The genomic natural history of the aurochs.

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia1. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs-European, Southwest Asian, North Asian and South Asian-each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago2, but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.

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

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

Population genomics of Bronze Age Eurasia.

The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans.

Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.

Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

New data for the Early Upper Paleolithic of Kostenki (Russia).

Several questions remain regarding the timing and nature of the Neanderthal-anatomically modern human (AMH) transition in Europe. The situation in Eastern Europe is generally less clear due to the relatively few sites and a dearth of reliable radiocarbon dates. Claims have been made for both notably early AMH and notably late Neanderthal presence, as well as for early AMH (Aurignacian) dispersal into the region from Central/Western Europe. The Kostenki-Borshchevo complex (European Russia) of Early Upper Paleolithic (EUP) sites offers high-quality data to address these questions. Here we revise the chronology and cultural status of the key sites of Kostenki 17 and Kostenki 14. The Kostenki 17/II lithic assemblage shares important features with Proto-Aurignacian material, strengthening an association with AMHs. New radiocarbon dates for Kostenki 17/II of ∼41-40 ka cal BP agree with new dates for the recently excavated Kostenki 14/IVw, which shows some similarities to Kostenki 17/II. Dates of ≥41 ka cal BP from other Kostenki sites cannot be linked to diagnostic archaeological material, and therefore cannot be argued to date AMH occupation. Kostenki 14's Layer in Volcanic Ash assemblage, on the other hand, compares to Early Aurignacian material. New radiocarbon dates targeting diagnostic lithics date to 39-37 ka cal BP. Overall, Kostenki's early EUP is in good agreement with the archaeological record further west. Our results are therefore consistent with models predicting interregional penecontemporaneity of diagnostic EUP assemblages. Most importantly, our work highlights ongoing challenges for reliably radiocarbon dating the period. Dates for Kostenki 14 agreed with the samples' chronostratigraphic positions, but standard pre-treatment methods consistently produced incorrect ages for Kostenki 17/II. Extraction of hydroxyproline from bone collagen using preparative high-performance liquid chromatography, however, yielded results consistent with the samples' chronostratigraphic position and with the layer's archaeological contents. This suggests that for some sites compound-specific techniques are required to build reliable radiocarbon chronologies.

Dogs accompanied humans during the Neolithic expansion into Europe.

Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near Eastern dogs spanning the Upper Palaeolithic to the Bronze Age to assess if incoming farmers brought Near Eastern dogs with them, or instead primarily adopted indigenous European dogs after they arrived. Our results show that European pre-Neolithic dogs all possessed the mitochondrial haplogroup C, and that the Neolithic and Post-Neolithic dogs associated with farmers from Southeastern Europe mainly possessed haplogroup D. Thus, the appearance of haplogroup D most probably resulted from the dissemination of dogs from the Near East into Europe. In Western and Northern Europe, the turnover is incomplete and haplogroup C persists well into the Chalcolithic at least. These results suggest that dogs were an integral component of the Neolithic farming package and a mitochondrial lineage associated with the Near East was introduced into Europe alongside pigs, cows, sheep and goats. It got diluted into the native dog population when reaching the Western and Northern margins of Europe.

Species-specific responses of Late Quaternary megafauna to climate and humans.

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.

Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings.

Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D. torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D. torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50 000 years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. All Holocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D. torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D. groenlandicus and D. richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D. groenlandicus had a more southern and D. richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.

Insights into subspecies classification and conservation priorities of Central Asian lynx populations revealed by morphometric and genetic analyses.

The Eurasian lynx (Lynx lynx) exhibits geographic variability and phylogenetic intraspecific relationships. Previous morphological studies have suggested the existence of multiple lynx subspecies, but recent genetic research has questioned this classification, particularly in Central Asia. In this study, we aimed to analyse the geographic and genetic variation in Central Asian lynx populations, particularly the Turkestan lynx and Altai lynx populations, using morphometric data and mtDNA sequences to contribute to their taxonomic classification. The comparative analysis of morphometric data revealed limited clinal variability between lynx samples from the Altai and Tien Shan regions. By examining mtDNA fragments (control region and cytochrome b) obtained from Kazakhstani lynx populations, two subspecies were identified: L. l. isabellinus (represented by a unique haplotype of the South clade, H46) and L. l. wrangeli (represented by haplotypes H36, H45, and H47 of the East clade). L. l. isabellinus was recognized only in Tien Shan Mountain, while Altai lynx was likely identical to L. l. wrangeli and found in northern Kazakhstan, Altai Mountain, Saur and Tarbagatai Mountains, and Tien Shan Mountain. The morphological and mtDNA evidence presented in this study, although limited in sample size and number of genetic markers, renders the differentiation of the two subspecies challenging. Further sampling and compilation of whole-genome sequencing data are necessary to confirm whether the proposed subspecies warrant taxonomic standing.

Holarctic genetic structure and range dynamics in the woolly mammoth.

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32-34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20-15 kyr BP, when a severe population size decline occurred.

Morphological differences between putative Paleolithic dogs and wolves: A commentary to Janssens et al. (2021).

Janssens et al. (2021, doi: 10.1002/ar.24624) recently commented on our article (Galeta et al., 2021, doi: 10.1002/ar.24500) regarding the morphological differences between putative Paleolithic dog and Pleistocene wolf crania. The authors argued that these differences reflect the normal population variation of wolves, that some of the cranial measurements used do not reflect morphological changes during domestication, and that our canid dataset was small because we inexplicably omitted several specimens we analyzed in our previous publications. In this commentary, we briefly address the issue of within and between morpho-population variability. The results based on our canid sample suggest that the magnitude of morphological differences between distinct morpho-populations (i.e., recent northern dogs and wolves) is at least twice as large as that observed within morpho-populations (between two groups of recent northern wolves segregated by cluster analysis). The morphological differences between putative Paleolithic dogs and Pleistocene wolves are relatively large, which may indicate that they did not likely represent a single Late Pleistocene morpho-population. Finally, we clarified the rationale behind the composition of our 2021 dataset to show that we did not adjust the list of the analyzed specimens. Although the sample size was small, the randomization analysis published in 2021 confirmed that the unbalanced composition of the reference sample did not affect the reliability of the morphological segregation of putative Paleolithic dogs and Pleistocene wolves.

Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFß signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

The evolution of dog diet and foraging: Insights from archaeological canids in Siberia.

Research on the evolution of dog foraging and diet has largely focused on scavenging during their initial domestication and genetic adaptations to starch-rich food environments following the advent of agriculture. The Siberian archaeological record evidences other critical shifts in dog foraging and diet that likely characterize Holocene dogs globally. By the Middle Holocene, body size reconstruction for Siberia dogs indicates that most were far smaller than Pleistocene wolves. This contributed to dogs' tendencies to scavenge, feed on small prey, and reduce social foraging. Stable carbon and nitrogen isotope analysis of Siberian dogs reveals that their diets were more diverse than those of Pleistocene wolves. This included habitual consumption of marine and freshwater foods by the Middle Holocene and reliance on C4 foods by the Late Holocene. Feeding on such foods and anthropogenic waste increased dogs' exposure to microbes, affected their gut microbiomes, and shaped long-term dog population history.

Morphological evidence for early dog domestication in the European Pleistocene: New evidence from a randomization approach to group differences.

The antiquity of the wolf/dog domestication has been recently pushed back in time from the Late Upper Paleolithic (~14,000 years ago) to the Early Upper Paleolithic (EUP; ~36,000 years ago). Some authors questioned this early dog domestication claiming that the putative (EUP) Paleolithic dogs fall within the morphological range of recent wolves. In this study, we reanalyzed a data set of large canid skulls using unbalanced- and balanced-randomized discriminant analyses to assess whether the putative Paleolithic dogs are morphologically unique or whether they represent a subsample of the wolf morpho-population. We evaluated morphological differences between 96 specimens of the 4 a priori reference groups (8 putative Paleolithic dogs, 41 recent northern dogs, 7 Pleistocene wolves, and 40 recent northern wolves) using discriminant analysis based on 5 ln-transformed raw and allometrically size-adjusted cranial measurements. Putative Paleolithic dogs are classified with high accuracies (87.5 and 100.0%, cross-validated) and randomization experiment suggests that these classification rates cannot be exclusively explained by the small and uneven sample sizes of reference groups. It indicates that putative Upper Paleolithic dogs may represent a discrete canid group with morphological signs of domestication (a relatively shorter skull and wider palate and braincase) that distinguish them from sympatric Pleistocene wolves. The present results add evidence to the view that these specimens could represent incipient Paleolithic dogs that were involved in daily activities of European Upper Paleolithic forager groups.

Origins and genetic legacy of prehistoric dogs.

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent.

Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift indicates rapid and widespread introgression of zebu, Bos indicus, from the Indus Valley. This process was likely stimulated at the onset of the current geological age, ~4.2 thousand years ago, by a widespread multicentury drought. In contrast to genome-wide admixture, mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival. This human-mediated migration of zebu-derived genetics has continued through millennia, altering tropical herding on each continent.

Stable isotopes reveal diet shift from pre-extinction to reintroduced Przewalski's horses.

The Przewalski's horse (Equus ferus przewalskii), the only remaining wild horse within the equid family, is one of only a handful of species worldwide that went extinct in the wild, was saved by captive breeding, and has been successfully returned to the wild. However, concerns remain that after multiple generations in captivity the ecology of the Przewalski's horse and / or the ecological conditions in its former range have changed in a way compromising the species' long term survival. We analyzed stable isotope chronologies from tail hair of pre-extinction and reintroduced Przewalski's horses from the Dzungarian Gobi and detected a clear difference in the isotopic dietary composition. The direction of the dietary shift from being a mixed feeder in winter and a grazer in summer in the past, to a year-round grazer nowadays, is best explained by a release from human hunting pressure. A changed, positive societal attitude towards the species allows reintroduced Przewalski's horses to utilize the scarce, grass-dominated pastures of the Gobi alongside local people and their livestock whereas their historic conspecifics were forced into less productive habitats dominated by browse.

Three-Dimensional Geometric Morphometric Analysis of Fossil Canid Mandibles and Skulls.

Much of the fossil record for dogs consists of mandibles. However, can fossil canid mandibles be reliably identified as dogs or wolves? 3D geometric morphometric analysis correctly classifies 99.5% of the modern dog and wolf mandibles. However, only 4 of 26 Ust'-Polui fossil mandibles, a Russian Arctic site occupied from 250BCE to 150CE, were identified as dogs and none of the 20 Ivolgin mandibles, an Iron Age site in southern Russia, were identified as dogs. Three of the Ust'-Polui mandibles and 8 of the Ivolgin mandibles were identified as wolves. In contrast, all 12 Ivolgin skulls and 5 Ust'-Polui skulls were clearly identified as dogs. Only the classification of the UP6571 skull as a dog (Dog Posterior Probability = 1.0) was not supported by the typical probability. Other evidence indicates these canids were domesticated: they were located within human dwellings, remains at both sites have butchery marks indicating that they were consumed, and isotope analysis of canid and human remains from Ust'-Polui demonstrate that both were consuming freshwater protein; indicating that the humans were feeding the canids. Our results demonstrate that the mandible may not evolve as rapidly as the cranium and the mandible is not reliable for identifying early dog fossils.