resolution entomological lidar to monitor a half-kilometer static transect positioned over rice fields outside a Tanzanian village. A quarter of a million in situ insect observations were classified, and several insect taxa were identified based on their modulation signatures. We observed distinct range distributions of male and female mosquitoes in relation to the village periphery, and spatio-temporal behavioral features, such as swarming. Furthermore, we observed that the spatial distributions of males and females change independently of each other during the day, and were able to estimate the daily dispersal of mosquitoes towards and away from the village. The findings of this study demonstrate how lidar-based monitoring could dramatically improve our understanding of malaria vector ecology and control options.

RevDate: 2021-10-20
CmpDate: 2021-10-20

Wang X, Zhang C, Wang C, et al (2021)

GIS-based for prediction and prevention of environmental geological disaster susceptibility: From a perspective of sustainable development.

Ecotoxicology and environmental safety, 226:112881.

Geological disasters seriously threaten the safety of human life, property, ecological resources, and the environment. Effective control of geological disasters is the focus of achieving sustainable social development. The Helong City (Jilin Province, China) was selected as the case study. Combined with GIS technology, a new integrated prediction model of geological disaster susceptibility was developed to improve the accuracy of geological disaster assessment, reduce the cost of geological disaster treatment, and ensure the sustainable development of ecological environment. The research results showed that elevation and normalized difference vegetation index (NDVI) were the key factors affecting susceptibility. Compared with the conventional model, the accuracy of the developing integrated model FR-DT and FR-RF was improved by more than 6%, and the disaster points were more concentrated in the high susceptibility zone. Statistical results of disaster treatment cost estimation and gross domestic product (GDP) value showed that the integrated model can save about 10% of treatment cost, and the ratio of total GDP/disaster governance cost was higher. The performance of the integrated model FR-DT and FR-RF had obvious advantages over the conventional model in terms of prediction accuracy, prevention pertinence, and prevention cost. These research results promote the advancement of geological disaster prevention and control technology, ensure the safety of the geological environment, and are of great significance to the sustainable development of the regional economy.

RevDate: 2021-10-18
CmpDate: 2021-10-18

Freschet GT, Pagès L, Iversen CM, et al (2021)

A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements.

The New phytologist, 232(3):973-1122.

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

RevDate: 2021-10-14
CmpDate: 2021-10-14

Upham NS, Poelen JH, Paul D, et al (2021)

Liberating host-virus knowledge from biological dark data.

The Lancet. Planetary health, 5(10):e746-e750.

Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host-pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems.

RevDate: 2021-10-04
CmpDate: 2021-10-04

Escamilla Molgora JM, Sedda L, PM Atkinson (2020)

Biospytial: spatial graph-based computing for ecological Big Data.

GigaScience, 9(5):.

BACKGROUND: The exponential accumulation of environmental and ecological data together with the adoption of open data initiatives bring opportunities and challenges for integrating and synthesising relevant knowledge that need to be addressed, given the ongoing environmental crises.

FINDINGS: Here we present Biospytial, a modular open source knowledge engine designed to import, organise, analyse and visualise big spatial ecological datasets using the power of graph theory. The engine uses a hybrid graph-relational approach to store and access information. A graph data structure uses linkage relationships to build semantic structures represented as complex data structures stored in a graph database, while tabular and geospatial data are stored in an efficient spatial relational database system. We provide an application using information on species occurrences, their taxonomic classification and climatic datasets. We built a knowledge graph of the Tree of Life embedded in an environmental and geographical grid to perform an analysis on threatened species co-occurring with jaguars (Panthera onca).

CONCLUSIONS: The Biospytial approach reduces the complexity of joining datasets using multiple tabular relations, while its scalable design eases the problem of merging datasets from different sources. Its modular design makes it possible to distribute several instances simultaneously, allowing fast and efficient handling of big ecological datasets. The provided example demonstrates the engine's capabilities in performing basic graph manipulation, analysis and visualizations of taxonomic groups co-occurring in space. The example shows potential avenues for performing novel ecological analyses, biodiversity syntheses and species distribution models aided by a network of taxonomic and spatial relationships.

RevDate: 2021-10-02

Westfall AK, Telemeco RS, Grizante MB, et al (2021)

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.

GigaScience, 10(10):.

BACKGROUND: High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources.

FINDINGS: We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length.

CONCLUSIONS: These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

RevDate: 2021-10-01
CmpDate: 2021-10-01

Miller KE, Polaszek A, DM Evans (2021)

A dearth of data: fitting parasitoids into ecological networks.

Trends in parasitology, 37(10):863-874.

Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.

RevDate: 2021-09-30
CmpDate: 2021-09-30

Sabatini FM, Bluhm H, Kun Z, et al (2021)

European primary forest database v2.0.

Scientific data, 8(1):220.

Primary forests, defined here as forests where the signs of human impacts, if any, are strongly blurred due to decades without forest management, are scarce in Europe and continue to disappear. Despite these losses, we know little about where these forests occur. Here, we present a comprehensive geodatabase and map of Europe's known primary forests. Our geodatabase harmonizes 48 different, mostly field-based datasets of primary forests, and contains 18,411 individual patches (41.1 Mha) spread across 33 countries. When available, we provide information on each patch (name, location, naturalness, extent and dominant tree species) and the surrounding landscape (biogeographical regions, protection status, potential natural vegetation, current forest extent). Using Landsat satellite-image time series (1985-2018) we checked each patch for possible disturbance events since primary forests were identified, resulting in 94% of patches free of significant disturbances in the last 30 years. Although knowledge gaps remain, ours is the most comprehensive dataset on primary forests in Europe, and will be useful for ecological studies, and conservation planning to safeguard these unique forests.

RevDate: 2021-09-30
CmpDate: 2021-09-30

Freedman R, Brown JA, Caldow C, et al (2021)

Species-specific thermal classification schemes can improve climate related marine resource decisions.

PloS one, 16(4):e0250792.

Global climate change increasingly contributes to large changes in ecosystem structure. Timely management of rapidly changing marine ecosystems must be matched with methods to rapidly quantify and assess climate driven impacts to ecological communities. Here we create a species-specific, classification system for fish thermal affinities, using three quantifiable datasets and expert opinion. Multiple sources of information limit potential data bias and avoid misclassification. Using a temperate kelp forest fish community in California, USA as a test case for this new methodology, we found the majority of species had high classification agreement across all four data sources (n = 78) but also a number of low agreement species (2 sources disagree from the others, n = 47). For species with low agreement, use of just one dataset to classify species, as is commonly done, would lead to high risk of misclassification. Differences in species classification between individual datasets and our composite classification were apparent. Applying different thermal classifications, lead to different conclusions when quantifying 'warm' and 'cool' species density responses to a marine heatwave. Managers can use this classification approach as a tool to generate accurate, timely and simple information for resource management.

RevDate: 2021-09-29

Fernandes-Martins MC, Keller LM, Munro-Ehrlich M, et al (2021)

Ecological dichotomies arise in microbial communities due to mixing of deep hydrothermal waters and atmospheric gas in a circumneutral hot spring.

Applied and environmental microbiology [Epub ahead of print].

Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen ∼2.4 Gya. IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral to alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼ 2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.

RevDate: 2021-09-29
CmpDate: 2021-09-29

Fatemi M, Rezaei-Moghaddam K, Karami E, et al (2021)

An integrated approach of Ecological Footprint (EF) and Analytical Hierarchy Process (AHP) in human ecology: A base for planning toward sustainability.

PloS one, 16(4):e0250167.

Environmental challenges to natural resources have been attributed to human behavior and traditional agricultural production techniques. Natural resource degradation in agriculture has always been a prime concern in agro ecological research and sustainability analysis. There are many techniques for assessing environmental performance; one of which, ecological footprint (EF), assesses human pressure on the environment and natural resources. The main purpose of this study was calculation of ecological indices including biocapacity (BC) and EF of rural areas of Fars province of Iran. The study was accomplished using survey and structured interviews consisting of three main questionnaires in two different steps. Different agricultural stakeholders, including farmers (for the first step) as well as the policymakers, extension managers and authorities (for the second step) were interviewed. Based on multi-stage stratified random sampling, 50 villages and 423 farmers were selected. Face validity and reliability of the questionnaires were assessed by a panel of specialists as well as conducting a pilot study, respectively. The paradigmatic perspectives of agricultural policy makers and managers (22 individuals) were also analyzed using another specific questionnaire by Analytical Hierarchy Process (AHP). Findings revealed that most of the studied villages faced a critical environmental condition due to the results of ecological indicator which was calculated in the study. According to the four main components of human ecology (POET model) including Population, Organization, Environment and Technology, village groups that differed in terms of sustainability level also showed significantly differences due to population, social participation, use of green technologies and attitude towards diverse environmental management paradigms. The causal model also revealed that population, green technology, social participation and attitude toward frontier economics, which were in accordance with the elements of human ecology model, were the main factors affecting the ecological index. Finally, AHP results determined the dominant economic perspectives of agricultural authorities. A paradigm shift toward the comprehensive paradigm of eco-development plus consideration of the results of the ecological indicator calculation as the base of agricultural planning at the local level were recommended.

RevDate: 2021-09-16

Remeš V, Remešová E, Friedman NR, et al (2021)

Functional diversity of avian communities increases with canopy height: From individual behavior to continental-scale patterns.

Ecology and evolution, 11(17):11839-11851.

Vegetation complexity is an important predictor of animal species diversity. Specifically, taller vegetation should provide more potential ecological niches and thus harbor communities with higher species richness and functional diversity (FD). Resource use behavior is an especially important functional trait because it links species to their resource base with direct relevance to niche partitioning. However, it is unclear how exactly the diversity of resource use behavior changes with vegetation complexity. To address this question, we studied avian FD in relation to vegetation complexity along a continental-scale vegetation gradient. We quantified foraging behavior of passerine birds in terms of foraging method and substrate use at 21 sites (63 transects) spanning 3,000 km of woodlands and forests in Australia. We also quantified vegetation structure on 630 sampling points at the same sites. Additionally, we measured morphological traits for all 111 observed species in museum collections. We calculated individual-based, abundance-weighted FD in morphology and foraging behavior and related it to species richness and vegetation complexity (indexed by canopy height) using structural equation modeling, rarefaction analyses, and distance-based metrics. FD of morphology and foraging methods was best predicted by species richness. However, FD of substrate use was best predicted by canopy height (ranging 10-30 m), but only when substrates were categorized with fine resolution (17 categories), not when categorized coarsely (8 categories). These results suggest that, first, FD might increase with vegetation complexity independently of species richness, but whether it does so depends on the studied functional trait. Second, patterns found might be shaped by how finely we categorize functional traits. More complex vegetation provided larger "ecological space" with more resources, allowing the coexistence of more species with disproportionately more diverse foraging substrate use. We suggest that the latter pattern was driven by nonrandom accumulation of functionally distinct species with increasing canopy height.

RevDate: 2021-08-31
CmpDate: 2021-08-31

Guo J, Zhang M, Shang Q, et al (2021)

River Basin Cyberinfrastructure in the Big Data Era: An Integrated Observational Data Control System in the Heihe River Basin.

Sensors (Basel, Switzerland), 21(16):.

River basin cyberinfrastructure with the Internet of Things (IoT) as the core has brought watershed data science into the big data era, greatly improving data acquisition and sharing efficiency. However, challenges in analyzing, processing, and applying very large quantities of observational data remain. Given the observational needs in watershed research, we studied the construction of river basin cyberinfrastructure and developed an integrated observational data control system (IODCS). The IODCS is an important platform for processing large quantities of observational data, including automated collection, storage, analysis, processing, and release. This paper presents various aspects of the IODCS in detail, including the system's overall design, function realization, big data analysis methods, and integrated models. We took the middle reaches of the Heihe River Basin (HRB) as the application research area to show the performance of the developed system. Since the system began operation, it has automatically received, analyzed, and stored more than 1.4 billion observational data records, with an average of more than 14 million observational data records processed per month and up to 21,011 active users. The demonstrated results show that the IODCS can effectively leverage the processing capability of massive observational data and provide a new perspective for facilitating ecological and hydrological scientific research on the HRB.

RevDate: 2021-08-26

Abdullah MM, Al-Ali ZM, S Srinivasan (2021)

The use of UAV-based remote sensing to estimate biomass and carbon stock for native desert shrubs.

MethodsX, 8:101399.

Unmanned Aerial Vehicles (UAVs) have started to receive more attention in the ecological field in the past 15 years, as they provide very high-resolution imagery that ranges from meters to millimeters. Very high-resolution multispectral imagery obtained from UAVs can help in assessing and monitoring native desert vegetation. Thus, this study use UAVs to develop a method to estimate the biomass and carbon stock of native desert shrubs. The method integrates different techniques and software to monitor native plants' coverage, biomass, and carbon stock. The techniques used in this work are also applicable for other native desert shrubs in the region and could support ecosystem managers in assessing and monitoring arid ecosystems and restoration and revegetation programs. A three-stage image and data management are discussed, including: (1) fieldwork and image acquisition using UAVs, (2) image pre-processing, and (3) image processing using different techniques and software.•Determining shrub biomass is not restricted to multispectral data only but could be applicable for RGB data since it mainly depends on the DSM and DTM.•Allometric parameters could help in estimating desert shrub biomass which could be measured easily and rapidly using UAV imagery.•SVM Supervised classification could help in distinguishing between native shrubs and grasses.

