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Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution. Siberian mammoth genomes from the Early and Middle Pleistocene subepochs reveal adaptive changes and a key hybridization event, highlighting the value of deep-time palaeogenomics for studies of speciation and long-term evolutionary trends.

Aim: Late Quaternary climate oscillations had major impacts on species distributions and abundances across the northern Holarctic. While many large mammals in this region went extinct towards the end of the Quaternary, some species survived and flourished. Here, we examine population dynamics and range shifts of one of the most widely distributed of these, the moose (Alces alces). Location: Northern Holarctic. Taxon: Moose (A. alces). Methods: We collected samples of modern and ancient moose from across their present and former range. We assessed their phylogeographical relations using part of the mitochondrial DNA in conjunction with radiocarbon dating to investigate the history of A. alces during the last glacial. Results: This species has a relatively shallow history, with the most recent common ancestor estimated at ca. 150–50 kyr. Ancient samples corroborate that its region of greatest diversity is in east Asia, supporting proposals that this is the region of origin of all extant moose. Both eastern and western haplogroups occur in the Ural Mountains during the last glacial period, implying a broader contact zone than previously proposed. It seems that this species went extinct over much of its northern range during the last glacial maximum (LGM) and recolonized the region with climate warming beginning around 15,000 yr bp. The post-LGM expansion included a movement from northeast Siberia to North America via Beringia, although the northeast Siberian source population is not the one currently occupying that area. Main conclusions: Moose are a relatively recently evolved species but have had a dynamic history. As a large-bodied subarctic browsing species, they were seemingly confined to refugia during full-glacial periods and expanded their range northwards when the boreal forest returned after the LGM. The main modern phylogeographical division is ancient, though its boundary has not remained constant. Moose population expansion into America was roughly synchronous with human and red deer expansion. © 2020 The Authors. Journal of Biogeography published by John Wiley & Sons Ltd We warmly thank the following museums, curators and people for access to samples: the late Andrei Sher, Severtsov Institute, Moscow; Andy Currant, Natural History Museum, London; Alfred Gardner, Smithsonian, Washington DC; R. Dale Guthrie, University of Alaska, Fairbanks; John de Vos, National Museum of Natural History (Naturalis), Leiden; Eileen Westwig, American Museum of Natural History, NY; Fyodor Shidlovsky, Ice-Age Museum, Moscow; Tong Haowen, Institute of Vertebrate Palaeontology and Paleoanthropology, Beijing; Mammoth Museum, Yakutsk; Geological Museum, Yakutsk; Paleontological Institute, Moscow; Royal Alberta Museum, Edmonton; Zoological Institute, Saint Petersburg; Museum of the Institute of Plant and Animal Ecology, Ekaterinburg. We thank our Yukon First Nation research partners for their continued support for our work on the ice age fossils of Yukon Territory. We are grateful to the placer gold mining community and the Tr'ond?k Hw?ch'in First Nation for their continued support and partnership with our research in the Klondike goldfields region; and the Vuntut Gwitchin First Nation for their collaboration with research in the Old Crow region. We would also like to thank Shai Meiri for help in drawing the map and useful discussion, Tony Stuart for access to radiocarbon dates, and Iris van Pijlen for laboratory assistance. This research was funded by NERC grant NE/G00269X/1 through the European Union FP7 ERA-NET program BiodivERsA. Funding for AMS dating was provided through NERC/AHRC/ORAU Grant NF/2008/2/15.

One major challenge in the study of late-Quaternary extinctions (LQEs) is providing better estimates of past megafauna abundance. To show how megaherbivore population size varied before and after the last extinctions in interior Alaska, we use both a database of radiocarbon-dated bone remains (spanning 25–0 ka) and spores of the obligate dung fungus,Sporormiella,recovered from radiocarbon-dated lake-sediment cores (spanning 17–0 ka). Bone fossils show that the last stage of LQEs in the region occurred at about 13 ka ago, but the number of megaherbivore bones remains high into the Holocene.Sporormiellaabundance also remains high into the Holocene and does not decrease with major vegetation changes recorded by arboreal pollen percentages. At two sites, the interpretation ofSporormiellawas enhanced by additional dung fungal spore types (e.g.,Sordaria). In contrast to many sites where the last stage of LQEs is marked by a sharp decline inSporormiellaabundance, in interior Alaska our results indicate the continuance of megaherbivore abundance, albeit with a major taxonomic turnover (includingMammuthusandEquusextinction) from predominantly grazing to browsing dietary guilds. This new and robust evidence implies that regional LQEs were not systematically associated with crashes of overall megaherbivore abundance.

