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Bibliography on: Paleontology Meets Genomics — Sequencing Ancient DNA

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ESP: PubMed Auto Bibliography 08 Mar 2021 at 01:35 Created: 

Paleontology Meets Genomics — Sequencing Ancient DNA

The ideas behind Jurassic Park have become real, kinda sorta. It is now possible to retrieve and sequence DNA from ancient specimens. Although these sequences are based on poor quality DNA and thus have many inferential steps (i,e, the resulting sequence is not likely to be a perfect replica of the living DNA), the insights to be gained from paleosequentcing are nonetheless great. For example, paleo-sequencing has shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.

Created with PubMed® Query: "ancient DNA" OR "ancient genome" OR paleogenetic OR paleogenetics NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2021-03-06

Kazarina A, Petersone-Gordina E, Kimsis J, et al (2021)

The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.

Genes, 12(2): pii:genes12020309.

Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16-17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.

RevDate: 2021-03-06

Lanubile A, Borrelli VMG, Soccio M, et al (2021)

Loss of ZmLIPOXYGENASE4 Decreases Fusarium verticillioides Resistance in Maize Seedlings.

Genes, 12(3): pii:genes12030335.

Fusarium verticillioides is one of the most relevant fungal species in maize responsible for ear, stalk and seedling rot, as well as the fumonisin contamination of kernels. Plant lipoxygenases (LOX) synthesize oxylipins that play a crucial role in the regulation of defense mechanisms against pathogens and influence the outcome of pathogenesis. To better uncover the role of these signaling molecules in maize resistance against F. verticillioides, the functional characterization of the 9-LOX gene, ZmLOX4, was carried out in this study by employing mutants carrying Mu insertions in this gene (named as UFMulox4). In this regard, the genotyping of five UFMulox4 identified the mutant UFMu10924 as the only one having an insertion in the coding region of the gene. The impact of ZmLOX4 mutagenesis on kernel defense against F. verticillioides and fumonisin accumulation were investigated, resulting in an increased fungal susceptibility compared to the inbred lines W22 and Tzi18. Moreover, the expression of most of the genes involved in the LOX, jasmonic acid (JA) and green leaf volatiles (GLV) pathways, as well as LOX enzymatic activity, decreased or were unaffected by fungal inoculation in the mutant UFMu10924. These results confirm the strategic role of ZmLOX4 in controlling defense against F. verticillioides and its influence on the expression of several LOX, JA and GLV genes.

RevDate: 2021-03-05

Kerner G, Laval G, Patin E, et al (2021)

Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years.

American journal of human genetics, 108(3):517-524.

Tuberculosis (TB), usually caused by Mycobacterium tuberculosis bacteria, is the first cause of death from an infectious disease at the worldwide scale, yet the mode and tempo of TB pressure on humans remain unknown. The recent discovery that homozygotes for the P1104A polymorphism of TYK2 are at higher risk to develop clinical forms of TB provided the first evidence of a common, monogenic predisposition to TB, offering a unique opportunity to inform on human co-evolution with a deadly pathogen. Here, we investigate the history of human exposure to TB by determining the evolutionary trajectory of the TYK2 P1104A variant in Europe, where TB is considered to be the deadliest documented infectious disease. Leveraging a large dataset of 1,013 ancient human genomes and using an approximate Bayesian computation approach, we find that the P1104A variant originated in the common ancestors of West Eurasians ∼30,000 years ago. Furthermore, we show that, following large-scale population movements of Anatolian Neolithic farmers and Eurasian steppe herders into Europe, P1104A has markedly fluctuated in frequency over the last 10,000 years of European history, with a dramatic decrease in frequency after the Bronze Age. Our analyses indicate that such a frequency drop is attributable to strong negative selection starting ∼2,000 years ago, with a relative fitness reduction on homozygotes of 20%, among the highest in the human genome. Together, our results provide genetic evidence that TB has imposed a heavy burden on European health over the last two millennia.

RevDate: 2021-03-03

Rahmat RA, Humphries MA, Austin JJ, et al (2021)

The development of a tool to predict temperature-exposure of incinerated teeth using colourimetric and hydroxyapatite crystal size data.

International journal of legal medicine [Epub ahead of print].

This study presents a novel tool to predict temperature-exposure of incinerated pig teeth as a proxy for understanding impacts of fire on human teeth. Previous studies on the estimation of temperature-exposure of skeletal elements have been limited to that of heat-exposed bone. This predictive tool was developed using a multinomial regression model of colourimetric and hydroxyapatite crystal size variables using data obtained from unheated pig teeth and teeth incinerated at 300 °C, 600 °C, 800 °C and 1000 °C. An additional variable based on the observed appearance of the tooth was included in the tool. This enables the tooth to be classified as definitely burnt (600 °C-1000 °C) or uncertain (27 °C/300 °C). As a result, the model predicting the temperature-exposure of the incinerated teeth had an accuracy of 95%. This tool is a holistic, robust and reliable approach to estimate temperature of heat-exposed pig teeth, with high accuracy, and may act as a valuable proxy to estimate heat exposure for human teeth in forensic casework.

RevDate: 2021-03-03

Aouizerat T, Maeir AM, Paz Y, et al (2020)

Isolation and Characterization of Live Yeast Cells from Ancient Clay Vessels.

Bio-protocol, 10(1):e3473 pii:3473.

Ancient fermented food has been studied mainly based on residue analysis and recipes and reconstruction attempts were performed using modern domesticated yeast. Furthermore, microorganisms which participated in fermentation were studied using ancient-DNA techniques. In a recent paper, we presented a novel approach based on the hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. Here we present a pipeline for isolation of yeast from clay vessels uncovered in archeological sites and transferred to the microbiology lab where they can be isolated and characterized. This method opens new avenues for experimental archeology and enables attempts to recreate ancient food and beverages using the original microorganisms.

RevDate: 2021-03-02

Yao H, Wang M, Zou X, et al (2021)

New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy.

Molecular genetics and genomics : MGG [Epub ahead of print].

Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f3/f4 statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.

RevDate: 2021-03-01

Liu Y, Wang M, Chen P, et al (2021)

Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians.

Frontiers in genetics, 12:582357.

The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3 , f4 , qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1-1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei's genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.

RevDate: 2021-02-28

Matsumura S, Terai Y, Hongo H, et al (2021)

Analysis of the Mitochondrial Genomes of Japanese Wolf Specimens in the Siebold Collection, Leiden.

Zoological science, 38(1):60-66.

The taxonomic status of extinct Japanese or Honshu wolves (Canis lupus hodophilax) has been disputed since the name hodophilax was first proposed by Temminck in 1839 on the basis of specimens stored in Leiden, the Netherlands. Points of controversy include whether the type specimen of hodophilax (Jentink c: RMNH.MAM.39181) and the other two specimens from Leiden (Jentink a: RMNH.MAM.39182 and Jentink b: RMNH.MAM.39183) represent different varieties or subspecies of Japanese wolves or not. Two Japanese names, ookami and jamainu, used to describe wild Canis species, further complicate the issue. In this study, the taxonomic status of Japanese wolves was clarified using mitochondrial DNA of the three specimens stored at the Naturalis Biodiversity Center in Leiden, in addition to three Japanese wolf specimens stored at the Museum für Naturkunde in Berlin and five new samples from Japan. The mitochondrial genomes of the type specimen of hodophilax (Jentink c) and another sample from Leiden (Jentink b) as well as Berlin specimens were included in the cluster of Japanese wolves distinct from other grey wolves. However, the other sample from Leiden (Jentink a) was identified as a domestic dog. A mitochondrial genome analysis suggested that Japanese wolves could be categorized into two distinct clusters. Studies of nuclear genomes are needed to further clarify the taxonomic status, divergence time, and population genetic structure of Japanese wolves.

RevDate: 2021-02-27

Yelmen B, Marnetto D, Molinaro L, et al (2021)

Improving selection detection with population branch statistic on admixed populations.

Genome biology and evolution pii:6151747 [Epub ahead of print].

Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. 2019 for cross population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared to the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.

RevDate: 2021-02-26
CmpDate: 2021-02-26

Grimm D (2021)

Siberia may be long-sought site of dog domestication.

Science (New York, N.Y.), 371(6528):451-452.

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

Datta S (2020)

Excavating new facts from ancient Hepatitis B virus sequences.

Virology, 549:89-99.

Recently, two independent studies discovered 15 ancient Hepatitis B virus (aHBV) sequences, of which 7 dated back to the Neolithic age (NA) and the Bronze Age (BA). In the present research, all the available aHBV sequences were collectively re-analysed with reference to extant HBV diversity to understand the role of these aHBV genotypes in evolution of extant HBV genetic diversity. Several intergenotype recombination events were documented, which corroborated well with population admixture and ancient human migration. Present analyses suggested replacement of HBV genotype associated with early Neolithic European farming cultures by the migrating steppe people, during Bronze Age Steppe migration. Additionally, detailed analyses of recombinations revealed evolution of a number of extant genotypes and suggested their possible site of origin. Through this manuscript, novel and important findings of the analyses are communicated.