RevDate: 2021-09-21
CmpDate: 2021-09-21

Li J, Chen X, Kurban A, et al (2021)

Identification of conservation priorities in the major basins of Central Asia: Using an integrated GIS-based ordered weighted averaging approach.

Journal of environmental management, 298:113442.

Ecosystem services (ESs) provided by the major basins of Central Asia are critical to human well-being and have attracted the attention of the international community. The identification of conservation priorities is of great significance for the maintenance and protection of key ESs. In this study, we quantified the spatiotemporal changes of net primary productivity (NPP), soil conservation (SC), water yield (WY) and habitat quality (HQ) in the major basins of Central Asia from 1995 to 2015. In addition, a GIS-based ordered weighted averaging (OWA) multi-criterion valuation method was adopted to identify potential conservation areas under 11 scenarios. Conservation priorities were determined by comparing the conservation efficiency under each scenario. Then, a broad range of indicators were considered to distinguish the driving factors affecting ESs in conservation priorities. The results show that the average conservation efficiency in the Issyk-Kul Basin was the highest, followed by the Am Darya Basin, Ili-Balkhash Basin and Syr Darya Basin. We observed that the conservation efficiency of the four ESs declined continuously in the Ili-Balkhash Basin from 1995 to 2015, while it changed steadily in the other three basins. Correlation analysis indicated that natural factors (e.g., precipitation and topography) were the main driving factors of WY, SR and NPP in conservation priorities, while HQ was more affected by socio-economic factors (e.g., population density and both cropland and urban percentages). The identification of conservation priorities and their driving factors plays an important role in ensuring the ecological security of the lower reaches, regulating the regional water balance and stabilizing the climate pattern.

RevDate: 2021-08-06

Jones B, Goodall T, George PBL, et al (2021)

Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database.

Frontiers in microbiology, 12:682886.

High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.

RevDate: 2021-08-02

Hagmann RK, Hessburg PF, Prichard SJ, et al (2021)

Evidence for widespread changes in the structure, composition, and fire regimes of western North American forests.

Ecological applications : a publication of the Ecological Society of America [Epub ahead of print].

Implementation of wildfire- and climate-adaptation strategies in seasonally dry forests of western North America is impeded by numerous constraints and uncertainties. After more than a century of resource and land use change, some question the need for proactive management, particularly given novel social, ecological, and climatic conditions. To address this question, we first provide a framework for assessing changes in landscape conditions and fire regimes. Using this framework, we then evaluate evidence of change and lack of change in contemporary conditions relative to those maintained by active fire regimes, i.e., those uninterrupted by a century or more of human-induced fire exclusion. The cumulative results of more than a century of research document a persistent and substantial fire deficit and widespread alterations to ecological structures and functions. These changes are not necessarily apparent at all spatial scales or in all dimensions of fire regimes and forest and nonforest conditions. Nonetheless, loss of the once abundant influence of low- and moderate-severity fires suggests that while some ecosystems within these landscapes may not be directly altered by fire exclusion, even the least fire-prone among them may be affected by alteration of the surrounding landscape and, consequently, ecosystem functions. Vegetation spatial patterns in fire-excluded forested landscapes no longer reflect the heterogeneity maintained by interacting fires of active fire regimes. Live and dead vegetation (surface and canopy fuels) is generally more abundant and continuous than before European colonization. As a result, current conditions are more vulnerable to the direct and indirect effects of seasonal and episodic increases in drought and fire, especially under a rapidly warming climate. Long-term fire exclusion and contemporaneous social-ecological influences continue to extensively modify seasonally dry forested landscapes. Management that realigns or adapts fire-excluded conditions to the seasonal and episodic increases in drought and fire can moderate ecosystem transitions as forests and human communities adapt to changing climatic and disturbance regimes. As adaptation strategies are developed, evaluated, and implemented, objective scientific evaluation of ongoing research and monitoring can aid differentiation of warranted and unwarranted uncertainties.

RevDate: 2021-09-10

Li YX, Rao YZ, Qi YL, et al (2021)

Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks.

mSystems, 6(4):e0060621.

"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.

RevDate: 2021-09-25

Liu C, Yang M, Hou Y, et al (2021)

Ecosystem service multifunctionality assessment and coupling coordination analysis with land use and land cover change in China's coastal zones.

The Science of the total environment, 797:149033.

Ecosystem services (ESs) have received widespread attention worldwide for their potential to solve sustainability issues. However, extensive land use and land cover change (LUCC) driven by human activities has raised concerns regarding its impacts on ESs, especially in coastal zones. More importantly, spatial-temporal changes, their coupling relationships with LUCC, and their underlying drivers have not been thoroughly analyzed. This study focuses on China's coastal zones to investigate the spatial-temporal changes of ecosystem service multifunctionality (ESM) from 2000 to 2018. Coupling coordination degree (CCD) analysis of the relationship between ESM and comprehensive intensity of land use was applied to identify coastal cities with low-level coordination and their main drivers in 2018. The results show that: (1) the proportion with high levels of ESM decreased by 1.01% from 2000 to 2010 and then increased by 3.29% from 2010 to 2018; (2) the ESM of China's coastal zones present significant spatial heterogeneity, and the low levels of ESM are mainly distributed in the north and urban areas, while most areas in the southern coastal zones have high levels of ESM; (3) forest land is the leading land cover type for ESM, and China's forest conservation policies significantly contribute to the increase in ESM; (4) the CCD of most cities in the southern coastal zones, apart from Shanghai and the Pearl River Delta, is at a relatively high level and experiences no significant changes, while most cities in the northern coastal zones display an improving trend; (5) the land use type, landform type, and leaf area index are the determinants of ESM, and the annual average temperature, population density, and surface elevation are the greatest influences on the CCD. The findings of this study can inform ecological conservation and landscape planning and are beneficial to the sustainable development of coastal zones in China.

RevDate: 2021-08-11
CmpDate: 2021-08-11

Ali EOM, Babalghith AO, Bahathig AOS, et al (2021)

Prevalence of Larval Breeding Sites and Seasonal Variations of Aedes aegypti Mosquitoes (Diptera: Culicidae) in Makkah Al-Mokarramah, Saudi Arabia.

International journal of environmental research and public health, 18(14):.

Since 1994, dengue fever (DF) transmission rates have increased significantly in Saudi Arabia (KSA). Climatic, geographic, and demographic conditions make KSA especially suitable for DF's spread. Still, there are insufficient strategies for controlling the Aedes species that transmit DF virus (DENV). To develop effective management strategies, it is necessary to identify Aedes species and the ecological habitat of larvae in Makkah Al-Mokarramah, KSA. We conducted a longitudinal survey of Aedes mosquitoes in 14 localities from January 2015 to December 2015. World Health Organization (WHO) inspection kits for larvae were used to detect and sample larvae, along with pictorial keys. A total of 42,981 potential Aedes larval breeding sites were surveyed. A total of 5403 (12.6%) sites had at least one water source positive for Aedes aegypti (Linnaeus) mosquitoes. Among the total of 15,133 water sources surveyed within the sampled sites, 1815 (12.0%) were positive for Aedes aegypti. Aedes aegypti was the only Aedes species identified in the course of the survey. The presence of such a large immature population may indicate an imminent outbreak of DF in the near future unless proper implementation of control and elimination of Aedes&nbsp;aegypti are undertaken. Additionally, the adaptation of Aedes&nbsp;aegypti to the arid climate of Makkah needs further investigation.

RevDate: 2021-07-22

Coutinho FH, Zaragoza-Solas A, López-Pérez M, et al (2021)

RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.

Patterns (New York, N.Y.), 2(7):100274.

Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.

RevDate: 2021-07-16

Rocchini D, Thouverai E, Marcantonio M, et al (2021)

rasterdiv-An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back.

Methods in ecology and evolution, 12(6):1093-1102.

Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow.In this paper, we present a new R package-rasterdiv-to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns.The rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open-source algorithms.

RevDate: 2021-08-31

Levi A, Z Barnett-Itzhaki (2021)

Effects of chronic exposure to ambient air pollutants, demographic, and socioeconomic factors on COVID-19 morbidity: The Israeli case study.

Environmental research, 202:111673 pii:S0013-9351(21)00967-1 [Epub ahead of print].

BACKGROUND: Recent studies conducted in several OECD countries have shown that chronic exposure to elevated levels of air pollutants (especially PM2.5, PM10 and NOx), might negatively impact COVID-19 morbidity and mortality rates. The aim of this study was to examine the association between chronic exposure to air pollution in Israeli cities and towns, their demographic and socioeconomic status, and COVID-19 morbidity, during the three local morbidity waves.

METHODS: We examined the associations between: (a) annual average concentrations of NOx, CO, PM10, PM2.5 and SO2 in 2016-2019, and demographic and socioeconomic parameters, and (b) COVID-19 positive cases in 279 Israeli cities and towns, in the four state-wide morbidity peaks: 1st wave peak: March 31st, 2020; 2nd wave peaks: July 24th and September 27th, 2020, and the 3rd wave peak: January 17th, 2021, which occurred after the beginning of the nationwide vaccination campaign. These associations were calculated using both Spearman correlations and multivariate linear regressions.

RESULTS: We found statistically significant positive correlations between the concentrations of most pollutants in 2016-19 and COVID-19 morbidity rate at the first three timepoints but not the 4th (January 17th, 2021). Population density and city/town total population were also positively associated with the COVID-19 morbidity rates at these three timepoints, but not the 4th, in which socioeconomic parameters were more dominant - we found a statistically significant negative correlation between socioeconomic cluster and COVID-19 morbidity. In addition, all multivariate models including PM2.5 concentrations were statistically significant, and PM2.5 concentrations were positively associated with the COVID-19 morbidity rates in all models.

CONCLUSIONS: We found a nationwide association between population chronic exposure to five main air pollutants in Israeli cities and towns, and COVID-19 morbidity rates during two of the three morbidity waves experienced in Israel. The widespread morbidity that was related to socioeconomic factors during the 3rd wave, emphasizes the need for special attention to morbidity prevention in socioeconomically vulnerable populations and especially in large household communities. Nevertheless, this ecological study has several limitations, such as the inability to draw conclusions about causality or mechanisms of action. The growing body of evidence, regarding association between exacerbated COVID-19 morbidity and mortality rates and long-term chronic exposure to elevated concentrations of air pollutants should serve as a wake-up call to policy makers regarding the urgent need to reduce air pollution and its harmful effects.

RevDate: 2021-07-21
CmpDate: 2021-07-21

Mehrshad M, Lopez-Fernandez M, Sundh J, et al (2021)

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.

Nature communications, 12(1):4253.

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

RevDate: 2021-07-29

Weinstein BG, Graves SJ, Marconi S, et al (2021)

A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network.

PLoS computational biology, 17(7):e1009180.

Broad scale remote sensing promises to build forest inventories at unprecedented scales. A crucial step in this process is to associate sensor data into individual crowns. While dozens of crown detection algorithms have been proposed, their performance is typically not compared based on standard data or evaluation metrics. There is a need for a benchmark dataset to minimize differences in reported results as well as support evaluation of algorithms across a broad range of forest types. Combining RGB, LiDAR and hyperspectral sensor data from the USA National Ecological Observatory Network's Airborne Observation Platform with multiple types of evaluation data, we created a benchmark dataset to assess crown detection and delineation methods for canopy trees covering dominant forest types in the United States. This benchmark dataset includes an R package to standardize evaluation metrics and simplify comparisons between methods. The benchmark dataset contains over 6,000 image-annotated crowns, 400 field-annotated crowns, and 3,000 canopy stem points from a wide range of forest types. In addition, we include over 10,000 training crowns for optional use. We discuss the different evaluation data sources and assess the accuracy of the image-annotated crowns by comparing annotations among multiple annotators as well as overlapping field-annotated crowns. We provide an example submission and score for an open-source algorithm that can serve as a baseline for future methods.

RevDate: 2021-07-08

Mairal M, Chown SL, Shaw J, et al (2021)

Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub-Antarctic.

Molecular ecology [Epub ahead of print].