A mammoth tusk contains an inner mineralized protein matrix of dentine and an outer layer of cementum. Enamel is only present on the tips of the tusks of young mammoths, and is worn away in older mammoths. Dentine is a mineralized connective tissue containing the inorganic component of dahlite [Ca10(PO4)6(CO3)H2O]. To determine the species from which ivory originated, often destructive methods are used. Raman spectroscopy is a non-invasive laser-based technique that has proven applications in the chemistry of mineralized tissue. Ivory and bone have similar biochemical properties. The aim of this study is to test the hypothesis that mammoth ivory is identifiable using Raman spectroscopy. Mammoth tusks were kindly loaned from the Natural History Museum, London, UK. All tusks were from the species Mammuthus primigenius discovered either in Lyakhov Islands or next to the Yenisei river, Krasnoyarsk (Siberia, Russia) and span the Pleistocene epoch, Cenerzoic era. The ivory was scanned with an inVia Raman micro spectrometer (Renishaw Ltd) equipped with a x50 objective lens and a 785nm laser. Spectra were acquired using line maps on cross sections of two samples, and individual spectral points were acquired independently at random or at points of interest on all samples. Data was analysed with principal component analysis (PCA) using an in-house Matlab script. To date, the results of this study establishes that well preserved mammoth ivory can be characterized through the comparison of peak intensity ratios between organic v(CH) collagen peaks and inorganic v(PO) hydroxyapatite peaks. Differences were observed in the hydroxyapatite peak from spectra acquired near the medulla of the tusk compared to the cortex. This suggests that the tusk is more mineralized towards the cortex compared to dentine found closer to the medulla. A comparison of the average data from each mammoth tusk demonstrated that the mammoth spectral ‘fingerprint’ remains similar for all samples, though there was some inter-variation in the mineralization of the tusks from mammoths of the same species. Further work in this study aims to compare the Raman spectra between mammoth and elephant ivory. This will have direct applications in archaeology, as the species from which an ivory sample is found could be identified without the need for more traditional, destructive techniques of valuable artefacts. Additionally, international trade regulations require proof of the species from which ivory is obtained. The information obtained in this study will be valuable in developing quick and non-destructive methods for the identification of ivory from an unknown origin.

Microwear data were analysed to study dietary traits in Elephantidae, Mammutidae, and Gomphotheriidae from Plio-Pleistocene localities from Europe and North America and included the following taxa: Palaeoloxodon antiquus, Mammuthus rumanus, M. meridionalis, M. trogontherii, M. primigenius, M. columbi, Mammut americanum, and Anancus arvernensis. Mammuthus shows a wide variety of dietary strategies, with an overall trend from browsing to grazing through the lineage from M. rumanus to M. primigenius. Nonetheless there is significant inter-population variability which is clearly related to the resources available or to limitations imposed by competition and niche partitioning with other large herbivores. Among the species, Mammuthus columbi (Late Pleistocene of North America) displays both browsing and grazing populations and individuals and also shows heavier pitting than the other species of Mammuthus studied, possibly indicating the occupation of a more arid habitat. The Middle and Late Pleistocene Palaeoloxodon antiquus from Europe also shows dietary plasticity, with browsing, grazing and mixed feeding patterns observed. Dietary variability appears to be lower in Mammut americanum from North America and Anancus arvernensis which were apparently committed browsers (except the grass-dominated mixed feeding A. arvernensis from Norwich Crag). Our results reveal interesting patterns involving Pleistocene vegetation structure and climate as well as aspects of niche utilization.

Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer ( Megaloceros giganteus ) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.

Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.