RevDate: 2021-02-22

Wang CC, Yeh HY, Popov AN, et al (2021)

Genomic Insights into the Formation of Human Populations in East Asia.

Nature pii:10.1038/s41586-021-03336-2 [Epub ahead of print].

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people1,2. We report genome-wide data from 166 East Asians dating to 6000 BCE - 1000 CE and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan plateau are linked by a deeply-splitting lineage likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ~3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ~84% to some groups and to the Central Plain where it contributed ~59-84% to Han Chinese. Third, people from Taiwan ~1300 BCE to 800 CE derived ~75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ~25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ~3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ~2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.

RevDate: 2021-02-19

Cooper A, Turney CSM, Palmer J, et al (2021)

A global environmental crisis 42,000 years ago.

Science (New York, N.Y.), 371(6531):811-818.

Geological archives record multiple reversals of Earth's magnetic poles, but the global impacts of these events, if any, remain unclear. Uncertain radiocarbon calibration has limited investigation of the potential effects of the last major magnetic inversion, known as the Laschamps Excursion [41 to 42 thousand years ago (ka)]. We use ancient New Zealand kauri trees (Agathis australis) to develop a detailed record of atmospheric radiocarbon levels across the Laschamps Excursion. We precisely characterize the geomagnetic reversal and perform global chemistry-climate modeling and detailed radiocarbon dating of paleoenvironmental records to investigate impacts. We find that geomagnetic field minima ~42 ka, in combination with Grand Solar Minima, caused substantial changes in atmospheric ozone concentration and circulation, driving synchronous global climate shifts that caused major environmental changes, extinction events, and transformations in the archaeological record.

RevDate: 2021-02-18

Callaway E (2021)

Million-year-old mammoth genomes shatter record for oldest ancient DNA.

RevDate: 2021-02-18
CmpDate: 2021-02-18

Piñar G, Tafer H, Schreiner M, et al (2020)

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value.

Environmental microbiology, 22(8):3218-3233.

This study provides an example in the emerging field of biocodicology showing how metagenomics can help answer relevant questions that may contribute to a better understanding of the history of ancient manuscripts. To this end, two Slavonic codices dating from the 11th century were investigated through shotgun metagenomics. Endogenous DNA enabled to infer the animal origin of the skins used in the manufacture of the two codices, while nucleic sequences recovered from viruses were investigated for the first time in this material, opening up new possibilities in the field of biocodicology. In addition, the microbiomes colonizing the surface of the parchments served to determine their conservation status and their latent risk of deterioration. The saline environment provided by the parchments selected halophilic and halotolerant microorganisms, which are known to be responsible for the biodegradation of parchment. Species of Nocardiopsis, Gracilibacillus and Saccharopolyspora, but also members of the Aspergillaceae family were detected in this study, all possessing enzymatic capabilities for the biodeterioration of this material. Finally, a relative abundance of microorganisms originating from the human skin microbiome were identified, most probably related to the intensive manipulation of the manuscripts throughout the centuries, which should be taken with caution as they can be potential pathogens.

RevDate: 2021-02-17

Sullivan AP, Marciniak S, O'Dea A, et al (2021)

Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama.

Molecular ecology resources [Epub ahead of print].

Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n=3), Late Holocene (984-1258 BP) archaeological midden (n=5), and a mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n=5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n=5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7x higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behavior on mollusc evolutionary biology.

RevDate: 2021-02-17

Lammers Y, Heintzman PD, IG Alsos (2021)

Environmental palaeogenomic reconstruction of an Ice Age algal population.

Communications biology, 4(1):220.

Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.

RevDate: 2021-02-16

Barlow A, Paijmans JLA, Alberti F, et al (2021)

Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.

Current biology : CB pii:S0960-9822(21)00138-X [Epub ahead of print].

Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.

RevDate: 2021-02-16

Librado P, L Orlando (2021)

Genomics and the Evolutionary History of Equids.

Annual review of animal biosciences, 9:81-101.

The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.

RevDate: 2021-02-15

Lan D, Tobler R, Souilmi Y, et al (2021)

Genozip - A Universal Extensible Genomic Data Compressor.

Bioinformatics (Oxford, England) pii:6135077 [Epub ahead of print].

We present Genozip, a universal and fully featured compression software for genomic data. Genozip is designed to be a general-purpose software and a development framework for genomic compression by providing five core capabilities - universality (support for all common genomic file formats), high compression ratios, speed, feature-richness, and extensibility. Genozip delivers high-performance compression for widely-used genomic data formats in genomics research, namely FASTQ, SAM/BAM/CRAM, VCF, GVF, FASTA, PHYLIP, and 23andMe formats. Our test results show that Genozip is fast and achieves greatly improved compression ratios, even when the files are already compressed. Further, Genozip is architected with a separation of the Genozip Framework from file-format-specific Segmenters and data-type-specific Codecs. With this, we intend for Genozip to be a general-purpose compression platform where researchers can implement compression for additional file formats, as well as new codecs for data types or fields within files, in the future. We anticipate that this will ultimately increase the visibility and adoption of these algorithms by the user community, thereby accelerating further innovation in this space. Availability: Genozip is written in C. The code is open-source and available on GitHub (https://github.com/divonlan/genozip). The package is free for non-commercial use. It is distributed as a Docker container on DockerHub and through the conda package manager. Genozip is tested on Linux, Mac, and Windows. Supplementary information: Supplementary data are available at Bioinformatics online.

RevDate: 2021-02-13

Harney É, Cheronet O, Fernandes DM, et al (2021)

A minimally destructive protocol for DNA extraction from ancient teeth.

Genome research pii:gr.267534.120 [Epub ahead of print].

Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

RevDate: 2021-02-10

Ontano AZ, Gainett G, Aharon S, et al (2021)

Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions.

Molecular biology and evolution pii:6132263 [Epub ahead of print].

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

RevDate: 2021-02-09

Yüncü E, Açan SC, Onar V, et al (2021)

Demography of swordfish (Xiphias gladius Linneus) populations from the coasts of Turkey, based on mitochondrial DNA and microsatellites.

Journal of fish biology [Epub ahead of print].

Genetic diversity of Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin; north of the Aegean Sea (Aegean-2013, n=26) and the Mediterranean coast of Turkey (N.Levantine-2013, n=42) were studied genetically, along with ancient samples from Yenikapı excavation (n=6). Partial mitochondrial DNA control region sequences (entire sequences, Clade I, and Clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., 2005b; Viñas et al., 2010; Righi et al., 2020) from the rest of the Mediterranean Sea. By pairwise FST and pairwise AMOVA tests we showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the last 20 years. On the other hand, our results confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One-tailed permutation tests revealed that the θ, which is directly proportional to long-term female effective population size (Ne) decreased significantly (p<0.05) in both regions over the last two decades. On the Turkish coasts, the θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. However, θ of the ancient sample was consistently and significantly (p<0.001) higher than those of the eastern and western Mediterranean populations in Clade I and Clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples suggesting that, the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite based present Ne estimate of the pooled Aegean-2013 and N.Levantine-2013 populations was lower than 1000 according to the upper limit of 95% confidence interval and possibly even lower than 100 according to the mean of MSVAR posterior distribution. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here shows that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need a stringent action and management plan, urgently. This article is protected by copyright. All rights reserved.

RevDate: 2021-02-09

Sun XF, Wen SQ, Lu CQ, et al (2021)

Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China.

Proceedings of the National Academy of Sciences of the United States of America, 118(8):.

The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS 14C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS 14C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.

RevDate: 2021-02-08

Plomp KA, Gestsdóttir H, Dobney K, et al (2021)

The composition of the founding population of Iceland: A new perspective from 3D analyses of basicranial shape.

PloS one, 16(2):e0246059 pii:PONE-D-20-31330.

The settlement of Iceland in the Viking Age has been the focus of much research, but the composition of the founding population remains the subject of debate. Some lines of evidence suggest that almost all the founding population were Scandinavian, while others indicate a mix of Scandinavians and people of Scottish and Irish ancestry. To explore this issue further, we used three-dimensional techniques to compare the basicrania of skeletons from archaeological sites in Iceland, Scandinavia, and the British Isles. Our analyses yielded two main results. One was that the founding population likely consisted of roughly equal numbers of Scandinavians and people from the British Isles. The other was that the immigrants who originated from the British Isles included individuals of southern British ancestry as well as individuals of Scottish and Irish ancestry. The first of these findings is consistent with the results of recent analyses of modern and ancient DNA, while the second is novel. Our study, therefore, strengthens the idea that the founding population was a mix of Scandinavians and people from the British Isles, but also raises a new possibility regarding the regions from which the settlers originated.