The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differently impacted by humans. We analysed microsatellite and genome size variation, and then compared the genetic diversity and structure of invasive Poa annua L. on two sub-Antarctic islands: human-occupied Marion Island and unoccupied Prince Edward Island. We also carried out niche modelling to map the potential distribution of the species on both islands. We found high levels of genetic diversity and evidence for extensive admixture between genetically distinct lineages of P. annua on Marion Island. By contrast, the Prince Edward Island populations showed low genetic diversity, no apparent admixture, and had smaller genomes. On both islands, high genetic diversity was apparent at human landing sites, and on Marion Island, also around human settlements, suggesting that these areas received multiple introductions and/or acted as initial introduction sites and secondary sources (bridgeheads) for invasive populations. More than 70 years of continuous human activity associated with a meteorological station on Marion Island led to a distribution of this species around human settlements and along footpaths, which facilitates ongoing gene flow among geographically separated populations. By contrast, this was not the case for Prince Edward Island, where P. annua populations showed high genetic structure. The high levels of genetic variation and admixture in P. annua facilitated by human activity, coupled with high habitat suitability on both islands, suggest that P. annua is likely to increase its distribution and abundance in the future.

RevDate: 2021-06-21

Tanner RL, Grover N, Anderson ML, et al (2021)

Examining cultural structures and functions in biology.

Integrative and comparative biology pii:6307025 [Epub ahead of print].

Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity-we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access-a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together-this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate-not reintegrate-the nuances of biology into our field.

RevDate: 2021-07-07
CmpDate: 2021-07-07

Borko Š, Trontelj P, Seehausen O, et al (2021)

A subterranean adaptive radiation of amphipods in Europe.

Nature communications, 12(1):3688.

Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.

RevDate: 2021-06-15
CmpDate: 2021-06-09

Colella JP, Bates J, Burneo SF, et al (2021)

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network.

PLoS pathogens, 17(6):e1009583.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO's virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

RevDate: 2021-07-14

Cadar D, Schmidt-Chanasit J, D Tappe (2021)

Genomic and Micro-Evolutionary Features of Mammalian 2 orthobornavirus (Variegated Squirrel Bornavirus 1, VSBV-1).

Microorganisms, 9(6):.

Mammalian 2 orthobornavirus (VSBV-1) is an emerging zoonotic pathogen discovered in several exotic squirrel species and associated with fatal human encephalitis. The dynamics of VSBV-1 spread and evolution in its presumed natural hosts are unknown. Here, we present the phylogeny, micro-evolution, cross-species transmission and spread of VSBV-1 at a temporal and spatial resolution within the limits of animal husbandry. The results showed that VSBV-1 can be classified into six distinct groups and that the most recent common ancestor of the known German strains emerged at least 20 years ago. We here demonstrate that the genetic diversity of the VSBV-1 groups is shaped primarily by in situ evolution and most of the amino acid changes are deleterious polymorphisms removed by purifying selection. Evidence of adaptive evolution has been found in the G and L genes which might have an influence on transmission fitness. Furthermore, there was also evidence for some form of adaptive changes in the glycoprotein which suggests that many sites might be subjected to positive pressure evolving under episodic directional selection, indicating past occurrence of positive selection. Host switching events were detected as dominant evolutionary mechanisms driving the virus-host associations. Virus spread by animal trade followed by subsequent local micro-evolution in zoos and holdings is responsible for diversifying strains. Time-resolved phylogeny indicated that Prevost's squirrels might be the original squirrel species carrying and seeding the virus in Germany. This study provides the first insight into the ecology and micro-evolutionary dynamics of this novel viral pathogen in the captive exotic squirrel population under artificial ecological conditions (zoos and animal husbandry) and co-housing of different squirrel species.

RevDate: 2021-07-08
CmpDate: 2021-07-08

Wright ES, Gupta R, KH Vetsigian (2021)

Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.

FEMS microbiology ecology, 97(6):.

Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment. This dataset led to several observations: (i) some pairwise competitions resulted in bistability with a separatrix near a 1:1 initial ratio across a range of population densities; (ii) bistability propagated to multi-stability in multispecies communities; and (iii) replicate microbial communities reached different stable states when starting close to initial conditions separating basins of attraction, indicating finite-sized regions where the dynamics are unpredictable. The generalized Lotka-Volterra equations qualitatively captured most competition outcomes but were unable to quantitatively recapitulate the observed dynamics. This was partly due to complex and diverse growth dynamics in monocultures that ranged from Allee effects to nonmonotonic behaviors. Overall, our results highlight that multi-stability might be generic in multispecies communities and, combined with ecological noise, can lead to unpredictable community assembly, even in simple environments.

RevDate: 2021-05-31
CmpDate: 2021-05-31

Rabosky DL, RBJ Benson (2021)

Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data.

Nature communications, 12(1):2945.

Estimates of evolutionary diversification rates - speciation and extinction - have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade's age and its extant species richness. This "age-richness rate" (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields "point estimates" that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness.

RevDate: 2021-05-25
CmpDate: 2021-05-24

Karatayev VA, Vasconcelos VV, Lafuite AS, et al (2021)

A well-timed shift from local to global agreements accelerates climate change mitigation.

Nature communications, 12(1):2908.

Recent attempts at cooperating on climate change mitigation highlight the limited efficacy of large-scale negotiations, when commitment to mitigation is costly and initially rare. Deepening existing voluntary mitigation pledges could require more stringent, legally-binding agreements that currently remain untenable at the global scale. Building-blocks approaches promise greater success by localizing agreements to regions or few-nation summits, but risk slowing mitigation adoption globally. Here, we show that a well-timed policy shift from local to global legally-binding agreements can dramatically accelerate mitigation compared to using only local, only global, or both agreement types simultaneously. This highlights the scale-specific roles of mitigation incentives: local agreements promote and sustain mitigation commitments in early-adopting groups, after which global agreements rapidly draw in late-adopting groups. We conclude that focusing negotiations on local legally-binding agreements and, as these become common, a renewed pursuit of stringent, legally-binding world-wide agreements could best overcome many current challenges facing climate mitigation.

RevDate: 2021-07-23
CmpDate: 2021-07-23

Baptiste YM (2021)

Digital Feast and Physical Famine: The Altered Ecosystem of Anatomy Education due to the Covid-19 Pandemic.

Anatomical sciences education, 14(4):399-407.

This article explores the effects of the coronavirus disease 2019 (Covid-19) pandemic on the evolution of both physical and digital cadavers within the unique ecosystem of the anatomy laboratory. A physical cadaver is a traditional and established learning tool in anatomy education, whereas a digital cadaver is a relatively recent phenomenon. The Covid-19 pandemic presented a major disturbance and disruption to all levels and types of education, including anatomy education. This article constructs a conceptual metaphor between a typical anatomy laboratory and an ecosystem, and considers the affordances, constraints, and changing roles of physical and digital cadavers within anatomy education through an ecological lens. Adaptation of physical and digital cadavers during the disturbance is analyzed, and the resiliency of digital cadaver technology is recognized. The evolving role of the digital cadaver is considered in terms of increasing accessibility and inclusivity within the anatomy laboratory ecosystem of the future.

RevDate: 2021-09-23
CmpDate: 2021-09-23

Huettmann F, K Hueffer (2021)

The ecological niche of reported rabies cases in Canada is similar to Alaska.

Zoonoses and public health, 68(6):677-683.

The ecology of rabies in the circumpolar North is still not well understood. We use machine learning, a geographic information system and data explicit in time and space obtained for reported rabies cases and predictors in Canada to develop an ecological niche model for the distribution of reported rabies cases in the American north (Alaska and Canada). The ecological niche model based on reported rabies cases in Canada predicted reported rabies cases in Alaska, suggesting a rather robust inference and even similar drivers on a continental scale. As found in Alaska, proximity to human infrastructure-specifically along the coast-was a strong predictor in the detection of rabies cases in Canada. Also, this finding highlights the need for a more systematic landscape sampling for rabies infection model predictions to better understand and tackle the ecology of this important zoonotic disease on a landscape scale at some distance from human infrastructure in wilderness areas.

RevDate: 2021-05-07

Santos FP, Levin SA, VV Vasconcelos (2021)

Biased perceptions explain collective action deadlocks and suggest new mechanisms to prompt cooperation.

iScience, 24(4):102375.

When individuals face collective action problems, their expectations about others' willingness to contribute affect their motivation to cooperate. Individuals, however, often misperceive the cooperation levels in a population. In the context of climate action, people underestimate the pro-climate positions of others. Designing incentives to enable cooperation and a sustainable future must thereby consider how social perception biases affect collective action. We propose a theoretical model and investigate the effect of social perception bias in non-linear public goods games. We show that different types of bias play a distinct role in cooperation dynamics. False uniqueness (underestimating own views) and false consensus (overestimating own views) both explain why communities get locked in suboptimal states. Such dynamics also impact the effectiveness of typical monetary incentives, such as fees. Our work contributes to understanding how targeting biases, e.g., by changing the information available to individuals, can comprise a fundamental mechanism to prompt collective action.

RevDate: 2021-04-30

Nasser M, Okely M, Nasif O, et al (2021)

Spatio-temporal analysis of Egyptian flower mantis Blepharopsis mendica (order: mantodea), with notes of its future status under climate change.

Saudi journal of biological sciences, 28(4):2049-2055.

Egyptian flower mantis Blepharopsis mendica (Order: Mantodea) is a widespread mantis species throughout the southwest Palearctic region. The ecological and geographical distribution of such interesting species is rarely known. So, through this work, habitat suitability models for its distribution through Egyptian territory were created using MaxEnt software from 90 occurrence records. One topographic (altitude) and eleven bioclimatic variables influencing the species distribution were selected to generate the models. The predicted distribution in Egypt was focused on the Delta, South Sinai, the north-eastern part of the country, and some areas in the west including Siwa Oasis. Temporal analysis between the two periods (1900-1961) and (1961-2017) show current reduction of this species distribution through Delta and its surrounding areas, may be due to urbanization. On the other hand, it increases in newly protected areas of South Sinai. Under the future climate change scenario, the MaxEnt model predicted the habitat gains for B. mendica in RCP 2.6 for 2070 and loss of habitat in RCP 8.5 for the same year. Our results can be used as a basis for conserving this species not only in Egypt, but also throughout the whole of its range, also, it show how the using of geo-information could help in studying animal ecology.

RevDate: 2021-05-20
CmpDate: 2021-05-20

Szabó B, Lang Z, Kövér S, et al (2021)

The inter-individual variance can provide additional information for the ecotoxicologists beside the mean.

Ecotoxicology and environmental safety, 217:112260.

The hypothesis that the inter-individual parameter variability is an unexploited area of ecotoxicology was proposed several decades ago. Although some illustrative examples were presented to support this hypothesis in the last decades, it has never been tested on an extensive, coherent database. In this study, variance changes of 105 dose-response curves were analysed. All data originated from the same experiment, where the effects of the insecticide Trebon EC were investigated in a dose-response manner on 15 traits of the collembolan Folsomia candida in four subsequent generations and two types of insecticide treatments. A consistent relationship between inter-individual variance and insecticide application was found in 2 (first clutch size and growth-reproduction trade-off) out of the 15 of the parameters. Contrary to the mean, the variance of the first clutch size showed consistent differences compared to the control. Furthermore, the variance of the growth-reproduction trade-off was consistently different from the control except in one case (F3 generation of the transgenerational treatment). Higher first clutch size variances were found in F1 and a lower one in the F2 and F3 generations than in that of the control. This overall pattern of the variance changes of the first clutch size and the trade-off seems to be a quick response to the insecticide application. In the short term, we have found that variance increased with insecticide treatment (P and F1 generation), because phenotypic variance generally increases due to environmental stress. Disruptive selection could be another mechanism between the more detoxification less reproduction strategy and the more reproduction less detoxification strategy. However, in the later generations (F2-F3) the variance decreases compared to the control, which could be because on short term selection stronger on the viability parameters and in long-term selection on reproduction becomes stronger. According to our results, analysis of the variance changes of some parameters may give information about the effects of the pesticide even when the mean does not predict any impact. Testing variance changes are important in ecotoxicology because variance change can signalise toxicant impact even when the mean does not change in certain cases.

RevDate: 2021-06-21
CmpDate: 2021-06-21

Ramakrishnan M, Yrjälä K, Satheesh V, et al (2021)

Bamboo Transposon Research: Current Status and Perspectives.

Methods in molecular biology (Clifton, N.J.), 2250:257-270.

Bamboo, a fast-growing non-timber forest plant with many uses, is a valuable species for green development. However, bamboo flowering is very infrequent, extending, in general, for up to 120 years. Ecologically, bamboo species are generally better adapted to various environments than other grasses. Therefore, the species deserves a special status in what could be called Ecological Bioeconomy. An understanding of the genetic processes of bamboo can help us sustainably develop and manage bamboo forests. Transposable elements (TEs), jumping genes or transposons, are major genetic elements in plant genomes. The rapid development of the bamboo reference genome, at the chromosome level, reveals that TEs occupy over 63.24% of the genome. This is higher than found in rice, Brachypodium, and sorghum. The bamboo genome contains diverse families of TEs, which play a significant role in bamboo's biological processes including growth and development. TEs provide important clues for understanding the evolution of the bamboo genome. In this chapter, we briefly describe the current status of research on TEs in the bamboo genome, their regulation, and transposition mechanisms. Perspectives for future research are also provided.

RevDate: 2021-08-13
CmpDate: 2021-08-13

Liu H, Jiang Y, Misa R, et al (2021)

Ecological environment changes of mining areas around Nansi lake with remote sensing monitoring.

