Razib Khan One-stop-shopping for all of my content

September 30, 2018

The shadow of the Ice Age

Filed under: paleontology,Wolves — Razib Khan @ 1:55 pm

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.

July 22, 2018

Wolves out of Beringia!

Filed under: Canids,Canine Evolution,Dog Evolution,Wolves — Razib Khan @ 9:05 pm
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.

May 18, 2011

A map of charismatic canid genomic variation

The Pith: Wolves and coyotes exhibit geographic population structure. The red wolf may “only” be a coyote with a minor admixture of wolf, instead of a “real species.”

I like dogs. For various structural reasons I am not able to live with a dog right now (not to mention the required investment of time & energy). But the whole military dog storyline associated with the killing of Osama Bin Laden has me thinking a bit more deeply of the co-evolutionary nature of dog-human relationships. Whether dogs have theory-of-mind is controversial, but there’s no doubt that they’re relatively well adapted to operate with humans relatively efficiently as part of a dual-species team. From an evolutionary and genomic perspective dogs are also of interest. Like humans dogs exhibit a huge range of phenotypic variation despite relatively recent common origin. The species which they presumably are derived from, wolves, are intelligent social creatures whose natural range is very expansive indeed. I believe that the general dynamics of evolution and genetics which are operative amongst canids can give us insight into the processes which shape our own species. In part that is ...

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