Basal Eurasians split off ca. 80kya and contributed ca. 10% to EEF

Efficiently inferring the demographic history of many populations with allele count data, by Kamm, Terhorst, Durbin, & Song (2018).


The sample frequency spectrum (SFS), or histogram of allele counts, is an important summary statistic in evolutionary biology, and is often used to infer the history of population size changes, migrations, and other demographic events affecting a set of populations. The expected multipopulation SFS under a given demographic model can be efficiently computed when the populations in the model are related by a tree, scaling to hundreds of populations. Admixture, back-migration, and introgression are common natural processes that violate the assumption of a tree-like population history, however, and until now the expected SFS could be computed for only a handful of populations when the demographic history is not a tree. In this article, we present a new method for efficiently computing the expected SFS and linear functionals of it, for demographies described by general directed acyclic graphs. This method can scale to more populations than previously possible for complex demographic histories including admixture. We apply our method to an 8-population SFS to estimate the timing and strength of a proposed “basal Eurasian” admixture event in human history. We implement and release our method in a new open-source software package momi2.

Inferred model and bootstraps for the 11 population demography described in Section 4. In the foreground (blue) is our point estimate from maximum composite likelihood; in the background (gray) are 300 bootstrap reestimates, which were created by splitting the data into 100 equally sized contiguous blocks, resampling these blocks with replacement, and refitting the model. The y-axis is linear below 5 x 104, then follows a logarithmic scale above 5 x 104.

Link to momi2 software package (GitHub).

Discovered via Iosif Lazaridis.

Featured image, from the article: “An example of a 3-population Moran model. The bottom of the graph corresponds to the present and the top to the past. Population 2 receives admixture from population 3 after splitting from population 1. Other features of the demography include archaic samples in population 1, and various size changes along the edges of this demography.”