Environmental science and pollution research international, 28(32):44152-44164.

Underground mining activity has existed for more than 100 years in Nansi lake. Coal mining not only plays a supporting role in local social and economic development but also has a significant impact on the ecological environment in the region. Landsat series remote sensing data (1988~2019) are used to research the impact of coal mining on the ecological environment in Nansi lake. Then support vector machine (SVM) classifier is applied to extract the water area of the upstream lake from 1988 to 2019, and ecological environment and spatiotemporal variation characteristics are analyzed by Remote Sensing Ecology Index (RSEI). The results illustrate that the water area change is associated with annual precipitation. In terms of ecological quality, the area of poor ecological quality areas increased by 101.782 km2, while the area of good and excellent quality areas decreased by 218.988 km2 from 2009 to 2019. So compared with 2009, the ecological quality of the lake is worse in 2019, and then the reason for this change is due to large-scale underground mining. Therefore, the coal mines from the natural reserve may be closed or limited to the mining boundary for protecting the lake's ecological environment.

RevDate: 2021-04-28

Pushkareva E, Sommer V, Barrantes I, et al (2021)

Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany.

Microorganisms, 9(4):.

Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.

RevDate: 2021-05-10
CmpDate: 2021-05-10

Peters K, Balcke G, Kleinenkuhnen N, et al (2021)

Untargeted In Silico Compound Classification-A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes.

International journal of molecular sciences, 22(6):.

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)-LC/MS-QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou's diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher's exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by "zooming in" and in ecology by "zooming out". The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies.

RevDate: 2021-05-13
CmpDate: 2021-05-13

Moghaddam VK, Dickerson AS, Bazrafshan E, et al (2021)

Socioeconomic determinants of global distribution of multiple sclerosis: an ecological investigation based on Global Burden of Disease data.

BMC neurology, 21(1):145.

BACKGROUND: Socioeconomic factors may be involved in risk of multiple sclerosis (MS), either indirectly or as confounding factors. In this study two comprehensive indicators reflecting socioeconomic differences, including the Human Development Index (HDI) and Prosperity Index (PI), were used to assess the impact of these factors on the worldwide distribution of MS.

METHODS: The data for this global ecological study were obtained from three comprehensive databases including the Global Burden of Disease (as the source of MS indices), United Nations Development Programme (source for HDI) and the Legatum Institute Database for PI. MS indices (including prevalence, incidence, mortality, and disability-adjusted life years) were all analyzed in the form of age- and sex-standardized. Correlation and regression analyses were used to investigate the relationship between HDI and PI and their subsets with MS indices.

RESULTS: All MS indices were correlated with HDI and PI. It was also found that developed countries had significantly higher prevalence and incidence rates of MS than developing countries. Education and governance from the PI, and gross national income and expected years of schooling from the HDI were more associated with MS. Education was significantly related to MS indices (p < 0.01) in both developed and developing countries.

CONCLUSION: In general, the difference in income and the socioeconomic development globally have created a landscape for MS that should be studied in more detail in future studies.

RevDate: 2021-07-28
CmpDate: 2021-07-28

Burthe SJ, Schäfer SM, Asaaga FA, et al (2021)

Reviewing the ecological evidence base for management of emerging tropical zoonoses: Kyasanur Forest Disease in India as a case study.

PLoS neglected tropical diseases, 15(4):e0009243.

Zoonoses disproportionately affect tropical communities and are associated with human modification and use of ecosystems. Effective management is hampered by poor ecological understanding of disease transmission and often focuses on human vaccination or treatment. Better ecological understanding of multi-vector and multi-host transmission, social and environmental factors altering human exposure, might enable a broader suite of management options. Options may include "ecological interventions" that target vectors or hosts and require good knowledge of underlying transmission processes, which may be more effective, economical, and long lasting than conventional approaches. New frameworks identify the hierarchical series of barriers that a pathogen needs to overcome before human spillover occurs and demonstrate how ecological interventions may strengthen these barriers and complement human-focused disease control. We extend these frameworks for vector-borne zoonoses, focusing on Kyasanur Forest Disease Virus (KFDV), a tick-borne, neglected zoonosis affecting poor forest communities in India, involving complex communities of tick and host species. We identify the hierarchical barriers to pathogen transmission targeted by existing management. We show that existing interventions mainly focus on human barriers (via personal protection and vaccination) or at barriers relating to Kyasanur Forest Disease (KFD) vectors (tick control on cattle and at the sites of host (monkey) deaths). We review the validity of existing management guidance for KFD through literature review and interviews with disease managers. Efficacy of interventions was difficult to quantify due to poor empirical understanding of KFDV-vector-host ecology, particularly the role of cattle and monkeys in the disease transmission cycle. Cattle are hypothesised to amplify tick populations. Monkeys may act as sentinels of human infection or are hypothesised to act as amplifying hosts for KFDV, but the spatial scale of risk arising from ticks infected via monkeys versus small mammal reservoirs is unclear. We identified 19 urgent research priorities for refinement of current management strategies or development of ecological interventions targeting vectors and host barriers to prevent disease spillover in the future.

RevDate: 2021-05-20
CmpDate: 2021-05-20

Todorov OS, Blomberg SP, Goswami A, et al (2021)

Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework.

Proceedings. Biological sciences, 288(1947):20210394.

Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalized linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying a much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age or gestation length. This supports suggestions that significant associations between behavioural or ecological variables with relative brain size may be due to a confounding influence of the extensive reproductive diversity of placental mammals.

RevDate: 2021-07-10

Modica MV, Ahmad R, Ainsworth S, et al (2021)

The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics.

GigaScience, 10(3):.

Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom investigation and applications. The COST Action CA19144-European Venom Network was recently launched to promote synergistic interactions among different stakeholders and foster venom research at the European level.

RevDate: 2021-06-28
CmpDate: 2021-06-28

Soria CD, Pacifici M, Di Marco M, et al (2021)

COMBINE: a coalesced mammal database of intrinsic and extrinsic traits.

Ecology, 102(6):e03344.

The use of species' traits in macroecological analyses has gained popularity in the last decade, becoming an important tool to understand global biodiversity patterns. Currently, trait data can be found across a wide variety of data sets included in websites, articles, and books, each one with its own taxonomic classification, set of traits, and data management methodology. Mammals, in particular, are among the most studied taxa, with large sources of trait information readily available. To facilitate the use of these data, we did an extensive review of published mammal trait data sources between 1999 and May 2020 and produced COMBINE: a COalesced Mammal dataBase of INtrinsic and Extrinsic traits. Our aim was to create a taxonomically integrated database of mammal traits that maximized trait number and coverage without compromising data quality. COMBINE contains information on 54 traits for 6,234 extant and recently extinct mammal species, including information on morphology, reproduction, diet, biogeography, life habit, phenology, behavior, home range, and density. Additionally, we calculated other relevant traits such as habitat and altitudinal breadths for all species and dispersal for terrestrial non-volant species. All data are compatible with the taxonomies of the IUCN Red List v. 2020-2 and PHYLACINE v. 1.2. Missing data were adequately flagged and imputed for non-biogeographical traits with 20% or more data available. We obtained full data sets for 21 traits such as female maturity, litter size, maximum longevity, trophic level, and dispersal, providing imputation performance statistics for all. This data set will be especially useful for those interested in including species' traits in large-scale ecological and conservation analyses. There are no copyright or proprietary restrictions; we request citation of this publication and all relevant underlying data sources (found in Data S1: trait_data_sources.csv), upon using these data.

RevDate: 2021-03-05

Kim HW, Yoon S, Kim M, et al (2021)

EcoBank: A flexible database platform for sharing ecological data.

Biodiversity data journal, 9:e61866.

Background: Environmental crisis challenges the human race harder than ever before. Ecologists have produced a massive amount of data to cope with the crisis. Accordingly, many national scale ecological database systems have been developed worldwide to manage and analyse these datasets. However, in Korea, ecological datasets produced by different research institutes for different purposes have not been integrated or serviced due to poorly designed information infrastructure. To address this obstacle, we present EcoBank (www.nie-ecobank.kr), an open, web-based ecological database platform designed to play an important role in ecosystem analysis, not only in Korea, but also worldwide.

New information: The architecture of EcoBank comprises core technologies of WebGIS, Application Programming Interface (API), responsive web and open-source software (OSS). Comprehensive ecological datasets from three different sources, including the National Institute of Ecology (NIE) in Korea, related national and international platforms and repositories, enter the three conceptual modules in EcoBank: data management, analysis and service. Diverse potential stakeholders of EcoBank can be classified into three groups: researchers, policy-makers and public users. EcoBank aims to expand its horizons through mutual communication amongst these stakeholders. We opened and launched the EcoBank service in December 2019 and have now begun to broaden its network by linking it to other data platforms and repositories over the globe to find possible solutions to ecological issues in Korea.

RevDate: 2021-03-17
CmpDate: 2021-03-17

Lei J, Booth DT, Rusli MU, et al (2021)

Spatial Ecology of Asian Water Monitors Adjacent to a Sea Turtle Nesting Beach.

Zoological science, 38(1):1-7.

Nest predation is the main cause of hatching failure for many turtle populations. For green turtles (Chelonia mydas) nesting at Chagar Hutang in Redang Island, Malaysia, Asian water monitors (Varanus salvator) are a potential nest predator. However, no studies have documented the space use of this species in coastal habitat adjacent to a sea turtle nesting beach to assess its potential impact on turtle nests. Here, we used Global Positioning System (GPS) data loggers to quantify space use of Asian water monitors in order to establish the extent to which they use sea turtle nesting areas. Asian water monitors had a diurnal activity pattern and spent most of their time in rain forest habitat behind the sea turtle nesting beach. The home range occupied by Asian water monitors varied between 0.015 and 0.198 km2 calculated by the Kernel Brownian Bridge method. The space use patterns of individual Asian water monitors varied between individuals. Two males had relatively small home ranges, whereas one male and the female had a relatively large home range. Because tracked Asian water monitors in this study rarely visited the sea turtle nesting areas, it is probable that only a few individuals are responsible for opening nests.

RevDate: 2021-02-23

Weinstein BG, Marconi S, Bohlman SA, et al (2021)

A remote sensing derived data set of 100 million individual tree crowns for the National Ecological Observatory Network.

eLife, 10:.

Forests provide biodiversity, ecosystem, and economic services. Information on individual trees is important for understanding forest ecosystems but obtaining individual-level data at broad scales is challenging due to the costs and logistics of data collection. While advances in remote sensing techniques allow surveys of individual trees at unprecedented extents, there remain technical challenges in turning sensor data into tangible information. Using deep learning methods, we produced an open-source data set of individual-level crown estimates for 100 million trees at 37 sites across the United States surveyed by the National Ecological Observatory Network's Airborne Observation Platform. Each canopy tree crown is represented by a rectangular bounding box and includes information on the height, crown area, and spatial location of the tree. These data have the potential to drive significant expansion of individual-level research on trees by facilitating both regional analyses and cross-region comparisons encompassing forest types from most of the United States.

RevDate: 2021-03-22
CmpDate: 2021-03-22

Boori MS, Choudhary K, Paringer R, et al (2021)

Spatiotemporal ecological vulnerability analysis with statistical correlation based on satellite remote sensing in Samara, Russia.

Journal of environmental management, 285:112138.

In the present global situation, when everywhere ecology is degraded due to the extreme exhaustion of natural resources. Therefore spatiotemporal ecological vulnerability analysis is necessary for the current situation for sustainable development with protection of fragile eco-environment. Remote sensing is a unique tool to provide complete and continuous land surface information at different scales, which can use for eco-environment analysis. A methodology constructed on the principal component analysis (PCA) to identify satellite remote sensing ecological index (RSEI) for ecological vulnerability analysis and distribution based on four land surface parameters (dryness, greenness, temperature and moisture) by using Landsat TM/ETM+/OLI/TIRS data in the Samara region Russia. The results were verified by the following four methods: location-based, categorization-based, correlation-based and city center to outwards distance-based comparisons. Results indicate that ecological condition was improved from 2010 to 2015 as RSEI increased from 0.79 to 0.98 and from 2015 to 2020 the ecological condition was degraded as RSEI decreased from 0.98 to 0.82 but overall it was improved in this decade. RSEI distribution curve shows moderate to good and excellent ecological conditions and degraded ecological condition was basically characterized by high human interference and socioeconomic activities in the study area. Such a technique is a baseline for highly accurate ecological conditions mapping, monitoring and can use for decision making, management and sustainable development.

RevDate: 2021-06-21
CmpDate: 2021-06-21

Titus M, Hagstrom G, JR Watson (2021)

Unsupervised manifold learning of collective behavior.

PLoS computational biology, 17(2):e1007811.

