@article {pmid41298920,
year = {2025},
author = {Dong, Y and Malhi, RS},
title = {Ancient DNA offers clues about mysterious prehistoric settlement in China.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41298920},
issn = {1476-4687},
}

@article {pmid41231995,
year = {2025},
author = {Zhang, SJ and Scarsbrook, L and Li, H and Carmagnini, A and Charlton, S and Feuerborn, T and Boeskorov, G and Chen, G and Deom, JM and Dimopoulos, EA and Dobney, K and Dong, J and Du, L and Hansen, AJ and Harris, A and Hernández-Alonso, G and Jia, X and Kim, A and Li, GM and Li, R and Linderholm, A and Outram, A and Qiu, M and Ren, L and Ruan, Q and Sala, R and Stepanov, A and Sun, Y and Tabbada, K and Thalmann, O and Varfolomeev, V and Wang, L and Wang, Q and Wang, S and Wei, W and Yang, Y and Yin, J and Zaibert, V and Zhang, Z and Dong, G and Rosengren, E and Sinding, MS and Ostrander, EA and Larson, G and Ma, M and Frantz, LAF and Wang, GD},
title = {Genomic evidence for the Holocene codispersal of dogs and humans across Eastern Eurasia.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {735-740},
doi = {10.1126/science.adu2836},
pmid = {41231995},
issn = {1095-9203},
mesh = {Animals ; *Dogs/genetics ; Humans ; Asia, Eastern ; DNA, Ancient ; Europe, Eastern ; *Genome ; History, Ancient ; *Human Migration ; Siberia ; *Animal Distribution ; },
abstract = {As the first domestic species, dogs likely dispersed with different cultural groups during the Late Pleistocene and Holocene. To test this hypothesis, we analyzed 73 ancient dog genomes, including 17 newly sequenced individuals sampled from East Asia to the West Eurasian Steppe spanning nearly 10,000 years. Our results indicate correlations between the ancestry of dogs and specific ancient human populations from eastern Europe to Eastern Siberia, including Ancient Paleo-Siberians, Eastern hunter-gatherers, East Asians, and Steppe pastoralists. We also identify multiple shifts in the ancestry of dogs that coincide with specific dispersals of hunter-gatherers, farmers, and pastoralists. Combined, our results reveal the long-term and integral role that dogs played in a multitude of human societies.},
}

Animals
*Dogs/genetics
Humans
Asia, Eastern
DNA, Ancient
Europe, Eastern
*Genome
History, Ancient
*Human Migration
Siberia
*Animal Distribution

@article {pmid40920634,
year = {2025},
author = {Fu, Q and Cao, P and Dai, Q and Bennett, EA and Feng, X and Yang, MA and Ping, W and Pääbo, S and Ji, Q},
title = {Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium.},
journal = {Cell},
volume = {188},
number = {15},
pages = {3919-3926.e9},
doi = {10.1016/j.cell.2025.05.040},
pmid = {40920634},
issn = {1097-4172},
mesh = {*DNA, Mitochondrial/genetics/isolation & purification ; *Dental Calculus/chemistry ; Animals ; *Fossils ; *Hominidae/genetics/classification/anatomy & histology ; *Skull/anatomy & histology ; China ; Phylogeny ; DNA, Ancient ; Humans ; },
abstract = {Denisovans have yet to be directly associated with a hominin cranium, limiting our understanding of their morphology and geographical distribution. We have attempted to retrieve DNA from a nearly complete Middle Pleistocene cranium from Harbin (>146 ka), northeastern China. Although no DNA could be retrieved from a tooth or the petrous bone, mitochondrial DNA (mtDNA) could be isolated from dental calculus. The mtDNA falls within Denisovan mtDNA variation and is related to an mtDNA branch carried by early Denisovan individuals in southern Siberia, previously observed in Denisova Cave. This suggests that Denisovans inhabited a large geographical range in Asia in the Middle Pleistocene. The association of Denisovan mtDNA with the Harbin cranium allows a better understanding of the morphological relationships between Denisovans and other East Asian Middle Pleistocene fossils. Furthermore, the retrieval of host DNA from dental calculus opens new possibilities for genetic research on Middle Pleistocene hominins.},
}

*DNA, Mitochondrial/genetics/isolation & purification
*Dental Calculus/chemistry
Animals
*Fossils
*Hominidae/genetics/classification/anatomy & histology
*Skull/anatomy & histology
China
Phylogeny
DNA, Ancient
Humans

@article {pmid40570118,
year = {2025},
author = {Yüncü, E and Doğu, AK and Kaptan, D and Kılıç, MS and Mazzucato, C and Güler, MN and Eker, E and Katırcıoğlu, B and Chyleński, M and Vural, KB and Sağlıcan, E and Atağ, G and Bozkurt, D and Pearson, J and Sevkar, A and Altınışık, NE and Milella, M and Karamurat, C and Aktürk, Ş and Yurttaş, ED and Yıldız, N and Koptekin, D and Yorulmaz, S and Kazancı, DD and Aydoğan, A and Gürün, K and Schotsmans, EMJ and Anvari, J and Rosenstock, E and Byrnes, J and Biehl, PF and Orton, D and Lagerholm, VK and Gemici, HC and Vasic, M and Marciniak, A and Atakuman, Ç and Erdal, YS and Kırdök, E and Pilloud, M and Larsen, CS and Haddow, SD and Götherström, A and Knüsel, CJ and Özer, F and Hodder, I and Somel, M},
title = {Female lineages and changing kinship patterns in Neolithic Çatalhöyük.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6754},
pages = {eadr2915},
doi = {10.1126/science.adr2915},
pmid = {40570118},
issn = {1095-9203},
mesh = {Female ; Humans ; Male ; Archaeology ; Burial/history ; Diet/history ; DNA, Ancient ; *Family ; History, Ancient ; Human Migration/history ; Turkey ; Sex Factors ; },
abstract = {Combining 131 paleogenomes with bioarchaeological and archaeological data, we studied social organization and gendered practices in Çatalhöyük East Mound (7100 to 5950 BCE), a major Neolithic settlement in Central Anatolia. In early Çatalhöyük, burials in the same building were frequently close genetic relatives, suggesting that houses were used by biological family members. In later periods, however, individuals buried in the same building were often genetically unrelated, despite sharing similar diets. We found no indication of sex-biased mobility into Çatalhöyük. Meanwhile, in all periods, within-building genetic connections were predominantly maternal rather than paternal. Burials of female subadults also received a higher frequency of gifts than male subadults. Our results reveal how kinship practices changed while specific practices prioritizing female lines persisted for 1000 years at Neolithic Çatalhöyük.},
}

Female
Humans
Male
Archaeology
Burial/history
Diet/history
DNA, Ancient
*Family
History, Ancient
Human Migration/history
Turkey
Sex Factors

@article {pmid40570102,
year = {2025},
author = {Koptekin, D and Aydoğan, A and Karamurat, C and Altınışık, NE and Vural, KB and Kazancı, DD and Doğu, AK and Kaptan, D and Gemici, HC and Yüncü, E and Moots, HM and Umurtak, G and Duru, R and Fidan, E and Çevik, Ö and Erdoğu, B and Korkut, T and Knüsel, CJ and Haddow, S and Larsen, CS and Özbal, R and Gerritsen, F and Özdoğan, E and Akbaba, A and Usanmaz, UO and Derici, YC and Uçmazoğlu, M and Jay, F and Özdoğan, M and Götherström, A and Erdal, YS and Malaspinas, AS and Atakuman, Ç and Özer, F and Somel, M},
title = {Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6754},
pages = {eadr3326},
doi = {10.1126/science.adr3326},
pmid = {40570102},
issn = {1095-9203},
mesh = {Humans ; History, Ancient ; *Human Migration/history ; Turkey ; *Cultural Evolution ; DNA, Ancient ; *Culture ; Archaeology ; },
abstract = {West Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. In this work, we describe the changing genetic and cultural landscapes of early Holocene West Anatolia using 30 new paleogenomes. We show that Neolithization in West Anatolia was a multifaceted process, characterized by the assimilation of Neolithic practices by local foragers, the influx of eastern populations, and their admixture, with their descendants subsequently establishing Neolithic Southeast Europe. We then coanalyzed genetic and cultural similarities across early Holocene Anatolian and Aegean Neolithic villages using 58 material culture elements. Cultural distances among villages correlate with their spatial distances but not with their genetic distances after controlling for geography. This suggests that cultural change was often decoupled from genetically visible mobility.},
}

Humans
History, Ancient
*Human Migration/history
Turkey
*Cultural Evolution
DNA, Ancient
*Culture
Archaeology

@article {pmid40440384,
year = {2025},
author = {Wang, T and Yang, MA and Zhu, Z and Ma, M and Shi, H and Speidel, L and Min, R and Yuan, H and Jiang, Z and Hu, C and Li, X and Zhao, D and Bai, F and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Wu, X and Liu, X and Zhang, M and Ping, W and Liu, Y and Wan, Y and Yang, F and Zhou, R and Kang, L and Dong, G and Stoneking, M and Fu, Q},
title = {Prehistoric genomes from Yunnan reveal ancestry related to Tibetans and Austroasiatic speakers.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6750},
pages = {eadq9792},
doi = {10.1126/science.adq9792},
pmid = {40440384},
issn = {1095-9203},
mesh = {Female ; Humans ; China ; DNA, Ancient ; *Genome, Human ; History, Ancient ; Language ; Tibet ; *East Asian People/genetics ; },
abstract = {The human landscape in East and Southeast Asia is vastly complex, and successful retrieval of genome-wide data from prehistoric humans of southern East Asia is sparse. We successfully sampled 127 ancient human genomes from southwestern China. A 7100-year-old female individual from central Yunnan shows a previously unsampled Basal Asian ancestry related to a ghost population that contributed to Tibetan Plateau populations. Central Yunnan populations dating to 5500 to 1400 years before present show an East Asian ancestry distinct from northern or southern East Asian ancestries that contributed to present-day East and Southeast Asians, particularly Austroasiatic speakers, and emphasizes the importance of the Red River valley for proto-Austroasiatic population history. Diverse Asian ancestries are represented in humans sampled from Yunnan, clarifying past population dynamics related to both Tibetan and Austroasiatic origins.},
}

Female
Humans
China
DNA, Ancient
*Genome, Human
History, Ancient
Language
Tibet
*East Asian People/genetics

@article {pmid39883774,
year = {2025},
author = {Daly, KG and Mullin, VE and Hare, AJ and Halpin, Á and Mattiangeli, V and Teasdale, MD and Rossi, C and Geiger, S and Krebs, S and Medugorac, I and Sandoval-Castellanos, E and Özbaşaran, M and Duru, G and Gülcür, S and Pöllath, N and Collins, M and Frantz, L and Vila, E and Zidarov, P and Stoddart, S and Boldgiv, B and Orlando, L and Pearson, MP and Mullville, J and Askeyev, IV and Askeyev, AO and Askeyev, OV and Shaymuratova, DN and Van den Hurk, Y and Zeeb-Lanz, A and Arbogast, RM and Hemmer, H and Davoudi, H and Amiri, S and Doost, SB and Decruyenaere, D and Fathi, H and Khazaeli, R and Hassanzadeh, Y and Sardari, A and Lhuillier, J and Abdolahi, M and Summers, GD and Marro, C and Bahshaliyev, V and Berthon, R and Çakirlar, C and Benecke, N and Scheu, A and Burger, J and Sauer, E and Horwitz, LK and Arbuckle, B and Buitenhuis, H and Gourichon, L and Bulatović, J and O'Connor, T and Orton, D and Jalabadze, M and Rhodes, S and Chazan, M and Özkaya, V and Zeder, M and Atıcı, L and Mashkour, M and Peters, J and Bradley, DG},
title = {Ancient genomics and the origin, dispersal, and development of domestic sheep.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6733},
pages = {492-497},
doi = {10.1126/science.adn2094},
pmid = {39883774},
issn = {1095-9203},
mesh = {Animals ; *Sheep, Domestic/genetics/growth & development ; Genomics ; *Genome ; DNA, Ancient ; Humans ; Domestication ; Pigmentation/genetics ; Europe ; History, Ancient ; Horns/anatomy & histology ; },
abstract = {The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Genomes from Central Türkiye ~8000 BCE are genetically proximal to the domestic origins of sheep but do not fully explain the ancestry of later populations, suggesting a mosaic of wild ancestries. Genomic signatures indicate selection by ancient herders for pigmentation patterns, hornedness, and growth rate. Although the first European sheep flocks derive from Türkiye, in a notable parallel with ancient human genome discoveries, we detected a major influx of Western steppe-related ancestry in the Bronze Age.},
}

Animals
*Sheep, Domestic/genetics/growth & development
Genomics
*Genome
DNA, Ancient
Humans
Domestication
Pigmentation/genetics
Europe
History, Ancient
Horns/anatomy & histology

@article {pmid39265004,
year = {2024},
author = {Ortega, RP},
title = {No 'collapse' for ancient people on Rapa Nui.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6714},
pages = {1146-1147},
doi = {10.1126/science.adt0781},
pmid = {39265004},
issn = {1095-9203},
mesh = {Humans ; Archaeology ; DNA, Ancient ; Genome, Human ; History, Ancient ; *Pacific Island People/genetics/history ; Polynesia ; *Population/genetics ; },
abstract = {New genomic, archaeological evidence counters influential tale of ecological suicide.},
}

Humans
Archaeology
DNA, Ancient
Genome, Human
History, Ancient
*Pacific Island People/genetics/history
Polynesia
*Population/genetics

@article {pmid39024443,
year = {2024},
author = {Gibbons, A},
title = {Oldest human genome comes from a Denisovan.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6706},
pages = {240-241},
doi = {10.1126/science.adr8007},
pmid = {39024443},
issn = {1095-9203},
mesh = {Animals ; Female ; Humans ; Male ; *DNA, Ancient ; Fossils ; *Genome, Human ; *Neanderthals/genetics ; Siberia ; },
abstract = {200,000-year-old DNA shows our now-extinct cousins mated with Neanderthals.},
}

Animals
Female
Humans
Male
*DNA, Ancient
Fossils
*Genome, Human
*Neanderthals/genetics
Siberia

@article {pmid38991076,
year = {2024},
author = {Stone, R},
title = {Stunning 3D chromosomes preserved in thawed mammoths.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6705},
pages = {130},
doi = {10.1126/science.adr6185},
pmid = {38991076},
issn = {1095-9203},
mesh = {Animals ; Chromosomes, Mammalian/genetics ; *Fossils ; *Mammoths/genetics ; *DNA, Ancient ; },
abstract = {"New type of fossil" may boost efforts to bring beasts back.},
}

Animals
Chromosomes, Mammalian/genetics
*Fossils
*Mammoths/genetics
*DNA, Ancient

@article {pmid38991073,
year = {2024},
author = {Gibbons, A},
title = {Neanderthals and moderns mingled early and often.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6705},
pages = {132-133},
doi = {10.1126/science.adr6187},
pmid = {38991073},
issn = {1095-9203},
mesh = {Animals ; Humans ; Fossils ; *Neanderthals/genetics ; *Extinction, Biological ; DNA, Ancient ; },
abstract = {Study of genes modern humans gave Neanderthals helps explain their end.},
}

