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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.

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity. [ABSTRACT FROM AUTHOR]

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800–9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene–Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction. [ABSTRACT FROM AUTHOR]

Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts. [ABSTRACT FROM AUTHOR]

Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment. [ABSTRACT FROM AUTHOR]

The high‐throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low‐quantity and low‐quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100‐year old museum‐preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample‐specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material. [ABSTRACT FROM AUTHOR]

Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods. [ABSTRACT FROM AUTHOR]

Aim: The distribution of hares (Lepus spp.) in southern Europe was markedly different at the Last Glacial Maximum. Historical hybridization during range replacements led to high frequencies of mtDNA introgression from Lepus timidus into populations of three other species in northern Iberian Peninsula, even though L. timidus subsequently disappeared from the region. We use palaeontological records to provide new insights on the biogeographic history of these range replacements, combining ancient DNA and ecological niche modelling. Location: Southern France. Taxon: Hares (genus Lepus). Methods: DNA was extracted from hare bones collected at Neolithic sites in southern France (5.5–7.5 thousand years before present; kyr bp) with uncertain species assignment. One mtDNA fragment was sequenced and 27 SNPs from 11 nuclear genes with species‐diagnostic information were genotyped. Distributions of L. granatensis, L. europaeus, and L. timidus were modelled using spatial and bioclimatic predictors, and the favourability function. Each model was transferred to 6 kyr bp and favourabilities were combined to determine the species with the highest environmental favourability in each sampled locality. Results: Ancient DNA analysis showed that the screened specimens belong to L. granatensis, a species presently confined to the Iberian Peninsula, but carried mtDNA haplotypes from L. timidus. Niche models show that L. granatensis achieved highest favourability in southern France 6 kyr bp reinforcing the molecular evidences. Main conclusions: L. granatensis replaced L. timidus populations from Iberia to southern France, being present in this region 5.5 kyr bp. Subsequent westwards invasion of L. europaeus likely replaced these L. granatensis populations towards northern Iberia, establishing current ranges. Despite successive species replacements, introgressed mtDNA haplotypes from L. timidus mark the distribution of the species in northern Iberian Peninsula before it disappeared in the region. Characterizing complex biogeographic histories of interacting species is a key to understand processes that led to current distributions of genetic diversity. [ABSTRACT FROM AUTHOR]

The present distribution of many species is a result of climatic changes during the Pleistocene and human activity. The impact of climate has been accompanied by restrictions of populations into refugia during glacial periods, and subsequent expansions during more favourable conditions, whereas human influence has been associated with hunting practices and translocations. One mammalian species that has been subject to such transformations is the red deer, Cervus elaphus, but the exact nature of these changes has been difficult to determine using only modern DNA. In this study, we obtained new cytochrome b sequences from subfossil remains of deer found in the Crimean Peninsula. A comparison of these sequences with the available recent and ancient sequences allowed to us to reconstruct phylogeographic relationships between Cervus lineages and to determine their potential migration routes at both local and Eurasian scales. Our analyses showed that the Crimean Peninsula was not a glacial refugium for red deer, but rather that red deer colonized Crimea in three independent waves from both Western and Eastern red deer populations. The immigrations were related to local extinctions and replacements of native populations. [ABSTRACT FROM AUTHOR]

Throughout time, climate changes have caused substantial rearrangements of habitats which have alternately promoted and disfavoured different types of taxa. At first glance, the mountain hare (Lepus timidus) shows the typical hallmarks of a cold-adapted species that has retreated to refugia since the onset of the current Holocene interglacial. In contrary to expectations, however, the species has a high contemporary genetic diversity with no clear differentiation between geographically isolated populations. In order to clarify the phylogeographic history of European mountain hares, we here analysed ancient DNA from the glacial populations that inhabited the previous midlatitude European tundra region. Our results reveal that the Ice Age hares had similar levels of genetic variation and lack of geographic structure as observed today, and the ancient samples were intermingled with modern individuals throughout the reconstructed evolutionary tree. This suggests a temporal genetic continuity in Europe, where the mountain hares were able to keep pace with the rapid changes at the last glacial/interglacial transition and successfully track their shifting habitat to northern and alpine regions. Further, the temporal demographic analyses showed that the species' population size in Europe appears to have been tightly linked with palaeoclimatic fluctuations, with increases and declines occurring during periods of global cooling and warming, respectively. Taken together, our results suggest that neither habitat shifts nor demographic fluctuations have had any substantial impact on the genetic diversity of European mountain hares. This remarkable resilience, which contrasts to a majority of previously investigated coldadapted species, is likely due to its generalist nature that makes it less vulnerable to environmental changes. [ABSTRACT FROM AUTHOR]

The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a ~750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history. [ABSTRACT FROM AUTHOR]

The Pleistocene glacial cycles resulted in significant changes in species distributions, and it has been discussed whether this caused increased rates of population divergence and speciation. One species that is likely to have evolved during the Pleistocene is the Norwegian lemming ( Lemmus lemmus). However, the origin of this species, both in terms of when and from what ancestral taxon it evolved, has been difficult to ascertain. Here, we use ancient DNA recovered from lemming remains from a series of Late Pleistocene and Holocene sites to explore the species' evolutionary history. The results revealed considerable genetic differentiation between glacial and contemporary samples. Moreover, the analyses provided strong support for a divergence time prior to the Last Glacial Maximum ( LGM), therefore likely ruling out a postglacial colonization of Scandinavia. Consequently, it appears that the Norwegian lemming evolved from a small population that survived the LGM in an ice-free Scandinavian refugium. [ABSTRACT FROM AUTHOR]