Collective behavior is an emergent property of numerous complex systems, from financial markets to cancer cells to predator-prey ecological systems. Characterizing modes of collective behavior is often done through human observation, training generative models, or other supervised learning techniques. Each of these cases requires knowledge of and a method for characterizing the macro-state(s) of the system. This presents a challenge for studying novel systems where there may be little prior knowledge. Here, we present a new unsupervised method of detecting emergent behavior in complex systems, and discerning between distinct collective behaviors. We require only metrics, d(1), d(2), defined on the set of agents, X, which measure agents' nearness in variables of interest. We apply the method of diffusion maps to the systems (X, d(i)) to recover efficient embeddings of their interaction networks. Comparing these geometries, we formulate a measure of similarity between two networks, called the map alignment statistic (MAS). A large MAS is evidence that the two networks are codetermined in some fashion, indicating an emergent relationship between the metrics d(1) and d(2). Additionally, the form of the macro-scale organization is encoded in the covariances among the two sets of diffusion map components. Using these covariances we discern between different modes of collective behavior in a data-driven, unsupervised manner. This method is demonstrated on a synthetic flocking model as well as empirical fish schooling data. We show that our state classification subdivides the known behaviors of the school in a meaningful manner, leading to a finer description of the system's behavior.

RevDate: 2021-05-14
CmpDate: 2021-05-14

Vörös D, Könnyű B, T Czárán (2021)

Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism.

PLoS computational biology, 17(1):e1008634.

The Metabolically Coupled Replicator System (MCRS) model of early chemical evolution offers a plausible and efficient mechanism for the self-assembly and the maintenance of prebiotic RNA replicator communities, the likely predecessors of all life forms on Earth. The MCRS can keep different replicator species together due to their mandatory metabolic cooperation and limited mobility on mineral surfaces, catalysing reaction steps of a coherent reaction network that produces their own monomers from externally supplied compounds. The complexity of the MCRS chemical engine can be increased by assuming that each replicator species may catalyse more than a single reaction of metabolism, with different catalytic activities of the same RNA sequence being in a trade-off relation: one catalytic activity of a promiscuous ribozyme can increase only at the expense of the others on the same RNA strand. Using extensive spatially explicit computer simulations we have studied the possibility and the conditions of evolving ribozyme promiscuity in an initial community of single-activity replicators attached to a 2D surface, assuming an additional trade-off between replicability and catalytic activity. We conclude that our promiscuous replicators evolve under weak catalytic trade-off, relatively strong activity/replicability trade-off and low surface mobility of the replicators and the metabolites they produce, whereas catalytic specialists benefit from very strong catalytic trade-off, weak activity/replicability trade-off and high mobility. We argue that the combination of conditions for evolving promiscuity are more probable to occur for surface-bound RNA replicators, suggesting that catalytic promiscuity may have been a significant factor in the diversification of prebiotic metabolic reaction networks.

RevDate: 2021-04-22
CmpDate: 2021-04-22

Wieters B, Steige KA, He F, et al (2021)

Polygenic adaptation of rosette growth in Arabidopsis thaliana.

PLoS genetics, 17(1):e1008748.

The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.

RevDate: 2021-03-18
CmpDate: 2021-03-18

Kang A, Ren L, Hua C, et al (2021)

Environmental management strategy in response to COVID-19 in China: Based on text mining of government open information.

The Science of the total environment, 769:145158.

Coronavirus disease 2019 (COVID-19) is a global pandemic and a major health emergency. In the process of fighting against COVID-19, the China Ministry of Ecology and Environment (MEE) responded quickly and set up a working group as soon as possible. This article uses text mining to retrospectively analyze the government's public information on the website of MEE during the epidemic, sort out the timeline of MEE's response to COVID-19. We find that MEE's work during the COVID-19 pandemic is focused on medical waste and wastewater treatment, environment emergency monitoring, pollution prevention, and other environmental management for supporting economic recovery. It drafted three main medical waste management plans, an emergency environmental monitoring plan, and formulated "two lists" - a Positive checklist for Environmental impact assessment (EIA) approval and a positive checklist for supervision and enforcement, to promote the resumption of work and production. 2020 is the final year of China's "three years of fighting pollution prevention and control". In the case of the sudden COVID-19 epidemic, the Chinese environment department has ensured that the quality of the ecological environment has not been affected by the epidemic prevention and control while ensuring the smooth progress of the fight against pollution. China's medical waste disposal capacity has also been greatly improved during this epidemic. The review of China's environmental management strategy in response to COVID-19 can provide a reference for countries in the world that are still in the critical period of epidemic control; it can provide action guidelines for the ecological environment system to respond to sudden pandemic events in the future.

RevDate: 2021-06-28
CmpDate: 2021-06-28

Marconi S, Graves SJ, Weinstein BG, et al (2021)

Estimating individual-level plant traits at scale.

Ecological applications : a publication of the Ecological Society of America, 31(4):e02300.

Functional ecology has increasingly focused on describing ecological communities based on their traits (measurable features affecting individuals' fitness and performance). Analyzing trait distributions within and among forests could significantly improve understanding of community composition and ecosystem function. Historically, data on trait distributions are generated by (1) collecting a small number of leaves from a small number of trees, which suffers from limited sampling but produces information at the fundamental ecological unit (the individual), or (2) using remote-sensing images to infer traits, producing information continuously across large regions, but as plots (containing multiple trees of different species) or pixels, not individuals. Remote-sensing methods that identify individual trees and estimate their traits would provide the benefits of both approaches, producing continuous large-scale data linked to biological individuals. We used data from the National Ecological Observatory Network (NEON) to develop a method to scale up functional traits from 160 trees to the millions of trees within the spatial extent of two NEON sites. The pipeline consists of three stages: (1) image segmentation, to identify individual trees and estimate structural traits; (2) an ensemble of models to infer leaf mass area (LMA), nitrogen, carbon, and phosphorus content using hyperspectral signatures, and DBH from allometry; and (3) predictions for segmented crowns for the full remote-sensing footprint at the NEON sites. The R2 values on held-out test data ranged from 0.41 to 0.75 on held-out test data. The ensemble approach performed better than single partial least-squares models. Carbon performed poorly compared to other traits (R2 of 0.41). The crown segmentation step contributed the most uncertainty in the pipeline, due to over-segmentation. The pipeline produced good estimates of DBH (R2 of 0.62 on held-out data). Trait predictions for crowns performed significantly better than comparable predictions on pixels, resulting in improvement of R2 on test data of between 0.07 and 0.26. We used the pipeline to produce individual-level trait data for ~5 million individual crowns, covering a total extent of ~360 km2 . This large data set allows testing ecological questions on landscape scales, revealing that foliar traits are correlated with structural traits and environmental conditions.

RevDate: 2021-07-29
CmpDate: 2021-06-09

Grunert K, Holden H, Jakobsen ER, et al (2021)

Evolutionarily stable strategies in stable and periodically fluctuating populations: The Rosenzweig-MacArthur predator-prey model.

Proceedings of the National Academy of Sciences of the United States of America, 118(4):.

An evolutionarily stable strategy (ESS) is an evolutionary strategy that, if adapted by a population, cannot be invaded by any deviating (mutant) strategy. The concept of ESS has been extensively studied and widely applied in ecology and evolutionary biology [M. Smith, On Evolution (1972)] but typically on the assumption that the system is ecologically stable. With reference to a Rosenzweig-MacArthur predator-prey model [M. Rosenzweig, R. MacArthur, Am. Nat. 97, 209-223 (1963)], we derive the mathematical conditions for the existence of an ESS when the ecological dynamics have asymptotically stable limit points as well as limit cycles. By extending the framework of Reed and Stenseth [J. Reed, N. C. Stenseth, J. Theoret. Biol. 108, 491-508 (1984)], we find that ESSs occur at values of the evolutionary strategies that are local optima of certain functions of the model parameters. These functions are identified and shown to have a similar form for both stable and fluctuating populations. We illustrate these results with a concrete example.

RevDate: 2021-01-28
CmpDate: 2021-01-28

Khataee H, Scheuring I, Czirok A, et al (2021)

Effects of social distancing on the spreading of COVID-19 inferred from mobile phone data.

Scientific reports, 11(1):1661.

A better understanding of how the COVID-19 pandemic responds to social distancing efforts is required for the control of future outbreaks and to calibrate partial lock-downs. We present quantitative relationships between key parameters characterizing the COVID-19 epidemiology and social distancing efforts of nine selected European countries. Epidemiological parameters were extracted from the number of daily deaths data, while mitigation efforts are estimated from mobile phone tracking data. The decrease of the basic reproductive number ([Formula: see text]) as well as the duration of the initial exponential expansion phase of the epidemic strongly correlates with the magnitude of mobility reduction. Utilizing these relationships we decipher the relative impact of the timing and the extent of social distancing on the total death burden of the pandemic.

RevDate: 2021-02-24
CmpDate: 2021-02-23

Pinkert S, Friess N, Zeuss D, et al (2020)

Mobility costs and energy uptake mediate the effects of morphological traits on species' distribution and abundance.

Ecology, 101(10):e03121.

Individuals of large or dark-colored ectothermic species often have a higher reproduction and activity than small or light-colored ones. However, investments into body size or darker colors should negatively affect the fitness of individuals as they increase their growth and maintenance costs. Thus, it is unlikely that morphological traits directly affect species' distribution and abundance. Yet, this simplification is frequently made in trait-based ecological analyses. Here, we integrated the energy allocation strategies of species into an ecophysiological framework to explore the mechanisms that link species' morphological traits and population dynamics. We hypothesized that the effects of morphological traits on species' distribution and abundance are not direct but mediated by components of the energy budget and that species can allocate more energy towards dispersal and reproduction if they compensate their energetic costs by reducing mobility costs or increasing energy uptake. To classify species' energy allocation strategies, we used easily measured proxies for the mobility costs and energy uptake of butterflies that can be also applied to other taxa. We demonstrated that contrasting effects of morphological traits on distribution and abundance of butterfly species offset each other when species' energy allocation strategies are not taken into account. Larger and darker butterfly species had wider distributions and were more abundant if they compensated the investment into body size and color darkness (i.e., melanin) by reducing their mobility costs or increasing energy uptake. Adults of darker species were more mobile and foraged less compared to lighter colored ones, if an investment into melanin was indirectly compensated via a size-dependent reduction of mobility costs or increase of energy uptake. Our results indicate that differences in the energy allocations strategies of species account for a considerable part of the variation in species' distribution and abundance that is left unexplained by morphological traits alone and ignoring these differences can lead to false mechanistic conclusions. Therefore, our findings highlight the potential of integrating proxies for species' energy allocation strategies into trait-based models not only for understanding the physiological mechanisms underlying variation in species' distribution and abundance, but also for improving predictions of the population dynamics of species.

RevDate: 2021-05-12
CmpDate: 2021-05-12

Hassine TB, Ali MB, Ghodhbane I, et al (2021)

Rabies in Tunisia: A spatio-temporal analysis in the region of CapBon-Nabeul.

Acta tropica, 216:105822.

Human rabies is a significant public health concern in Tunisia. However, the spatiotemporal spread pattern of rabies in dogs, the major reservoir and vector, and its determinants are poorly understood. We collected geographic locations and timeline of reported animal rabies cases in the region of CapBon (study area), for the years 2015-2019 and integrated them in Geographical Information System (GIS) approach to explore the spatio-temporal pattern of dog rabies. The results show that roads and irrigated areas can act as ecological corridors to viral spread. Our study showed that there was a significant seasonal variation in the number of cases of rabies recorded, with a strong peak in spring and lower peak in winter and summer. These findings may play a role in updating and directing public health policy, as well as providing opportunities for authorities to explore control options in time and space. A better knowledge of the ecology and dog population dynamics is still necessary and important to achieve an effective rabies control.

RevDate: 2021-05-12

Zhou Y, Shearwin-Whyatt L, Li J, et al (2021)

Platypus and echidna genomes reveal mammalian biology and evolution.

Nature, 592(7856):756-762.

Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.

RevDate: 2021-05-10
CmpDate: 2021-05-10

Keshavarzi A, Kumar V, Ertunç G, et al (2021)

Ecological risk assessment and source apportionment of heavy metals contamination: an appraisal based on the Tellus soil survey.

Environmental geochemistry and health, 43(5):2121-2142.

It is imperative to comprehend the level and spatial distribution of soil pollution with heavy metals to find sustainable management approaches for affected soils. Selected heavy metals (Mn, Zn, Pb, Cu, Cr, Ni, As, Co, and Cd) and physiochemical parameters were appraised for 620 samples from industrial, agricultural and urban sites in Northern Ireland using the Tellus database. The findings of this study showed that among the analyzed heavy metals, Mn content was the highest and Cd content the lowest. Pearson's correlation analysis revealed that heavy metals were highly correlated with each other, signifying similar sources for the heavy metals. Mixed factors (anthropogenic and lithogenic) were responsible for the contribution of heavy metals as revealed by multivariate statistical analysis. The results of contamination factor and enrichment factor analyses suggest that As, Cd, and Pb showed very high risk for pollution in the study area. The geoaccumulation index revealed that with the exception of Cd, all analyzed heavy metals showed severe accumulation in the soils. The potential and modified ecological risk indices inferred that Cd, As, and Pb represented ecological threats in the soils of Northern Ireland. The findings of this study will aid in forming approaches to decrease the risks associated with heavy metals in industrial, urban and agricultural soils, and help create guidelines to protect the environment from long-term accumulation of heavy metals.