RevDate: 2021-02-06

Rampelli S, Turroni S, Mallol C, et al (2021)

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.

Communications biology, 4(1):169.

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

RevDate: 2021-02-06

Armbrecht L, Hallegraeff G, Bolch CJS, et al (2021)

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes.

Scientific reports, 11(1):3220.

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

RevDate: 2021-02-05

Davidson R, Fehren-Schmitz L, B Llamas (2021)

A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations.

Genes, 12(2): pii:genes12020215.

The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.

RevDate: 2021-02-01

Ma X, Zhang L, Pei Z, et al (2021)

Hydrogen sulfide promotes flowering in heading Chinese cabbage by S-sulfhydration of BraFLCs.

Horticulture research, 8(1):19.

Heading Chinese cabbage (Brassica rapa L. syn. B. campestris L. ssp. chinensis Makino var. pekinensis (Rupr.) J. Cao et Sh. Cao) is a cruciferous Brassica vegetable that has a triplicate genome, owing to an ancient genome duplication event. It is unclear whether the duplicated homologs have conserved or diversified functions. Hydrogen sulfide (H2S) is a plant gasotransmitter that plays important physiological roles in growth, development, and responses to environmental stresses. The modification of cysteines through S-sulfhydration is an important mechanism of H2S, which regulates protein functions. H2S promotes flowering in Arabidopsis and heading Chinese cabbage. Here we investigated the molecular mechanisms of H2S used to promote flowering in the latter. Four, five, and four BraFLC, BraSOC I, and BraFT homologs were identified in heading Chinese cabbage. Different BraFLC proteins were bound to different CArG boxes in the promoter regions of the BraSOC I and BraFT homologs, producing different binding patterns. Thus, there may be functionally diverse BraFLC homologs in heading Chinese cabbage. Exogenous H2S at 100 μmol L-1 significantly promoted flowering by compensating for insufficient vernalization. BraFLC 1 and BraFLC 3 underwent S-sulfhydration by H2S, after which their abilities to bind most BraSOC I or BraFT promoter probes weakened or even disappeared. These changes in binding ability were consistent with the expression pattern of the BraFT and BraSOC I homologs in seedlings treated with H2S. These results indicated that H2S signaling regulates flowering time. In summary, H2S signaling promoted plant flowering by weakening or eliminating the binding abilities of BraFLCs to downstream promoters through S-sulfhydration.

RevDate: 2021-01-30

De Angelis F, Pellegrini M, Martínez-Labarga C, et al (2021)

Exploring mobility in Italian Neolithic and Copper Age communities.

Scientific reports, 11(1):2697.

As a means for investigating human mobility during late the Neolithic to the Copper Age in central and southern Italy, this study presents a novel dataset of enamel oxygen and carbon isotope values (δ18Oca and δ13Cca) from the carbonate fraction of biogenic apatite for one hundred and twenty-six individual teeth coming from two Neolithic and eight Copper Age communities. The measured δ18Oca values suggest a significant role of local sources in the water inputs to the body water, whereas δ13Cca values indicate food resources, principally based on C3 plants. Both δ13Cca and δ18Oca ranges vary substantially when samples are broken down into local populations. Statistically defined thresholds, accounting for intra-site variability, allow the identification of only a few outliers in the eight Copper Age communities, suggesting that sedentary lifestyle rather than extensive mobility characterized the investigated populations. This seems to be also typical of the two studied Neolithic communities. Overall, this research shows that the investigated periods in peninsular Italy differed in mobility pattern from the following Bronze Age communities from more northern areas.

RevDate: 2021-01-30

García-Rodríguez O, Hardouin EA, Hambleton E, et al (2021)

Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia.

BMC ecology and evolution, 21(1):9.

BACKGROUND: The earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period.

RESULTS: From these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N = 6) and D (N = 2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D.

CONCLUSIONS: The presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age.

RevDate: 2021-01-28

Hayer S, Brandis D, Immel A, et al (2021)

Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.

Scientific reports, 11(1):2307.

The historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s-including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.

RevDate: 2021-01-27

Fellows Yates JA, Andrades Valtueña A, Vågene ÅJ, et al (2021)

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.

Scientific data, 8(1):31.

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

RevDate: 2021-01-27

Hu J, Westbury MV, Yuan J, et al (2021)

Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta.

Proceedings. Biological sciences, 288(1943):20202934.

Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62-2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.

RevDate: 2021-01-27

Xavier C, Eduardoff M, Bertoglio B, et al (2021)

Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age.

Genes, 12(2): pii:genes12020146.

The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille's overall increased gain of DNA when enough tissue is available and Dabney's improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.

RevDate: 2021-01-27

Taron UH, Paijmans JLA, Barlow A, et al (2021)

Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe.

Genes, 12(2): pii:genes12020144.

The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.

RevDate: 2021-01-27
CmpDate: 2021-01-27

Li Z, MS Barker (2020)

Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions.

GigaScience, 9(2):.

BACKGROUND: Polyploidy, or whole-genome duplications (WGDs), repeatedly occurred during green plant evolution. To examine the evolutionary history of green plants in a phylogenomic framework, the 1KP project sequenced >1,000 transcriptomes across the Viridiplantae. The 1KP project provided a unique opportunity to study the distribution and occurrence of WGDs across the green plants. As an accompaniment to the capstone publication, this article provides expanded methodological details, results validation, and descriptions of newly released datasets that will aid researchers who wish to use the extended data generated by the 1KP project.

RESULTS: In the 1KP capstone analyses, we used a total evidence approach that combined inferences of WGDs from Ks and phylogenomic methods to infer and place 244 putative ancient WGDs across the Viridiplantae. Here, we provide an expanded explanation of our approach by describing our methodology and walk-through examples. We also evaluated the consistency of our WGD inferences by comparing them to evidence from published syntenic analyses of plant genome assemblies. We find that our inferences are consistent with whole-genome synteny analyses and our total evidence approach may minimize the false-positive rate throughout the dataset.

CONCLUSIONS: We release 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots from the 1KP capstone paper. These resources will be useful for many future analyses on gene and genome evolution in green plants.

RevDate: 2021-01-26

Perri AR, Feuerborn TR, Frantz LAF, et al (2021)

Dog domestication and the dual dispersal of people and dogs into the Americas.

Proceedings of the National Academy of Sciences of the United States of America, 118(6):.

Advances in the isolation and sequencing of ancient DNA have begun to reveal the population histories of both people and dogs. Over the last 10,000 y, the genetic signatures of ancient dog remains have been linked with known human dispersals in regions such as the Arctic and the remote Pacific. It is suspected, however, that this relationship has a much deeper antiquity, and that the tandem movement of people and dogs may have begun soon after the domestication of the dog from a gray wolf ancestor in the late Pleistocene. Here, by comparing population genetic results of humans and dogs from Siberia, Beringia, and North America, we show that there is a close correlation in the movement and divergences of their respective lineages. This evidence places constraints on when and where dog domestication took place. Most significantly, it suggests that dogs were domesticated in Siberia by ∼23,000 y ago, possibly while both people and wolves were isolated during the harsh climate of the Last Glacial Maximum. Dogs then accompanied the first people into the Americas and traveled with them as humans rapidly dispersed into the continent beginning ∼15,000 y ago.

RevDate: 2021-01-26

Singh G, Yellapu S, Sandhu HS, et al (2021)

Genetic Characterization of the North-West Indian Population: Analysis of Mitochondrial DNA Control Region Variation.

Annals of human biology [Epub ahead of print].

BACKGROUND: Human mitochondrial DNA presents several interesting characteristics, making it a favourable tool in the field of molecular anthropology, medical genetics, population history and forensic science.

AIM: The present study investigated the mitochondrial DNA (mtDNA) control region variations in diverse ethnic groups of North-West India for which population data is insufficient.

SUBJECTS AND METHODS: The complete mtDNA control regions of 197 unrelated (for up to three generations) healthy individuals belonging to different ethnic groups of North-West India were sequenced. The haplotype frequencies, haplogroup distribution and pairwise FST values between the studied and other worldwide populations were generated to study patterns of variation in human mtDNA.

RESULTS: The results ascertained high gene diversity (0.998) in the studied maternal lineages, identifying 166 distinct haplotypes, of which 158 were unique and characterised by 117 variable sites. Three haplogroups: M3, M30 and U7 were observed to be the most prevalent and phylogeographically a total of 55.86% of sequences were characterised into South Asian, followed by West Eurasian (40.18%) and East Asian (3.96%), ancestry haplogroups. Pairwise genetic differentiation comparisons revealed maternal homogeneity in the studied groups. No population substructure was detected within the North-West Indian populations.

CONCLUSION: The results of this preliminary study will contribute to an existing database of mtDNA variations of the Indian population and facilitate prospective studies investigating population genetics and human diseases.