The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted herbivore, widely distributed from western Europe to north-east Siberia during the Late Pleistocene. Previous studies associate the extinction of the species ~14,000 years before present to climatic and vegetational changes, and suggest that later survival of populations in north-east Siberia may relate to the later persistence of open vegetation in that region. Here, we analyzed carbon (δ13C) and nitrogen (δ15N) stable isotopes and mitochondrial DNA sequences to elucidate the evolutionary ecology of the species. Our dataset comprised 286 woolly rhinoceros isotopic records, including 192 unpublished records, from across the species range, dating from >58,600 14C years to ~14,000 years before present. Crucially, we present the first 71 isotopic records available to date of the 15,000 years preceding woolly rhinoceros extinction. The data reveal ecological flexibility and geographical variation in woolly rhinoceros stable isotope compositions through time. In north-east Siberia, we detected δ15N stability through time. This could reflect long-term environmental stability, and might have enabled the later survival of the species in the region. To further investigate the palaeoecology of woolly rhinoceroses, we compared their isotopic compositions with that of other contemporary herbivores. This analysis suggests possible niche partitioning between woolly rhinoceros and both horse (Equus spp.) and woolly mammoth (Mammuthus primigenius), and isotopic similarities between woolly rhinoceros and both musk ox (Ovibos moschatus) and saiga (Saiga tatarica) at different points in time. To provide phylogeographical context to the isotopic data, we analyzed 61 published mitochondrial control region sequences. The data show a lack of geographic structuring; we found three haplogroups with overlapping distributions, all of which show a signal of expansion during the Last Glacial Maximum. Furthermore, our genetic findings support the notion that environmental stability in Siberia had an impact on the paleoecology of woolly rhinoceroses in the region. Our study highlights the utility of combining stable isotopic records with ancient DNA to advance our knowledge of the evolutionary ecology of past populations and extinct species.

The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted herbivore, widely distributed from western Europe to north-east Siberia during the Late Pleistocene. Previous studies have associated the extinction of the species ∼14,000 calendar years before present to climatic and vegetational changes, suggesting the later survival of populations in north-east Siberia may have related to the later persistence of open vegetation in the region. Here, we analyzed carbon (δ13C) and nitrogen (δ15N) stable isotopes and mitochondrial DNA sequences to elucidate the evolutionary ecology of the species. Our dataset comprised 286 woolly rhinoceros isotopic records, including 192 unpublished records, from across the species range, dating from >58,600 to 12,135 14C years before present (equivalent to 14,040 calendar years ago). Crucially, we present the first 71 isotopic records available to date of the 15,000 years preceding woolly rhinoceros extinction. The data revealed ecological flexibility and geographic variation in woolly rhinoceros stable isotope compositions across time. In north-east Siberia, we detected stability in δ15N through time, which could reflect long-term environmental stability, and may have enabled the later survival of the species in the region. To further investigate the paleoecology of woolly rhinoceroses, we compared their isotopic compositions with other contemporary herbivores. Our findings suggested isotopic similarities between woolly rhinoceros and both musk ox (Ovibos moschatus) and saiga (Saiga tatarica), albeit at varying points in time, and possible niche partitioning between woolly rhinoceros and both horse (Equus spp.) and woolly mammoth (Mammuthus primigenius). To provide phylogeographic context to the isotopic data, we compiled and analyzed the 61 published mitochondrial control region sequences. The genetic data showed a lack of geographic structuring; we found three haplogroups with overlapping distributions, all of which showed a signal of expansion during the Last Glacial Maximum. Furthermore, our genetic findings support the notion that environmental stability in Siberia influenced the paleoecology of woolly rhinoceroses in the region. Our study highlights the utility of combining stable isotopic records with ancient DNA to advance our knowledge of the evolutionary ecology of past populations and extinct species.

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines., The authors acknowledge support from the Science for Life Laboratory, the Garvan Institute of Medical Research, the Knut and Alice Wallenberg Foundation, and the National Genomics Infrastructure funded by the Swedish Research Council and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Natural History Museum at the University of Oslo for providing the Javan rhinoceros sample. We thank the Museum of the Institute of Plant and Animal Ecology (UB RAS, Ekaterinburg) for providing the sample of Siberian unicorn. M.T.P.G. was supported by European Research Council (ERC) Consolidator grant 681396 (Extinction Genomics). E.D.L. was supported by Independent Research Fund Denmark grant 8021-00218B. A.C. was supported by an Australian Research Council Laureate Fellowship (FL140100260). T.M.B. is supported by funding from the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement 864203), grant BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu” funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). L.D. was supported by the Swedish Research Council (2017-04647) and Formas (2018-01640)., With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2018-000792-M).

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.

Excavations from 2013 to 2015 at the site of Shishan Marsh 1 (SM1) in the Azraq Basin of eastern Jordan have yielded substantial late middle Pleistocene lithic assemblages in association with faunal remains. Faunal preservation is poor, but multiple taxa have been identified, including cf.Panthera leo,Gazellasp.,Boscf.primigenius,Camelussp.,Equusspp., cf.Stephanorhinus hemitoechus,Palaeoloxodoncf.recki, andElephascf.hysudricus. The overall Azraq habitat may have been most similar to a savanna ecosystem, with a mixture of open grassland/shrub habitats and more closed vegetation along the wetlands margins. These taxa were drawn to the relatively lush oasis environment, where they were a dietary resource of the hominin groups exploiting the wetlands resources.

