F. L. Mendez; G. D. Poznik; C. D. Bustamante; 1000 Genomes Project Consortium
Department of Genetics, Stanford University, Stanford, CA.
Evolutionary processes affecting a population influence gene genealogies across the genome. Coalescent theory provides the mathematical framework to connect realized genealogies to the underlying evolutionary processes. However, in most cases, information about the genealogies is obtained only indirectly through the observation of genetic variation. Therefore, in general, very limited information about any individual locus is available. As the longest non-recombining portion of the human genome, the Y chromosome accumulates mutations relatively quickly. When large amounts of sequence are used, the Y chromosome provides an unparalleled ability to resolve the structure and coalescence times of its genealogy. Because patterns of variation in the Y chromosome are only influenced by processes affecting men, they can be used to study both demographic and social phenomena. The 1000 Genomes Project includes whole Y-chromosome data from more than 1000 men and has an extensive representation of most lineages that have experienced recent massive expansions in size. Though the dynamics of population growth have likely changed over time, we are more interested in the growth rates at the times of these rapid expansions than on an average effect. To study this, we have developed a new method that takes advantage of the temporal resolution provided by Y-chromosome data and of historical data, while accounting for the uncertainties associated with the coalescent and mutational processes. We estimate the growth rates for several branches of the Y-chromosome tree, including those in Europe, sub-Saharan Africa and South Asia. We estimate that several lineages within the European R1b, sub-Saharan African E1b, and South Asian R1a haplogroups experienced growth rates of at least 20-60% per generation at the onset of their massive expansions, some 3-5 thousand years ago. These high growth rates are comparable to those experienced by human populations during the 20th century. However, we find that most observed genealogies are unlikely to be the result of whole population expansion or of natural selection.