RevDate: 2021-04-23
CmpDate: 2021-04-23

Lemm JU, Venohr M, Globevnik L, et al (2021)

Multiple stressors determine river ecological status at the European scale: Towards an integrated understanding of river status deterioration.

Global change biology, 27(9):1962-1975.

The biota of European rivers are affected by a wide range of stressors impairing water quality and hydro-morphology. Only about 40% of Europe's rivers reach 'good ecological status', a target set by the European Water Framework Directive (WFD) and indicated by the biota. It is yet unknown how the different stressors in concert impact ecological status and how the relationship between stressors and status differs between river types. We linked the intensity of seven stressors to recently measured ecological status data for more than 50,000 sub-catchment units (covering almost 80% of Europe's surface area), which were distributed among 12 broad river types. Stressor data were either derived from remote sensing data (extent of urban and agricultural land use in the riparian zone) or modelled (alteration of mean annual flow and of base flow, total phosphorous load, total nitrogen load and mixture toxic pressure, a composite metric for toxic substances), while data on ecological status were taken from national statutory reporting of the second WFD River Basin Management Plans for the years 2010-2015. We used Boosted Regression Trees to link ecological status to stressor intensities. The stressors explained on average 61% of deviance in ecological status for the 12 individual river types, with all seven stressors contributing considerably to this explanation. On average, 39.4% of the deviance was explained by altered hydro-morphology (morphology: 23.2%; hydrology: 16.2%), 34.4% by nutrient enrichment and 26.2% by toxic substances. More than half of the total deviance was explained by stressor interaction, with nutrient enrichment and toxic substances interacting most frequently and strongly. Our results underline that the biota of all European river types are determined by co-occurring and interacting multiple stressors, lending support to the conclusion that fundamental management strategies at the catchment scale are required to reach the ambitious objective of good ecological status of surface waters.

RevDate: 2021-08-29

Allen DC, Datry T, Boersma KS, et al (2020)

River ecosystem conceptual models and non-perennial rivers: A critical review.

WIREs. Water, 7(5):.

Conceptual models underpin river ecosystem research. However, current models focus on continuously flowing rivers and few explicitly address characteristics such as flow cessation and drying. The applicability of existing conceptual models to nonperennial rivers that cease to flow (intermittent rivers and ephemeral streams, IRES) has not been evaluated. We reviewed 18 models, finding that they collectively describe main drivers of biogeochemical and ecological patterns and processes longitudinally (upstream-downstream), laterally (channel-riparian-floodplain), vertically (surface water-groundwater), and temporally across local and landscape scales. However, perennial rivers are longitudinally continuous while IRES are longitudinally discontinuous. Whereas perennial rivers have bidirectional lateral connections between aquatic and terrestrial ecosystems, in IRES, this connection is unidirectional for much of the time, from terrestrial-to-aquatic only. Vertical connectivity between surface and subsurface water occurs bidirectionally and is temporally consistent in perennial rivers. However, in IRES, this exchange is temporally variable, and can become unidirectional during drying or rewetting phases. Finally, drying adds another dimension of flow variation to be considered across temporal and spatial scales in IRES, much as flooding is considered as a temporally and spatially dynamic process in perennial rivers. Here, we focus on ways in which existing models could be modified to accommodate drying as a fundamental process that can alter these patterns and processes across spatial and temporal dimensions in streams. This perspective is needed to support river science and management in our era of rapid global change, including increasing duration, frequency, and occurrence of drying.

RevDate: 2021-01-23
CmpDate: 2021-01-07

Grantham HS, Duncan A, Evans TD, et al (2020)

Anthropogenic modification of forests means only 40% of remaining forests have high ecosystem integrity.

Nature communications, 11(1):5978.

Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.

RevDate: 2021-04-21
CmpDate: 2021-04-21

Hassell JM, Bettridge JM, Ward MJ, et al (2021)

Socio-ecological drivers of vertebrate biodiversity and human-animal interfaces across an urban landscape.

Global change biology, 27(4):781-792.

Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large-scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co-exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio-ecological drivers occurring across the city. By characterizing landscape-scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy.

RevDate: 2021-04-22
CmpDate: 2021-04-22

Dührkop K, Nothias LF, Fleischauer M, et al (2021)

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.

Nature biotechnology, 39(4):462-471.

Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is limited to structures present in libraries or databases, restricting analysis and interpretation of experimental data. Here we describe CANOPUS (class assignment and ontology prediction using mass spectrometry), a computational tool for systematic compound class annotation. CANOPUS uses a deep neural network to predict 2,497 compound classes from fragmentation spectra, including all biologically relevant classes. CANOPUS explicitly targets compounds for which neither spectral nor structural reference data are available and predicts classes lacking tandem mass spectrometry training data. In evaluation using reference data, CANOPUS reached very high prediction performance (average accuracy of 99.7% in cross-validation) and outperformed four baseline methods. We demonstrate the broad utility of CANOPUS by investigating the effect of microbial colonization in the mouse digestive system, through analysis of the chemodiversity of different Euphorbia plants and regarding the discovery of a marine natural product, revealing biological insights at the compound class level.

RevDate: 2021-04-26
CmpDate: 2021-04-26

McLean BS, RP Guralnick (2021)

Digital biodiversity data sets reveal breeding phenology and its drivers in a widespread North American mammal.

Ecology, 102(3):e03258.

Shifts in reproductive timing are among the most commonly documented responses of organisms to global climate change. However, our knowledge of these responses is biased towards taxa that are easily observable and abundant in existing biodiversity data sets. Mammals are common subjects in reproductive biology, but mammalian phenology and its drivers in the wild remain poorly understood because many species are small, secretive, or too labor-intensive to monitor. We took an informatics-based approach to reconstructing breeding phenology in the widespread North American deer mouse (Peromyscus maniculatus) using individual-level reproductive observations from digitized museum specimens and field censuses spanning >100 yr and >45 degrees of latitude. We reconstructed female phenology in different regions and tested the importance of three environmental variables (photoperiod, temperature, precipitation) as breeding cues. Photoperiod and temperature were strong positive and negative breeding cues, respectively, whereas precipitation was not a significant predictor of breeding phenology. However, phenologies and the use of environmental cues varied substantially among regions, and we found evidence that these cueing repertoires are tuned to ecosystem-specific limiting conditions. Our results reiterate the importance of ecological context in optimizing reproduction and demonstrate how harmonization across biodiversity data resources allows new insight into phenology and its drivers in wild mammals.

RevDate: 2021-05-14
CmpDate: 2021-05-14

Wu X, Li X, Wang W, et al (2020)

Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients.

BMC genomics, 21(Suppl 10):697.

BACKGROUND: Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people's health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is very limited.

RESULTS: An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling of Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao tissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao.

CONCLUSIONS: The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.

RevDate: 2021-09-16

Culina A, Adriaensen F, Bailey LD, et al (2021)

Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub.

The Journal of animal ecology, 90(9):2147-2160.

The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.

RevDate: 2021-08-12
CmpDate: 2021-03-08

Tripathi A, Vázquez-Baeza Y, Gauglitz JM, et al (2021)

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.

Nature chemical biology, 17(2):146-151.

Untargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on the hierarchical organization of molecular fingerprints predicted from fragmentation spectra. Qemistree allows mass spectrometry data to be represented in the context of sample metadata and chemical ontologies. By expressing molecular relationships as a tree, we can apply ecological tools that are designed to analyze and visualize the relatedness of DNA sequences to metabolomics data. Here we demonstrate the use of tree-guided data exploration tools to compare metabolomics samples across different experimental conditions such as chromatographic shifts. Additionally, we leverage a tree representation to visualize chemical diversity in a heterogeneous collection of samples. The Qemistree software pipeline is freely available to the microbiome and metabolomics communities in the form of a QIIME2 plugin, and a global natural products social molecular networking workflow.

RevDate: 2020-11-17

Rosen GL, P Hammrich (2020)

Teaching Microbiome Analysis: From Design to Computation Through Inquiry.

Frontiers in microbiology, 11:528051.

In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre- and post-surveys of these individual classes still showed progress toward learning objectives. It is expected that students trained will enter the workforce with skills needed to innovate in the biotechnology, health, and environmental industries. Students are trained to maximize impact and tackle real world problems in biology and medicine with their learned knowledge of data science and machine learning. The course materials for the new microbiome analysis course are available on Github: https://github.com/EESI/Comp_Metagenomics_resources.

RevDate: 2021-03-22
CmpDate: 2021-03-22

García-Jiménez R, Margalida A, JM Pérez-García (2020)

Influence of individual biological traits on GPS fix-loss errors in wild bird tracking.

Scientific reports, 10(1):19621.

In recent decades, global positioning system (GPS) location data and satellite telemetry systems for data transmission have become fundamental in the study of basic ecological traits in wildlife biology. Evaluating GPS location errors is essential in assessing detailed information about the behaviour of an animal species such as migration, habitat selection, species distribution or foraging strategy. While many studies of the influence of environmental and technical factors on the fix errors of solar-powered GPS transmitters have been published, few studies have focussed on the performance of GPS systems in relation to a species' biological traits. Here, we evaluate the possible effects of the biological traits of a large raptor on the frequency of lost fixes-the fix-loss rate (FLR). We analysed 95,686 records obtained from 20 Bearded Vultures Gypaetus barbatus tracked with 17 solar-powered satellite transmitters in the Pyrenees (Spain, France and Andorra), between 2006 and 2019 to evaluate the influence of biological, technical, and environmental factors on the fix-loss rate of transmitters. We show that combined effects of technical factors and the biological traits of birds explained 23% of the deviance observed. As expected, the transmitter usage time significantly increased errors in the fix-loss rate, although the flight activity of birds revealed an unexpected trade-off: the greater the proportion of fixes recorded from perched birds, the lower the FLR. This finding seems related with the fact that territorial and breeding birds spend significantly more time flying than non-territorial individuals. The fix success rate is apparently due to the interactions between a complex of factors. Non-territorial adults and subadults, males, and breeding individuals showed a significantly lower FLR than juveniles-immatures females, territorial birds or non-breeding individuals. Animal telemetry tracking studies should include error analyses before reaching any ecological conclusions or hypotheses about spatial distribution.

RevDate: 2020-12-24
CmpDate: 2020-12-24

Altamiranda-Saavedra M, Osorio-Olvera L, Yáñez-Arenas C, et al (2020)

Geographic abundance patterns explained by niche centrality hypothesis in two Chagas disease vectors in Latin America.

PloS one, 15(11):e0241710.

Ecoepidemiological scenarios for Chagas disease transmission are complex, so vector control measures to decrease human-vector contact and prevent infection transmission are difficult to implement in all geographic contexts. This study assessed the geographic abundance patterns of two vector species of Chagas disease: Triatoma maculata (Erichson, 1848) and Rhodnius pallescens (Barber, 1932) in Latin America. We modeled their potential distribution using the maximum entropy algorithm implemented in Maxent and calculated distances to their niche centroid by fitting a minimum-volume ellipsoid. In addition, to determine which method would accurately explain geographic abundance patterns, we compared the correlation between population abundance and the distance to the ecological niche centroid (DNC) and between population abundance and Maxent environmental suitability. The potential distribution estimated for T. maculata showed that environmental suitability covers a large area, from Panama to Northern Brazil. R. pallescens showed a more restricted potential distribution, with environmental suitability covering mostly the coastal zone of Costa Rica and some areas in Nicaragua, Honduras, Belize and the Yucatán Peninsula in Mexico, northern Colombia, Acre, and Rondônia states in Brazil, as well as a small region of the western Brazilian Amazon. We found a negative slope in the relationship between population abundance and the DNC in both species. R. pallecens has a more extensive potential latitudinal range than previously reported, and the distribution model for T. maculata corroborates previous studies. In addition, population abundance increases according to the niche centroid proximity, indicating that population abundance is limited by the set of scenopoetic variables at coarser scales (non-interactive variables) used to determine the ecological niche. These findings might be used by public health agencies in Latin America to implement actions and support programs for disease prevention and vector control, identifying areas in which to expand entomological surveillance and maintain chemical control, in order to decrease human-vector contact.

RevDate: 2021-03-26
CmpDate: 2021-03-26

Petrushin I, Belikov S, L Chernogor (2020)

Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskia baicalensis.

International journal of molecular sciences, 21(21):.