The type material (holotypes, paratypes, syntypes and neotypes) and nomenclatural history of North American mammoth species are described in detail, focusing on names that have been in recent use: Mammuthus columbi, M. imperator, M. jeffersonii, M. meridionalis, M. hayi, M. haroldcooki and M. primigenius. Biometric study of the type specimens of M. meridionalis nebrascensis, M. hayi and M. haroldcooki shows them to be within the range of variation of M. columbi. These and other specimens referred to these species have a misleadingly ‘primitive’ appearance that is due to advanced individual age or, in the case of M. hayi, to inaccurate reconstruction of fragmentary fossils. The type material of M. imperator is also indistinguishable from M. columbi, but this taxon has been used to categorise mammoth fossils thought to be of intermediate grade between M. meridionalis and M. columbi. Biometric data indicate no clear morphocline in North American mammoths through the Pleistocene, except for ‘advancement’ in some Late Pleistocene samples that have been categorised as Mammuthus jeffersonii. Genetic and morphometric data suggest that these represent part of a complex metapopulation that arose with the immigration of M. primigenius into the continent, followed by varying degrees of hybridization with endemic M. columbi. Where adequate single-site Late Pleistocene samples are available they span the whole range of morphologies from ‘typical’ M. columbi to ‘M. jeffersonii’. It is difficult to impose taxonomic boundaries on a complex evolutionary process, but a suggested compromise is to treat the whole range of Late Pleistocene variation as M. columbi but informally, if desired, using ‘Jeffersonian’ as a descriptive term for the more advanced individuals or samples.

The bone-bearing beds of Bethlehem were excavated by Gardner and Bate in the late 1930s, yielding an important Plio-Pleistocene faunal assemblage. In the 1950s, Hooijer revised the fauna and described elephant remains, including a large tusk, a mandible, several molars and some post-cranial elements, identified by him as Archidiskodon cf. planifrons . Recent preparation and Computed Tomography has given new insights into the early elephant remains from Bethlehem – both in terms of their anatomy and their post-depositional deformation. This includes two further mandibles, distorted and almost totally obscured by sediment, whose morphology has been revealed. The elephant material has been studied in detail and compared morphometrically with key taxa including Siwalik Elephas planifrons and European Mammuthus rumanus . The morphology of the molars cannot definitively distinguish between Elephas or Mammuthus , but their evolutionary grade, and the morphology of the mandible, are most conformable with a primitive mammoth intermediate between African M. subplanifrons and European M. rumanus. Conversely a largely complete tusk shows none of the spiral twisting associated with Mammuthus and is more conformable with Elephas. The possibility that two elephantid taxa are represented in the Bethlehem deposit cannot be discounted, and is consistent with a wide size variation seen among the postcranial bones. These remains, together with some others recently described, represent the most primitive known elephantines out of Africa.

Summary Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily). 1 Despite the challenges associated with recovering ancient DNA from warm climates, 2 we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived 3 to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 and 200.95 kg and height reduction between 0.15 and 41.49 mm per generation. We show that combining ancient DNA with paleontological and geochronological evidence can constrain the timing of phenotypic changes with greater accuracy than could be achieved using any source of evidence in isolation.

Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1–3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species’ extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species. Here, Lord et al. sequence a complete nuclear genome and 14 mitogenomes from the extinct woolly rhinoceros. Demographic analyses show that the woolly rhinoceros population size was large until close to extinction and not affected by modern human arrival in northeastern Siberia. The extinction may have been mostly driven by climate warming.

Evolution on islands, and the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of a particular phenotypic trait of extinct animals can be challenging, due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily). Despite the challenges associated with recovering ancient DNA from warm climates, we successfully retrieved a mitogenome from a sample with an estimated age between 147,000 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals in the Pleistocene to a comparatively small-bodied island species, with an estimated average mass reduction of 0.79 - 18.45 kg and height reduction of 0.15 - 3.41 mm per generation. We show that combining ancient DNA, palaeontological and geochronological evidence can constrain the timing of phenotypic changes within narrower age boundaries than could be achieved using any source of evidence in isolation.