Animals
Humans
Fossils
*Neanderthals/genetics
*Extinction, Biological
DNA, Ancient

@article {pmid38488477,
year = {2024},
author = {Seeber, PA and Batke, L and Dvornikov, Y and Schmidt, A and Wang, Y and Stoof-Leichsenring, K and Moon, K and Vohr, SH and Shapiro, B and Epp, LS},
title = {Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {38488477},
issn = {2050-084X},
support = {EP-98/3-1//Deutsche Forschungsgemeinschaft/ ; BiodivScen ERA-Net COFUND//Biodiversa+/ ; },
mesh = {Humans ; *Genome, Mitochondrial ; Lakes ; Ecosystem ; DNA ; Sequence Analysis, DNA ; DNA, Ancient ; },
abstract = {Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.},
}

Humans
*Genome, Mitochondrial
Lakes
Ecosystem
DNA
Sequence Analysis, DNA
DNA, Ancient

@article {pmid38297138,
year = {2024},
author = {Smith, GM and Ruebens, K and Zavala, EI and Sinet-Mathiot, V and Fewlass, H and Pederzani, S and Jaouen, K and Mylopotamitaki, D and Britton, K and Rougier, H and Stahlschmidt, M and Meyer, M and Meller, H and Dietl, H and Orschiedt, J and Krause, J and Schüler, T and McPherron, SP and Weiss, M and Hublin, JJ and Welker, F},
title = {The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany.},
journal = {Nature ecology & evolution},
volume = {8},
number = {3},
pages = {564-577},
pmid = {38297138},
issn = {2397-334X},
support = {101027850//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 948365//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; Horses ; Animals ; Infant, Newborn ; Germany ; Diet ; Bone and Bones/chemistry ; Europe ; DNA ; Mammals ; *Reindeer ; DNA, Ancient ; Nitrogen Isotopes/analysis ; *Ursidae ; },
abstract = {Recent excavations at Ranis (Germany) identified an early dispersal of Homo sapiens into the higher latitudes of Europe by 45,000 years ago. Here we integrate results from zooarchaeology, palaeoproteomics, sediment DNA and stable isotopes to characterize the ecology, subsistence and diet of these early H. sapiens. We assessed all bone remains (n = 1,754) from the 2016-2022 excavations through morphology (n = 1,218) or palaeoproteomics (zooarchaeology by mass spectrometry (n = 536) and species by proteome investigation (n = 212)). Dominant taxa include reindeer, cave bear, woolly rhinoceros and horse, indicating cold climatic conditions. Numerous carnivore modifications, alongside sparse cut-marked and burnt bones, illustrate a predominant use of the site by hibernating cave bears and denning hyaenas, coupled with a fluctuating human presence. Faunal diversity and high carnivore input were further supported by ancient mammalian DNA recovered from 26 sediment samples. Bulk collagen carbon and nitrogen stable isotope data from 52 animal and 10 human remains confirm a cold steppe/tundra setting and indicate a homogenous human diet based on large terrestrial mammals. This lower-density archaeological signature matches other Lincombian-Ranisian-Jerzmanowician sites and is best explained by expedient visits of short duration by small, mobile groups of pioneer H. sapiens.},
}

Humans
Horses
Animals
Infant, Newborn
Germany
Diet
Bone and Bones/chemistry
Europe
DNA
Mammals
*Reindeer
DNA, Ancient
Nitrogen Isotopes/analysis
*Ursidae

@article {pmid37803274,
year = {2023},
author = {Pittman, M and Wang, Y},
title = {Paleoecology of extinct species.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {59},
pmid = {37803274},
issn = {2730-7182},
mesh = {*DNA, Ancient ; *Extinction, Biological ; },
abstract = {Recent developments, including new imaging and ancient environmental DNA (aeDNA) technologies, are providing unprecedented insights into the past, which can also help researchers predict future ecological change. BMC Ecology and Evolution has launched a new article Collection on the "Paleoecology of extinct species" to provide an open-access resource for all interested in this multidisciplinary field.},
}

*DNA, Ancient
*Extinction, Biological

@article {pmid37230884,
year = {2023},
author = {Williams, JW and Spanbauer, TL and Heintzman, PD and Blois, J and Capo, E and Goring, SJ and Monchamp, ME and Parducci, L and Von Eggers, JM and , },
title = {Strengthening global-change science by integrating aeDNA with paleoecoinformatics.},
journal = {Trends in ecology & evolution},
volume = {38},
number = {10},
pages = {946-960},
doi = {10.1016/j.tree.2023.04.016},
pmid = {37230884},
issn = {1872-8383},
mesh = {*Biodiversity ; *DNA, Ancient ; Computational Biology ; DNA Barcoding, Taxonomic ; },
abstract = {Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.},
}

*Biodiversity
*DNA, Ancient
Computational Biology
DNA Barcoding, Taxonomic

@article {pmid37095409,
year = {2023},
author = {Callaway, E},
title = {'Truly gobsmacked': Ancient-human genome count surpasses 10,000.},
journal = {Nature},
volume = {617},
number = {7959},
pages = {20},
pmid = {37095409},
issn = {1476-4687},
mesh = {Humans ; *Anthropology/trends ; *Archaeology/trends ; *DNA, Ancient ; *Genome, Human/genetics ; },
}

Humans
*Anthropology/trends
*Archaeology/trends
*DNA, Ancient
*Genome, Human/genetics

@article {pmid36546258,
year = {2022},
author = {Wang, Y},
title = {Ancient environmental DNA reveals Arctic ecosystem dynamics in last 50,000 years.},
journal = {Science bulletin},
volume = {67},
number = {13},
pages = {1304-1306},
doi = {10.1016/j.scib.2022.04.018},
pmid = {36546258},
issn = {2095-9281},
mesh = {*Ecosystem ; DNA, Ancient ; *DNA, Environmental ; Arctic Regions ; },
}

*Ecosystem
DNA, Ancient
*DNA, Environmental
Arctic Regions

@article {pmid36536113,
year = {2022},
author = {D'Agostino, A and Di Marco, G and Marvelli, S and Marchesini, M and Rizzoli, E and Rolfo, MF and Canini, A and Gismondi, A},
title = {Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1384},
pmid = {36536113},
issn = {2399-3642},
mesh = {Humans ; Animals ; *Fruit ; Plants, Edible ; Pollen ; Poaceae ; Forests ; DNA, Ancient ; *Calculi ; },
abstract = {Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.},
}

Humans
Animals
*Fruit
Plants, Edible
Pollen
Poaceae
Forests
DNA, Ancient
*Calculi

@article {pmid36458990,
year = {2023},
author = {Flohr, S},
title = {Canine dimensions for estimation of sex in adult and non-adult individuals with external validation by aDNA.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {80},
number = {2},
pages = {225-231},
doi = {10.1127/anthranz/2022/1653},
pmid = {36458990},
issn = {0003-5548},
mesh = {Humans ; Female ; *Tooth ; DNA, Ancient ; Discriminant Analysis ; Germany ; *Sex Determination by Skeleton/methods ; },
abstract = {Using discriminant functions obtained from canine dimensions for sex estimation in human skeletons has frequently been proposed as a promising approach within assemblages, even when used in non-adult individuals. However, applicability of this method to adult and non-adult individuals from other assemblages was rarely investigated, probably due to frequently observed inter-population differences in tooth dimensions. In the present study, discriminant functions obtained for permanent canine dimensions at the cemento-enamel junction in a previous study of the early medieval assemblage from Greding, were applied to individuals from a late medieval Jewish cemetery at Erfurt, Germany. The results were validated by aDNA analyses. Prior to the application of the functions, canine dimensions of the assemblages were compared. The comparison showed largely corresponding canine dimensions between the two assemblages. The application of the formulae obtained on the early medieval assemblage to the late medieval assemblage at Erfurt revealed a 100 % correct classification rate in the adult individuals. In non-adults, the correct classification rate was poorer, with 7 of 9 (77.8 %) individuals correctly classified. The study showed that the application of discriminant functions for sex estimation from canine measurements to assemblages other than those for which the functions were developed can lead to high correct classification rates in adults if the average canine dimensions are similar in the respective assemblages. An application to non-adult individuals should only be made with caution as canine dimensions in the "non-survivors" can lead to an over-estimation of the proportion of female non-adults.},
}

Humans
Female
*Tooth
DNA, Ancient
Discriminant Analysis
Germany
*Sex Determination by Skeleton/methods

@article {pmid36454815,
year = {2022},
author = {Curry, A},
title = {Meeting the ancestors.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6623},
pages = {940-943},
doi = {10.1126/science.adg0308},
pmid = {36454815},
issn = {1095-9203},
mesh = {*Jews/genetics ; Population/genetics ; Germany ; Cemeteries/history ; DNA, Ancient ; Humans ; },
abstract = {DNA from a medieval German cemetery opens a window on the history of today's largest Jewish population.},
}

*Jews/genetics
Population/genetics
Germany
Cemeteries/history
DNA, Ancient
Humans

@article {pmid36333301,
year = {2022},
author = {Garcés-Pastor, S and Coissac, E and Lavergne, S and Schwörer, C and Theurillat, JP and Heintzman, PD and Wangensteen, OS and Tinner, W and Rey, F and Heer, M and Rutzer, A and Walsh, K and Lammers, Y and Brown, AG and Goslar, T and Rijal, DP and Karger, DN and Pellissier, L and , and Heiri, O and Alsos, IG},
title = {High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6559},
pmid = {36333301},
issn = {2041-1723},
mesh = {Humans ; *Climate Change ; *DNA, Ancient ; Plants/genetics ; Lakes ; Pollen ; },
abstract = {The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.},
}

Humans
*Climate Change
*DNA, Ancient
Plants/genetics
Lakes
Pollen

@article {pmid36264804,
year = {2022},
author = {Gibbons, A},
title = {How the Black Death left its mark on immune system genes.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6617},
pages = {237-238},
doi = {10.1126/science.adf3947},
pmid = {36264804},
issn = {1095-9203},
mesh = {Humans ; Immune System ; *Plague/genetics/history/immunology ; *Immunity/genetics ; *Selection, Genetic ; *Pandemics/history ; DNA, Ancient ; },
abstract = {Study of DNA from medieval victims and survivors finds gene that helped protect people from deadly pathogen.},
}

Humans
Immune System
*Plague/genetics/history/immunology
*Immunity/genetics
*Selection, Genetic
*Pandemics/history
DNA, Ancient

@article {pmid36192444,
year = {2022},
author = {Callaway, E and Ledford, H},
title = {Geneticist who unmasked lives of ancient humans wins medicine Nobel.},
journal = {Nature},
volume = {610},
number = {7930},
pages = {16-17},
pmid = {36192444},
issn = {1476-4687},
mesh = {*DNA, Ancient ; Humans ; *Medicine/standards ; *Nobel Prize ; },
}

*DNA, Ancient
Humans
*Medicine/standards
*Nobel Prize

@article {pmid36137029,
year = {2022},
author = {Curry, A},
title = {How the Anglo-Saxons settled England.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6613},
pages = {1371},
doi = {10.1126/science.ade9808},
pmid = {36137029},
issn = {1095-9203},
mesh = {Burial ; DNA, Ancient ; *Emigration and Immigration/history ; England ; History, Ancient ; Humans ; Sequence Analysis, DNA ; *White People/genetics ; },
abstract = {Genetic study of burials suggests whole families migrated to the island in the first millennium C.E.},
}

Burial
DNA, Ancient
*Emigration and Immigration/history
England
History, Ancient
Humans
Sequence Analysis, DNA
*White People/genetics

@article {pmid35931723,
year = {2022},
author = {Silva, NM and Kreutzer, S and Souleles, A and Triantaphyllou, S and Kotsakis, K and Urem-Kotsou, D and Halstead, P and Efstratiou, N and Kotsos, S and Karamitrou-Mentessidi, G and Adaktylou, F and Chondroyianni-Metoki, A and Pappa, M and Ziota, C and Sampson, A and Papathanasiou, A and Vitelli, K and Cullen, T and Kyparissi-Apostolika, N and Lanz, AZ and Peters, J and Rio, J and Wegmann, D and Burger, J and Currat, M and Papageorgopoulou, C},
title = {Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {13474},
pmid = {35931723},
issn = {2045-2322},
support = {31003A_156853/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Bayes Theorem ; DNA, Ancient ; *DNA, Mitochondrial/genetics ; Europe ; Genetics, Population ; Greece ; History, Ancient ; Humans ; *Mitochondria/genetics ; Population Dynamics ; },
abstract = {The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.},
}

Bayes Theorem
DNA, Ancient
*DNA, Mitochondrial/genetics
Europe
Genetics, Population
Greece
History, Ancient
Humans
*Mitochondria/genetics
Population Dynamics

@article {pmid35901158,
year = {2022},
author = {O'Grady, C},
title = {Ancient Europeans farmed dairy-but couldn't digest milk.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6605},
pages = {456},
doi = {10.1126/science.ade1300},
pmid = {35901158},
issn = {1095-9203},
mesh = {Animals ; DNA, Ancient ; *Dairying/history ; Digestion ; Europe ; *Farms/history ; History, Ancient ; Humans ; *Lactase/genetics ; *Lactose Intolerance/enzymology/genetics/history ; *Milk ; *Selection, Genetic ; Starvation/epidemiology ; *White People/genetics/history ; },
abstract = {Giant study of ancient pottery and DNA challenges common evolutionary explanation for lactase persistence.},
}

Animals
DNA, Ancient
*Dairying/history
Digestion
Europe
*Farms/history
History, Ancient
Humans
*Lactase/genetics
*Lactose Intolerance/enzymology/genetics/history
*Milk
*Selection, Genetic
Starvation/epidemiology
*White People/genetics/history

@article {pmid35709925,
year = {2022},
author = {Raveane, A and Molinaro, L and Aneli, S and Capodiferro, MR and de Gennaro, L and Ongaro, L and Rambaldi Migliore, N and Soffiati, S and Scarano, T and Torroni, A and Achilli, A and Ventura, M and Pagani, L and Capelli, C and Olivieri, A and Bertolini, F and Semino, O and Montinaro, F},
title = {Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy.},
journal = {Genomics},
volume = {114},
number = {4},
pages = {110405},
doi = {10.1016/j.ygeno.2022.110405},
pmid = {35709925},
issn = {1089-8646},
mesh = {Archaeology ; *DNA, Ancient ; *Genome, Human ; Humans ; Iran ; Italy ; },
abstract = {Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.},
}

Archaeology
*DNA, Ancient
*Genome, Human
Humans
Iran
Italy

@article {pmid35580179,
year = {2022},
author = {Slavin, P and Sebbane, F},
title = {Emergence and spread of ancestral Yersinia pestis in Late-Neolithic and Bronze-Age Eurasia, ca. 5,000 to 1,500 y B.P.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {21},
pages = {e2204044119},
pmid = {35580179},
issn = {1091-6490},
mesh = {Asia ; DNA, Ancient ; Europe ; Humans ; *Plague/epidemiology ; *Yersinia pestis/genetics ; *Yersinia pseudotuberculosis/genetics ; },
}

Asia
DNA, Ancient
Europe
Humans
*Plague/epidemiology
*Yersinia pestis/genetics
*Yersinia pseudotuberculosis/genetics

