Kidd Lab Interpretation of "phylogenetic" trees of populations based on gene frequency data.
In the abstract a tree is simply one of many graphical ways to represent similarities. An additive tree is simply a representation of a set of linear equations that gives graphically the segment lengths that best fit the pairwise distances. However, it is unavoidable that a tree be thought of in terms of historical divisions and diversifications of populations. Without major qualifications that would be an incorrect interpretation for most human populations. Few extant populations have had complete endogamy for many generations and it is unlikely that ancient populations were any different. Moreover, at most loci that have been studied on many populations, the allele frequencies tend to show a clinal pattern.
In spite of these and other problems with an evolutionary interpretation of trees, there are plausible historical inferences that can be made. For example, in the interim analyses depicted the Native American branch separates from the East Asian branch considerably before the majority of the East Asian populations diverge from one another. The exception is the Siberian Yakut, which seems intermediate between the two clusters. Once North America was colonized there was probably little gene flow between there and the bulk of East Asia. This pattern in the tree argues that the ancestors of Native Americans were a separate group of populations prior to the diversification of modern East Asians. The Yakut may be descended from a less diversified ancestral lineage or may be more recently the result of amalgamation of modern East Asians and populations related to the ancestors of American Indians, giving the impression in a tree diagram of a more intermediate origin.
To the degree various simplifying
assumptions are met the branch lengths are in units of t/2Ne,
time in generations divided by twice the effective population size. These
additive trees are unrooted – from the data analyzed there is no information
on where the population ancestral to all modern populations connects to
the tree shown. However, many sets of data indicate that our species arose
in Africa, placing the root among the African populations. Assuming the
root of this tree is among the African populations, the distance along
the tree to each extant population has the same elapsed time – the differences
are in the effective population sizes over that time period. Populations
that have recently been very small and isolated are on long terminal branches,
something particularly noticeable for the Samaritans. But, if the population
is not isolated and/or its history does not fit a model of successive bifurcations
of ancestry, its position in the tree may be misleading if one assumes
an always-branching ancestry. Thus, a population arising from amalgamation
of already diversified lineages would in effect represent a population
with higher effective population size giving a shorter terminal branch.
It would also have more intermediate gene frequencies and tend to be placed
in the tree roughly intermediate between the lineages that founded it.
The Yakut are an excellent example of this possibility.
© 1999 Kenneth K. Kidd, Yale University.
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