The largest antlers of any known deer species belonged to the extinct giant deer Megaloceros giganteus. It has been argued that their antlers were too large for use in fighting, instead being used only in ritualized displays to attract mates. Here, we used finite-element analysis to test whether the antlers of M. giganteus could have withstood forces generated during fighting. We compared the mechanical performance of antlers in M. giganteus with three extant deer species: red deer (Cervus elaphus), fallow deer (Dama dama) and elk (Alces alces). Von Mises stress results suggest that M. giganteus was capable of withstanding some fighting loads, provided that their antlers interlocked proximally, and that their antlers were best adapted for withstanding loads from twisting rather than pushing actions, as are other deer with palmate antlers. We conclude that fighting in M. giganteus was probably more constrained and predictable than in extant deer.

Reconstructing the dynamics and drivers of late Quaternary megafaunal extinctions requires direct radiometric date series that are assessed within probabilistic statistical frameworks. Extinction chronologies are poorly understood for many tropical regions, including Madagascar, which had a diverse, now-extinct Holocene large vertebrate fauna including a “megaherbivore” guild of endemic hippopotami and elephant birds. Madagascar's megaherbivores likely played vital roles in regulating ecosystem structure and nutrient cycling, but few direct dates are available for megaherbivore specimens identified to species level, with uncertainty over when and why different representatives of this guild disappeared. Here, we conduct a new investigation into Malagasy megaherbivore extinction dynamics, including 30 new AMS dates and 63 audited published dates. We use Gaussian-resampled inverse-weighted McInerny (GRIWM) analysis to estimate species-specific extinction dates for three elephant bird species (Aepyornis hildebrandti, Mullerornis modestus, Vorombe titan), eggshell representing Aepyornis or Vorombe, and two hippo species (Hippopotamus lemerlei, H. madagascariensis), and to estimate extinction dates for megaherbivore communities in different biomes. Megaherbivores persisted for millennia after first human arrival. Extinction date estimates vary significantly between biomes, with disappearance from dry deciduous forest over a millennium earlier than other biomes, possibly reflecting local variation in megaherbivore population densities or human pressures. However, megaherbivore communities including all elephant bird and hippo species persisted elsewhere across Madagascar until ∼1200-900 bp , when they collapsed suddenly. Extinctions are closely correlated in time with intensive conversion of forests to grassland at ∼1100-1000 bp , probably associated with a shift to agro-pastoralism and representing a radical change in sustainability of prehistoric human interactions with biodiversity.

DOI: 10.1016/j.quascirev.2016.06.007 URL: http://www.sciencedirect.com/science/article/pii/S0277379116302086 Filiació URV: SI Tooth wear analysis techniques (mesowear and microwear) are employed to analyze dietary traits in proboscideans, perissodactyls and artiodactyls from 33 Pleistocene localities in Britain. The objectives of this study are to examine the variability in each taxon, to track dietary shifts through time, and to investigate resource partitioning among species.The integration of mesowear and microwear results first allowed us to examine dietary variability. We identified differences in variability among species, from more stenotopic species such as Capreolus capreolus to more eurytopic species such as Megaloceros giganteus and Cervus elaphus. Broad dietary shifts at the community level are seen between climatic phases, and are the result of species turnover as well as dietary shifts in the more flexible species. The species present at each locality are generally spread over a large part of the dietary spectrum, and resource partitioning was identified at most of these localities. Mixed feeders always coexist with at least one of the two strict dietary groups, grazers or browsers. Finally, for some species, a discrepancy is observed between meso- and microwear signals and may imply that individuals tended to die at a time of year when their normal food was in short supply.

Microwear analyses have proven to be reliable for elucidating dietary differences in taxa with similar gross tooth morphologies. We analyzed enamel microwear of a large sample of Channel Island pygmy mammoth (Mammuthus exilis) molars from Santa Rosa Island, California and compared our results to those of extant proboscideans, extant ungulates, and mainland fossil mammoths and mastodons from North America and Europe. Our results show a distinct narrowing in mammoth dietary niche space after mainland mammoths colonized Santa Rosa as M. exilis became more specialized on browsing on leaves and twigs than the Columbian mammoth and modern elephant pattern of switching more between browse and grass. Scratch numbers and scratch width scores support this interpretation as does the Pleistocene vegetation history of Santa Rosa Island whereby extensive conifer forests were available during the last glacial when M. exilis flourished. The ecological disturbances and alteration of this vegetation (i.e., diminishing conifer forests) as the climate warmed suggests that climatic factors may have been a contributing factor to the extinction of M. exilis on Santa Rosa Island in the Late Pleistocene.

Understanding global patterns of late Quaternary megafaunal extinction is impeded by geographic variation in data quality and quantity. The magnitude, timing and drivers of megafaunal extinctions remain poorly understood for India, a region with a strong history of palaeontological research. We review available data for all putative extinct Indian megafaunal taxa with direct or indirect reported evidence of potential survival into the global “megafaunal extinction window” (from ∼50,000 years onwards). Assessment of late Quaternary megafaunal species richness is confused by multiple levels of taxonomic uncertainty, including the relationship of named Late Pleistocene taxa to extant taxa, and nomenclatural confusion over correct species names. There is sufficient evidence to recognise up to four genuine global megafaunal species-level extinctions in India during the Late Pleistocene: two proboscideans (Palaeoloxodon namadicus, Stegodon sp.), a hippopotamus (Hexaprotodon sp.), and possibly a horse (Equus namadicus). A fifth extinct megafaunal species, the Indian aurochs Bos [primigenius] namadicus, definitely persisted into the Holocene. Other Indian late Quaternary megafaunal species (Rhinoceros spp., Bubalus palaeindicus, Sus “palaeindicus”, Crocodylus palaeindicus) are likely to be synonyms of extant species. Reconstructing regional extinction dynamics is further impeded by chronological uncertainty; however, attempts to obtain new dates for vertebrate samples from six late Quaternary sites in five regions were unsuccessful. Accurate understanding of the dynamics of megafaunal extinctions in India will require robust taxonomic, chronological and palaeoecological data, and we encourage further investigation of the region’s rich late Quaternary record.

The giant deer, Megaloceros giganteus, is one of the most celebrated of late Quaternary megafaunal species. Here we present new radiocarbon data on the pattern of its extinction, and compare this, on a region-by-region basis, with evidence of environmental change and human occupation. Following strict auditing criteria for the acceptance of radiocarbon dates, 51 dates are published here for the first time, bringing the total number of accepted dates for the species to 134. For western Europe, extirpation around the start of the Younger Dryas stadial is corroborated. Previous early-to mid-Holocene records for the Urals and Siberia are augmented by new dates that together provide an almost continuous radiocarbon record from the late-glacial to the mid-Holocene. Newly-rediscovered skeletal material of giant deer from the Maloarchangelsk region of European Russia has provided the latest date for the species known so far, and extends the mid-Holocene range substantially westward almost to Ukraine. The relatively narrow overall distribution of M. giganteus through its history, and direct palaeoecological evidence, demonstrate the species’ requirement for a mixed, partially open habitat providing both graze and browse. Its extirpation from western Europe remains strongly linked to deterioration of climate and productivity in the Younger Dryas, while its disappearance from more eastern areas correlates chronologically with the spread of closed forest. However, these intervals also coincide with the arrival of (probably sparse) human populations in the regions occupied by giant deer in Ireland and across Russia. The pattern of distributional changes leading to the Holocene restriction of giant deer populations strongly suggests environmental causation, but a contribution of human hunting to the extirpation of terminal populations cannot be ruled out.

Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the ‘Siberian unicorn’, was believed to have gone extinct around 200,000 years ago—well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the ‘Siberian unicorn’ marked the extinction of this subfamily.

Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables age estimation over the Quaternary. We postulate that enamel is a suitable biomineral for the long-term survival of endogenous amino acids. Analysis of multiple amino acids for geochronological studies is typically achieved using a RP-HPLC method. However, the low concentrations of amino acids coupled with high concentrations of inorganic species make accurate determination of amino concentrations challenging. We have developed a method for the routine preparation of multiple enamel samples using biphasic separation. Furthermore, we have shown that amino acids that exhibit effectively closed system behaviour can be isolated from enamel through an exposure time of 72 h to bleach. Elevated temperature experiments investigating the processes of intra-crystalline protein degradation (IcPD) do not appear to match the patterns from fossil samples, reinforcing the need for a comprehensive understanding of the underlying mechanisms of protein degradation. This novel preparative method isolates intra-crystalline amino acids suitable for the development of mammalian geochronologies based on enamel protein degradation. The lower rates of racemisation in enamel (cf.Bithyniaopercula) suggest that the enamel AAR may be able to be used as a relative dating technique over time scales > 2.8 Ma. Enamel AAR has the potential to estimate the age of mammalian remains past the limit of all other current direct dating methods, providing an invaluable tool for geochronological studies.