@article {pmid35508651,
year = {2022},
author = {Gelabert, P and Schmidt, RW and Fernandes, DM and Karsten, JK and Harper, TK and Madden, GD and Ledogar, SH and Sokhatsky, M and Oota, H and Kennett, DJ and Pinhasi, R},
title = {Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7242},
pmid = {35508651},
issn = {2045-2322},
support = {PACE #70245/MCCC_/Marie Curie/United Kingdom ; },
mesh = {Agriculture ; *DNA, Ancient ; Europe ; Genome, Human ; History, Ancient ; *Human Migration ; Humans ; Ukraine ; },
abstract = {The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000-3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935-825 cal BCE). Results reveal that the CTCC individuals' ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980-825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.},
}

Agriculture
*DNA, Ancient
Europe
Genome, Human
History, Ancient
*Human Migration
Humans
Ukraine

@article {pmid35201891,
year = {2022},
author = {Wohns, AW and Wong, Y and Jeffery, B and Akbari, A and Mallick, S and Pinhasi, R and Patterson, N and Reich, D and Kelleher, J and McVean, G},
title = {A unified genealogy of modern and ancient genomes.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6583},
pages = {eabi8264},
pmid = {35201891},
issn = {1095-9203},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Africa ; Chromosomes, Human, Pair 20/genetics ; Computer Simulation ; *DNA, Ancient ; Databases, Nucleic Acid ; Datasets as Topic ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; *Genome, Human ; *Genomics ; Geography ; Haplotypes ; Human Migration ; Humans ; Mutation ; *Pedigree ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Statistics, Nonparametric ; },
abstract = {The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.},
}

Africa
Chromosomes, Human, Pair 20/genetics
Computer Simulation
*DNA, Ancient
Databases, Nucleic Acid
Datasets as Topic
Evolution, Molecular
Genetic Variation
Genetics, Population
*Genome, Human
*Genomics
Geography
Haplotypes
Human Migration
Humans
Mutation
*Pedigree
Sequence Analysis, DNA
Spatio-Temporal Analysis
Statistics, Nonparametric

@article {pmid34949860,
year = {2022},
author = {Carlin, N},
title = {A grave matter of ancient kinship in Neolithic Britain.},
journal = {Nature},
volume = {601},
number = {7894},
pages = {510-512},
pmid = {34949860},
issn = {1476-4687},
mesh = {*Archaeology ; *DNA, Ancient ; United Kingdom ; },
}

*Archaeology
*DNA, Ancient
United Kingdom

@article {pmid34937885,
year = {2022},
author = {Bradley, DG},
title = {Bronze Age genomes reveal migration to Britain.},
journal = {Nature},
volume = {601},
number = {7894},
pages = {512-513},
pmid = {34937885},
issn = {1476-4687},
mesh = {*DNA, Ancient ; *Human Migration ; United Kingdom ; },
}

*DNA, Ancient
*Human Migration
United Kingdom

@article {pmid34782694,
year = {2021},
author = {Guellil, M and Rinaldo, N and Zedda, N and Kersten, O and Gonzalez Muro, X and Stenseth, NC and Gualdi-Russo, E and Bramanti, B},
title = {Bioarchaeological insights into the last plague of Imola (1630-1632).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {22253},
pmid = {34782694},
issn = {2045-2322},
support = {324249//FP7 Ideas: European Research Council/ ; 324249//FP7 Ideas: European Research Council/ ; 324249//FP7 Ideas: European Research Council/ ; },
mesh = {Adult ; *Archaeology/history ; Child ; Child, Preschool ; DNA, Ancient ; DNA, Bacterial ; *Disease Outbreaks/history ; Female ; Geography, Medical ; History, 17th Century ; Humans ; Italy/epidemiology ; Male ; Metagenome ; Metagenomics ; Plague/*epidemiology/history/*microbiology ; Yersinia pestis/genetics ; },
abstract = {The plague of 1630-1632 was one of the deadliest plague epidemics to ever hit Northern Italy, and for many of the affected regions, it was also the last. While accounts on plague during the early 1630s in Florence and Milan are frequent, much less is known about the city of Imola. We analyzed the full skeletal assemblage of four mass graves (n = 133 individuals) at the Lazaretto dell'Osservanza, which date back to the outbreak of 1630-1632 in Imola and evaluated our results by integrating new archival sources. The skeletons showed little evidence of physical trauma and were covered by multiple layers of lime, which is characteristic for epidemic mass mortality sites. We screened 15 teeth for Yersinia pestis aDNA and were able to confirm the presence of plague in Imola via metagenomic analysis. Additionally, we studied a contemporaneous register, in which a friar recorded patient outcomes at the lazaretto during the last year of the epidemic. Our multidisciplinary approach combining historical, osteological and genomic data provided a unique opportunity to reconstruct an in-depth picture of the last plague of Imola through the city's main lazaretto.},
}

Adult
*Archaeology/history
Child
Child, Preschool
DNA, Ancient
DNA, Bacterial
*Disease Outbreaks/history
Female
Geography, Medical
History, 17th Century
Humans
Italy/epidemiology
Male
Metagenome
Metagenomics
Plague/*epidemiology/history/*microbiology
Yersinia pestis/genetics

@article {pmid34718543,
year = {2021},
author = {Colbran, LL and Johnson, MR and Mathieson, I and Capra, JA},
title = {Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment.},
journal = {Genome biology and evolution},
volume = {13},
number = {11},
pages = {},
pmid = {34718543},
issn = {1759-6653},
support = {T32 GM080178/GM/NIGMS NIH HHS/United States ; R35 GM133708/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; R01 GM115836/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adaptation, Biological/genetics ; Adaptation, Physiological ; Biological Evolution ; DNA, Ancient ; *Genome, Human ; Humans ; Multifactorial Inheritance ; Selection, Genetic ; },
abstract = {As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple noncoding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, for example, at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2,999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits.},
}

*Adaptation, Biological/genetics
Adaptation, Physiological
Biological Evolution
DNA, Ancient
*Genome, Human
Humans
Multifactorial Inheritance
Selection, Genetic

@article {pmid34671162,
year = {2021},
author = {Librado, P and Khan, N and Fages, A and Kusliy, MA and Suchan, T and Tonasso-Calvière, L and Schiavinato, S and Alioglu, D and Fromentier, A and Perdereau, A and Aury, JM and Gaunitz, C and Chauvey, L and Seguin-Orlando, A and Der Sarkissian, C and Southon, J and Shapiro, B and Tishkin, AA and Kovalev, AA and Alquraishi, S and Alfarhan, AH and Al-Rasheid, KAS and Seregély, T and Klassen, L and Iversen, R and Bignon-Lau, O and Bodu, P and Olive, M and Castel, JC and Boudadi-Maligne, M and Alvarez, N and Germonpré, M and Moskal-Del Hoyo, M and Wilczyński, J and Pospuła, S and Lasota-Kuś, A and Tunia, K and Nowak, M and Rannamäe, E and Saarma, U and Boeskorov, G and Lōugas, L and Kyselý, R and Peške, L and Bălășescu, A and Dumitrașcu, V and Dobrescu, R and Gerber, D and Kiss, V and Szécsényi-Nagy, A and Mende, BG and Gallina, Z and Somogyi, K and Kulcsár, G and Gál, E and Bendrey, R and Allentoft, ME and Sirbu, G and Dergachev, V and Shephard, H and Tomadini, N and Grouard, S and Kasparov, A and Basilyan, AE and Anisimov, MA and Nikolskiy, PA and Pavlova, EY and Pitulko, V and Brem, G and Wallner, B and Schwall, C and Keller, M and Kitagawa, K and Bessudnov, AN and Bessudnov, A and Taylor, W and Magail, J and Gantulga, JO and Bayarsaikhan, J and Erdenebaatar, D and Tabaldiev, K and Mijiddorj, E and Boldgiv, B and Tsagaan, T and Pruvost, M and Olsen, S and Makarewicz, CA and Valenzuela Lamas, S and Albizuri Canadell, S and Nieto Espinet, A and Iborra, MP and Lira Garrido, J and Rodríguez González, E and Celestino, S and Olària, C and Arsuaga, JL and Kotova, N and Pryor, A and Crabtree, P and Zhumatayev, R and Toleubaev, A and Morgunova, NL and Kuznetsova, T and Lordkipanize, D and Marzullo, M and Prato, O and Bagnasco Gianni, G and Tecchiati, U and Clavel, B and Lepetz, S and Davoudi, H and Mashkour, M and Berezina, NY and Stockhammer, PW and Krause, J and Haak, W and Morales-Muñiz, A and Benecke, N and Hofreiter, M and Ludwig, A and Graphodatsky, AS and Peters, J and Kiryushin, KY and Iderkhangai, TO and Bokovenko, NA and Vasiliev, SK and Seregin, NN and Chugunov, KV and Plasteeva, NA and Baryshnikov, GF and Petrova, E and Sablin, M and Ananyevskaya, E and Logvin, A and Shevnina, I and Logvin, V and Kalieva, S and Loman, V and Kukushkin, I and Merz, I and Merz, V and Sakenov, S and Varfolomeyev, V and Usmanova, E and Zaibert, V and Arbuckle, B and Belinskiy, AB and Kalmykov, A and Reinhold, S and Hansen, S and Yudin, AI and Vybornov, AA and Epimakhov, A and Berezina, NS and Roslyakova, N and Kosintsev, PA and Kuznetsov, PF and Anthony, D and Kroonen, GJ and Kristiansen, K and Wincker, P and Outram, A and Orlando, L},
title = {The origins and spread of domestic horses from the Western Eurasian steppes.},
journal = {Nature},
volume = {598},
number = {7882},
pages = {634-640},
pmid = {34671162},
issn = {1476-4687},
mesh = {Animals ; Archaeology ; Asia ; DNA, Ancient ; *Domestication ; Europe ; *Genetics, Population ; Genome ; Grassland ; *Horses/genetics ; Phylogeny ; },
abstract = {Domestication of horses fundamentally transformed long-range mobility and warfare[1]. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling[2-4] at Botai, Central Asia around 3500 BC[3]. Other longstanding candidate regions for horse domestication, such as Iberia[5] and Anatolia[6], have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association[7] between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC[8,9] driving the spread of Indo-European languages[10]. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture[11,12].},
}

Animals
Archaeology
Asia
DNA, Ancient
*Domestication
Europe
*Genetics, Population
Genome
Grassland
*Horses/genetics
Phylogeny

@article {pmid34584164,
year = {2021},
author = {Wang, CC and Posth, C and Furtwängler, A and Sümegi, K and Bánfai, Z and Kásler, M and Krause, J and Melegh, B},
title = {Genome-wide autosomal, mtDNA, and Y chromosome analysis of King Bela III of the Hungarian Arpad dynasty.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19210},
pmid = {34584164},
issn = {2045-2322},
mesh = {Asian People/genetics ; Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Female ; *Genetics, Population ; *Haplotypes ; Humans ; Hungary ; Male ; Pedigree ; },
abstract = {The ancient Hungarians, "Madzsars", established their control of the Carpathian Basin in the late ninth century and founded the Hungarian Kingdom around 1000AD. The origin of the Magyars as a tribal federation has been much debated in the past. From the time of the conquest to the early fourteenth century they were ruled by descendants of the Arpad family. In order to learn more about the genetic origin of this family, we here analyzed the genome of Bela III one of the most prominent members of the early Hungarian dynasty that ruled the Hungarian Kingdom from 1172 to 1196. The Y-Chromosome of Bela III belongs to haplogroup R1a-Z2123 that is today found in highest frequency in Central Asia, supporting a Central Asian origin for the ruling lineage of the Hungarian kingdom. The autosomal DNA profile of Bela III, however, falls within the genetic variation of present-day east European populations. This is further supported through his mtDNA genome that belongs to haplogroup H, the most common European maternal lineage, but also found in Central Asia. However, we didn't find an exact haplotype match for Bela III. The typical autosomal and maternal Central Eastern European ancestry among Bela III autosomes might be best explained by consecutive intermarriage with local European ruling families.},
}

Asian People/genetics
Chromosomes, Human, Y/genetics
*DNA, Ancient
DNA, Mitochondrial/genetics
Female
*Genetics, Population
*Haplotypes
Humans
Hungary
Male
Pedigree

@article {pmid34516814,
year = {2021},
author = {Gibbons, A},
title = {How farming shaped Europeans' immunity.},
journal = {Science (New York, N.Y.)},
volume = {373},
number = {6560},
pages = {1186},
doi = {10.1126/science.acx9047},
pmid = {34516814},
issn = {1095-9203},
mesh = {Agriculture/*history ; Animals ; Communicable Diseases/*history/immunology/mortality ; DNA, Ancient ; Europe ; Genetic Variation ; History, Ancient ; Humans ; *Immune System ; Immunity/genetics ; Zoonoses/history/immunology ; },
}

Agriculture/*history
Animals
Communicable Diseases/*history/immunology/mortality
DNA, Ancient
Europe
Genetic Variation
History, Ancient
Humans
*Immune System
Immunity/genetics
Zoonoses/history/immunology

@article {pmid34480555,
year = {2021},
author = {Ferreira, JC and Alshamali, F and Montinaro, F and Cavadas, B and Torroni, A and Pereira, L and Raveane, A and Fernandes, V},
title = {Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations.},
journal = {Genome biology and evolution},
volume = {13},
number = {9},
pages = {},
pmid = {34480555},
issn = {1759-6653},
mesh = {Animals ; DNA, Ancient ; Genetics, Population ; Genome, Human ; Human Migration ; Humans ; Indian Ocean ; Iran ; *Neanderthals/genetics ; },
abstract = {The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.},
}

Animals
DNA, Ancient
Genetics, Population
Genome, Human
Human Migration
Humans
Indian Ocean
Iran
*Neanderthals/genetics

@article {pmid34425243,
year = {2021},
author = {Ma, P and Yang, X and Yan, S and Li, C and Gao, S and Han, B and Hou, K and Robbeets, M and Wei, LH and Cui, Y},
title = {Ancient Y-DNA with reconstructed phylogeny provides insights into the demographic history of paternal haplogroup N1a2-F1360.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {48},
number = {12},
pages = {1130-1133},
doi = {10.1016/j.jgg.2021.07.018},
pmid = {34425243},
issn = {1673-8527},
mesh = {Chromosomes, Human, Y ; *DNA, Ancient ; *Ethnicity ; Genetics, Population ; Haplotypes/genetics ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; },
}

Chromosomes, Human, Y
*DNA, Ancient
*Ethnicity
Genetics, Population
Haplotypes/genetics
Humans
Phylogeny
Polymorphism, Single Nucleotide

@article {pmid34349118,
year = {2021},
author = {Maisano Delser, P and Jones, ER and Hovhannisyan, A and Cassidy, L and Pinhasi, R and Manica, A},
title = {A curated dataset of modern and ancient high-coverage shotgun human genomes.},
journal = {Scientific data},
volume = {8},
number = {1},
pages = {202},
pmid = {34349118},
issn = {2052-4463},
support = {649307//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 263441//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 647797//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; 647797//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; },
mesh = {Computational Biology ; DNA, Ancient ; *Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; *Whole Genome Sequencing ; },
abstract = {Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.},
}

