The Deep History of Human Populations

By Alan R. Rogers

Departments of Anthropology and Biology, University of Utah

Our lab has developed a new statistical method, called “Legofit,” which uses genetic data to estimate the history of population size, subdivision, and gene flow. Our recent publications have used it to study human evolution over the past 2 million years. Legofit studies the frequencies of “nucleotide site patterns,” which are illustrated in the figure. The solid black lines and arrows represent a network of populations. The dashed and colored lines show one of many possible gene genealogies that might occur at different nucleotide sites within the genome. Upper-case letters refer to populations. X represents an African population (the Yorubans), Y a European population, A Altai Neanderthals, and D Denisovans. S is an unsampled “superarchaic” population that is distantly related to other humans. Lowercase letters at the bottom of the figure label nucleotide site patterns. A nucleotide site exhibits pattern xya if random nucleotides sampled from X, Y, and A carry the derived allele, but those sampled from other populations are ancestral. Site pattern probabilities can be calculated from models of population history, and their frequencies can be estimated from data. Legofit estimates parameters by fitting models to these relative frequencies. 

Nucleotide site patterns contain only a portion of the information available in genome sequence data. This portion, however, is of particular relevance to the study of deep population history. Site pattern frequencies are unaffected by recent population history because they ignore the within population component of variation. This reduces the number of parameters we must estimate and allows us to focus on the distant past. The archaeology of the early middle Pleistocene provided an additional clue. At this time, the “neandersovan” ancestors of Neanderthals and Denisovans separated from the ancestors of modern humans. Modern humans seem to have evolved in Africa, so it seemed plausible that neandersovans separated from an African population and emigrated to Eurasia. Had they done so, they would have encountered the previous “superarchaic” inhabitants of Eurasia, who had been there since about 1.85 million years ago. This suggested a fourth episode of admixture, labeled δ in the figure, from superarchaics into neandersovans.

For more information, see our Spring 2020 newsletter here.

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