RevDate: 2021-01-24

Selberg AGA, Gaucher EA, DA Liberles (2021)

Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond.

Journal of molecular evolution [Epub ahead of print].

As both a computational and an experimental endeavor, ancestral sequence reconstruction remains a timely and important technique. Modern approaches to conduct ancestral sequence reconstruction for proteins are built upon a conceptual framework from journal founder Emile Zuckerkandl. On top of this, work on maximum likelihood phylogenetics published in Journal of Molecular Evolution in 1996 was one of the first approaches for generating maximum likelihood ancestral sequences of proteins. From its computational history, future model development needs as well as potential applications in areas as diverse as computational systems biology, molecular community ecology, infectious disease therapeutics and other biomedical applications, and biotechnology are discussed. From its past in this journal, there is a bright future for ancestral sequence reconstruction in the field of evolutionary biology.

RevDate: 2021-01-22

Melo L, Matos VMJ, Santos AL, et al (2021)

The first probable evidence of leprosy in a male individual (17th-19th century AD) unearthed in Northern Portugal (Travanca, Santa Maria da Feira).

International journal of paleopathology, 32:80-86 pii:S1879-9817(20)30068-1 [Epub ahead of print].

OBJECTIVE: This study describes the first evidence of a probable paleopathological case of leprosy from northern Portugal.

MATERIALS: An adult male, skeleton 403, exhumed from the Christian cemetery associated with the church dedicated to Saint Mamede (Travanca, Santa Maria da Feira), dated from the 17th-19th century AD.

METHODS: Standard bioarchaeological methods were used for sex and age-at-death determinations, and leprosy-related bone lesions were identified through macroscopic analysis guided by paleopathological diagnostic criteria.

RESULTS: The macroscopic observation revealed probable leprosy-related skeletal lesions, namely tenuous rhinomaxillary changes, bilateral proliferative periosteal reactions on the tibiae and fibulae, as well as concentric atrophy, acro-osteolysis and ankyloses of foot bones.

CONCLUSIONS: Skeleton 403 represents a probable case of leprosy according to the nature and distribution pattern of bony lesions observed.

SIGNIFICANCE: This finding fills an important gap in the history of leprosy in Portugal. Although historical sources show that the majority of leprosaria were located in the northern part of the country, suggesting that leprosy was more prevalent in this area of Portugal in the past, no paleopathological evidence of this disease was reported for this region to date. Furthermore, the inhumation of a leprosy sufferer in a 17th-19th century AD Christian parish cemetery is deeply imbued with social meaning.

The future detailed study of the remaining skeletons unearthed from the cemetery of the Church of São Mamede will hopefully reveal further osteological evidence of leprosy in addition to the application of ancient DNA analysis to confirm the presence of the pathogen of this disease. Also, further documentary research is needed in order to expand appreciation of the epidemiological and social impact of leprosy in the 17th-19th century AD Portugal.

RevDate: 2021-01-22

Phillips MJ, S Shazwani Zakaria (2021)

Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals.

Molecular phylogenetics and evolution pii:S1055-7903(21)00015-4 [Epub ahead of print].

Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.

RevDate: 2021-01-21

Gowland R, Stewart NA, Crowder KD, et al (2021)

Sex estimation of teeth at different developmental stages using dimorphic enamel peptide analysis.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: This study tests, for the first time, the applicability of a new method of sex estimation utilizing enamel peptides on a sample of deciduous and permanent teeth at different stages of mineralization, from nonadults of unknown sex, including perinates.

MATERIALS AND METHODS: A total of 43 teeth from 29 nonadult individuals aged from 40 gestational weeks to 19 years old were analyzed. The sample included pairs of fully mineralized and just developing teeth from the same individual. The individuals were from four archaeological sites in England: Piddington (1st-2nd centuries AD), Coach Lane, Victoria Gate, and Fewston (all 18th-19th centuries). A method that identifies sex chromosome-linked isoforms of the peptide amelogenin from human tooth enamel was applied. The method utilizes a minimally destructive acid etching procedure and subsequent nano liquid chromatography tandem mass spectrometry.

RESULTS: It was possible to determine the sex of 28 of the nonadult individuals sampled (males = 20, females = 8, undetermined = 1). Only one sample failed (CL9), due to insufficient mineralization of the sampled tooth enamel. Data are available via ProteomeXchange with identifier PXD021683.

DISCUSSION: Sufficient peptide material to determine sex can be recovered even from the crowns of developing perinatal teeth that are not fully mineralized. The minimally destructive and inexpensive (compared to ancient DNA) nature of this procedure has significant implications for bioarchaeological studies of infancy and childhood.

RevDate: 2021-01-21

Kornienko IV, Faleeva TG, Oreshkova NV, et al (2018)

Complete mitochondrial genome of a woolly mammoth (Mammuthus primigenius) from Maly Lyakhovsky Island (New Siberian Islands, Russia) and its phylogenetic assessment.

Mitochondrial DNA. Part B, Resources, 3(2):596-598 pii:1473721.

We present a complete sequence and an annotation of the mitochondrial genome of the woolly mammoth (Mammuthus primigenius) found in 2012 on Maly Lyakhovsky Island (North-Eastern Siberia, Russia). The genome was 16,851 bp long and contained 13 protein-coding, 22 tRNA, and 2 rRNA genes. It was AT reach (61.3%) with A = 32.9%, T = 28.4%, C = 25.3%, and G = 13.4%.

RevDate: 2021-01-21

de Flamingh A, Mallott EK, Roca AL, et al (2018)

Species identification and mitochondrial genomes of ancient fish bones from the Riverine Kachemak tradition of the Kenai Peninsula, Alaska.

Mitochondrial DNA. Part B, Resources, 3(1):409-411 pii:1456371.

Seven fish vertebrae were chosen for analysis from the 49-KEN-147 archaeological site in the Kenai Peninsula, Alaska. Mitochondrial DNA analysis of the ancient fish bones revealed that they were from sockeye and coho salmon. Here, we report the ancient mitochondrial genomes for three sockeye salmon and one coho salmon fish bone.

RevDate: 2021-01-19

Keighley X, Bro-Jørgensen MH, Ahlgren H, et al (2021)

Predicting sample success for large-scale ancient DNA studies on marine mammals.

Molecular ecology resources [Epub ahead of print].

In recent years, non-human ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to the feasibility of such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, the skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.

RevDate: 2021-01-18

Mitchell KJ, NJ Rawlence (2020)

Examining Natural History through the Lens of Palaeogenomics.

Trends in ecology & evolution pii:S0169-5347(20)30282-2 [Epub ahead of print].

The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.

RevDate: 2021-01-18
CmpDate: 2021-01-18

Cheng JY, T Mailund (2020)

Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model.

Methods in molecular biology (Clifton, N.J.), 2090:167-189.

Coalescence theory lets us probe the past demographics of present-day genetic samples and much information about the past can be gleaned from variation in rates of coalescence event as we trace genetic lineages back in time. Fewer and fewer lineages will remain, however, so there is a limit to how far back we can explore. Without recombination, we would not be able to explore ancient speciation events because of this-any meaningful species concept would require that individuals of one species are closer related than they are to individuals of another species, once speciation is complete. Recombination, however, opens a window to the deeper past. By scanning along a genomic alignment, we get a sequential variant of the coalescence process as it looked at the time of the speciation. This pattern of coalescence times is fixed at speciation time and does not erode with time; although accumulated mutations and genomic rearrangements will eventually hide the signal, it enables us to glance at events in the past that would not be observable without recombination. So-called coalescence hidden Markov models allow us to exploit this, and in this chapter, we present the tool Jocx that uses a framework of these models to infer demographic parameters in ancient speciation events.

RevDate: 2021-01-16

Ramirez DA, Saka HA, R Nores (2021)

Detection of Vibrio cholerae aDNA in human burials from the fifth cholera pandemic in Argentina (1886-1887 AD).

International journal of paleopathology, 32:74-79 pii:S1879-9817(20)30071-1 [Epub ahead of print].

OBJECTIVE: Detecting traces of ancient DNA of Vibrio cholerae to provide genetic information associated with the fifth cholera pandemic.

MATERIALS: Sediment samples from the sacral foramina of four individuals were analyzed, recovered from a mass grave near an institution dedicated exclusively to the isolation and treatment of citizens infected with cholera in the late 19th century in the city of Cordoba, Argentina.

METHODS: Paleogenetic techniques (ancient DNA extraction, PCR amplification, and Sanger sequencing) were applied. Specific primers for Vibrio cholerae (VCR, ctxA, ctxB, and tcpA) were designed.

RESULTS: By amplifying and sequencing the Vibrio cholerae repeats fragment, the infection in at least one individual was confirmed.