Computational Biology
DNA, Ancient
*Genome, Human
High-Throughput Nucleotide Sequencing
Humans
Sequence Analysis, DNA
*Whole Genome Sequencing

@article {pmid34302465,
year = {2021},
author = {Wang, W and Han, GZ},
title = {Ancient Adaptative Evolution of ACE2 in East Asians.},
journal = {Genome biology and evolution},
volume = {13},
number = {8},
pages = {},
pmid = {34302465},
issn = {1759-6653},
mesh = {Adaptation, Physiological ; Angiotensin-Converting Enzyme 2/*genetics ; Asian People/*genetics ; DNA, Ancient ; *Evolution, Molecular ; Haplotypes ; Humans ; Selection, Genetic ; },
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been posing an unprecedented challenge to global public health. SARS-CoV-2 and several other coronaviruses utilize angiotensin-converting enzyme 2 (ACE2) as their entry receptors. The ACE2 gene has been found to experience episodic positive selection across mammals. However, much remains unknown about how the ACE2 gene evolved in human populations. Here, we use population genetics approaches to investigate the evolution of the ACE2 gene in 26 human populations sampled globally. We find the ACE2 gene exhibits an extremely low nucleotide diversity in the East Asian populations. Strong signals of selective sweep are detected in the East Asian populations, but not in the other human populations. The selective sweep in ACE2 is estimated to begin in East Asian populations ∼23,600 years ago. Our study provides novel insights into the evolution of the ACE2 gene within human populations.},
}

Adaptation, Physiological
Angiotensin-Converting Enzyme 2/*genetics
Asian People/*genetics
DNA, Ancient
*Evolution, Molecular
Haplotypes
Humans
Selection, Genetic

@article {pmid33986160,
year = {2021},
author = {Curry, A},
title = {Ancient poop reveals extinction in gut bacteria.},
journal = {Science (New York, N.Y.)},
volume = {372},
number = {6543},
pages = {671},
doi = {10.1126/science.372.6543.671},
pmid = {33986160},
issn = {1095-9203},
mesh = {*Bacteria/classification/genetics ; *DNA, Ancient ; *DNA, Bacterial ; Diet ; Extinction, Biological ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Mexico ; Utah ; },
}

*Bacteria/classification/genetics
*DNA, Ancient
*DNA, Bacterial
Diet
Extinction, Biological
Feces/*microbiology
*Gastrointestinal Microbiome
Genome, Bacterial
Humans
Mexico
Utah

@article {pmid33878301,
year = {2021},
author = {Pedersen, MW and De Sanctis, B and Saremi, NF and Sikora, M and Puckett, EE and Gu, Z and Moon, KL and Kapp, JD and Vinner, L and Vardanyan, Z and Ardelean, CF and Arroyo-Cabrales, J and Cahill, JA and Heintzman, PD and Zazula, G and MacPhee, RDE and Shapiro, B and Durbin, R and Willerslev, E},
title = {Environmental genomics of Late Pleistocene black bears and giant short-faced bears.},
journal = {Current biology : CB},
volume = {31},
number = {12},
pages = {2728-2736.e8},
pmid = {33878301},
issn = {1879-0445},
support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; 220023/WT_/Wellcome Trust/United Kingdom ; 207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Humans ; Metagenomics ; Phylogeny ; *Ursidae/genetics ; },
abstract = {Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,[1-3] by allowing for parallel sequencing of DNA from all trophic levels.[4-8] However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,[9] the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.[5][,][6][,][10][,][11] This is in contrast to data from fossils[12][,][13] where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.[14-16] Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.},
}

Animals
DNA, Ancient
DNA, Mitochondrial
Fossils
Humans
Metagenomics
Phylogeny
*Ursidae/genetics

@article {pmid33833103,
year = {2021},
author = {Gibbons, A},
title = {When modern humans met Neanderthals.},
journal = {Science (New York, N.Y.)},
volume = {372},
number = {6538},
pages = {115-116},
doi = {10.1126/science.372.6538.115},
pmid = {33833103},
issn = {1095-9203},
mesh = {Animals ; Bulgaria ; Czech Republic ; *DNA, Ancient ; Female ; Genetics, Population ; *Genome, Human ; Hominidae/*genetics ; Humans ; Male ; Neanderthals/*genetics ; Sexual Behavior ; Sexual Behavior, Animal ; },
}

Animals
Bulgaria
Czech Republic
*DNA, Ancient
Female
Genetics, Population
*Genome, Human
Hominidae/*genetics
Humans
Male
Neanderthals/*genetics
Sexual Behavior
Sexual Behavior, Animal

@article {pmid33802878,
year = {2021},
author = {Wang, X and Vlok, M and Flibotte, S and Jan, E},
title = {Resurrection of a Viral Internal Ribosome Entry Site from a 700 Year Old Ancient Northwest Territories Cripavirus.},
journal = {Viruses},
volume = {13},
number = {3},
pages = {},
pmid = {33802878},
issn = {1999-4915},
support = {PJT-148761//CIHR/Canada ; },
mesh = {Animals ; DNA, Ancient ; DNA, Intergenic/metabolism ; *Dicistroviridae/genetics/physiology ; Feces/virology ; *Internal Ribosome Entry Sites ; Northwest Territories ; Reindeer/*virology ; Ribosomes/metabolism ; },
abstract = {The dicistrovirus intergenic region internal ribosome entry site (IGR IRES) uses an unprecedented, streamlined mechanism whereby the IRES adopts a triple-pseudoknot (PK) structure to directly bind to the conserved core of the ribosome and drive translation from a non-AUG codon. The origin of this IRES mechanism is not known. Previously, a partial fragment of a divergent dicistrovirus RNA genome, named ancient Northwest territories cripavirus (aNCV), was extracted from 700-year-old caribou feces trapped in a subarctic ice patch. The aNCV IGR sequence adopts a secondary structure similar to contemporary IGR IRES structures, however, there are subtle differences including 105 nucleotides upstream of the IRES of unknown function. Using filter binding assays, we showed that the aNCV IRES could bind to purified ribosomes, and toeprinting analysis pinpointed the start site at a GCU alanine codon adjacent to PKI. Using a bicistronic reporter RNA, the aNCV IGR can direct translation in vitro in a PKI-dependent manner. Lastly, a chimeric infectious clone swapping in the aNCV IRES supported translation and virus infection. The characterization and resurrection of a functional IGR IRES from a divergent 700-year-old virus provides a historical framework for the importance of this viral translational mechanism.},
}

Animals
DNA, Ancient
DNA, Intergenic/metabolism
*Dicistroviridae/genetics/physiology
Feces/virology
*Internal Ribosome Entry Sites
Northwest Territories
Reindeer/*virology
Ribosomes/metabolism

@article {pmid33769498,
year = {2021},
author = {Sjödin, P and McKenna, J and Jakobsson, M},
title = {Estimating divergence times from DNA sequences.},
journal = {Genetics},
volume = {217},
number = {4},
pages = {},
pmid = {33769498},
issn = {1943-2631},
mesh = {Animals ; DNA, Ancient ; Genetic Drift ; Humans ; *Mutation Rate ; Neanderthals/genetics ; *Polymorphism, Genetic ; Population/*genetics ; Time ; },
abstract = {The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.},
}

Animals
DNA, Ancient
Genetic Drift
Humans
*Mutation Rate
Neanderthals/genetics
*Polymorphism, Genetic
Population/*genetics
Time

@article {pmid33564028,
year = {2021},
author = {Kehlmaier, C and Albury, NA and Steadman, DW and Graciá, E and Franz, R and Fritz, U},
title = {Ancient mitogenomics elucidates diversity of extinct West Indian tortoises.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3224},
pmid = {33564028},
issn = {2045-2322},
mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; *Extinction, Biological ; *Genome, Mitochondrial ; *Phylogeny ; Turtles/*genetics ; West Indies ; },
abstract = {We present 10 nearly complete mitochondrial genomes of the extinct tortoise Chelonoidis alburyorum from the Bahamas. While our samples represent morphologically distinct populations from six islands, their genetic divergences were shallow and resembled those among Galápagos tortoises. Our molecular clock estimates revealed that divergence among Bahamian tortoises began ~ 1.5 mya, whereas divergence among the Galápagos tortoises (C. niger complex) began ~ 2 mya. The inter-island divergences of tortoises from within the Bahamas and within the Galápagos Islands are much younger (0.09-0.59 mya, and 0.08-1.43 mya, respectively) than the genetic differentiation between any other congeneric pair of tortoise species. The shallow mitochondrial divergences of the two radiations on the Bahamas and the Galápagos Islands suggest that each archipelago sustained only one species of tortoise, and that the taxa currently regarded as distinct species in the Galápagos should be returned to subspecies status. The extinct tortoises from the Bahamas have two well-supported clades: the first includes one sample from Great Abaco and two from Crooked Island; the second clade includes tortoises from Great Abaco, Eleuthera, Crooked Island, Mayaguana, Middle Caicos, and Grand Turk. Tortoises belonging to both clades on Great Abaco and Crooked Island suggest late Holocene inter-island transport by prehistoric humans.},
}

Animals
*DNA, Ancient
DNA, Mitochondrial/*genetics
*Extinction, Biological
*Genome, Mitochondrial
*Phylogeny
Turtles/*genetics
West Indies

@article {pmid33510007,
year = {2021},
author = {Grimm, D},
title = {Siberia may be long-sought site of dog domestication.},
journal = {Science (New York, N.Y.)},
volume = {371},
number = {6528},
pages = {451-452},
doi = {10.1126/science.371.6528.451},
pmid = {33510007},
issn = {1095-9203},
mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; *Domestication ; Humans ; Phenotype ; Siberia ; Wolves/genetics ; },
}

Animals
DNA, Ancient
DNA, Mitochondrial/genetics
Dogs/*genetics
*Domestication
Humans
Phenotype
Siberia
Wolves/genetics

@article {pmid33444387,
year = {2021},
author = {Egfjord, AF and Margaryan, A and Fischer, A and Sjögren, KG and Price, TD and Johannsen, NN and Nielsen, PO and Sørensen, L and Willerslev, E and Iversen, R and Sikora, M and Kristiansen, K and Allentoft, ME},
title = {Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244872},
pmid = {33444387},
issn = {1932-6203},
mesh = {*Archaeology ; DNA, Ancient ; Denmark ; Female ; *Genomics ; Haplotypes ; History, Ancient ; Human Migration ; Humans ; Male ; Sex Determination Analysis ; Skeleton/*metabolism ; },
abstract = {The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500-2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.},
}

*Archaeology
DNA, Ancient
Denmark
Female
*Genomics
Haplotypes
History, Ancient
Human Migration
Humans
Male
Sex Determination Analysis
Skeleton/*metabolism

@article {pmid33122839,
year = {2020},
author = {Callaway, E},
title = {Ancient dog DNA reveals 11,000 years of canine evolution.},
journal = {Nature},
volume = {587},
number = {7832},
pages = {20},
pmid = {33122839},
issn = {1476-4687},
mesh = {Animals ; *DNA, Ancient ; Dogs ; Evolution, Molecular ; *Heredity ; Phylogeny ; },
}

Animals
*DNA, Ancient
Dogs
Evolution, Molecular
*Heredity
Phylogeny

@article {pmid33122380,
year = {2020},
author = {Massilani, D and Skov, L and Hajdinjak, M and Gunchinsuren, B and Tseveendorj, D and Yi, S and Lee, J and Nagel, S and Nickel, B and Devièse, T and Higham, T and Meyer, M and Kelso, J and Peter, BM and Pääbo, S},
title = {Denisovan ancestry and population history of early East Asians.},
journal = {Science (New York, N.Y.)},
volume = {370},
number = {6516},
pages = {579-583},
doi = {10.1126/science.abc1166},
pmid = {33122380},
issn = {1095-9203},
support = {324139/ERC_/European Research Council/International ; 694707/ERC_/European Research Council/International ; },
mesh = {Animals ; Asian People/*genetics ; DNA, Ancient ; *Evolution, Molecular ; Female ; Hominidae/*genetics ; Humans ; Mongolia ; Population ; Skull ; },
abstract = {We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in northeastern Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.},
}

Animals
Asian People/*genetics
DNA, Ancient
*Evolution, Molecular
Female
Hominidae/*genetics
Humans
Mongolia
Population
Skull

@article {pmid32970680,
year = {2020},
author = {Toncheva, D and Serbezov, D and Karachanak-Yankova, S and Nesheva, D},
title = {Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease.},
journal = {PloS one},
volume = {15},
number = {9},
pages = {e0233666},
pmid = {32970680},
issn = {1932-6203},
mesh = {*DNA, Ancient ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Female ; *Genes, Mitochondrial ; Humans ; Male ; Mitochondria/genetics ; Mitochondrial Diseases/*genetics ; Mutation ; RNA, Transfer/genetics ; },
abstract = {Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.},
}

*DNA, Ancient
DNA, Mitochondrial/*genetics
Databases, Genetic
Female
*Genes, Mitochondrial
Humans
Male
Mitochondria/genetics
Mitochondrial Diseases/*genetics
Mutation
RNA, Transfer/genetics

@article {pmid32888485,
year = {2020},
author = {Burger, J and Link, V and Blöcher, J and Schulz, A and Sell, C and Pochon, Z and Diekmann, Y and Žegarac, A and Hofmanová, Z and Winkelbach, L and Reyna-Blanco, CS and Bieker, V and Orschiedt, J and Brinker, U and Scheu, A and Leuenberger, C and Bertino, TS and Bollongino, R and Lidke, G and Stefanović, S and Jantzen, D and Kaiser, E and Terberger, T and Thomas, MG and Veeramah, KR and Wegmann, D},
title = {Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years.},
journal = {Current biology : CB},
volume = {30},
number = {21},
pages = {4307-4315.e13},
doi = {10.1016/j.cub.2020.08.033},
pmid = {32888485},
issn = {1879-0445},
mesh = {Adult ; Body Remains ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Europe ; Female ; Gene Frequency ; Humans ; Lactase/*genetics ; Male ; *Selection, Genetic ; White People/*genetics ; Young Adult ; },
abstract = {Lactase persistence (LP), the continued expression of lactase into adulthood, is the most strongly selected single gene trait over the last 10,000 years in multiple human populations. It has been posited that the primary allele causing LP among Eurasians, rs4988235-A [1], only rose to appreciable frequencies during the Bronze and Iron Ages [2, 3], long after humans started consuming milk from domesticated animals. This rapid rise has been attributed to an influx of people from the Pontic-Caspian steppe that began around 5,000 years ago [4, 5]. We investigate the spatiotemporal spread of LP through an analysis of 14 warriors from the Tollense Bronze Age battlefield in northern Germany (∼3,200 before present, BP), the oldest large-scale conflict site north of the Alps. Genetic data indicate that these individuals represent a single unstructured Central/Northern European population. We complemented these data with genotypes of 18 individuals from the Bronze Age site Mokrin in Serbia (∼4,100 to ∼3,700 BP) and 37 individuals from Eastern Europe and the Pontic-Caspian Steppe region, predating both Bronze Age sites (∼5,980 to ∼3,980 BP). We infer low LP in all three regions, i.e., in northern Germany and South-eastern and Eastern Europe, suggesting that the surge of rs4988235 in Central and Northern Europe was unlikely caused by Steppe expansions. We estimate a selection coefficient of 0.06 and conclude that the selection was ongoing in various parts of Europe over the last 3,000 years.},
}