The understanding of Earth's biodiversity depends critically on the accurate identification and nomenclature of species. Many species were described centuries ago, and in a surprising number of cases their nomenclature or type material remain unclear or inconsistent. A prime example is provided by Elephas maximus, one of the most iconic and well-known mammalian species, described and named by Linnaeus (1758) and today designating the Asian elephant. We used morphological, ancient DNA (aDNA), and high-throughput ancient proteomic analyses to demonstrate that a widely discussed syntype specimen of E. maximus, a complete foetus preserved in ethanol, is actually an African elephant, genus Loxodonta. We further discovered that an additional E. maximus syntype, mentioned in a description by John Ray (1693) cited by Linnaeus, has been preserved as an almost complete skeleton at the Natural History Museum of the University of Florence. Having confirmed its identity as an Asian elephant through both morphological and ancient DNA analyses, we designate this specimen as the lectotype of E. maximus. The mass spectrometry proteomics data have been deposited in the Proteome Xchange Consortium with the data set identifier PXD000423. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]

Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age. [ABSTRACT FROM AUTHOR]

Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recent western European neandertals (<48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison with both eastern and older (>48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region. [ABSTRACT FROM PUBLISHER]

The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths ( Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species' final disappearance c. 4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9 ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event. [ABSTRACT FROM AUTHOR]

Models for the development of species distribution in Europe typically invoke restriction in three temperate Mediterranean refugia during glaciations, from where recolonization of central and northern Europe occurred. The brown bear, Ursus arctos, is one of the taxa from which this model is derived. Sequence data generated from brown bear fossils show a complex phylogeographical history for western European populations. Long-term isolation in separate refugia is not required to explain our data when considering the palaeontological distribution of brown bears. We propose continuous gene flow across southern Europe, from which brown bear populations expanded after the last glaciation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Many species have undergone dramatic population size declines over the past centuries. Although stochastic genetic processes during and after such declines are thought to elevate the risk of extinction, comparative analyses of genomic data from several endangered species suggest little concordance between genome-wide diversity and current population sizes. This is likely because species-specific life-history traits and ancient bottlenecks overshadow the genetic effect of recent demographic declines. Therefore, we advocate that temporal sampling of genomic data provides a more accurate approach to quantify genetic threats in endangered species. Specifically, genomic data from predecline museum specimens will provide valuable baseline data that enable accurate estimation of recent decreases in genome-wide diversity, increases in inbreeding levels, and accumulation of deleterious genetic variation. [ABSTRACT FROM AUTHOR]

The Sardinian dhole (Cynotherium sardous) 1 was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene. 2–5 Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor. 3,6–9 Morphometric analyses 3,6,8–12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca -21,100-year-old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found that it represents a separate taxon from all other living canids from Eurasia, Africa, and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, which ended approximately 500-300 ka, when the land bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids—probably a result of the long-term isolation—that could have contributed to the subsequent extinction of the Sardinian dhole. • The Sardinian dhole lineage diverged from the Asian dholes around 885 ka • Post-divergence gene flow between the dhole lineages ended between 560 and 310 ka • Our sample also showed a reduced genome-wide diversity • The gene flow between Lycaon and the dholes' ancestor ended around 1.05–0.83 Ma Ciucani et al. sequence the genome of a 21,100-year-old Sardinian dhole. The sample represents a different lineage from the current Asian dholes and split from them ca 885 ka. Post-divergence gene flow between the two lineages ended later— ca 560–310 ka—followed by a stable but long-term population decline and extinction of the Sardinian dhole. [ABSTRACT FROM AUTHOR]

To understand the causes and implications of an extinction event, detailed information is necessary. However, this can be challenging when working with poorly resolved paleontological data sets. One approach to increase the data resolution is by combining different methods. In this study, we used both radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. We generated 88 new radiocarbon dates and combined these with previously published dates from 626 specimens to construct Bayesian age models. These models show that mammoths disappeared on the eastern Siberian mainland before the onset of the Younger Dryas (12.9–11.7 ky cal BP). Mammoths did however persist in the northernmost parts of central and western Siberia until the early Holocene. Further genetic results of 131 high quality mitogenomes, including 22 new mitogenomes generated in this study, support the hypothesis that mammoths from, or closely related to, a central and/or west- Siberian population recolonized Wrangel Island over the now submerged northern Siberian plains. As mammoths became trapped on the island due to rising sea levels, they lived another ca. 6000 years on Wrangel Island before eventually going extinct ca. 4000 years ago. • Woolly mammoth population and extinction dynamics in northern Siberia. • Extensive dataset combining 720 radiocarbon dates and 131 complete mitogenomes. • Radiocarbon model suggests mammoths first disappeared from eastern Siberia. • Final mammoth refugium colonized from central and/or western Siberia. • Global extinction of woolly mammoth ca. 4000 years ago. [ABSTRACT FROM AUTHOR]

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

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

Summary While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [ 1, 2 ]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [ 3 ]). Here we use genomic data to determine the sex of 98 woolly mammoth ( Mammuthus primigenius ) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species’ existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. We hypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely. [ABSTRACT FROM AUTHOR]