CONCLUSIONS: The synthesis of the paleogenetic results with the archaeological and historical evidence strongly supports that at least one individual from the mass grave in Cordoba, Argentina, was a victim of the fifth cholera pandemic.

SIGNIFICANCE: Confirming the presence of the disease through multiple lines of evidence, including genetic, archaeological, and historical analyses, strengthens and affirms our understanding of the presence, effects, and potential evolutionary paths of the disease in the past.

LIMITATIONS: Vibrio cholerae repeats were sequenced in one individual, while the remaining genes could not be amplified, which is likely related to gene copy number.

Paleogenetic examination of ancient samples from different locations will broaden our understanding of the origin, evolution, and past dissemination of Vibrio cholerae epidemic strains.

RevDate: 2021-01-14

Ju D, I Mathieson (2021)

The evolution of skin pigmentation-associated variation in West Eurasia.

Proceedings of the National Academy of Sciences of the United States of America, 118(1):.

Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.

RevDate: 2021-01-14

Pugach I, Hübner A, Hung HC, et al (2021)

Ancient DNA from Guam and the peopling of the Pacific.

Proceedings of the National Academy of Sciences of the United States of America, 118(1):.

Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.

RevDate: 2021-01-14

Perri AR, Mitchell KJ, Mouton A, et al (2021)

Dire wolves were the last of an ancient New World canid lineage.

Nature [Epub ahead of print].

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

RevDate: 2021-01-13

Xu W, Lin Y, Zhao K, et al (2021)

An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data.

Ecology and evolution, 11(1):390-401 pii:ECE37056.

Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.

RevDate: 2021-01-12

Seguin-Orlando A, Donat R, Der Sarkissian C, et al (2021)

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.

Current biology : CB pii:S0960-9822(20)31835-2 [Epub ahead of print].

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.

RevDate: 2021-01-12
CmpDate: 2021-01-12

Sazzini M, Abondio P, Sarno S, et al (2020)

Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans.

BMC biology, 18(1):51.

BACKGROUND: The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes.

RESULTS: We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition.

CONCLUSIONS: We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.

RevDate: 2021-01-11

Kévin R, Nicolas C, Elsa P, et al (2021)

Gastrointestinal parasite burden in 4th-5th c. AD Florence highlighted by microscopy and paleogenetics.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases pii:S1567-1348(21)00010-1 [Epub ahead of print].

The study of ancient parasites, named paleoparasitology, traditionally focused on microscopic eggs disseminated in past environments and archaeological structures by humans and other animals infested by gastrointestinal parasites. Since the development of paleogenetics in the early 1980s, few paleoparasitological studies have been based on the ancient DNA (aDNA) of parasites, although such studies have clearly proven their utility and reliability. In this paper, we describe our integrative approach for the paleoparasitological study of an ancient population from Florence in Italy, dated to the 4th-5th c. CE. The first stage consisted in the study of sediment samples from the pelvic area of 18 individuals under light microscopy. This allowed us to detect Ascarid-type eggs belonging very probably to the human-infesting roundworm Ascaris lumbricoides. Ten subsamples were selected corresponding to five individuals, and we extracted their whole DNA following sediment aDNA protocols. A targeted approach allowed us to detect two nematodes and one trematode aDNA fragments, namely Ascaris sp., Trichuris trichiura, and Dicrocoelium dendriticum. Among the five individuals tested for microscopic eggs and aDNA, three of them showed the remains of eggs (only Ascarid-type), but all of them tested positive to the presence of at least one parasite aDNA. Microscopic diagnosis first guided our research for the selection of promising samples while the targeted aDNA approach significantly improved our knowledge in terms of parasitic diversity and frequency in this population subgroup. These results enabled us to discuss the possible impact of latent parasitism in this past population at the time of an epidemic, as suggested in Florence. In particular, the singular case of D. dendriticum detection is discussed in light of the present-day scarcity of genuine human infections. Nevertheless, actual infections are known in the paleoparasitological record, and food habits may have led to false parasitism in this historical context. aDNA leaching from overlying strata may also explain this detection. This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology.

RevDate: 2021-01-08

Nowaczewska W, Binkowski M, Benazzi S, et al (2021)

New hominin teeth from Stajnia Cave, Poland.

Journal of human evolution, 151:102929 pii:S0047-2484(20)30190-1 [Epub ahead of print].

RevDate: 2021-01-08

Greer C, Bhakta H, Ghanem L, et al (2021)

Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.

Human reproduction (Oxford, England) pii:6071469 [Epub ahead of print].

STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction?

SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis.

WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average ∼2%) present in non-African extant humans.

STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction.

Ancient DNA from six Neanderthals and two Denisovans dated between ∼82 000 and 43 000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database.

Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage ≥20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma.

While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae.

This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction.

This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare.

TRIAL REGISTRATION NUMBER: N/A.

RevDate: 2021-01-08
CmpDate: 2021-01-08

Vorobieva NV, Makunin AI, Druzhkova AS, et al (2020)

High genetic diversity of ancient horses from the Ukok Plateau.

PloS one, 15(11):e0241997.

A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.

RevDate: 2021-01-05

Mckinnon M, D Higgins (2020)

Comparison of bone demineralisation procedures for DNA recovery from burned remains.

Forensic science international. Genetics, 51:102448 pii:S1872-4973(20)30220-9 [Epub ahead of print].

Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.

RevDate: 2020-12-31

Nedoluzhko AV, Sharko FS, Boulygina ES, et al (2019)

The complete mitochondrial genome of the extinct Pleistocene horse (Equus cf. lenensis) from Kotelny Island (New Siberian Islands, Russia) and its phylogenetic assessment.

Mitochondrial DNA. Part B, Resources, 5(1):243-245.

The complete mitochondrial genome from the Pleistocene stallion horse (Equus cf. lenensis) which complete skull was found in 1901 on Kotelny Island (New Siberian Archipelago, Sakha Republic, Russia) is published in this paper. The mitochondrial DNA (mtDNA) is 16,584 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. The overall base composition of the genome in descending order was 32.3% - A, 28.5% - C, 13.4% - G, 25.8% - T without a significant AT bias of 58.2%.

RevDate: 2020-12-31

Grond J, Płecha M, Hahn C, et al (2019)

Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard.

Mitochondrial DNA. Part B, Resources, 4(2):4152-4154.

The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215-8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.

RevDate: 2020-12-22

Friedlaender JS, S Tucci (2020)

Human Migrations: Tales of the Pacific.

Current biology : CB, 30(24):R1478-R1481.

The mode and tempo of human dispersal to the far-flung Pacific Islands has been a source of fascination for centuries. New ancient DNA data from the archipelago of Vanuatu shed light on the ancient migrations that shaped the history of human settlement in the Pacific.

RevDate: 2021-01-03

Hong JH, Seo M, Oh CS, et al (2020)

Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty.

The Journal of parasitology, 106(6):802-808.

Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics.

RevDate: 2021-01-05

Senovska A, Drozdova E, Vaculik O, et al (2020)

Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA.

Forensic science international, 319:110638 pii:S0379-0738(20)30500-4 [Epub ahead of print].

Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.

RevDate: 2020-12-19

Lewis D (2019)

Head of ancient-DNA lab sacked for 'serious misconduct'.

RevDate: 2020-12-15

Schulte L, Bernhardt N, Stoof-Leichsenring K, et al (2020)

Hybridization capture of larch (Larix Mill) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest.

Molecular ecology resources [Epub ahead of print].

Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA - metabarcoding - focuses on small fragments which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborate an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.

RevDate: 2020-12-30

Kistler L, Thakar HB, VanDerwarker AM, et al (2020)

Archaeological Central American maize genomes suggest ancient gene flow from South America.

Proceedings of the National Academy of Sciences of the United States of America, 117(52):33124-33129.

Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300-1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.

RevDate: 2020-12-12

Padró J, Lambertucci SA, Perrig PL, et al (2020)

Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories.

Ecology and evolution, 10(23):13011-13021.

While genetic diversity of threatened species is a major concern of conservation biologists, historic patterns of genetic variation are often unknown. A powerful approach to assess patterns and processes of genetic erosion is via ancient DNA techniques. Herein, we analyzed mtDNA from historical samples (1800s to present) of Andean Condors (Vultur gryphus) to investigate whether contemporary low genetic variability is the result of recent human expansion and persecution, and compared this genetic history to that of California condors (Gymnogyps californianus).We then explored historic demographies for both species via coalescent simulations. We found that Andean condors have lost at least 17% of their genetic variation in the early 20th century. Unlike California condors, however, low mtDNA diversity in the Andean condor was mostly ancient, before European arrival. However, we found that both condor species shared similar demographies in that population bottlenecks were recent and co-occurred with the introduction of livestock to the Americas and the global collapse of marine mammals. Given the combined information on genetic and demographic processes, we suggest that the protection of key habitats should be targeted for conserving extant genetic diversity and facilitate the natural recolonization of lost territories, while nuclear genomic data should be used to inform translocation plans.