Endemic freshwater sponges (demosponges, Lubomirskiidae) dominate in Lake Baikal, Central Siberia, Russia. These sponges are multicellular filter-feeding animals that represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of Lubomirskia baicalensis has been a significant problem in Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria from the families Flavobacteriaceae and Oxalobacteraceae dominate the microbiomes of diseased sponges. Both species are opportunistic pathogens common in freshwater ecosystems. The aim of our study was to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. Janthinobacterium sp. SLB01 attacks other cells using a type VI secretion system and suppresses gram-positive bacteria with violacein, and regulates its own activity via quorum sensing. It produces floc and strong biofilm by exopolysaccharide biosynthesis and PEP-CTERM/XrtA protein expression. Flavobacterium sp. SLB02 utilizes the fragments of cell walls produced by polysaccharides. These two strains have a marked difference in carbohydrate acquisition. We described a possible means of joint occupation of the ecological niche in the freshwater sponge microbial community. This study expands the understanding of the symbiotic relationship of microorganisms with freshwater Baikal sponges.

RevDate: 2021-08-27

Yamaguchi K, Koyanagi M, S Kuraku (2021)

Visual and nonvisual opsin genes of sharks and other nonosteichthyan vertebrates: Genomic exploration of underwater photoreception.

Journal of evolutionary biology, 34(6):968-976.

Vision of sharks embraces various biological and ecological themes ranging from predation and adaptation to deep-sea life. However, behavioural and genetic studies have been limited by their elusive lifestyles, repeatedly reported declines of wild populations, and their unique life-history traits including low fecundity and enhanced longevity. Sharks have also not been actively studied on the cellular and molecular levels, because of additional difficulties in cell culture, tissue collection and genome sequencing. A recent study circumvented some of these obstacles by means of genome informatics thereby portrayed the variation of visual opsin gene repertoires among elasmobranchs (sharks and rays) and spectral shifts of the rhodopsin pigment. Comprehensive surveys in whole-genome sequences are also revealing the repertoires of nonvisual opsins with unknown functions. This review is aimed to summarize existing studies on shark opsins with an emphasis on genomic investigation of gene repertoires and to provide insights into the better understanding of underwater ecology of marine megafauna with in vitro experimentation.

RevDate: 2020-11-17
CmpDate: 2020-11-17

Sala C, Giampieri E, Vitali S, et al (2020)

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging.

PloS one, 15(10):e0237207.

In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.

RevDate: 2020-11-12
CmpDate: 2020-11-06

Cai W, Snyder J, Hastings A, et al (2020)

Mutualistic networks emerging from adaptive niche-based interactions.

Nature communications, 11(1):5470.

Mutualistic networks are vital ecological and social systems shaped by adaptation and evolution. They involve bipartite cooperation via the exchange of goods or services between actors of different types. Empirical observations of mutualistic networks across genres and geographic conditions reveal correlated nested and modular patterns. Yet, the underlying mechanism for the network assembly remains unclear. We propose a niche-based adaptive mechanism where both nestedness and modularity emerge simultaneously as complementary facets of an optimal niche structure. Key dynamical properties are revealed at different timescales. Foremost, mutualism can either enhance or reduce the network stability, depending on competition intensity. Moreover, structural adaptations are asymmetric, exhibiting strong hysteresis in response to environmental change. Finally, at the evolutionary timescale we show that the adaptive mechanism plays a crucial role in preserving the distinctive patterns of mutualism under species invasions and extinctions.

RevDate: 2021-08-16
CmpDate: 2021-08-16

Zrimec J (2020)

Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.

MicrobiologyOpen, 9(12):e1129.

Antimicrobial resistance poses a great danger to humanity, in part due to the widespread horizontal gene transfer of plasmids via conjugation. Modeling of plasmid transfer is essential to uncovering the fundamentals of resistance transfer and for the development of predictive measures to limit the spread of resistance. However, a major limitation in the current understanding of plasmids is the incomplete characterization of the conjugative DNA transfer mechanisms, which conceals the actual potential for plasmid transfer in nature. Here, we consider that the plasmid-borne origin-of-transfer substrates encode specific DNA structural properties that can facilitate finding these regions in large datasets and develop a DNA structure-based alignment procedure for typing the transfer substrates that outperforms sequence-based approaches. Thousands of putative DNA transfer substrates are identified, showing that plasmid mobility can be twofold higher and span almost twofold more host species than is currently known. Over half of all putative mobile plasmids contain the means for mobilization by conjugation systems belonging to different mobility groups, which can hypothetically link previously confined host ranges across ecological habitats into a robust plasmid transfer network. This hypothetical network is found to facilitate the transfer of antimicrobial resistance from environmental genetic reservoirs to human pathogens, which might be an important driver of the observed rapid resistance development in humans and thus an important point of focus for future prevention measures.

RevDate: 2021-05-20
CmpDate: 2021-05-20

de Mestral C, Hussain MA, Austin PC, et al (2020)

Regional health care services and rates of lower extremity amputation related to diabetes and peripheral artery disease: an ecological study.

CMAJ open, 8(4):E659-E666.

BACKGROUND: The care necessary to prevent amputation from diabetes and peripheral artery disease (PAD) remains disjointed in many jurisdictions. To help inform integrated regional care, this study explores the correlation between regional health care services and rates of lower extremity amputation.

METHODS: This ecological study included 14 administrative health regions in Ontario, Canada. All diabetes- or PAD-related major (above ankle) amputations (Apr. 1, 2007, to Mar. 31, 2017) were identified among residents 40 years of age and older. For each region, age-and sex-adjusted amputation rates were calculated as well as per capita counts of key health providers (podiatrists and chiropodists, as well as surgeons) and health care utilization among study patients in the year before the first major amputation (physician visits, publicly funded podiatry visits, emergency department visits, hospital admissions, home care nursing, minor amputation, limb revascularization).

RESULTS: A total of 11 658 patients with major amputation were identified (of whom 79.2% had diabetes and 96.5% had PAD). There was wide regional variation in amputation rates: 2.53 to 11.77 per 100 000 person-quarters. At a regional level, the proportion of study patients who received revascularization showed the strongest negative correlation with amputation rates. The regional proportion of study patients who saw a vascular surgeon showed the strongest negative correlation with amputation rates, relative to other health provider visits. Other measures of health care utilization among patients correlated poorly with regional amputation rates, as did the regional provider counts. The results were similar when we restricted the analysis to diabetes-related amputations.

INTERPRETATION: Amputation rates related to diabetes and PAD vary widely across Ontario. Access to vascular assessment and revascularization must be integrated into regional amputation prevention efforts.

RevDate: 2020-12-21
CmpDate: 2020-12-21

Snell Taylor S, Coyle JR, White EP, et al (2020)

A simulation study of the use of temporal occupancy for identifying core and transient species.

PloS one, 15(10):e0241198.

Transient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.

RevDate: 2021-04-06
CmpDate: 2021-04-06

Maák I, Tóth E, Lenda M, et al (2020)

Behaviours indicating cannibalistic necrophagy in ants are modulated by the perception of pathogen infection level.

Scientific reports, 10(1):17906.

Cannibalistic necrophagy is rarely observed in social hymenopterans, although a lack of food could easily favour such behaviour. One of the main supposed reasons for the rarity of necrophagy is that eating of nestmate corpses carries the risk of rapid spread of pathogens or parasites. Here we present an experimental laboratory study on behaviour indicating consumption of nestmate corpses in the ant Formica polyctena. We examined whether starvation and the fungal infection level of the corpses affects the occurrence of cannibalistic necrophagy. Our results showed that the ants distinguished between corpses of different types and with different levels of infection risk, adjusting their behaviour accordingly. The frequency of behaviours indicating cannibalistic necrophagy increased during starvation, although these behaviours seem to be fairly common in F. polyctena even in the presence of other food sources. The occurrence and significance of cannibalistic necrophagy deserve further research because, in addition to providing additional food, it may be part of the hygienic behaviour repertoire. The ability to detect infections and handle pathogens are important behavioural adaptations for social insects, crucial for the fitness of both individual workers and the entire colony.

RevDate: 2021-01-13
CmpDate: 2021-01-13

Middleton-Welling J, Dapporto L, García-Barros E, et al (2020)

A new comprehensive trait database of European and Maghreb butterflies, Papilionoidea.

Scientific data, 7(1):351.

Trait-based analyses explaining the different responses of species and communities to environmental changes are increasing in frequency. European butterflies are an indicator group that responds rapidly to environmental changes with extensive citizen science contributions to documenting changes of abundance and distribution. Species traits have been used to explain long- and short-term responses to climate, land-use and vegetation changes. Studies are often characterised by limited trait sets being used, with risks that the relative roles of different traits are not fully explored. Butterfly trait information is dispersed amongst various sources and descriptions sometimes differ between sources. We have therefore drawn together multiple information sets to provide a comprehensive trait database covering 542 taxa and 25 traits described by 217 variables and sub-states of the butterflies of Europe and Maghreb (northwest Africa) which should serve for improved trait-based ecological, conservation-related, phylogeographic and evolutionary studies of this group of insects. We provide this data in two forms; the basic data and as processed continuous and multinomial data, to enhance its potential usage.

RevDate: 2021-08-09
CmpDate: 2021-08-09

Riginos C, Crandall ED, Liggins L, et al (2020)

Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.

Molecular ecology resources, 20(6):1458-1469.

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.

RevDate: 2021-09-09
CmpDate: 2021-08-31

Martínez Martínez J, Martinez-Hernandez F, M Martinez-Garcia (2020)

Single-virus genomics and beyond.

Nature reviews. Microbiology, 18(12):705-716.

Viruses are extremely diverse and modulate important biological and ecological processes globally. However, much of viral diversity remains uncultured and yet to be discovered. Several powerful culture-independent tools, in particular metagenomics, have substantially advanced virus discovery. Among those tools is single-virus genomics, which yields sequenced reference genomes from individual sorted virus particles without the need for cultivation. This new method complements virus culturing and metagenomic approaches and its advantages include targeted investigation of specific virus groups and investigation of genomic microdiversity within viral populations. In this Review, we provide a brief history of single-virus genomics, outline how this emergent method has facilitated advances in virus ecology and discuss its current limitations and future potential. Finally, we address how this method may synergistically intersect with other single-virus and single-cell approaches.

RevDate: 2021-08-03
CmpDate: 2021-08-03

Loxley GM, Hooks DO, Antonopoulos A, et al (2020)

Vulpeculin: a novel and abundant lipocalin in the urine of the common brushtail possum, Trichosurus vulpecula.

Open biology, 10(10):200218.

Lipocalins are a family of secreted proteins. They are capable of binding small lipophilic compounds and have been extensively studied for their role in chemosignalling in rodent urine. Urine of the common brushtail possum (Trichosurus vulpecula) contains a prominent glycoprotein of 20 kDa, expressed in both sexes. We have isolated this protein and determined its primary sequence by mass spectrometry, including the use of metabolic labelling to resolve the leucine/isoleucine isobaric ambiguity. The protein sequence was identified as a lipocalin, and phylogenetic analysis grouped the protein with other marsupial lipocalin sequences in a phylogenetic clade distinct from established cross-species lipocalin sub-families. The pattern of expression in possum urine and the similarity in sequence and structure to other lipocalins suggests this protein may have a role in brushtail possum chemosignalling.

RevDate: 2021-04-19
CmpDate: 2021-04-19

Smith JE, N Pinter-Wollman (2021)

Observing the unwatchable: Integrating automated sensing, naturalistic observations and animal social network analysis in the age of big data.

The Journal of animal ecology, 90(1):62-75.

In the 4.5 decades since Altmann (1974) published her seminal paper on the methods for the observational study of behaviour, automated detection and analysis of social interaction networks have fundamentally transformed the ways that ecologists study social behaviour. Methodological developments for collecting data remotely on social behaviour involve indirect inference of associations, direct recordings of interactions and machine vision. These recent technological advances are improving the scale and resolution with which we can dissect interactions among animals. They are also revealing new intricacies of animal social interactions at spatial and temporal resolutions as well as in ecological contexts that have been hidden from humans, making the unwatchable seeable. We first outline how these technological applications are permitting researchers to collect exquisitely detailed information with little observer bias. We further recognize new emerging challenges from these new reality-mining approaches. While technological advances in automating data collection and its analysis are moving at an unprecedented rate, we urge ecologists to thoughtfully combine these new tools with classic behavioural and ecological monitoring methods to place our understanding of animal social networks within fundamental biological contexts.

RevDate: 2020-11-25
CmpDate: 2020-11-25

Sannigrahi S, Pilla F, Zhang Q, et al (2021)

Examining the effects of green revolution led agricultural expansion on net ecosystem service values in India using multiple valuation approaches.

Journal of environmental management, 277:111381.

