Tag: Wolves

Wolf paleogenomics

Posted on by Razib Khan

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 (Canis familiaris) lived1,2,3,4,5,6,7,8. 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 IFT88 40,000–30,000 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.

Dog stuff makes the headlines, but I think the wolf stuff is the most interesting in this paper.

The shadow of the Ice Age

Posted on by Razib Khan

As ancient DNA becomes a more standard part of archaeological science it’s going really yield up some doozies. You’ve probably read Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, and how it’s upended old paradigms. But with the human past we probably have a better idea of the range of possibilities. When it comes to other organisms it’s going to be a weirder and wilder ride I predict.

This is why a new preliminary result does not shock me, Ancient Japanese wolf may be rare remnant of ice age wolves:

The wolf’s DNA more closely resembled that of a long-extinct wolf that lived in Siberia more than 35,000 years ago than that of living Eurasian and American wolves, Niemann reported here on Friday at the International Symposium on Biomolecular Archaeology. Most ancient wolves went extinct when the ice sheets that covered the Northern Hemisphere began to melt more than 20,000 years ago and the large mammals the wolves hunted, such as mammoth, died off. But some of their DNA lived on in the Honshū wolf, which could offer a new window on the evolution of wolves as well as dogs, says paleogeneticist Mikkel Sinding of the Greenland Institute of Natural Resources in Nuuk, who extracted the DNA.

Unfortunately the last Honshu wolves were killed more than a century ago. But for the purposes of DNA extract that’s basically yesterday.

From everything I can see the “megafauna” that inhabit the Palearctic ecozone seem to have through a lot of mass extinctions over the last 50,000 years. This extends from Neanderthals, to mammoths, to large canids and felids. Some lineages, such as that of humans and wolves, also underwent expansions from the remaining branches of the phylogenetic tree. But it’s reasonable that various relic groups of earlier diversifications might persist here and there.

Wolves out of Beringia!

Posted on by Razib Khan
Citation: Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Do Eurasian and North American wolves come from Beringia? That’s the conclusion of a new preprint, Modern wolves trace their origin to a late Pleistocene expansion from Beringia. The figure above is the main result, using ancient and modern mitochondrial genomes to construct a phylogeny. It’s not surprising that the ancient lineages are basal. Y and mtDNA lineages have a tendency to go extinct (lower effective population, etc.). But it’s a surprising result that the older Beringian individuals are distributed basal to the modern lineages, as opposed to more of the ancient samples from Europe and the Middle East.

The basic argument here is very similar to “mitochondrial Eve.” If Beringian lineages tend to be basal to modern wolves, then the former is likely to be ancestral to the latter. Additionally, as noted in the preprint there is whole-genome inference which indicates that modern gray wolves across the Palearctic ecozone underwent a rather recent demographic expansion, in particular, after the Last Glacial Maximum (~20,000 years BP). That being said, I am curious if modern Alaskan and (east) Siberian wolves exhibit greater mtDNA diversity than elsewhere, in keeping with the human analogy.

Needless to say, mtDNA has limitations. It’s a single locus, and in other animal research, there have been confusions and misunderstandings due to the usage of mtDNA. The authors did some explicit formal demographic modeling using their data. It’s fine, but generally, I ignore this stuff because it rarely tells us things we don’t know to a high degree of certainty.  Rather, I would rather focus on paleoclimate data and a model where coexistence with Beringian humans might explain a possible break-out of Beringian wolves to the west and the east after the Pleistocene. The Beringian landscape may have been particularly fertile territory for the Palearctic wolf. Though modern wolves seem to prefer some forest, rather than open territory.

One thing human evolutionary genomics has taught us is that the first-pass story is always far simpler than reality. I think this is a decent framework to start with, though it may still turn out to be wrong. But in the preprint, the authors note some peculiarities in South Asians and Tibetan wolves. So peculiar that they were discarded from the analysis. We know wolves hybridize with both jackals and coyotes, so the emergence of the modern lineages are likely more complex than a simple expansion and replacement. The whole-genome analysis will probably offer up curious wrinkles.

Though the preprint tries to put the emergence of the wolf from Beringia in the context of the domestication of the dog, I suspect we’ll find that the dog derives from an extinct Eurasian wolf lineage. This was the implication of Freedman et al., and ancient canine genomics is producing some erratic finds which are in keeping with a possible complex divergence of the dog lineage from wolves.