RevDate: 2020-12-12

Garrett Vieira F, Samaniego Castruita JA, MTP Gilbert (2020)

Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.

Ecology and evolution, 10(23):12700-12709.

Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.

RevDate: 2020-12-15

Balzeau A, Turq A, Talamo S, et al (2020)

Pluridisciplinary evidence for burial for the La Ferrassie 8 Neandertal child.

Scientific reports, 10(1):21230.

The origin of funerary practices has important implications for the emergence of so-called modern cognitive capacities and behaviour. We provide new multidisciplinary information on the archaeological context of the La Ferrassie 8 Neandertal skeleton (grand abri of La Ferrassie, Dordogne, France), including geochronological data -14C and OSL-, ZooMS and ancient DNA data, geological and stratigraphic information from the surrounding context, complete taphonomic study of the skeleton and associated remains, spatial information from the 1968-1973 excavations, and new (2014) fieldwork data. Our results show that a pit was dug in a sterile sediment layer and the corpse of a two-year-old child was laid there. A hominin bone from this context, identified through Zooarchaeology by Mass Spectrometry (ZooMS) and associated with Neandertal based on its mitochondrial DNA, yielded a direct 14C age of 41.7-40.8 ka cal BP (95%), younger than the 14C dates of the overlying archaeopaleontological layers and the OSL age of the surrounding sediment. This age makes the bone one of the most recent directly dated Neandertals. It is consistent with the age range for the Châtelperronian in the site and in this region and represents the third association of Neandertal taxa to Initial Upper Palaeolithic lithic technocomplex in Western Europe. A detailed multidisciplinary approach, as presented here, is essential to advance understanding of Neandertal behavior, including funerary practices.

RevDate: 2020-12-08

Verma S, Sharma I, Sharma V, et al (2020)

MassArray analysis of genomic susceptibility variants in ovarian cancer.

Scientific reports, 10(1):21101.

Ovarian cancer (OC), a multifaceted and genetically heterogeneous malignancy is one of the most common cancers among women. The aim of the study is to unravel the genetic factors associated with OC and the extent of genetic heterogeneity in the populations of Jammu and Kashmir (J&K).Using the high throughput Agena MassARRAY platform, present case control study was designed which comprises 200 histopathological confirmed OC patients and 400 age and ethnicity matched healthy controls to ascertain the association of previously reported eleven single nucleotide polymorphisms (SNPs) spread over ten genes (DNMT3A, PIK3CA, FGFR2, GSTP1, ERCC5, AKT1, CASC16, CYP19A1, BCL2 and ERCC1) within the OC population of Jammu and Kashmir, India. The association of each variant was estimated using logistic regression analyses. Out of the 11 SNPs the odds ratio observed for three SNPs; rs2699887 was (1.72 at 95% CI: 1.19-2.48, p = 0.004), rs1695 was (1.87 at 95% CI: 1.28-2.71, p = 0.001), and rs2298881 was (0.66 at 95% CI: 0.46-0.96, p = 0.03) were found significantly associated with the OC after correction with confounding factors i.e. age & BMI. Furthermore, the estimation of interactive analyses was performed and odds ratio observed was 2.44 (1.72-3.47), p value < 0. 001 suggests that there was a strong existence of interplay between the selected genetic variants in OC, which demonstrate that interactive analysis highlights the role of gene-gene interaction that provides an insight among multiple little effects of various polymorphisms in OC.

RevDate: 2020-12-11

Duggan AT, Holmes EC, HN Poinar (2020)

Response to Brinkmann et al. "Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States".

Genome biology, 21(1):287.

We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA.

RevDate: 2020-12-07

Dussex N, Alberti F, Heino MT, et al (2020)

Moose genomes reveal past glacial demography and the origin of modern lineages.

BMC genomics, 21(1):854.

BACKGROUND: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.

RESULTS: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.

CONCLUSIONS: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

RevDate: 2021-01-01

Wellman HP, Austin RM, Dagtas ND, et al (2020)

Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction.

Proceedings. Biological sciences, 287(1940):20202343.

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters (n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.

RevDate: 2020-12-07

Feuerborn TR, Palkopoulou E, van der Valk T, et al (2020)

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.

BMC genomics, 21(1):844.

BACKGROUND: After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.

RESULTS: Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.

CONCLUSIONS: We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

RevDate: 2020-12-26

Koupadi K, Fontani F, Ciucani MM, et al (2020)

Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age.

Genes, 11(12):.

Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.

RevDate: 2020-12-14
CmpDate: 2020-12-04

García-Rodríguez F, Piccini C, Carrizo D, et al (2021)

Centennial glacier retreat increases sedimentation and eutrophication in Subantarctic periglacial lakes: A study case of Lake Uruguay.

The Science of the total environment, 754:142066.

High resolution XRF scanning documented inter-annual paleolimnological changes of a Subantarctic periglacial lake, during a process of centennial glacier retreat in King George Island, Antarctica. Two major paleoenvironmental stages were inferred from the combined analysis of elemental, molecular and isotopic biomarkers, with a boundary or transition set at about 3200 yr BP. The first stage was characterized by a relatively low allochthonous organic content, reduced productivity and nitrogen levels. Such paleoenvironmental conditions are interpreted as a terrestrial system under periglacial influence, where material influx was related to erosion process from the melt water discharge, because of the proximity to the Collins Glacier ice cap. After the major Holocene glacier advance dated at about 3500 yr BP, the ice cap retreat led to the formation of Lake Uruguay, which involved in filling processes leading to moraine deposits, proglacial meltwater channels, and lakes next to the land glacier. During the second stage, with the onset of the Current Warm Period, prior to 1900 CE the stabilization of the Zr/Rb ratio within the laminated sediments documented the origin of the lacustrine sedimentation system, with subsequent increases in the sedimentation rate and biomass content (total nitrogen and organic carbon). Time series analyses revealed that the lake displayed variability cycles related to El Niño Southern Oscillation (ENSO), as reflected by high resolution sedimentological proxies for grain size, weathering, allochthonous inputs from the watershed, increase of biomass and productivity, and changes in redox conditions, all of which displayed similar oscillation cycles from 2 to 6 yr. During this periglacial recession and associated eutrophication process, we detected a striking loss in both bacterial specific richness and diversity as inferred from preliminary selected ancient DNA analyses. Thus, the Antarctic warming scenario leading to glacier depletion appears to exert deterioration consequences on the Subantarctic microbial web.

RevDate: 2020-12-22

Loog L (2021)

Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 376(1816):20190719.

Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.

RevDate: 2020-12-22

Wester JVWC, Vilchez VJS, Torre CEW, et al (2020)

Molecular characterization of mitochondrial Amerindian haplogroups and the amelogenin gene in human ancient DNA from three archaeological sites in Lambayeque - Peru.

Genetics and molecular biology, 43(4):e20190265.

Important pre-Inca civilizations, known by their great political and religious structures, inhabited the northern coast of Peru. Archeological and anthropological studies have shown that people from these villages have hierarchical strata, but the genetic structure has been poorly studied. Here, we aimed to perform a molecular characterization of the Amerindian maternal lineages and the amelogenin gene in skeletons collected from three archeological sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial haplogroup B and the identification of haplogroups A, C, and D were obtained with PCR-RFLP experiments. The sex was characterized via amplification of the AMEL(X/Y) locus. Haplogroup frequencies were compared with available data from other ancient and modern civilizations from the Peruvian coast and highlands using statistical methods. Our results showed that haplogroup C had the highest frequency, while haplogroup B showed variable diversity in the analyzed populations. The meta-analysis revealed a positive correlation among some coastal villages. We concluded that ancient populations analyzed in our study showed the presence of four Amerindian mitochondrial haplogroups, which is consistent with previous studies.

RevDate: 2020-11-26

Sun J, Ma PC, Cheng HZ, et al (2020)

Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins.

MATERIALS AND METHODS: Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software.

RESULTS: C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves.

DISCUSSION: We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.

RevDate: 2020-12-04

Weyrich LS (2021)

The evolutionary history of the human oral microbiota and its implications for modern health.

Periodontology 2000, 85(1):90-100.

Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.

RevDate: 2020-12-29

Gregory MD, Kippenhan JS, Kohn P, et al (2020)

Neanderthal-Derived Genetic Variation Is Associated with Functional Connectivity in the Brains of Living Humans.

Brain connectivity [Epub ahead of print].