Adult
Body Remains
*DNA, Ancient
DNA, Mitochondrial/genetics
Europe
Female
Gene Frequency
Humans
Lactase/*genetics
Male
*Selection, Genetic
White People/*genetics
Young Adult

@article {pmid32612278,
year = {2020},
author = {Gansauge, MT and Aximu-Petri, A and Nagel, S and Meyer, M},
title = {Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA.},
journal = {Nature protocols},
volume = {15},
number = {8},
pages = {2279-2300},
pmid = {32612278},
issn = {1750-2799},
mesh = {Automation ; Base Sequence ; *DNA, Ancient ; DNA, Single-Stranded/*genetics ; *Gene Library ; Sequence Analysis, DNA/*methods ; },
abstract = {It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3' ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5' adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30-35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired.},
}

Automation
Base Sequence
*DNA, Ancient
DNA, Single-Stranded/*genetics
*Gene Library
Sequence Analysis, DNA/*methods

@article {pmid32554575,
year = {2020},
author = {Curry, A},
title = {Incest in ancient Ireland suggests an elite ruled early farmers.},
journal = {Science (New York, N.Y.)},
volume = {368},
number = {6497},
pages = {1299},
doi = {10.1126/science.368.6497.1299},
pmid = {32554575},
issn = {1095-9203},
mesh = {Archaeology ; DNA, Ancient ; Farmers/*history ; History, Ancient ; Humans ; Incest/*history ; Ireland ; Middle Aged ; },
}

Archaeology
DNA, Ancient
Farmers/*history
History, Ancient
Humans
Incest/*history
Ireland
Middle Aged

@article {pmid32437661,
year = {2020},
author = {Yu, H and Spyrou, MA and Karapetian, M and Shnaider, S and Radzevičiūtė, R and Nägele, K and Neumann, GU and Penske, S and Zech, J and Lucas, M and LeRoux, P and Roberts, P and Pavlenok, G and Buzhilova, A and Posth, C and Jeong, C and Krause, J},
title = {Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia.},
journal = {Cell},
volume = {181},
number = {6},
pages = {1232-1245.e20},
doi = {10.1016/j.cell.2020.04.037},
pmid = {32437661},
issn = {1097-4172},
mesh = {Asia ; DNA, Ancient ; Europe ; Genome, Human/*genetics ; History, Ancient ; Human Migration/*history ; Humans ; Racial Groups/*genetics/*history ; Siberia ; },
abstract = {Modern humans have inhabited the Lake Baikal region since the Upper Paleolithic, though the precise history of its peoples over this long time span is still largely unknown. Here, we report genome-wide data from 19 Upper Paleolithic to Early Bronze Age individuals from this Siberian region. An Upper Paleolithic genome shows a direct link with the First Americans by sharing the admixed ancestry that gave rise to all non-Arctic Native Americans. We also demonstrate the formation of Early Neolithic and Bronze Age Baikal populations as the result of prolonged admixture throughout the eighth to sixth millennium BP. Moreover, we detect genetic interactions with western Eurasian steppe populations and reconstruct Yersinia pestis genomes from two Early Bronze Age individuals without western Eurasian ancestry. Overall, our study demonstrates the most deeply divergent connection between Upper Paleolithic Siberians and the First Americans and reveals human and pathogen mobility across Eurasia during the Bronze Age.},
}

Asia
DNA, Ancient
Europe
Genome, Human/*genetics
History, Ancient
Human Migration/*history
Humans
Racial Groups/*genetics/*history
Siberia

@article {pmid32313080,
year = {2020},
author = {Furtwängler, A and Rohrlach, AB and Lamnidis, TC and Papac, L and Neumann, GU and Siebke, I and Reiter, E and Steuri, N and Hald, J and Denaire, A and Schnitzler, B and Wahl, J and Ramstein, M and Schuenemann, VJ and Stockhammer, PW and Hafner, A and Lösch, S and Haak, W and Schiffels, S and Krause, J},
title = {Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1915},
pmid = {32313080},
issn = {2041-1723},
mesh = {Archaeology ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Europe ; *Evolution, Molecular ; France ; Genetics, Population/*history ; Genome, Human/*genetics ; Germany ; History, Ancient ; Humans ; Switzerland ; White People/genetics ; },
abstract = {Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860-2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region.},
}

Archaeology
*DNA, Ancient
DNA, Mitochondrial/genetics
Europe
*Evolution, Molecular
France
Genetics, Population/*history
Genome, Human/*genetics
Germany
History, Ancient
Humans
Switzerland
White People/genetics

@article {pmid32132541,
year = {2020},
author = {Gokhman, D and Nissim-Rafinia, M and Agranat-Tamir, L and Housman, G and García-Pérez, R and Lizano, E and Cheronet, O and Mallick, S and Nieves-Colón, MA and Li, H and Alpaslan-Roodenberg, S and Novak, M and Gu, H and Osinski, JM and Ferrando-Bernal, M and Gelabert, P and Lipende, I and Mjungu, D and Kondova, I and Bontrop, R and Kullmer, O and Weber, G and Shahar, T and Dvir-Ginzberg, M and Faerman, M and Quillen, EE and Meissner, A and Lahav, Y and Kandel, L and Liebergall, M and Prada, ME and Vidal, JM and Gronostajski, RM and Stone, AC and Yakir, B and Lalueza-Fox, C and Pinhasi, R and Reich, D and Marques-Bonet, T and Meshorer, E and Carmel, L},
title = {Differential DNA methylation of vocal and facial anatomy genes in modern humans.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1189},
pmid = {32132541},
issn = {2041-1723},
support = {P51 OD011133/OD/NIH HHS/United States ; R01 AI058715/AI/NIAID NIH HHS/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adult ; Aged ; Animals ; Cells, Cultured ; Child ; Chondrocytes ; *DNA Methylation ; *DNA, Ancient ; Evolution, Molecular ; Face/*anatomy & histology ; Female ; Gene Regulatory Networks ; Genetic Speciation ; Humans ; Larynx/anatomy & histology ; Male ; Middle Aged ; Neanderthals/genetics ; Pan troglodytes/genetics ; *Phenotype ; Phonation/*genetics ; Primary Cell Culture ; Tongue/anatomy & histology ; Vocal Cords/anatomy & histology ; Vocalization, Animal ; },
abstract = {Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.},
}

Adult
Aged
Animals
Cells, Cultured
Child
Chondrocytes
*DNA Methylation
*DNA, Ancient
Evolution, Molecular
Face/*anatomy & histology
Female
Gene Regulatory Networks
Genetic Speciation
Humans
Larynx/anatomy & histology
Male
Middle Aged
Neanderthals/genetics
Pan troglodytes/genetics
*Phenotype
Phonation/*genetics
Primary Cell Culture
Tongue/anatomy & histology
Vocal Cords/anatomy & histology
Vocalization, Animal

@article {pmid32079752,
year = {2020},
author = {Gibbons, A},
title = {Strange bedfellows for human ancestors.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6480},
pages = {838-839},
doi = {10.1126/science.367.6480.838},
pmid = {32079752},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; DNA, Ancient ; Extinction, Biological ; Fossils ; *Hominidae/anatomy & histology/genetics ; Humans ; Inbreeding ; *Mating Preference, Animal ; },
}

Animals
*Biological Evolution
DNA, Ancient
Extinction, Biological
Fossils
*Hominidae/anatomy & histology/genetics
Humans
Inbreeding
*Mating Preference, Animal

@article {pmid32043527,
year = {2020},
author = {Li, Z and Barker, MS},
title = {Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions.},
journal = {GigaScience},
volume = {9},
number = {2},
pages = {},
pmid = {32043527},
issn = {2047-217X},
mesh = {DNA, Ancient ; Evolution, Molecular ; *Genome, Plant ; *Phylogeny ; Plants/classification/*genetics ; *Polyploidy ; },
abstract = {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.},
}

DNA, Ancient
Evolution, Molecular
*Genome, Plant
*Phylogeny
Plants/classification/*genetics
*Polyploidy

@article {pmid31892727,
year = {2019},
author = {Laza, IM and Hervella, M and Neira Zubieta, M and de-la-Rúa, C},
title = {Environmental factors modulated ancient mitochondrial DNA variability and the prevalence of rheumatic diseases in the Basque Country.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {20380},
pmid = {31892727},
issn = {2045-2322},
mesh = {*DNA, Ancient ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Predisposition to Disease ; Humans ; Prevalence ; Rheumatic Diseases/epidemiology/*genetics ; Spain ; },
abstract = {Among the factors that would explain the distribution of mitochondrial lineages in Europe, climate and diseases may have played an important role. A possible explanation lies in the nature of the mitochondrion, in which the energy generation process produces reactive oxygen species that may influence the development of different diseases. The present study is focused on the medieval necropolis of San Miguel de Ereñozar (13[th]-16[th] centuries, Basque Country), whose inhabitants presented a high prevalence of rheumatic diseases and lived during the Little Ice Age (LIA). Our results indicate a close relationship between rheumatic diseases and mitochondrial haplogroup H, and specifically between spondyloarthropathies and sub-haplogroup H2. One possible explanation may be the climate change that took place in the LIA that favoured those haplogroups that were more energy-efficient, such as haplogroup H, to endure lower temperatures and food shortage. However, it had a biological trade-off: the increased risk of developing rheumatic diseases.},
}

*DNA, Ancient
DNA, Mitochondrial/*genetics
*Evolution, Molecular
Genetic Predisposition to Disease
Humans
Prevalence
Rheumatic Diseases/epidemiology/*genetics
Spain

@article {pmid31844110,
year = {2019},
author = {Mastrantonio, V and Urbanelli, S and Porretta, D},
title = {Ancient hybridization and mtDNA introgression behind current paternal leakage and heteroplasmy in hybrid zones.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {19177},
pmid = {31844110},
issn = {2045-2322},
mesh = {Animals ; Base Sequence ; Coleoptera/*genetics ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; *Hybridization, Genetic ; Phylogeny ; },
abstract = {Hybridization between heterospecific individuals has been documented as playing a direct role in promoting paternal leakage and mitochondrial heteroplasmy in both natural populations and laboratory conditions, by relaxing the egg-sperm recognition mechanisms. Here, we tested the hypothesis that hybridization can lead to mtDNA heteroplasmy also indirectly via mtDNA introgression. By using a phylogenetic approach, we showed in two reproductively isolated beetle species, Ochthebius quadricollis and O. urbanelliae, that past mtDNA introgression occurred between them in sympatric populations. Then, by developing a multiplex allele-specific PCR assay, we showed the presence of heteroplasmic individuals and argue that their origin was through paternal leakage following mating between mtDNA-introgressed and pure conspecific individuals. Our results highlight that mtDNA introgression can contribute to promote paternal leakage, generating genetic novelty in a way that has been overlooked to date. Furthermore, they highlight that the frequency and distribution of mtDNA heteroplasmy can be deeply underestimated in natural populations, as i) the commonly used PCR-Sanger sequencing approach can fail to detect mitochondrial heteroplasmy, and ii) specific studies aimed at searching for it in populations where mtDNA-introgressed and pure individuals co-occur remain scarce, despite the fact that mtDNA introgression has been widely documented in several taxa and populations.},
}

Animals
Base Sequence
Coleoptera/*genetics
*DNA, Ancient
DNA, Mitochondrial/*genetics
Electron Transport Complex IV/genetics
Genetic Variation
Genetics, Population
Geography
Haplotypes/genetics
*Hybridization, Genetic
Phylogeny

@article {pmid31721774,
year = {2019},
author = {Wasef, S and Subramanian, S and O'Rorke, R and Huynen, L and El-Marghani, S and Curtis, C and Popinga, A and Holland, B and Ikram, S and Millar, C and Willerslev, E and Lambert, D},
title = {Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0223964},
pmid = {31721774},
issn = {1932-6203},
mesh = {Africa ; Animal Husbandry/history ; Animals ; Birds/classification/*genetics ; DNA, Ancient ; DNA, Mitochondrial/blood/genetics/history ; Egypt, Ancient ; Genetic Variation ; *Genome, Mitochondrial ; History, Ancient ; *Mummies ; Phylogeny ; Religion/history ; },
abstract = {The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these 'votive' mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.},
}

Africa
Animal Husbandry/history
Animals
Birds/classification/*genetics
DNA, Ancient
DNA, Mitochondrial/blood/genetics/history
Egypt, Ancient
Genetic Variation
*Genome, Mitochondrial
History, Ancient
*Mummies
Phylogeny
Religion/history

@article {pmid31601754,
year = {2019},
author = {Vogel, G},
title = {Seeing fossils in a new light.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6462},
pages = {176-178},
doi = {10.1126/science.366.6462.176},
pmid = {31601754},
issn = {1095-9203},
mesh = {Animals ; DNA, Ancient ; *Dinosaurs ; *Fossils ; Proteins/analysis/*chemistry ; Proteolysis ; Tissue Preservation ; Tooth/chemistry ; },
}

Animals
DNA, Ancient
*Dinosaurs
*Fossils
Proteins/analysis/*chemistry
Proteolysis
Tissue Preservation
Tooth/chemistry

@article {pmid31601705,
year = {2019},
author = {Mittnik, A and Massy, K and Knipper, C and Wittenborn, F and Friedrich, R and Pfrengle, S and Burri, M and Carlichi-Witjes, N and Deeg, H and Furtwängler, A and Harbeck, M and von Heyking, K and Kociumaka, C and Kucukkalipci, I and Lindauer, S and Metz, S and Staskiewicz, A and Thiel, A and Wahl, J and Haak, W and Pernicka, E and Schiffels, S and Stockhammer, PW and Krause, J},
title = {Kinship-based social inequality in Bronze Age Europe.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6466},
pages = {731-734},
doi = {10.1126/science.aax6219},
pmid = {31601705},
issn = {1095-9203},
mesh = {Anthropology ; DNA, Ancient ; Family Characteristics/*history ; Female ; Germany ; History, Ancient ; Humans ; Male ; Pedigree ; Polymorphism, Single Nucleotide ; Social Class/*history ; },
abstract = {Revealing and understanding the mechanisms behind social inequality in prehistoric societies is a major challenge. By combining genome-wide data, isotopic evidence, and anthropological and archaeological data, we have gone beyond the dominating supraregional approaches in archaeogenetics to shed light on the complexity of social status, inheritance rules, and mobility during the Bronze Age. We applied a deep microregional approach and analyzed genome-wide data of 104 human individuals deriving from farmstead-related cemeteries from the Late Neolithic to the Middle Bronze Age in southern Germany. Our results reveal individual households, lasting several generations, that consisted of a high-status core family and unrelated low-status individuals; a social organization accompanied by patrilocality and female exogamy; and the stability of this system over 700 years.},
}

Anthropology
DNA, Ancient
Family Characteristics/*history
Female
Germany
History, Ancient
Humans
Male
Pedigree
Polymorphism, Single Nucleotide
Social Class/*history

