Wednesday, November 27, 2013

Within-species networks

In this blog we have consistently championed the idea that within-species relationships are better represented by a network than by a tree. We have done this for humans and their relatives:
Networks and human inter-population variation
Human races, networks and fuzzy clusters
Why do we still use trees for the Neandertal genealogy?
and for other species as well:
Are phylogenetic trees useful for domesticated organisms?
Why do we still use trees for the dog genealogy?
Network of apple cultivars
Genetically, a within-species network is a haplotype network. Also, when dealing with individuals in a sexually reproducing species it is a hybridization network, as I have noted:
Family trees, pedigrees and hybridization networks
Charles Darwin's family pedigree network
Toulouse-Lautrec: family trees and networks
We are not the only blog to emphasize intra-species networks, of course. As far as humans are concerned, one of the more vocal blogs has been Gene Expression, run by Razib Khan over at Discover magazine. For example, when discussing phylogenetic trees (Burning down the trees in historical population genetics), Khan notes:
These sorts of trees range from Ernst Haeckel's classical attempt, depicting relationships which biologists derived from intuition within the framework of a grand evolutionary scheme, all the way down to modern methods implemented in software packages such as Mr. Bayes, which many frankly utilize in a "turnkey" manner. These trees are abstractions, in that they reduce down a wide range of phenomena into schematic representations which impart aspects of particular interest in a stylized form. This is important, because the actual nature of the phenomena being represented may be more complex than is being represented.
Phylogenetic analysis involving distinct species has its own problems, but they are dwarfed by what must confront those who attempt to parse out relatedness of populations within species. Because of the ubiquity of gene flow across populations within species, attempts to generate a tree of relationships of populations is always bound to be a gross simplification. Instead of a sequence of bifurcations the true relationship of putative populations is more accurately represented by a networked graph.
When discussing alternative evolutionary models (Unveiling the genealogical lattice), Khan notes:
It seems that the bifurcating model of the tree must now be strongly tinted by the shades of reticulation. In a stylized sense inter-specific phylogenies, which assume the approximate truth of the biological species concept (i.e., little gene flow across lineages), mislead us when we think of the phylogeny of species on the microevolutionary scale of population genetics. On an intra-specific scale gene flow is not just a nuisance parameter in the model, it is an essential phenomenon which must be accommodated into the framework.
And here the takeaway for me is that we may need to rethink our whole conception of pure ancestral populations, and imagine a human phylogenetic tree as a series of lattices in eternal flux, with admixed nodes periodically expanding so as to generate the artifice of a diversifying tree. The closer we look, the more likely it seems that most of the populations which have undergone demographic expansion in the past 10,000 years are also the products of admixture. Any story of the past 10,000 years, and likely the past 100,000 years, must give space at the center of the narrative arc to lateral gene flow across populations.
Mind you, the network and lattice metaphors are not the only ones he has up his sleeve (When trees turn into brambles):
With the expansion of genomics from humans to a wide range of species I suspect that we’ll see a lot more blurring of distinctions between species on the margins. This will be particularly true of those lineages with wide and continuous distributions. It will also be most salient and surprising for mammalian populations, where our prejudices about the primacy of a biological species concept are most strongly developed. In a phylogenetic sense when you shift the grain of analysis to a finer scale the tree of life becomes much more of a bramble in many cases.

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