Plants and animals influence biomass production and nutrient cycling in terrestrial ecosystems; however their relative importance remains unclear. We assessed the extent to which mega-herbivore species controlled plant community composition and nutrient cycling, relative to other factors during and after the Late Quaternary extinction event in Britain and Ireland, when two-thirds of the region’s mega-herbivore species went extinct. Warmer temperatures, plant-soil and plant-plant interactions, and reduced burning contributed to the expansion of woody plants and declining nitrogen availability in our five study ecosystems. Shrub biomass in particular was consistently one of the strongest predictors of ecosystem change, equaling or exceeding the effects of other biotic and abiotic factors. In contrast, there was relatively little evidence for mega-herbivore control on plant community composition and nitrogen availability. The ability of plants to determine the fate of terrestrial ecosystems during periods of global environmental change may therefore be greater than previously thought.

The Aghnadarragh site presents the most complete known Midlandian (last cold stage) sequence in Ireland. Above a glacial till and below organic deposits of the Aghnadarragh Interstadial, a unit of poorly sorted gravel and diamicton yielded numerous fossils of woolly mammoth and rarer musk ox, the first record of that species in Ireland. The mammoth molars are of relatively small size and distinctive morphology that probably relate to local environmental conditions. Dating of three mammoth molars by Electron-Spin-Resonance indicates an age for the faunal horizon in the range 109 to 74 ka, corresponding to the later part of MIS 5, presumably MIS 5d or 5b in view of the cold-adapted flora and fauna, or possibly early MIS 4. This in turn suggests that the underlying glacigenic deposits, assigned to the Fermanagh Stadial, formed during a cold stage preceding the last interglacial, rather than being early Midlandian in age as generally assumed. Copyright © 2015 John Wiley & Sons, Ltd.

Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.

The extirpation of spotted hyaena, Crocuta crocuta, in northern Eurasia can be seen as part of the late Quaternary megafaunal extinction event. The radiocarbon record for this species is less substantial than for other megafaunal species, but with the addition of new dates we have significantly increased the tally to approximately 100 reliable direct dates. These suggest extirpation at ca 40 ka (calendar years) in Central Europe and Russia, and ca 31 ka in north-west and southern Europe, so that the species was probably restricted to the Mediterranean and the Atlantic seaboard after 40 ka. Previous records suggesting Lateglacial or even Holocene survival (especially in eastern Asia) are not substantiated. The current estimate of 31 ka for extirpation of the spotted hyaena in northern Eurasia is close to the estimated extinction date of cave bear (Ursus spelaeus), suggesting a possible common cause. Factors likely to have impacted the spotted hyaena include, in particular, physiological cold intolerance in the face of deteriorating climate, as well as reduction of prey abundance driven by depressed vegetational productivity, and increased competition for food or space with lions, bears and people, possibly exacerbated by the arrival of modern humans.

House mice from 24 Scottish and Faroese islands show positive correlation of skeletal size with island area, conforming to a model of resource limitation in very small islands. Molar size is not correlated with island size, suggesting greater genetic canalization; smaller individuals have larger tooth to body size ratio. The size variation may have a simple genetic basis or may be ecophenotypic. The offset between skeletal and molar size has potential use in the fossil record as a marker for these rapid effects, while longer-term evolutionary change reverts to approximate tooth—body size isometry. Collation of related studies indicates frequently deterministic relationships of small-mammal body size to island size. The parameters of the relationship (positive, negative or parabolic) vary widely with case study according to biotic and abiotic factors. In the present study there was no relationship of mouse size to any variable (e.g. presence of competitors) except island area.

The largest antlers of any known deer species belonged to the extinct giant deerMegaloceros giganteus. It has been argued that their antlers were too large for use in fighting, instead being used only in ritualized displays to attract mates. Here, we used finite-element analysis to test whether the antlers ofM. giganteuscould have withstood forces generated during fighting. We compared the mechanical performance of antlers inM. giganteuswith three extant deer species: red deer (Cervus elaphus), fallow deer (Dama dama) and elk (Alces alces). Von Mises stress results suggest thatM. giganteuswas capable of withstanding some fighting loads, provided that their antlers interlocked proximally, and that their antlers were best adapted for withstanding loads from twisting rather than pushing actions, as are other deer with palmate antlers. We conclude that fighting inM. giganteuswas probably more constrained and predictable than in extant deer.

