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 remain contentious. 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, underscoring the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.This paper is in the memory of our friend and colleague Dr. Andrei Sher, who was a major contributor of this study. Dr Sher died unexpectedly, but his major contributions to the field of Quaternary science will be remembered and appreciated for many years to come. We are grateful to Dr. Adrian Lister and Dr. Tony Stuart for guides and discussions. Thanks to Tina B. Brandt, Dr. Bryan Hockett and Alice Telka for laboratory help and samples and to L. Malik R. Thrane for his work on the megafauna locality database. Data taken from the Stage 3 project was partly funded by Grant #F/757/A from the Leverhulme Trust, together with a grant from the McDonald Grants and Awards Fund. We acknowledge the Danish National Research Foundation, the Lundbeck Foundation, the Danish Council for Independent Research and the US National Science Foundation for financial suppor

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canisfamiliaris) lived(1-8). Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT8840,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.Peer reviewe

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

Magyar Pszichológiai Szemle

The first objective of this study is to examine temporal patterns in ancient dog burials in the Lake Baikal region of Eastern Siberia. The second objective is to determine if the practice of dog burial here can be correlated with patterns in human subsistence practices, in particular a reliance on terrestrial mammals. Direct radiocarbon dating of a suite of the region's dog remains indicates that these animals were given burial only during periods in which human burials were common. Dog burials of any kind were most common during the Early Neolithic (∼7-8000 B.P.), and rare during all other time periods. Further, only foraging groups seem to have buried canids in this region, as pastoralist habitation sites and cemeteries generally lack dog interments, with the exception of sacrificed animals. Stable carbon and nitrogen isotope data indicate that dogs were only buried where and when human diets were relatively rich in aquatic foods, which here most likely included river and lake fish and Baikal seal (Phoca sibirica). Generally, human and dog diets appear to have been similar across the study subregions, and this is important for interpreting their radiocarbon dates, and comparing them to those obtained on the region's human remains, both of which likely carry a freshwater old carbon bias. Slight offsets were observed in the isotope values of dogs and humans in our samples, particularly where both have diets rich in aquatic fauna. This may result from dietary differences between people and their dogs, perhaps due to consuming fish of different sizes, or even different tissues from the same aquatic fauna. This paper also provides a first glimpse of the DNA of ancient canids in Northeast Asia

Reindeer from Sámi offering sites document the replacement of wild reindeer genetic lineages by domestic ones in Northern Finland starting from 1400 to 1600 AD

Abstract Reindeer herding emerged among the indigenous Sámi of Northern Fennoscandia between ca. 800 and 1500 CE. While the details of the reindeer domestication process are still actively debated, it has been hypothesized that the transition to reindeer herding affected Sámi ritual practice, especially animal offerings given at various sacred sites. To explore this hypothesis, we analyzed DNA from reindeer bone samples dating to ca. 1200–1700 CE from Sámi offering sites located in present-day Northern Finland as well as from samples originating from ancient dwelling site in Southern Finland and Kola Peninsula, Russia. The results show that haplotypes related to wild Finnish forest reindeer (Rangifer tarandus fennicus) began to be replaced by haplotypes common in modern domesticated reindeer in the faunal assemblages from offering sites starting between 1400 and 1600 CE. The results suggest that, although the role of reindeer herding in the economy of the Sámi communities varied greatly, the transition to reindeer herding may have affected ritual practices, testifying to a shared way of reciprocating with the land and animals

Maximum likelihood phylogeny of recent and ancient dogs and wolves (prefix lu), rooted with coyotes (prefix la).

<p>The dogs form the previously identified four clades (labeled dog clades I–IV) within the diversity of wolves. Specimen 2010-19 is Ust’-Belaia dog 2 in the text, 2010-021 is Ust’-Belaia dog 3, 2010-023 Pad’ Kalashnikova dog 1, 1997.282 Khotoruk, and 2010-001 Ulan-Khada.</p

The cranium of the Ust’-Khaita canid with the location of the partially healed puncture to the cranium indicated.

<p>The cranium of the Ust’-Khaita canid with the location of the partially healed puncture to the cranium indicated.</p

Comparison of Cis-Baikal canid long bone lengths with those of modern and ancient wolves, and large northern dogs. Shoulder heights are estimates based on regression equations on long bone lengths [32].

a<p>This study.</p>b<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063740#pone.0063740-Meachen1" target="_blank">[27]</a>.</p>c<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063740#pone.0063740-BoudadiMagali1" target="_blank">[26]</a>.</p

Minimum spanning network of haplotypes in dog clade I.

<p>Previously published sequences are in white and the ancient Baikal dogs presented here are in the shaded ovals. The American clade has been collapsed and is represented by the oval labeled “American clade”. Each link represents a single mutation, and bars across them additional mutations. The black circle represents a hypothetical haplotype. Not all alternative links are shown.</p