@article {pmid31517044,
year = {2019},
author = {Raveane, A and Aneli, S and Montinaro, F and Athanasiadis, G and Barlera, S and Birolo, G and Boncoraglio, G and Di Blasio, AM and Di Gaetano, C and Pagani, L and Parolo, S and Paschou, P and Piazza, A and Stamatoyannopoulos, G and Angius, A and Brucato, N and Cucca, F and Hellenthal, G and Mulas, A and Peyret-Guzzon, M and Zoledziewska, M and Baali, A and Bycroft, C and Cherkaoui, M and Chiaroni, J and Di Cristofaro, J and Dina, C and Dugoujon, JM and Galan, P and Giemza, J and Kivisild, T and Mazieres, S and Melhaoui, M and Metspalu, M and Myers, S and Pereira, L and Ricaut, FX and Brisighelli, F and Cardinali, I and Grugni, V and Lancioni, H and Pascali, VL and Torroni, A and Semino, O and Matullo, G and Achilli, A and Olivieri, A and Capelli, C},
title = {Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.},
journal = {Science advances},
volume = {5},
number = {9},
pages = {eaaw3492},
pmid = {31517044},
issn = {2375-2548},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *DNA, Ancient ; *Databases, Genetic ; *Genetic Drift ; *Genome, Human ; Genome-Wide Association Study ; History, Ancient ; Human Genetics ; Humans ; Italy ; Neanderthals/genetics ; White People/*genetics ; },
abstract = {European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.},
}

Animals
*DNA, Ancient
*Databases, Genetic
*Genetic Drift
*Genome, Human
Genome-Wide Association Study
History, Ancient
Human Genetics
Humans
Italy
Neanderthals/genetics
White People/*genetics

@article {pmid31405970,
year = {2019},
author = {Frantz, LAF and Haile, J and Lin, AT and Scheu, A and Geörg, C and Benecke, N and Alexander, M and Linderholm, A and Mullin, VE and Daly, KG and Battista, VM and Price, M and Gron, KJ and Alexandri, P and Arbogast, RM and Arbuckle, B and Bӑlӑşescu, A and Barnett, R and Bartosiewicz, L and Baryshnikov, G and Bonsall, C and Borić, D and Boroneanţ, A and Bulatović, J and Çakirlar, C and Carretero, JM and Chapman, J and Church, M and Crooijmans, R and De Cupere, B and Detry, C and Dimitrijevic, V and Dumitraşcu, V and du Plessis, L and Edwards, CJ and Erek, CM and Erim-Özdoğan, A and Ervynck, A and Fulgione, D and Gligor, M and Götherström, A and Gourichon, L and Groenen, MAM and Helmer, D and Hongo, H and Horwitz, LK and Irving-Pease, EK and Lebrasseur, O and Lesur, J and Malone, C and Manaseryan, N and Marciniak, A and Martlew, H and Mashkour, M and Matthews, R and Matuzeviciute, GM and Maziar, S and Meijaard, E and McGovern, T and Megens, HJ and Miller, R and Mohaseb, AF and Orschiedt, J and Orton, D and Papathanasiou, A and Pearson, MP and Pinhasi, R and Radmanović, D and Ricaut, FX and Richards, M and Sabin, R and Sarti, L and Schier, W and Sheikhi, S and Stephan, E and Stewart, JR and Stoddart, S and Tagliacozzo, A and Tasić, N and Trantalidou, K and Tresset, A and Valdiosera, C and van den Hurk, Y and Van Poucke, S and Vigne, JD and Yanevich, A and Zeeb-Lanz, A and Triantafyllidis, A and Gilbert, MTP and Schibler, J and Rowley-Conwy, P and Zeder, M and Peters, J and Cucchi, T and Bradley, DG and Dobney, K and Burger, J and Evin, A and Girdland-Flink, L and Larson, G},
title = {Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {35},
pages = {17231-17238},
pmid = {31405970},
issn = {1091-6490},
support = {/WT_/Wellcome Trust/United Kingdom ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; *Domestication ; Europe ; *Gene Flow ; History, Ancient ; Middle East ; *Phylogeny ; Skin Pigmentation/genetics ; Swine/*genetics ; },
abstract = {Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.},
}

Animals
*DNA, Ancient
DNA, Mitochondrial/*genetics
*Domestication
Europe
*Gene Flow
History, Ancient
Middle East
*Phylogeny
Skin Pigmentation/genetics
Swine/*genetics

@article {pmid31273106,
year = {2019},
author = {Gibbons, A},
title = {DNA reveals European roots of the ancient Philistines.},
journal = {Science (New York, N.Y.)},
volume = {365},
number = {6448},
pages = {17},
doi = {10.1126/science.365.6448.17},
pmid = {31273106},
issn = {1095-9203},
mesh = {Archaeology ; DNA, Ancient ; Europe/ethnology ; History, Ancient ; Human Migration/*history ; Israel/ethnology ; },
}

Archaeology
DNA, Ancient
Europe/ethnology
History, Ancient
Human Migration/*history
Israel/ethnology

@article {pmid31095634,
year = {2019},
author = {Yuan, JX and Hou, XD and Barlow, A and Preick, M and Taron, UH and Alberti, F and Basler, N and Deng, T and Lai, XL and Hofreiter, M and Sheng, GL},
title = {Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0216883},
pmid = {31095634},
issn = {1932-6203},
mesh = {Animals ; *Biological Evolution ; *DNA, Ancient ; *Equidae/classification/genetics ; *Genome, Mitochondrial ; *Haplotypes ; *Phylogeny ; },
abstract = {The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus.},
}

Animals
*Biological Evolution
*DNA, Ancient
*Equidae/classification/genetics
*Genome, Mitochondrial
*Haplotypes
*Phylogeny

@article {pmid30545868,
year = {2018},
author = {Gibbons, A},
title = {Why modern humans have round heads.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6420},
pages = {1229},
doi = {10.1126/science.362.6420.1229-a},
pmid = {30545868},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Brain/*anatomy & histology ; *DNA, Ancient ; Head/*anatomy & histology ; Humans ; Neanderthals/*genetics ; },
}

Animals
*Biological Evolution
Brain/*anatomy & histology
*DNA, Ancient
Head/*anatomy & histology
Humans
Neanderthals/*genetics

@article {pmid30366251,
year = {2018},
author = {Molinaro, L and Pagani, L},
title = {Human evolutionary history of Eastern Africa.},
journal = {Current opinion in genetics & development},
volume = {53},
number = {},
pages = {134-139},
doi = {10.1016/j.gde.2018.10.002},
pmid = {30366251},
issn = {1879-0380},
mesh = {Africa, Eastern/epidemiology ; Animals ; Anthropology/trends ; *Biological Evolution ; *DNA, Ancient ; Fossils ; Hominidae/*genetics ; Humans ; Paleontology/trends ; },
abstract = {Since the discovery of the first hominin fossils, East Africa has been in the spotlight of palaeo-anthropological investigation for its role as a potential cradle of humanity and as a gateway out of Africa. With the advent of the genomic era an ever increasing amount of information has started to complement this notion, and to place the area within a broader, Pan-African scenario. Here we examine the most recent genetic and fossil results that recapitulate the last hundreds of thousands of years of human evolution in the area, and point to a number of uncharted avenues that may complement the emerging scenario in the coming years.},
}

Africa, Eastern/epidemiology
Animals
Anthropology/trends
*Biological Evolution
*DNA, Ancient
Fossils
Hominidae/*genetics
Humans
Paleontology/trends

@article {pmid30072694,
year = {2018},
author = {Juras, A and Chyleński, M and Ehler, E and Malmström, H and Żurkiewicz, D and Włodarczak, P and Wilk, S and Peška, J and Fojtík, P and Králík, M and Libera, J and Bagińska, J and Tunia, K and Klochko, VI and Dabert, M and Jakobsson, M and Kośko, A},
title = {Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {11603},
pmid = {30072694},
issn = {2045-2322},
mesh = {*DNA, Ancient ; Female ; *Genome, Mitochondrial ; *Grassland ; History, Ancient ; Humans ; Male ; Russia ; White People/*genetics ; },
abstract = {From around 4,000 to 2,000 BC the forest-steppe north-western Pontic region was occupied by people who shared a nomadic lifestyle, pastoral economy and barrow burial rituals. It has been shown that these groups, especially those associated with the Yamnaya culture, played an important role in shaping the gene pool of Bronze Age Europeans, which extends into present-day patterns of genetic variation in Europe. Although the genetic impact of these migrations from the forest-steppe Pontic region into central Europe have previously been addressed in several studies, the contribution of mitochondrial lineages to the people associated with the Corded Ware culture in the eastern part of the North European Plain remains contentious. In this study, we present mitochondrial genomes from 23 Late Eneolithic and Bronze Age individuals, including representatives of the north-western Pontic region and the Corded Ware culture from the eastern part of the North European Plain. We identified, for the first time in ancient populations, the rare mitochondrial haplogroup X4 in two Bronze Age Catacomb culture-associated individuals. Genetic similarity analyses show close maternal genetic affinities between populations associated with both eastern and Baltic Corded Ware culture, and the Yamnaya horizon, in contrast to larger genetic differentiation between populations associated with western Corded Ware culture and the Yamnaya horizon. This indicates that females with steppe ancestry contributed to the formation of populations associated with the eastern Corded Ware culture while more local people, likely of Neolithic farmer ancestry, contributed to the formation of populations associated with western Corded Ware culture.},
}

*DNA, Ancient
Female
*Genome, Mitochondrial
*Grassland
History, Ancient
Humans
Male
Russia
White People/*genetics

@article {pmid30002235,
year = {2018},
author = {Pennisi, E and Price, M},
title = {Molecular 'barcodes' reveal lost whale hunts.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6398},
pages = {119},
doi = {10.1126/science.361.6398.119},
pmid = {30002235},
issn = {1095-9203},
mesh = {Animals ; *Biodiversity ; Bone and Bones ; *DNA Barcoding, Taxonomic ; DNA, Ancient ; Phylogeny ; Whales/*classification/*genetics ; },
}

Animals
*Biodiversity
Bone and Bones
*DNA Barcoding, Taxonomic
DNA, Ancient
Phylogeny
Whales/*classification/*genetics

@article {pmid29976827,
year = {2018},
author = {McColl, H and Racimo, F and Vinner, L and Demeter, F and Gakuhari, T and Moreno-Mayar, JV and van Driem, G and Gram Wilken, U and Seguin-Orlando, A and de la Fuente Castro, C and Wasef, S and Shoocongdej, R and Souksavatdy, V and Sayavongkhamdy, T and Saidin, MM and Allentoft, ME and Sato, T and Malaspinas, AS and Aghakhanian, FA and Korneliussen, T and Prohaska, A and Margaryan, A and de Barros Damgaard, P and Kaewsutthi, S and Lertrit, P and Nguyen, TMH and Hung, HC and Minh Tran, T and Nghia Truong, H and Nguyen, GH and Shahidan, S and Wiradnyana, K and Matsumae, H and Shigehara, N and Yoneda, M and Ishida, H and Masuyama, T and Yamada, Y and Tajima, A and Shibata, H and Toyoda, A and Hanihara, T and Nakagome, S and Deviese, T and Bacon, AM and Duringer, P and Ponche, JL and Shackelford, L and Patole-Edoumba, E and Nguyen, AT and Bellina-Pryce, B and Galipaud, JC and Kinaston, R and Buckley, H and Pottier, C and Rasmussen, S and Higham, T and Foley, RA and Lahr, MM and Orlando, L and Sikora, M and Phipps, ME and Oota, H and Higham, C and Lambert, DM and Willerslev, E},
title = {The prehistoric peopling of Southeast Asia.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6397},
pages = {88-92},
doi = {10.1126/science.aat3628},
pmid = {29976827},
issn = {1095-9203},
mesh = {Asia, Southeastern ; Asian People/genetics ; DNA, Ancient ; Genetic Variation ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Population/genetics ; Sequence Analysis, DNA ; },
abstract = {The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.},
}

Asia, Southeastern
Asian People/genetics
DNA, Ancient
Genetic Variation
*Genome, Human
History, Ancient
Human Migration/*history
Humans
Population/genetics
Sequence Analysis, DNA

@article {pmid29976826,
year = {2018},
author = {Daly, KG and Maisano Delser, P and Mullin, VE and Scheu, A and Mattiangeli, V and Teasdale, MD and Hare, AJ and Burger, J and Verdugo, MP and Collins, MJ and Kehati, R and Erek, CM and Bar-Oz, G and Pompanon, F and Cumer, T and Çakırlar, C and Mohaseb, AF and Decruyenaere, D and Davoudi, H and Çevik, Ö and Rollefson, G and Vigne, JD and Khazaeli, R and Fathi, H and Doost, SB and Rahimi Sorkhani, R and Vahdati, AA and Sauer, EW and Azizi Kharanaghi, H and Maziar, S and Gasparian, B and Pinhasi, R and Martin, L and Orton, D and Arbuckle, BS and Benecke, N and Manica, A and Horwitz, LK and Mashkour, M and Bradley, DG},
title = {Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6397},
pages = {85-88},
doi = {10.1126/science.aas9411},
pmid = {29976826},
issn = {1095-9203},
mesh = {Africa ; Animals ; Animals, Domestic/classification/genetics ; Asia ; DNA, Ancient ; DNA, Mitochondrial/genetics ; *Domestication ; Europe ; Follistatin/genetics ; Genetic Variation ; Genome ; Goats/classification/*genetics ; *Mosaicism ; Phylogeny ; },
abstract = {Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.},
}

Africa
Animals
Animals, Domestic/classification/genetics
Asia
DNA, Ancient
DNA, Mitochondrial/genetics
*Domestication
Europe
Follistatin/genetics
Genetic Variation
Genome
Goats/classification/*genetics
*Mosaicism
Phylogeny

@article {pmid29895902,
year = {2018},
author = {Kılınç, GM and Kashuba, N and Yaka, R and Sümer, AP and Yüncü, E and Shergin, D and Ivanov, GL and Kichigin, D and Pestereva, K and Volkov, D and Mandryka, P and Kharinskii, A and Tishkin, A and Ineshin, E and Kovychev, E and Stepanov, A and Alekseev, A and Fedoseeva, SA and Somel, M and Jakobsson, M and Krzewińska, M and Storå, J and Götherström, A},
title = {Investigating Holocene human population history in North Asia using ancient mitogenomes.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8969},
pmid = {29895902},
issn = {2045-2322},
mesh = {Asia, Northern ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; *Genome, Microbial ; History, Ancient ; Humans ; Male ; },
abstract = {Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.},
}

Asia, Northern
*DNA, Ancient
DNA, Mitochondrial/*genetics
Female
*Genetic Variation
*Genome, Microbial
History, Ancient
Humans
Male

@article {pmid29853688,
year = {2018},
author = {Ebenesersdóttir, SS and Sandoval-Velasco, M and Gunnarsdóttir, ED and Jagadeesan, A and Guðmundsdóttir, VB and Thordardóttir, EL and Einarsdóttir, MS and Moore, KHS and Sigurðsson, Á and Magnúsdóttir, DN and Jónsson, H and Snorradóttir, S and Hovig, E and Møller, P and Kockum, I and Olsson, T and Alfredsson, L and Hansen, TF and Werge, T and Cavalleri, GL and Gilbert, E and Lalueza-Fox, C and Walser, JW and Kristjánsdóttir, S and Gopalakrishnan, S and Árnadóttir, L and Magnússon, ÓÞ and Gilbert, MTP and Stefánsson, K and Helgason, A},
title = {Ancient genomes from Iceland reveal the making of a human population.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6392},
pages = {1028-1032},
doi = {10.1126/science.aar2625},
pmid = {29853688},
issn = {1095-9203},
mesh = {*Biological Evolution ; DNA, Ancient ; Female ; Founder Effect ; Gene Pool ; *Genetic Drift ; *Genome, Human ; Genotype ; Humans ; Iceland ; Male ; Phenotype ; Population/*genetics ; },
abstract = {Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.},
}