Ecosystem Services (ESs) are bundles of natural processes and functions that are essential for human well-being, subsistence, and livelihoods. The 'Green Revolution' (GR) has substantial impact on the agricultural landscape and ESs in India. However, the effects of GR on ESs have not been adequately documented and analyzed. This leads to the main hypothesis of this work - 'the incremental trend of ESs in India is mainly prompted by GR led agricultural innovations that took place during 1960 - 1970'. The analysis was carried out through five successive steps. First, the spatiotemporal Ecosystem Service Values (ESVs) in Billion US$ for 1985, 1995, and 2005 were estimated using several value transfer approaches. Second, the sensitivity and elasticity of different ESs to land conversion were carried out using coefficient of sensitivity and coefficient of elasticity. Third, the Geographically Weighted Regression model was performed using five explanatory factors, i.e., total crop area, crop production, crop yield, net irrigated area, and cropping intensity, to explore the cumulative and individual effects of these driving factors on ESVs. Fourth, Multi-Layer Perceptron based Artificial Neural Network was employed to estimate the normalized importance of these explanatory factors. Fifth, simple and multiple linear regression modeling was done to assess the linear associations between the driving factors and the ESs. During the observation periods, cropland, forestland and water bodies contributed to 80%-90% of ESVs, followed by grassland, mangrove, wetland and urban built-up. In all three evaluation years, the highest estimated ESVs among the nine ES categories was provided by water regulation, followed by soil formation and soil-water retention, biodiversity maintenance, waste treatment, climate regulation, and greenhouse gas regulation. Among the five explanatory factors, total crop area, crop production, and net irrigated area showed strong positive associations with ESVs, while cropping intensity exhibited a negative association. Therefore, the study reveals a strong association between GR led agricultural expansion and ESVs in India. This study suggests that there should be an urgent need for formulation of rigorous ecosystem management strategies and policies to preserve ecological integrity and flow of uninterrupted ESs and to sustain human well-being.

RevDate: 2021-07-20
CmpDate: 2021-07-20

Dueholm MS, Andersen KS, McIlroy SJ, et al (2020)

Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax).

mBio, 11(5):.

High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.

RevDate: 2020-10-16

Juhász O, Fürjes-Mikó Á, Tenyér A, et al (2020)

Consequences of Climate Change-Induced Habitat Conversions on Red Wood Ants in a Central European Mountain: A Case Study.

Animals : an open access journal from MDPI, 10(9):.

The consequences of anthropogenic climate change are one of the major concerns of conservation biology. A cascade of negative effects is expected to affect various ecosystems, one of which is Central European coniferous forests and their unique biota. These coniferous forests are the primary habitat of many forest specialist species such as red wood ants. Climate change-induced rising of temperature allows trees to skip winter hibernation, making them more vulnerable to storms that cause wind felling, and in turn, promotes bark beetle infestations that results in unscheduled clear-cuttings. Red wood ants can also be exposed to such habitat changes. We investigated the effects of bark beetle-induced clear-cutting and the absence of coniferous trees on colonies of Formica polyctena, including a mixed-coniferous forest as a reference. Our aim was to investigate how these habitat features affect the nest characteristics and nesting habits of F. polyctena. Our results indicate that, in the absence of conifers, F. polyctena tend to use different alternatives for nest material, colony structure, and food sources. However, the vitality of F. polyctena colonies significantly decreased (smaller nest mound volumes). Our study highlights the ecological flexibility of this forest specialist and its potential to survive under extreme conditions.

RevDate: 2021-02-22
CmpDate: 2021-02-22

Laubmeier AN, Cazelles B, Cuddington K, et al (2020)

Ecological Dynamics: Integrating Empirical, Statistical, and Analytical Methods.

Trends in ecology & evolution, 35(12):1090-1099.

Understanding ecological processes and predicting long-term dynamics are ongoing challenges in ecology. To address these challenges, we suggest an approach combining mathematical analyses and Bayesian hierarchical statistical modeling with diverse data sources. Novel mathematical analysis of ecological dynamics permits a process-based understanding of conditions under which systems approach equilibrium, experience large oscillations, or persist in transient states. This understanding is improved by combining ecological models with empirical observations from a variety of sources. Bayesian hierarchical models explicitly couple process-based models and data, yielding probabilistic quantification of model parameters, system characteristics, and associated uncertainties. We outline relevant tools from dynamical analysis and hierarchical modeling and argue for their integration, demonstrating the value of this synthetic approach through a simple predator-prey example.

RevDate: 2021-09-10
CmpDate: 2021-03-25

Pârvulescu L, Iorgu EI, Zaharia C, et al (2020)

The future of endangered crayfish in light of protected areas and habitat fragmentation.

Scientific reports, 10(1):14870.

The long-term survival of a species requires, among other things, gene flow between populations. Approaches for the evaluation of fragmentation in the frame of freshwater habitats consider only a small amount of the information that combined demography and geography are currently able to provide. This study addresses two species of Austropotamobius crayfish in the light of population genetics, spatial ecology and protected areas of the Carpathians. Advancing the classical approaches, we defined ecological distances upon the rasterised river network as a surrogate of habitat resistance to migration, quantifying the deviations from the species´ suitability range for a set of relevant geospatial variables in each cell of the network. Molecular analyses revealed the populations of the two Austropotamobius crayfish species are clearly distinct, lacking hybridisation. Comparing pairs of populations, we found, in some cases, a strong disagreement regarding genetic and ecological distances, potentially due to human-mediated translocations or the geophysical phenomena of regressive erosion, which may have led to unexpected colonisation routes. Protected areas were found to offer appropriate local habitat conditions but failed to ensure connectivity. The methodology applied in this study allowed us to quantify the contribution of each geospatial (environmental) variable to the overall effect of fragmentation, and we found that water quality was the most important variable. A multilevel approach proved to reveal a better understanding of drivers behind the distribution patterns, which can lead to more adequate conservation measures.

RevDate: 2020-10-29
CmpDate: 2020-09-21

Guo Y, Wang H, Wu Z, et al (2020)

Modified Red Blue Vegetation Index for Chlorophyll Estimation and Yield Prediction of Maize from Visible Images Captured by UAV.

Sensors (Basel, Switzerland), 20(18):.

The vegetation index (VI) has been successfully used to monitor the growth and to predict the yield of agricultural crops. In this paper, a long-term observation was conducted for the yield prediction of maize using an unmanned aerial vehicle (UAV) and estimations of chlorophyll contents using SPAD-502. A new vegetation index termed as modified red blue VI (MRBVI) was developed to monitor the growth and to predict the yields of maize by establishing relationships between MRBVI- and SPAD-502-based chlorophyll contents. The coefficients of determination (R2s) were 0.462 and 0.570 in chlorophyll contents' estimations and yield predictions using MRBVI, and the results were relatively better than the results from the seven other commonly used VI approaches. All VIs during the different growth stages of maize were calculated and compared with the measured values of chlorophyll contents directly, and the relative error (RE) of MRBVI is the lowest at 0.355. Further, machine learning (ML) methods such as the backpropagation neural network model (BP), support vector machine (SVM), random forest (RF), and extreme learning machine (ELM) were adopted for predicting the yields of maize. All VIs calculated for each image captured during important phenological stages of maize were set as independent variables and the corresponding yields of each plot were defined as dependent variables. The ML models used the leave one out method (LOO), where the root mean square errors (RMSEs) were 2.157, 1.099, 1.146, and 1.698 (g/hundred grain weight) for BP, SVM, RF, and ELM. The mean absolute errors (MAEs) were 1.739, 0.886, 0.925, and 1.356 (g/hundred grain weight) for BP, SVM, RF, and ELM, respectively. Thus, the SVM method performed better in predicting the yields of maize than the other ML methods. Therefore, it is strongly suggested that the MRBVI calculated from images acquired at different growth stages integrated with advanced ML methods should be used for agricultural- and ecological-related chlorophyll estimation and yield predictions.

RevDate: 2021-05-13
CmpDate: 2021-02-25

Nam S, Dunton GF, Ordway MR, et al (2020)

Feasibility and acceptability of intensive, real-time biobehavioral data collection using ecological momentary assessment, salivary biomarkers, and accelerometers among middle-aged African Americans.

Research in nursing & health, 43(5):453-464.

Perceived racial discrimination is linked to unhealthy behaviors and stress-related morbidities. A compelling body of research indicates that perceived racial discrimination may contribute to health disparities among African Americans (AAs). The purposes of this study were to describe the study protocol including data collection procedures and study measures and to evaluate the feasibility and acceptability of intensive biobehavioral data collection using ecological momentary assessment (EMA), salivary biomarkers, and accelerometers over 7 days among middle-aged AAs with a goal of understanding the relationships between perceived racial discrimination and biobehavioral responses to stress. Twelve AA men and women participated in the feasibility/acceptability study. They completed surveys, anthropometrics, and received in-person training in EMA and saliva sample collection at baseline. Participants were asked to respond to the random prompt text message-based EMA five times a day, wear an accelerometer daily for 7 days, and to self-collect saliva samples four times a day for 4 consecutive days. The EMA surveys included perceived racial discrimination, affective states, lifestyle behaviors, and social and physical contexts. The mean EMA response rate was 82.8%. All participants collected saliva samples four times a day for 4 consecutive days. About 83% of participants wore the accelerometer on the hip 6 out of 7 days. Despite the perception that the intensive nature of assessments would result in high participant burden, the acceptability of the study procedures was uniformly favorable.

RevDate: 2020-10-15
CmpDate: 2020-10-15

Xu J, Yin P, Hu W, et al (2020)

Assessing the ecological regime and spatial spillover effects of a reclaimed mining subsided lake: A case study of the Pan'an Lake wetland in Xuzhou.

PloS one, 15(8):e0238243.

In the North China Plain, coal mining subsided lakes are surface water bodies that form after the conclusion of coal mining. In China, mining subsided lakes are often transformed into artificial wetland parks for ecological restoration. While many studies have focused on evaluating coal mining subsidence lake ecosystem service value and water pollution, little attention has been paid to changes in ecological regimes and ecological spillover effects before and after the reclamation of mining areas. This paper examines the Pan'an Lake artificial wetland in Jiawang District, Xuzhou, as a case study. Changes in the ecological regime of the mining subsidence area before and after land reclamation and corresponding spatial spillover effect on land prices are assessed based on remote sensing, GIS raster calculations and geostatistical methods. The results show that the ecosystem service value and ecological storage capacity changed significantly after the mining subsided lake was transformed into an artificial wetland and the wetland ecosystem has been developing well with significantly positive spillover effects on surrounding land prices. From 2008 to 2017, service functions of the artificial wetland ecosystem of Pan'an Lake increased by 81.95%, and the system's ecological storage capacity increased from RMB 6,754 yuan/hm2 in 2008 to RMB 12,289 yuan/hm2 in 2017. The average impact of the Pan'an Lake artificial wetland on the spillover effects of surrounding residential land prices was measured at RMB 195.18 yuan/m2, and the total spillover value of planned residential land in the study area was measured at RMB 805,422,100 yuan. The present study can serve as a useful guide for evaluating the economic feasibility of land reclamation planning and ecological restoration in mining subsidence areas.

RevDate: 2021-02-17

Kaufman D, McKay N, Routson C, et al (2020)

Publisher Correction: A global database of Holocene paleotemperature records.

Scientific data, 7(1):271 pii:10.1038/s41597-020-00611-1.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

RevDate: 2021-02-16
CmpDate: 2020-12-07

Hansen AJ, Burns P, Ervin J, et al (2020)

A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.

Nature ecology & evolution, 4(10):1377-1384.

Tropical forests vary in composition, structure and function such that not all forests have similar ecological value. This variability is caused by natural and anthropogenic disturbance regimes, which influence the ability of forests to support biodiversity, store carbon, mediate water yield and facilitate human well-being. While international environmental agreements mandate protecting and restoring forests, only forest extent is typically considered, while forest quality is ignored. Consequently, the locations and loss rates of forests of high ecological value are unknown and coordinated strategies for conserving these forests remain undeveloped. Here, we map locations high in forest structural integrity as a measure of ecological quality on the basis of recently developed fine-resolution maps of three-dimensional forest structure, integrated with human pressure across the global moist tropics. Our analyses reveal that tall forests with closed canopies and low human pressure typical of natural conditions comprise half of the global humid or moist tropical forest estate, largely limited to the Amazon and Congo basins. Most of these forests have no formal protection and, given recent rates of loss, are at substantial risk. With the rapid disappearance of these 'best of the last' forests at stake, we provide a policy-driven framework for their conservation and restoration, and recommend locations to maintain protections, add new protections, mitigate deleterious human impacts and restore forest structure.

RevDate: 2021-01-14
CmpDate: 2020-10-13

Cichocki N, Hübschmann T, Schattenberg F, et al (2020)

Bacterial mock communities as standards for reproducible cytometric microbiome analysis.

Nature protocols, 15(9):2788-2812.

Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.

RevDate: 2020-09-28

Carraro L, Bertuzzo E, Fronhofer EA, et al (2020)

Generation and application of river network analogues for use in ecology and evolution.

Ecology and evolution, 10(14):7537-7550.

Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well-known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R-package OCNet. Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.We describe the main functionalities of the package and its integration with other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general.

RevDate: 2021-03-24
CmpDate: 2021-03-24

Baker BJ, Appler KE, X Gong (2021)

New Microbial Biodiversity in Marine Sediments.

Annual review of marine science, 13:161-175.

Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.

LOAD NEXT 100 CITATIONS

ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

cover-pic

SUPPORT ESP: Order from Amazon
The ESP project will earn a commission.

This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @ gmail.com

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).

Timelines

ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.

Biographies

Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )