Trees, networks and dogs

One of the perennially most popular posts in this blog has been the one about the domestication of dogs: Why do we still use trees for the dog genealogy?

In that post I noted that, up to 2012, there were three distinct trends in the presentation of the genealogy of dog breeds:

1. the study of whole-genome data, in which the results are presented solely as a neighbor-joining tree
2. the study of mtDNA sequence data, in which the results are presented both as a tree and as a haplotype network
3. the study of combined Y-chromosome and mtDNA sequence data, in which the results are presented solely as a haplotype network.

This pattern has continued. For example, the following diagram is taken from:

Skoglund P, Ersmark E, Palkopoulou E, Dalén L (2015) Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Current Biology 25:1515-1519.

The tree is based on mitochondrial genome data for the highlighted fossil, compared to the mitochondrial sequences of modern-day dogs and wolves, as well as ancient canids. The use of a phylogenetic tree seems to be based on the idea that mitochondria consist of tightly linked genes that are uniparentally inherited. However, neither of these characteristics is universal, and so a network might be more appropriate.

The dog genealogy is recognized as being characterized by introgression with wolves, as the authors themselves note. Also, the origin of dogs is not directly from wolf ancestors, but both modern wolves and modern dogs are derived from a common ancestor. For example, this next diagram is from:

Freedman AH, et alia (2014) Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics 10:e1004016.

The width of each population branch is proportional to inferred population size. Note that wolves and dogs originated at roughly the same time, as the result of bottlenecks in the ancestral population size. Wolves diversified slightly earlier than dogs. Also, Skoglund et al. dispute the dating of the splits, suggesting that the dog-wolf divergence was "at least 27,000 years ago".

As a final note, there is a tendency to credit Charles Darwin with originating just about everything in the study of genealogy, although he was a synthesizer as much as an innovator. For example, David Grimm suggests (Dawn of the dog. Science 348: 274-279):

Charles Darwin fired the first shot in the dog wars. Writing in 1868 in The Variation of Animals and Plants under Domestication, he wondered whether dogs had evolved from a single species or from an unusual mating, perhaps between a wolf and a jackal.

However, the first hypothesized genealogy was actually published more than a century earlier, by Georges-Louis Leclerc, comte de Buffon (see the blog post on The first phylogenetic network), who suggested a common origin with wolves.