*Biological Evolution
DNA, Ancient
Female
Founder Effect
Gene Pool
*Genetic Drift
*Genome, Human
Genotype
Humans
Iceland
Male
Phenotype
Population/*genetics

@article {pmid29743352,
year = {2018},
author = {de Barros Damgaard, P and Martiniano, R and Kamm, J and Moreno-Mayar, JV and Kroonen, G and Peyrot, M and Barjamovic, G and Rasmussen, S and Zacho, C and Baimukhanov, N and Zaibert, V and Merz, V and Biddanda, A and Merz, I and Loman, V and Evdokimov, V and Usmanova, E and Hemphill, B and Seguin-Orlando, A and Yediay, FE and Ullah, I and Sjögren, KG and Iversen, KH and Choin, J and de la Fuente, C and Ilardo, M and Schroeder, H and Moiseyev, V and Gromov, A and Polyakov, A and Omura, S and Senyurt, SY and Ahmad, H and McKenzie, C and Margaryan, A and Hameed, A and Samad, A and Gul, N and Khokhar, MH and Goriunova, OI and Bazaliiskii, VI and Novembre, J and Weber, AW and Orlando, L and Allentoft, ME and Nielsen, R and Kristiansen, K and Sikora, M and Outram, AK and Durbin, R and Willerslev, E},
title = {The first horse herders and the impact of early Bronze Age steppe expansions into Asia.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6396},
pages = {},
pmid = {29743352},
issn = {1095-9203},
support = {206194/WT_/Wellcome Trust/United Kingdom ; 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; T32 GM007197/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Asia ; Asian People/*genetics ; Chromosomes, Human, Y/genetics ; DNA, Ancient ; DNA, Mitochondrial/genetics ; *Domestication ; Europe ; *Genetic Drift ; *Genome, Human ; Grassland ; History, Ancient ; *Horses ; Human Migration/*history ; Humans ; Language ; Whole Genome Sequencing ; },
abstract = {The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.},
}

Animals
Asia
Asian People/*genetics
Chromosomes, Human, Y/genetics
DNA, Ancient
DNA, Mitochondrial/genetics
*Domestication
Europe
*Genetic Drift
*Genome, Human
Grassland
History, Ancient
*Horses
Human Migration/*history
Humans
Language
Whole Genome Sequencing

@article {pmid29608727,
year = {2018},
author = {Shriner, D and Tekola-Ayele, F and Adeyemo, A and Rotimi, CN},
title = {Genetic Ancestry of Hadza and Sandawe Peoples Reveals Ancient Population Structure in Africa.},
journal = {Genome biology and evolution},
volume = {10},
number = {3},
pages = {875-882},
pmid = {29608727},
issn = {1759-6653},
support = {ZIA HG200362/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Black People/*genetics ; DNA, Ancient ; *Genetics, Population ; Genome, Human/*genetics ; Haplotypes/genetics ; Humans ; Tanzania ; },
abstract = {The Hadza and Sandawe populations in present-day Tanzania speak languages containing click sounds and therefore thought to be distantly related to southern African Khoisan languages. We analyzed genome-wide genotype data for individuals sampled from the Hadza and Sandawe populations in the context of a global data set of 3,528 individuals from 163 ethno-linguistic groups. We found that Hadza and Sandawe individuals share ancestry distinct from and most closely related to Omotic ancestry; share Khoisan ancestry with populations such as ≠Khomani, Karretjie, and Ju/'hoansi in southern Africa; share Niger-Congo ancestry with populations such as Yoruba from Nigeria and Luhya from Kenya, consistent with migration associated with the Bantu Expansion; and share Cushitic ancestry with Somali, multiple Ethiopian populations, the Maasai population in Kenya, and the Nama population in Namibia. We detected evidence for low levels of Arabian, Nilo-Saharan, and Pygmy ancestries in a minority of individuals. Our results indicate that west Eurasian ancestry in eastern Africa is more precisely the Arabian parent of Cushitic ancestry. Relative to the Out-of-Africa migrations, Hadza ancestry emerged early whereas Sandawe ancestry emerged late.},
}

Black People/*genetics
DNA, Ancient
*Genetics, Population
Genome, Human/*genetics
Haplotypes/genetics
Humans
Tanzania

@article {pmid29545507,
year = {2018},
author = {van de Loosdrecht, M and Bouzouggar, A and Humphrey, L and Posth, C and Barton, N and Aximu-Petri, A and Nickel, B and Nagel, S and Talbi, EH and El Hajraoui, MA and Amzazi, S and Hublin, JJ and Pääbo, S and Schiffels, S and Meyer, M and Haak, W and Jeong, C and Krause, J},
title = {Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6388},
pages = {548-552},
doi = {10.1126/science.aar8380},
pmid = {29545507},
issn = {1095-9203},
mesh = {Africa South of the Sahara ; Africa, Northern ; Animals ; Black People/*genetics ; DNA, Ancient ; *Evolution, Molecular ; Female ; Gene Flow ; *Genome, Human ; *Genome, Mitochondrial ; Genome-Wide Association Study ; Humans ; Mice ; Middle East ; Polymorphism, Single Nucleotide ; White People ; },
abstract = {North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans, attributed to the Iberomaurusian culture, from Morocco. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans to Late Pleistocene North Africans. The Taforalt individuals derive one-third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.},
}

Africa South of the Sahara
Africa, Northern
Animals
Black People/*genetics
DNA, Ancient
*Evolution, Molecular
Female
Gene Flow
*Genome, Human
*Genome, Mitochondrial
Genome-Wide Association Study
Humans
Mice
Middle East
Polymorphism, Single Nucleotide
White People

@article {pmid29522562,
year = {2018},
author = {Hamilton-Brehm, SD and Hristova, LT and Edwards, SR and Wedding, JR and Snow, M and Kruger, BR and Moser, DP},
title = {Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194223},
pmid = {29522562},
issn = {1932-6203},
mesh = {Archaeology ; *Carbon Radioisotopes ; *DNA, Ancient ; *DNA, Mitochondrial ; Evolution, Molecular ; Genetic Variation ; Humans ; Nevada ; Population Dynamics ; *Radiometric Dating ; Sequence Analysis, DNA ; },
abstract = {Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource.},
}

Archaeology
*Carbon Radioisotopes
*DNA, Ancient
*DNA, Mitochondrial
Evolution, Molecular
Genetic Variation
Humans
Nevada
Population Dynamics
*Radiometric Dating
Sequence Analysis, DNA

@article {pmid29472463,
year = {2018},
author = {Wade, L},
title = {'Extinct' Caribbeans have living descendants.},
journal = {Science (New York, N.Y.)},
volume = {359},
number = {6378},
pages = {858},
doi = {10.1126/science.359.6378.858},
pmid = {29472463},
issn = {1095-9203},
mesh = {Caribbean Region ; *DNA, Ancient ; Female ; *Genome, Human ; Humans ; *Women ; },
}

Caribbean Region
*DNA, Ancient
Female
*Genome, Human
Humans
*Women

@article {pmid29472442,
year = {2018},
author = {Gaunitz, C and Fages, A and Hanghøj, K and Albrechtsen, A and Khan, N and Schubert, M and Seguin-Orlando, A and Owens, IJ and Felkel, S and Bignon-Lau, O and de Barros Damgaard, P and Mittnik, A and Mohaseb, AF and Davoudi, H and Alquraishi, S and Alfarhan, AH and Al-Rasheid, KAS and Crubézy, E and Benecke, N and Olsen, S and Brown, D and Anthony, D and Massy, K and Pitulko, V and Kasparov, A and Brem, G and Hofreiter, M and Mukhtarova, G and Baimukhanov, N and Lõugas, L and Onar, V and Stockhammer, PW and Krause, J and Boldgiv, B and Undrakhbold, S and Erdenebaatar, D and Lepetz, S and Mashkour, M and Ludwig, A and Wallner, B and Merz, V and Merz, I and Zaibert, V and Willerslev, E and Librado, P and Outram, AK and Orlando, L},
title = {Ancient genomes revisit the ancestry of domestic and Przewalski's horses.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6384},
pages = {111-114},
doi = {10.1126/science.aao3297},
pmid = {29472442},
issn = {1095-9203},
support = {W 1225/FWF_/Austrian Science Fund FWF/Austria ; /ERC_/European Research Council/International ; },
mesh = {Animals ; DNA, Ancient ; Genome ; Horses/anatomy & histology/*classification/*genetics ; Phenotype ; Phylogeny ; },
abstract = {The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski's horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.},
}

Animals
DNA, Ancient
Genome
Horses/anatomy & histology/*classification/*genetics
Phenotype
Phylogeny

@article {pmid29466337,
year = {2018},
author = {Olalde, I and Brace, S and Allentoft, ME and Armit, I and Kristiansen, K and Booth, T and Rohland, N and Mallick, S and Szécsényi-Nagy, A and Mittnik, A and Altena, E and Lipson, M and Lazaridis, I and Harper, TK and Patterson, N and Broomandkhoshbacht, N and Diekmann, Y and Faltyskova, Z and Fernandes, D and Ferry, M and Harney, E and de Knijff, P and Michel, M and Oppenheimer, J and Stewardson, K and Barclay, A and Alt, KW and Liesau, C and Ríos, P and Blasco, C and Miguel, JV and García, RM and Fernández, AA and Bánffy, E and Bernabò-Brea, M and Billoin, D and Bonsall, C and Bonsall, L and Allen, T and Büster, L and Carver, S and Navarro, LC and Craig, OE and Cook, GT and Cunliffe, B and Denaire, A and Dinwiddy, KE and Dodwell, N and Ernée, M and Evans, C and Kuchařík, M and Farré, JF and Fowler, C and Gazenbeek, M and Pena, RG and Haber-Uriarte, M and Haduch, E and Hey, G and Jowett, N and Knowles, T and Massy, K and Pfrengle, S and Lefranc, P and Lemercier, O and Lefebvre, A and Martínez, CH and Olmo, VG and Ramírez, AB and Maurandi, JL and Majó, T and McKinley, JI and McSweeney, K and Mende, BG and Modi, A and Kulcsár, G and Kiss, V and Czene, A and Patay, R and Endrődi, A and Köhler, K and Hajdu, T and Szeniczey, T and Dani, J and Bernert, Z and Hoole, M and Cheronet, O and Keating, D and Velemínský, P and Dobeš, M and Candilio, F and Brown, F and Fernández, RF and Herrero-Corral, AM and Tusa, S and Carnieri, E and Lentini, L and Valenti, A and Zanini, A and Waddington, C and Delibes, G and Guerra-Doce, E and Neil, B and Brittain, M and Luke, M and Mortimer, R and Desideri, J and Besse, M and Brücken, G and Furmanek, M and Hałuszko, A and Mackiewicz, M and Rapiński, A and Leach, S and Soriano, I and Lillios, KT and Cardoso, JL and Pearson, MP and Włodarczak, P and Price, TD and Prieto, P and Rey, PJ and Risch, R and Rojo Guerra, MA and Schmitt, A and Serralongue, J and Silva, AM and Smrčka, V and Vergnaud, L and Zilhão, J and Caramelli, D and Higham, T and Thomas, MG and Kennett, DJ and Fokkens, H and Heyd, V and Sheridan, A and Sjögren, KG and Stockhammer, PW and Krause, J and Pinhasi, R and Haak, W and Barnes, I and Lalueza-Fox, C and Reich, D},
title = {The Beaker phenomenon and the genomic transformation of northwest Europe.},
journal = {Nature},
volume = {555},
number = {7695},
pages = {190-196},
pmid = {29466337},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; },
mesh = {Chromosomes, Human, Y/genetics ; Cultural Evolution/*history ; DNA, Ancient ; Europe ; Gene Pool ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Male ; Spatio-Temporal Analysis ; },
abstract = {From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.},
}

Chromosomes, Human, Y/genetics
Cultural Evolution/*history
DNA, Ancient
Europe
Gene Pool
Genetics, Population
Genome, Human/*genetics
*Genomics
Haplotypes
History, Ancient
Human Migration/*history
Humans
Male
Spatio-Temporal Analysis

@article {pmid29300040,
year = {2018},
author = {Gibney, E},
title = {What to expect in 2018: science in the new year.},
journal = {Nature},
volume = {553},
number = {7686},
pages = {12-13},
doi = {10.1038/d41586-018-00009-5},
pmid = {29300040},
issn = {1476-4687},
mesh = {Astronauts ; Astronomy/trends ; Climate Change ; Clinical Trials as Topic ; DNA, Ancient ; Drug Resistance, Microbial ; European Union/organization & administration ; Gene Editing/trends ; Genomics/trends ; Human Migration ; Humans ; Indians, North American/genetics ; Induced Pluripotent Stem Cells/transplantation ; Moon ; Neoplasms/genetics ; Open Access Publishing/trends ; Parkinson Disease/pathology/therapy ; Phage Therapy/trends ; Physics ; Politics ; Science/*trends ; Space Flight/trends ; Synchrotrons ; },
}

Astronauts
Astronomy/trends
Climate Change
Clinical Trials as Topic
DNA, Ancient
Drug Resistance, Microbial
European Union/organization & administration
Gene Editing/trends
Genomics/trends
Human Migration
Humans
Indians, North American/genetics
Induced Pluripotent Stem Cells/transplantation
Moon
Neoplasms/genetics
Open Access Publishing/trends
Parkinson Disease/pathology/therapy
Phage Therapy/trends
Physics
Politics
Science/*trends
Space Flight/trends
Synchrotrons

@article {pmid29146789,
year = {2017},
author = {Pickrell, J},
title = {Ancient Australian goes home.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6365},
pages = {853},
doi = {10.1126/science.358.6365.853},
pmid = {29146789},
issn = {1095-9203},
mesh = {Australia/ethnology ; Bone and Bones ; DNA, Ancient ; Fossils ; History, Ancient ; Humans ; },
}

Australia/ethnology
Bone and Bones
DNA, Ancient
Fossils
History, Ancient
Humans

@article {pmid29074745,
year = {2017},
author = {Gibbons, A},
title = {Neandertals gave 'lost' African DNA back to moderns.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6362},
pages = {431},
doi = {10.1126/science.358.6362.431},
pmid = {29074745},
issn = {1095-9203},
mesh = {Alleles ; Animals ; Asian People/*genetics ; Black People/genetics ; *DNA, Ancient ; Humans ; Neanderthals/*genetics ; Smoking/*genetics ; Waist Circumference/*genetics ; White People/*genetics ; },
}

Alleles
Animals
Asian People/*genetics
Black People/genetics
*DNA, Ancient
Humans
Neanderthals/*genetics
Smoking/*genetics
Waist Circumference/*genetics
White People/*genetics

@article {pmid28983028,
year = {2017},
author = {Gibbons, A},
title = {Neandertal genome reveals greater legacy in the living.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6359},
pages = {21},
doi = {10.1126/science.358.6359.21},
pmid = {28983028},
issn = {1095-9203},
mesh = {Animals ; DNA, Ancient ; Disease/*genetics ; Extinction, Biological ; Genome ; Neanderthals/*genetics ; Sequence Analysis, DNA ; },
}

Animals
DNA, Ancient
Disease/*genetics
Extinction, Biological
Genome
Neanderthals/*genetics
Sequence Analysis, DNA

@article {pmid28982795,
year = {2017},
author = {Sikora, M and Seguin-Orlando, A and Sousa, VC and Albrechtsen, A and Korneliussen, T and Ko, A and Rasmussen, S and Dupanloup, I and Nigst, PR and Bosch, MD and Renaud, G and Allentoft, ME and Margaryan, A and Vasilyev, SV and Veselovskaya, EV and Borutskaya, SB and Deviese, T and Comeskey, D and Higham, T and Manica, A and Foley, R and Meltzer, DJ and Nielsen, R and Excoffier, L and Mirazon Lahr, M and Orlando, L and Willerslev, E},
title = {Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6363},
pages = {659-662},
doi = {10.1126/science.aao1807},
pmid = {28982795},
issn = {1095-9203},
mesh = {DNA, Ancient ; *Genome, Human ; History, Ancient ; Humans ; Population Density ; Reproductive Behavior/*history ; Russia ; Social Behavior/*history ; },
abstract = {Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.},
}

DNA, Ancient
*Genome, Human
History, Ancient
Humans
Population Density
Reproductive Behavior/*history
Russia
Social Behavior/*history

@article {pmid28982794,
year = {2017},
author = {Prüfer, K and de Filippo, C and Grote, S and Mafessoni, F and Korlević, P and Hajdinjak, M and Vernot, B and Skov, L and Hsieh, P and Peyrégne, S and Reher, D and Hopfe, C and Nagel, S and Maricic, T and Fu, Q and Theunert, C and Rogers, R and Skoglund, P and Chintalapati, M and Dannemann, M and Nelson, BJ and Key, FM and Rudan, P and Kućan, Ž and Gušić, I and Golovanova, LV and Doronichev, VB and Patterson, N and Reich, D and Eichler, EE and Slatkin, M and Schierup, MH and Andrés, AM and Kelso, J and Meyer, M and Pääbo, S},
title = {A high-coverage Neandertal genome from Vindija Cave in Croatia.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6363},
pages = {655-658},
pmid = {28982794},
issn = {1095-9203},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 GM040282/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 694707/ERC_/European Research Council/International ; R01 HG002385/HG/NHGRI NIH HHS/United States ; },
mesh = {Alleles ; Animals ; *Biological Evolution ; Caves ; Croatia ; DNA, Ancient ; Genome ; Humans ; Neanderthals/*genetics ; },
abstract = {To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.},
}

Alleles
Animals
*Biological Evolution
Caves
Croatia
DNA, Ancient
Genome
Humans
Neanderthals/*genetics

@article {pmid28971970,
year = {2017},
author = {Schlebusch, CM and Malmström, H and Günther, T and Sjödin, P and Coutinho, A and Edlund, H and Munters, AR and Vicente, M and Steyn, M and Soodyall, H and Lombard, M and Jakobsson, M},
title = {Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.},
journal = {Science (New York, N.Y.)},
volume = {358},
number = {6363},
pages = {652-655},
doi = {10.1126/science.aao6266},
pmid = {28971970},
issn = {1095-9203},
mesh = {*Biological Evolution ; Black People/*genetics ; DNA, Ancient ; *Genetic Variation ; *Genome, Human ; Humans ; South Africa/ethnology ; },
abstract = {Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.},
}

*Biological Evolution
Black People/*genetics
DNA, Ancient
*Genetic Variation
*Genome, Human
Humans
South Africa/ethnology

@article {pmid28851849,
year = {2017},
author = {Kacar, B and Garmendia, E and Tuncbag, N and Andersson, DI and Hughes, D},
title = {Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs.},
journal = {mBio},
volume = {8},
number = {4},
pages = {},
pmid = {28851849},
issn = {2150-7511},
mesh = {Bacterial Proteins ; *DNA, Ancient ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Essential ; Genetic Fitness ; Genome, Bacterial ; Peptide Elongation Factor Tu/*genetics/metabolism ; Phylogeny ; *Protein Biosynthesis ; Proteobacteria/genetics ; },
abstract = {Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 billion years ago (bya). Our results demonstrate that all of the foreign tuf genes are transferable to the E. coli genome, provided that an additional copy of the EF-Tu gene, tufB, remains present in the E. coli genome. However, when the tufB gene was removed, only the variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth which demonstrates the limited functional interchangeability of E. coli tuf with its homologs. Relative bacterial fitness correlated with the evolutionary distance of the extant tuf homologs inserted into the E. coli genome. This reduced fitness was associated with reduced levels of EF-Tu and reduced rates of protein synthesis. Increasing the expression of tuf partially ameliorated these fitness costs. In summary, our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.IMPORTANCE Horizontal gene transfer (HGT) is a fundamental driving force in bacterial evolution. However, whether essential genes can be acquired by HGT and whether they can be acquired from distant organisms are very poorly understood. By systematically replacing tuf with ancestral homologs and homologs from distantly related organisms, we investigated the constraints on HGT of a highly conserved gene with multiple interaction partners. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 bya. Only variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth, demonstrating the limited functional interchangeability of E. coli tuf with its homologs. Our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.},
}

Bacterial Proteins
*DNA, Ancient
Escherichia coli/*genetics
Gene Transfer, Horizontal
*Genes, Bacterial
*Genes, Essential
Genetic Fitness
Genome, Bacterial
Peptide Elongation Factor Tu/*genetics/metabolism
Phylogeny
*Protein Biosynthesis
Proteobacteria/genetics

@article {pmid28838680,
year = {2020},
author = {Shaughnessy, PD},
title = {On the identity of the 'Upland seal' with comments on the paper by Salis et al. (2016).},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {105902},
doi = {10.1016/j.ympev.2017.08.012},
pmid = {28838680},
issn = {1095-9513},
mesh = {*DNA, Ancient ; Phylogeny ; },
}

*DNA, Ancient
Phylogeny

@article {pmid28684477,
year = {2017},
author = {Gibbons, A},
title = {Neandertals mated early with modern humans.},
journal = {Science (New York, N.Y.)},
volume = {357},
number = {6346},
pages = {14},
doi = {10.1126/science.357.6346.14},
pmid = {28684477},
issn = {1095-9203},
mesh = {Animals ; Anthropology ; *Biological Evolution ; DNA, Ancient ; DNA, Mitochondrial/*genetics ; Female ; Fossils ; Germany ; Humans ; Male ; Neanderthals/*genetics ; *Sexual Behavior, Animal ; },
}

Animals
Anthropology
*Biological Evolution
DNA, Ancient
DNA, Mitochondrial/*genetics
Female
Fossils
Germany
Humans
Male
Neanderthals/*genetics
*Sexual Behavior, Animal

@article {pmid28655202,
year = {2017},
author = {Smith, O and Palmer, SA and Clapham, AJ and Rose, P and Liu, Y and Wang, J and Allaby, RG},
title = {Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment.},
journal = {Molecular biology and evolution},
volume = {34},
number = {10},
pages = {2555-2562},
pmid = {28655202},
issn = {1537-1719},
support = {BBG0177941//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adaptation, Physiological ; Base Sequence ; DNA, Ancient ; Gene Expression Regulation, Plant/genetics ; Germination/genetics ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Hordeum/*genetics ; MicroRNAs/genetics ; RNA/analysis ; RNA, Plant/*genetics/history ; Sequence Analysis, RNA/methods ; Stress, Physiological/genetics ; },
abstract = {The recovery of ancient RNA from archeological material could enable the direct study of microevolutionary processes. Small RNAs are a rich source of information because their small size is compatible with biomolecular preservation, and their roles in gene regulation make them likely foci of evolutionary change. We present here the small RNA fraction from a sample of archeological barley generated using high-throughput sequencing that has previously been associated with localized adaptation to drought. Its microRNA profile is broadly similar to 19 globally distributed modern barley samples with the exception of three microRNAs (miRNA159, miRNA319, and miR396), all of which are known to have variable expression under stress conditions. We also found retrotransposon activity to be significantly reduced in the archeological barley compared with the controls, where one would expect the opposite under stress conditions. We suggest that the archeological barley's conflicting stress signals could be the result of long-term adaptation to its local environment.},
}

Adaptation, Physiological
Base Sequence
DNA, Ancient
Gene Expression Regulation, Plant/genetics
Germination/genetics
High-Throughput Nucleotide Sequencing
History, Ancient
Hordeum/*genetics
MicroRNAs/genetics
RNA/analysis
RNA, Plant/*genetics/history
Sequence Analysis, RNA/methods
Stress, Physiological/genetics

@article {pmid28619897,
year = {2017},
author = {Johannsen, NN and Larson, G and Meltzer, DJ and Vander Linden, M},
title = {A composite window into human history.},
journal = {Science (New York, N.Y.)},
volume = {356},
number = {6343},
pages = {1118-1120},
doi = {10.1126/science.aan0737},
pmid = {28619897},
issn = {1095-9203},
support = {//European Research Council/International ; },
mesh = {Anthropology/*standards/trends ; Archaeology/*trends ; *Biological Evolution ; *DNA, Ancient ; History ; Humans ; },
}

Anthropology/*standards/trends
Archaeology/*trends
*Biological Evolution
*DNA, Ancient
History
Humans

@article {pmid28502003,
year = {2017},
author = {Warner, JF and Harpole, MG and Crerar, LD},
title = {Microsatellite Analysis for Identification of Individuals Using Bone from the Extinct Steller's Sea Cow (Hydrodamalis gigas).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1606},
number = {},
pages = {205-217},
doi = {10.1007/978-1-4939-6990-6_14},
pmid = {28502003},
issn = {1940-6029},
mesh = {Animals ; Bone and Bones/*metabolism ; *DNA, Ancient ; Dugong/classification/*genetics/metabolism ; Extinction, Biological ; Genetics, Population/*methods ; *Microsatellite Repeats ; Molecular Typing/*methods ; },
abstract = {Microsatellite DNA can provide more detailed population genetic information than mitochondrial DNA which is normally used to research ancient bone. The methods detailed in this chapter can be utilized for any type of bone. However, for this example, four microsatellite loci were isolated from Steller's sea cow (Hydrodamalis gigas) using published primers for manatee and dugong microsatellites. The primers DduC05 (Broderick et al., Mol Ecol Notes 6:1275-1277, 2007), Tmakb60, TmaSC5 (Pause et al., Mol Ecol Notes 6: 1073-1076, 2007), and TmaE11 (Garcia-Rodriguez et al., Mol Ecol 12:2161-2163, 2000) all successfully amplified microsatellites from H. gigas. The DNA samples were from bone collected on Bering or St. Lawrence Islands. DNA was analyzed using primers with the fluorescent label FAM-6. Sequenced alleles were then used to indicate a difference in the number of repeats and thus a difference in individuals. This is the first time that H. gigas microsatellite loci have been isolated. These techniques for ancient bone microsatellite analysis allow an estimate of population size for a newly discovered St. Lawrence Island sea cow population.},
}

Animals
Bone and Bones/*metabolism
*DNA, Ancient
Dugong/classification/*genetics/metabolism
Extinction, Biological
Genetics, Population/*methods
*Microsatellite Repeats
Molecular Typing/*methods

@article {pmid28450643,
year = {2017},
author = {Librado, P and Gamba, C and Gaunitz, C and Der Sarkissian, C and Pruvost, M and Albrechtsen, A and Fages, A and Khan, N and Schubert, M and Jagannathan, V and Serres-Armero, A and Kuderna, LFK and Povolotskaya, IS and Seguin-Orlando, A and Lepetz, S and Neuditschko, M and Thèves, C and Alquraishi, S and Alfarhan, AH and Al-Rasheid, K and Rieder, S and Samashev, Z and Francfort, HP and Benecke, N and Hofreiter, M and Ludwig, A and Keyser, C and Marques-Bonet, T and Ludes, B and Crubézy, E and Leeb, T and Willerslev, E and Orlando, L},
title = {Ancient genomic changes associated with domestication of the horse.},
journal = {Science (New York, N.Y.)},
volume = {356},
number = {6336},
pages = {442-445},
doi = {10.1126/science.aam5298},
pmid = {28450643},
issn = {1095-9203},
mesh = {Animals ; *Breeding ; DNA, Ancient ; DNA, Mitochondrial/genetics ; *Domestication ; Genetic Variation ; Genome ; Horses/*genetics ; Neural Crest ; Quantitative Trait, Heritable ; Selection, Genetic ; },
abstract = {The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.},
}

Animals
*Breeding
DNA, Ancient
DNA, Mitochondrial/genetics
*Domestication
Genetic Variation
Genome
Horses/*genetics
Neural Crest
Quantitative Trait, Heritable
Selection, Genetic

@article {pmid28379502,
year = {2017},
author = {Demars, J and Cano, M and Drouilhet, L and Plisson-Petit, F and Bardou, P and Fabre, S and Servin, B and Sarry, J and Woloszyn, F and Mulsant, P and Foulquier, D and Carrière, F and Aletru, M and Rodde, N and Cauet, S and Bouchez, O and Pirson, M and Tosser-Klopp, G and Allain, D},
title = {Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep.},
journal = {Molecular biology and evolution},
volume = {34},
number = {7},
pages = {1722-1729},
pmid = {28379502},
issn = {1537-1719},
mesh = {Animals ; Biological Evolution ; Carrier Proteins/genetics ; DNA, Ancient ; Genetic Variation/genetics ; Genome ; Genome-Wide Association Study/methods ; Mutation ; Phenotype ; Sheep/*genetics ; Sheep, Domestic/*genetics ; Transcription Factors/genetics ; Wool ; },
abstract = {The composition and structure of fleece variation observed in mammals is a consequence of a strong selective pressure for fiber production after domestication. In sheep, fleece variation discriminates ancestral species carrying a long and hairy fleece from modern domestic sheep (Ovis aries) owning a short and woolly fleece. Here, we report that the "woolly" allele results from the insertion of an antisense EIF2S2 retrogene (called asEIF2S2) into the 3' UTR of the IRF2BP2 gene leading to an abnormal IRF2BP2 transcript. We provide evidence that this chimeric IRF2BP2/asEIF2S2 messenger 1) targets the genuine sense EIF2S2 RNA and 2) creates a long endogenous double-stranded RNA which alters the expression of both EIF2S2 and IRF2BP2 mRNA. This represents a unique example of a phenotype arising via a RNA-RNA hybrid, itself generated through a retroposition mechanism. Our results bring new insights on the sheep population history thanks to the identification of the molecular origin of an evolutionary phenotypic variation.},
}

Animals
Biological Evolution
Carrier Proteins/genetics
DNA, Ancient
Genetic Variation/genetics
Genome
Genome-Wide Association Study/methods
Mutation
Phenotype
Sheep/*genetics
Sheep, Domestic/*genetics
Transcription Factors/genetics
Wool