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

Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion

The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of C-14 and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52- 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species

Approximate original fatty acid profiles calculated for frozen mammals.

<p>^a Only the major FAs have been considered.</p><p>^b A superscript number indicates the FA percentages found in frozen samples, while all derived percentages appear in italics. In reconstructed figures, C18 PUFA percentages are partially subtracted from PA figures; C20 PUFAs from EA. For both bison, reconstructed OA percentages are partially subtracted from PA.</p><p>^c PUFA ratios and PA percentage in agreement with those of grass-fed elephants <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084480#pone.0084480-Meyer1" target="_blank">[19]</a>.</p><p>^d PUFA ratios and PA percentage as grass-fed Siberian <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084480#pone.0084480-Mordovskaya1" target="_blank">[20]</a> and Galician horses <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084480#pone.0084480-GuilGuerrero1" target="_blank">[21]</a>.</p><p>^e PUFA ratios and PA percentage as grass-fed Bison subcutaneous fat <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084480#pone.0084480-Turner1" target="_blank">[22]</a>.</p

Unsaturated fatty acids composition of the fat from frozen mammals^a.

<p>^a Mean ± SD of three independent determinations performed by GLC-MS.</p

Mammoth calf Lyuba had a hump on the neck consisting of special fat cavities.

<p>Mammoth calf Lyuba had a hump on the neck consisting of special fat cavities.</p

Gas-liquid chromatogram of fatty acid methyl esters from under skin fat from the belly of mammoth Lyuba.

<p>As noted in the chromatogram, palmitic acid (16∶0) is the main FA component, but the peaks due to the monounsaturated 18∶1<i>n</i>-9<i>E</i> and 18∶1<i>n</i>-9<i>Z</i> FAs can be clearly seen too.</p

Data from: X-Ray computed tomography of two mammoth calf mummies

Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (∼2,300 cm3) than that of neonate elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques

Total fatty acids and saturated fatty acids composition of the fat from frozen mammals ^a.

<p>^a Mean ± SD of three independent determinations performed by GLC-MS.</p

Sample characteristics of frozen mammals.

<p>Sample characteristics of frozen mammals.</p

Supplemental Data 1

Animation based on segmented or thresholded features from a full-body CT-scan of Lyuba, a woolly mammoth neonate from the Yamal Peninsula, Siberi