Aim: To determine whether Neanderthal-derived genetic variation relates to functional connectivity patterns in the brains of living modern humans. Introduction: Nearly 50,000 years ago, Neanderthals interbred with ancestors of modern humans, imparting a genetic legacy that lives on today. The vestiges of this Neanderthal-derived genetic variation have been previously shown to be enriched in genes coding for neurogenesis and myelination and to alter skull shape and brain structure in living people. Materials and Methods: Using two independent cohorts totaling 553 healthy individuals, we employed multivariate distance matrix regression (MDMR) to determine whether any brain areas exhibited whole-brain functional connectivity patterns that significantly related to the degree of Neanderthal introgression. Identified clusters were then used as regions of interest in follow-up seed-based functional connectivity analyses to determine the connectivity patterns driving the relationships. Results: The MDMR analysis revealed that the percentage of Neanderthal-originating polymorphisms was significantly associated with the functional connectivity patterns of an area of the intraparietal sulcus (IPS) that was nearly identical in both cohorts. Using these IPS clusters as regions of interest in seed-based connectivity analyses, we found, again in both cohorts, that individuals with a higher proportion of Neanderthal-derived genetic variation showed increased IPS functional connectivity with visual processing regions, but decreased IPS connectivity with regions underlying social cognition. Conclusions: These findings demonstrate that the remnants of Neanderthal admixture continue to influence human brain function today, in ways that are consistent with anthropological conceptualizations of Neanderthal phenotypes, including the possibility that Neanderthals may have depended upon visual processing capabilities at the expense of social cognition, and this may have contributed to the extinction of this species through reduced cultural maintenance and inability to cope with fluctuating resources. This and other studies capitalizing on the emerging science surrounding ancient DNA provide a window through which to view an ancient lineage long past.

RevDate: 2020-12-14
CmpDate: 2020-12-14

Latorre SM, Lang PLM, Burbano HA, et al (2020)

Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA.

Current protocols in plant biology, 5(4):e20121.

The ability to sequence DNA retrieved from ancient and historical material plays a crucial role in reinforcing evolutionary and anthropological inference. While the focus of the field is largely on analyzing DNA from ancient hominids and other animals, we have also learned from plant ancient DNA (aDNA), in particular, about human farming practices, crop domestication, environment management, species invasion, and adaptation to various environmental conditions. In the following protocols, we outline best practices for plant aDNA isolation, preparation for sequencing, bioinformatic processing, and authentication. We describe the process all the way from processing of archaeological or historical plant material to characterizing and authenticating sequencing reads. In alternative protocols, we include modifications to this process that are tailored to strongly degraded DNA. Throughout, we stress the importance of precautionary measures to successfully analyze aDNA. Finally, we discuss the evolution of the archaeogenomics field and the development of new methods, which both shaped this protocol. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Isolation of aDNA Alternate Protocol 1: Isolation of ultra-short DNA (Dabney modification) Support Protocol 1: Preparation of PTB-based mix Support Protocol 2: Preparation of binding buffer Basic Protocol 2: Preparation of genomic libraries Alternate Protocol 2: Preparation of genomic libraries with uracil removal Basic Protocol 3: Bioinformatic processing and authentication of aDNA.

RevDate: 2020-12-01

Roca-Rada X, Souilmi Y, Teixeira JC, et al (2020)

Ancient DNA Studies in Pre-Columbian Mesoamerica.

Genes, 11(11):.

Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.

RevDate: 2020-11-17

Wang T, Dong Q, Wang W, et al (2020)

Evolution of AITR family genes in cotton and their functions in abiotic stress tolerance.

Plant biology (Stuttgart, Germany) [Epub ahead of print].

Abiotic stresses are major environmental factors inhibiting plant growth and development. AITRs (ABA-induced transcription repressors) are a novel family of transcription factors regulating ABA (abscisic acid) signaling and plant responses to abiotic stresses in Arabidopsis. However, the composition and evolution history of AITRs and their roles in cotton genus are largely unknown. Here, a total of 12 putative AITR genes were identified in cultivated tetraploid cotton Gossypium hirsutum. Phylogenetic analysis of GhAITRs in these cottons and their closely related species implicate the ancient genome-wide duplication occurring after speciation of Gossypium and Theobroma could generate the duplicates of GhAITRs. Duplicated GhAITRs were stably inherited in following diploid speciation and further allotetraploidy in Gossypium. Homologous GhAITRs shared common expression patterns in response to ABA, drought and salinity treatments, and drought tolerance could be affected in transgenic Arabidopsis plants expressing GhAITR-A1. Together, our findings reveal that duplicates in GhAITR gene family were achieved by whole genome duplication rather than three individual duplication events, and GhAITRs function as transcription repressors and are involved in the regulation of plant responses to ABA and drought stress. These results may provide insights towards the improvement of abiotic stress tolerance in cotton by using GhAITRs.

RevDate: 2020-12-23
CmpDate: 2020-12-23

Sjögren KG, Olalde I, Carver S, et al (2020)

Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries.

PloS one, 15(11):e0241278.

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0-14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.

RevDate: 2020-12-07

Froment C, Zanolli C, Hourset M, et al (2021)

Protein sequence comparison of human and non-human primate tooth proteomes.

Journal of proteomics, 231:104045.

In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time to provide biomolecular information useful for the phylogenetic reconstruction of hominid taxa. In this study, we used a shotgun proteomics approach to compare the tooth proteomes of extant human and non-human primates (gorilla, chimpanzee, orangutan and baboon) in order to search for a panel of peptides able to discriminate between taxa and further help reconstructing the evolutionary relationships of fossil primates. Among the 25 proteins shared by the five genera datasets, we found a combination of peptides with sequence variations allowing to differentiate the hominid taxa in the proteins AHSG, AMBN, APOA1, BGN, C9, COL11A2, COL22A1, COL3A1, DSPP, F2, LUM, OMD, PCOLCE and SERPINA1. The phylogenetic tree confirms the placement of the samples in the appropriate genus branches. Altogether, the results provide experimental evidence that a shotgun proteomics approach on dental tissue has the potential to detect taxonomic variation, which is promising for future investigations of uncharacterized and/or fossil hominid/hominin specimens. SIGNIFICANCE: A shotgun proteomics approach on human and non-human primate teeth allowed to identify peptides with taxonomic interest, highlighting the potential for future studies on hominid fossils.

RevDate: 2020-11-12

Bonsu DOM, Higgins D, Henry J, et al (2020)

Evaluation of the efficiency of Isohelix™ and Rayon swabs for recovery of DNA from metal surfaces.

Forensic science, medicine, and pathology pii:10.1007/s12024-020-00329-x [Epub ahead of print].

PURPOSE: We investigated the recovery and extraction efficiency of DNA from three metal surfaces (brass, copper, steel) relevant to forensic casework, and plastic (control) using two different swabbing systems; Rayon and Isohelix™ swabs, with sterile water and isopropyl alcohol respectively, as the wetting solutions.

METHODS: Twenty nanograms of human genomic DNA were applied directly to Isohelix™ and Rayon swabs; and to the metal and plastic substrates. All substrates were left to dry for 24 h, followed by single wet swabbing and extraction with the DNA IQ™ System. DNA extracts were quantified using real time quantitative PCR assays with SYBR green chemistry.

RESULTS: DNA was extracted from directly seeded Isohelix™ swabs with a high efficiency of 98%, indicating effective DNA-release from the swab into the extraction buffer. In contrast, only 58% of input DNA was recovered from seeded Rayon swabs, indicating higher DNA retention by these swabs. Isohelix™ swabs recovered 32 - 53% of DNA from metal surfaces, whilst the Rayon swabs recovered 11-29%. DNA recovery was lowest from copper and highest from brass. Interestingly, Rayon swabs appeared to collect more DNA from the plastic surface than Isohelix™ swabs, however, due to the lower release of DNA from Rayon swabs they returned less DNA overall following extraction than Isohelix™ swabs.

CONCLUSION: These results demonstrate that DNA samples deposited on metal surfaces can be more efficiently recovered using Isohelix™ swabs wetted with isopropyl alcohol than Rayon swabs wetted with sterile water, although recovery is affected by the substrate type.

RevDate: 2020-11-19

Silva M, Pratas D, AJ Pinho (2020)

Efficient DNA sequence compression with neural networks.

GigaScience, 9(11):.

BACKGROUND: The increasing production of genomic data has led to an intensified need for models that can cope efficiently with the lossless compression of DNA sequences. Important applications include long-term storage and compression-based data analysis. In the literature, only a few recent articles propose the use of neural networks for DNA sequence compression. However, they fall short when compared with specific DNA compression tools, such as GeCo2. This limitation is due to the absence of models specifically designed for DNA sequences. In this work, we combine the power of neural networks with specific DNA models. For this purpose, we created GeCo3, a new genomic sequence compressor that uses neural networks for mixing multiple context and substitution-tolerant context models.

