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

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.

July 26, 2017

18,000 years BC (the film)

Filed under: Dog Evolution,Human Evolution,Paleolithic — Razib Khan @ 5:42 pm

Alpha, set 20,000 years ago in Europe, was apparently originally titled “Solutrean.” The change is probably for the best. It will come out next spring. I really hope that this movie is good and does well. It isn’t often that you have something which takes place during the Last Glacial Maximum.

The plot seems to reflect the what you might read in Pat Shipman’s The Invaders, but it’s about 20,000 years too late for her model to work. One of the major criticisms of the idea that dogs and modern humans operated as a team is that it seems way too early. But of late there have been suggestions that the date is earlier than we’d previous thought in relation to when dogs as we understand them arose: Ancient European dog genomes reveal continuity since the Early Neolithic. Here’s the relevant section: “By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000–40,000 years ago.”

Please note though that the divergence of the dog lineage from the ancestors of modern wolves is a distinct question and process from domestication as such as we understand it. Though it seems likely these events didn’t occur too far apart in time.

December 18, 2011

Dogs are necessary when man is sufficient

Filed under: Anthroplogy,Dog Evolution,Dogs — Razib Khan @ 10:17 pm

Wolf-to-dog transition had little to do with humans, ancient skull suggests. I think the headline here is deceptive. This is the important part:

A Canadian researcher who specializes in the biology of ancient dogs co-authored one of the most significant studies of the year in canine science: a paper detailing the world’s earliest evidence of an animal in transition from wild wolf to domesticated dog.

The “extraordinary preservation” of the creature’s 33,000-year-old skull — found in a cave in southern Siberia — has helped show that dog domestication “was, in most cases, entirely natural” and not really a “human accomplishment,” says B.C. evolutionary biologist Susan Crockford.

She was part of a six-member team of researchers from Russia, Britain, the U.S. and the Netherlands that turned the clock back on wolf-dog transformations by thousands of years and showed that the phenomenon probably happened many times in many places around the globe.

I am leaning toward this direction, because I suspect that hominins were themselves moving in an “inevitable” direction after a few initial contingent stages. The co-evolution between social canids and primates is I think not a random chance event. To some extent I think “man’s best friend” was a necessary outcome of evolutionary forces. Barring the total extermination of one lineage or the other, some sort of cooperative relationship is I suspect something that will naturally reoccur. Dogs are not simply a specific derived lineage of wolves, they’re an ecological niche created by the existence of hominins with social complexity. Humans may not have domesticated wolves per se, but human societies are the ecological niche which a certain subset of wolves naturally adapt themselves to. And, I believe humans are pre-adapted to tolerate, accept, and even extol, the presence of philo-anthropic canids. In some ways they may be a preview for what is to come with intelligent social robots, which will draw upon the same cognitive reflexes.

Image credit: Wikipedia

November 25, 2011

Man is the environment of the rat

Filed under: Dog Evolution,Evolution,Human Evolution,Rat Evolution — Razib Khan @ 3:58 pm

The above is a figure from a new paper in PLoS ONE, Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats. Here’s the abstract:

The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.

Since it is open access you can read the paper for the full details. The main result is that it looks like separate and distinction lineages of R. rattus piggybacked on the expansion of humans. The main caveat, admitted in the article, is a reliance on mtDNA and the possibility of admixture and introgression across lineages explaining the current extant variance. The authors refer to paraphyly because it may be that all the descendants of modern black rats, as we understand them, may not be identified as black rats, probably due to their lack of adaptation and coexistence with humans.

Obviously we’ll need to wait for autosomal studies which utilize many more markers. But let’s grant the robustness of this finding: that the modern black rat lineages are a compound of a recent demographic expansion from a small population in western India, as well as long standing deep rooted populations across South and Southeast Asia, which independently entered into coexistence and parasitism with humans. I find this broadly plausible. The reason is not the rat, but the dog.

A new paper just came out which established an East Asian origin for dogs. Or at least for now, as there have been multiple candidates for point of origin. Additionally there are some who argue for evidence of pre-Neolithic domestication or coexistence of dogs and humans. I am beginning to suspect that this hodgepodge of confusing results on the origin of the dog, both in location and period, indicates that in some deep way the wild ancestors of dogs were pre-adapted for coexistence with humans, and it may have occurred multiple times. This is the argument in Mark Derr’s How the Dog Became the Dog: From Wolves to Our Best Friends. My position isn’t that modern dogs aren’t the descendants of a small ancient population which crystallized in the early Neolithic. Rather, it may be that they’re just the last in a long line of dog-human co-socialization experiments.

With the radiation of the hominin clade, and its shift toward more complex social organizational structures, the evolution of parasites like rats and companion species like dogs was inevitable. Out of the set of species which exhibit a potential toward close interaction with humans you have a small number which are ideally pre-adapted. Often this pre-adaptation isn’t a universal feature of a species, but part of the quantitative range of trait value. In other words, there may have been wolves always present which would be more congenial to interaction with hominins, and rats which were optimized for living on the margins and within human settlements. When humans become numerous, these previously neutral or lower frequency morphs became strong targets of natural selection.

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