There has been much discussion of the role of behaviour in evolution, especially its potential to lead morphological evolution by placing the organism in a novel selective environment. Many adaptations of living species can be imagined to have originated in this way, although documented examples are relatively few. A fruitful arena for testing hypotheses about behavioural innovation is the fossil record. Traditionally, the behaviour of fossil species has been deduced from their morphology, precluding the observation of a behavioural lead preceding morphological evolution. This circularity can be broken by examining behavioural proxies independent of the adaptive morphology itself. Examples applicable to fossil remains include dietary information (e.g. wear traces on teeth, stable isotopes) and trace fossils indicating locomotor mode (footprints). The signature of a behavioural lead would be an observed shift in behaviour from one horizon (or taxon) to another, followed later by a functionally-related morphological change. This pattern can be sought either in finely-stratified anagenetic sequences of fossils (stratophenetic approach) or among fossils with well-resolved species-level phylogenies (cladistic approach). An array of case studies from the literature is presented. These include feeding shifts in finely-resolved sequences of vertebrates ranging from freshwater fish to terrestrial ungulates, as well as locomotor changes crucial to major evolutionary transitions in the origin of tetrapods, birds, and humans. The latter examples highlight the role of behaviour in initiating exaptation (the requisitioning of structure for a new function). The case studies also illustrate the challenges of using fossil sequences to elucidate behavioural roles, including insufficient stratigraphic resolution and uncertainty over the adaptive function of observed traits. By the same token, they suggest criteria for choosing promising cases for research, as well as for formulating testable hypotheses about evolutionary modes. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 315–331.

We describe new fossil remains of elephant (Elephas cf. hysudricus) from archaeological sites in the Levant: Ma'ayan Baruch (Israel) and 'Ain Soda (Jordan). Both sites date to the Middle Pleistocene based on stone artefacts typical of Levantine Late Acheulian assemblages. The elephant remains show ‘primitive’ dental features reminiscent of E. hysudricus from the Plio-Pleistocene of the Siwaliks (northern India), the species thought to be ancestral to Asian elephant E. maximus. Regionally, the new fossils are chronologically intermediate between an earlier (ca. 1 Ma) record of Elephas sp. from Evron Quarry (Israel), and Holocene remains of E. maximus from archaeological sites in NW Syria, Turkey, Iraq and Iran. It is unclear at present whether this represents continuity of occupation or, more plausibly, independent westward expansions.

Late Quaternary megafaunal extinction chronologies are poorly understood across eastern and southeast Asia. Previous radiometric studies suggested that surprisingly many extinct late Pleistocene large mammal species survived into the Holocene in northern China (Bos primigenius, Coelodonta antiquitatis, Mammuthus primigenius) and southern China (Ailuropoda baconi, Crocuta [crocuta] ultima, Megatapirus augustus, Stegodon orientalis, Sus cf. xiaozhu), indicating that Chinese megafaunal extinctions may have been "staggered" across the Late Quaternary. We critically re-examined all radiometric evidence suggesting Holocene survival of Chinese Late Quaternary megafauna, and conducted new dating of mammal material from reportedly Holocene sites containing characteristically Late Pleistocene faunas. Evidence for Holocene survival of any Chinese Late Pleistocene megafaunal species is weak or untenable. No previous radiometric dates used to support Holocene megafaunal survival represent direct bone dates for species of interest, and stratigraphic association between material yielding Holocene dates and megafaunal remains is dubious at most sites. Concerns over accurate identification of faunal material further confuse claims for Holocene survival of many species. Robust radiometric last-occurrence dates for extinct Chinese megafauna are all restricted to the Late Pleistocene, similar to the timing of many other Late Quaternary megafaunal species extinctions elsewhere in Eurasia and the Americas. (c) 2013 Elsevier Ltd. All rights reserved.

The fossil record richly illustrates the origin of morphological adaptation through time. However, our understanding of the selective forces responsible in a given case, and the role of behaviour in the process, is hindered by assumptions of synchrony between environmental change, behavioural innovation and morphological response. Here I show, from independent proxy data through a 20-million-year sequence of fossil proboscideans in East Africa, that changes in environment, diet and morphology are often significantly offset chronologically, allowing dissection of the roles of behaviour and different selective drivers. These findings point the way to hypothesis-driven testing of the interplay between habitat change, behaviour and morphological adaptation with the use of independent proxies in the fossil record.