FINDINGS: We benchmark GeCo3 as a reference-free DNA compressor in 5 datasets, including a balanced and comprehensive dataset of DNA sequences, the Y-chromosome and human mitogenome, 2 compilations of archaeal and virus genomes, 4 whole genomes, and 2 collections of FASTQ data of a human virome and ancient DNA. GeCo3 achieves a solid improvement in compression over the previous version (GeCo2) of $2.4\%$, $7.1\%$, $6.1\%$, $5.8\%$, and $6.0\%$, respectively. To test its performance as a reference-based DNA compressor, we benchmark GeCo3 in 4 datasets constituted by the pairwise compression of the chromosomes of the genomes of several primates. GeCo3 improves the compression in $12.4\%$, $11.7\%$, $10.8\%$, and $10.1\%$ over the state of the art. The cost of this compression improvement is some additional computational time (1.7-3 times slower than GeCo2). The RAM use is constant, and the tool scales efficiently, independently of the sequence size. Overall, these values outperform the state of the art.

CONCLUSIONS: GeCo3 is a genomic sequence compressor with a neural network mixing approach that provides additional gains over top specific genomic compressors. The proposed mixing method is portable, requiring only the probabilities of the models as inputs, providing easy adaptation to other data compressors or compression-based data analysis tools. GeCo3 is released under GPLv3 and is available for free download at https://github.com/cobilab/geco3.

RevDate: 2020-12-07

Thomas C, Francke A, Vogel H, et al (2020)

Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka.

Microorganisms, 8(11):.

Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. We found significant environmental parameters influencing the overall microbial community distribution, but no strong relationship with given phylotypes and paleoclimatic signals or sediment age. Our results support a weak recording of early diagenetic processes and their actors by bulk prokaryotic sedimentary DNA in Lake Ohrid, replaced by specialized low-energy clades of the deep biosphere and a marked imprint of erosional processes on the subsurface DNA pool of Lake Ohrid.

RevDate: 2020-11-16

Psonis N, de Carvalho CN, Figueiredo S, et al (2020)

Molecular identification and geographic origin of a post-Medieval elephant finding from southwestern Portugal using high-throughput sequencing.

Scientific reports, 10(1):19252.

Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable. Molecular markers have been used in forensic science to trace the geographic origin of wildlife products, such as ivory. So far, only a few studies have applied genetic methods to both identify the species and circumscribe the provenance of historic wildlife trade material. Here, by combining ancient DNA methods and genome skimming on a historical elephantid tooth found in southwestern Portugal, we aimed to identify its species, infer its placement in the elephantid phylogenetic tree, and triangulate its geographic origin. According to our results the specimen dates back to the eighteenth century CE and belongs to a female African forest elephant (non-hybrid Loxodonta cyclotis individual) geographically originated from west-west-central Africa, from areas where one of the four major mitochondrial clades of L. cyclotis is distributed. Historical evidence supports our inference, pointing out that the tooth should be considered as post-Medieval raw ivory trade material between West Africa and Portugal. Our study provides a comprehensive approach to study historical products and artefacts using archaeogenetics and contributes towards enlightening cultural and biological historical aspects of ivory trade in western Europe.

RevDate: 2020-11-13

Teschler-Nicola M, Fernandes D, Händel M, et al (2020)

Ancient DNA reveals monozygotic newborn twins from the Upper Palaeolithic.

Communications biology, 3(1):650.

The Upper Palaeolithic double burial of newborns and the single burial of a ca. 3-month-old infant uncovered at the Gravettian site of Krems-Wachtberg, Austria, are of paramount importance given the rarity of immature human remains from this time. Genome-wide ancient DNA shows that the male infants of the double grave are the earliest reported case of monozygotic twins, while the single grave´s individual was their 3rd-degree male relative. We assessed the individuals´ age at death by applying histological and µCT inspection of the maxillary second incisors (i2) in conjunction with C- and N-isotope ratios and Barium (Ba) intake as biomarker for breastfeeding. The results show that the twins were full-term newborns, and that while individual 2 died at birth, individual 1 survived for about 50 days. The findings show that Gravettian mortuary behaviour also included re-opening of a grave and manipulation of its layout and content.

RevDate: 2020-12-11

Jeong C, Wang K, Wilkin S, et al (2020)

A Dynamic 6,000-Year Genetic History of Eurasia's Eastern Steppe.

Cell, 183(4):890-904.e29.

The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region's population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

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

Abbona CC, Adolfo GN, Johnson J, et al (2020)

Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study.

PloS one, 15(11):e0240474.

The southern boundary of prehispanic farming in South America occurs in central Mendoza Province, Argentina at approximately 34 degrees south latitude. Archaeological evidence of farming includes the recovery of macrobotanical remains of cultigens and isotopic chemistry of human bone. Since the 1990s, archaeologists have also hypothesized that the llama (Lama glama), a domesticated South American camelid, was also herded near the southern boundary of prehispanic farming. The remains of a wild congeneric camelid, the guanaco (Lama guanicoe), however, are common in archaeological sites throughout Mendoza Province. It is difficult to distinguish bones of the domestic llama from wild guanaco in terms of osteological morphology, and therefore, claims that llama were in geographic areas where guanaco were also present based on osteometric analysis alone remain equivocal. A recent study, for example, claimed that twenty-five percent of the camelid remains from the high elevation Andes site of Laguna del Diamante S4 were identified based on osteometric evidence as domestic llama, but guanaco are also a likely candidate since the two species overlap in size. We test the hypothesis that domesticated camelids occurred in prehispanic, southern Mendoza through analysis of ancient DNA. We generated whole mitochondrial genome datasets from 41 samples from southern Mendoza late Holocene archaeological sites, located between 450 and 3400 meters above sea level (masl). All camelid samples from those sites were identified as guanaco; thus, we have no evidence to support the hypothesis that the domestic llama occurred in prehispanic southern Mendoza.

RevDate: 2020-11-06

Skelly E, Johnson NW, Kapellas K, et al (2020)

Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children.

Journal of oral microbiology, 12(1):1830623.

A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren-a population with disproportionately poorer oral health than non-Indigenous Australian children-in the Northern Peninsula Area (NPA) of Far North Queensland (FNQ), which significantly improved their oral health. Here, we examine the salivary microbiota of these children (mean age = 10 ± 2.96 years; n = 103), reconstructing the bacterial community composition with high-throughput sequencing of the V4 region of bacterial 16S rRNA gene. Microbial communities of children who received the Intervention had lower taxonomic diversity than those who did not receive treatment (Shannon, p < 0.05). Moreover, the Intervention resulted in further decreased microbial diversity in children with active carious lesions existing at the time of saliva collection. Microbial species associated with caries were detected; Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus gasseri, Prevotella multisaccharivorax, Parascardovia denticolens, and Mitsuokella HMT 131 were significantly increased (p < 0.05) in children with severe caries, especially in children who did not receive the Intervention. These insights into microbial associations and community differences prompt future considerations to the mechanisms behind caries-preventive therapy induced change; important for understanding the long-term implications of like treatment to improve oral health disparities within Australia. Trial registration: ANZCTR, ACTRN12615000693527. Registered 3 July 2015, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368750&isReview=true.

RevDate: 2020-11-03

Saag L (2020)

Human Genetics: Lactase Persistence in a Battlefield.

Current biology : CB, 30(21):R1311-R1313.

Lactase persistence is a common genetic trait in Europeans and other pastoralists. New ancient DNA evidence from a Bronze Age battlefield indicates that selection for lactase persistence was strong and on-going in the last 3,000 years.

RevDate: 2020-11-04

Lall GM, Larmuseau MHD, Wetton JH, et al (2020)

Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain.

European journal of human genetics : EJHG pii:10.1038/s41431-020-00747-z [Epub ahead of print].

The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.

RevDate: 2020-12-15

Furtwängler A, Neukamm J, Böhme L, et al (2020)

Comparison of target enrichment strategies for ancient pathogen DNA.

BioTechniques, 69(6):455-459.

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods - array-based hybridization capture and in-solution capture using either RNA or DNA baits - have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.

RevDate: 2020-11-03

Hao S, Han K, Meng L, et al (2020)

African Arowana Genome Provides Insights on Ancient Teleost Evolution.

iScience, 23(11):101662.

Osteoglossiformes is a basal clade of teleost, evolving since the Jurassic period. The genomes of Osteoglossiformes species would shed light on the evolution and adaptation of teleost. Here, we established a chromosome-level genome of African arowana. Together with the genomes of pirarucu and Asian arowana, we found that they diverged at ∼106.1 million years ago (MYA) and ∼59.2 MYA, respectively, which are coincident with continental separation. Interestingly, we identified a dynamic genome evolution characterized by a fast evolutionary rate and a high pseudogenization rate in African arowana and pirarucu. Additionally, more transposable elements were found in Asian arowana which confer more gene duplications. Moreover, we found the contraction of olfactory receptor and the expansion of UGT in African arowana might be related to its transformation from carnivore to be omnivore. Taken together, we provided valuable genomic resource of Osteoglossidae and revealed the correlation of biogeography and teleost evolution.

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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.

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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 )