The Empirical Distribution of Singletons for Geographic Samples of DNA Sequences
Résumé
Rare variants are important for drawing inference about past demographic events in
a species history. A singleton is a rare variant for which genetic variation is carried by
a unique chromosome in a sample. How singletons are distributed across geographic
space provides a local measure of genetic diversity that can be measured at the individual
level. Here, we define the empirical distribution of singletons in a sample of chromosomes
as the proportion of the total number of singletons that each chromosome carries, and
we present a theoretical background for studying this distribution. Next, we use computer
simulations to evaluate the potential for the empirical distribution of singletons to provide
a description of genetic diversity across geographic space. In a Bayesian framework,
we show that the empirical distribution of singletons leads to accurate estimates of the
geographic origin of range expansions. We apply the Bayesian approach to estimating
the origin of the cultivated plant species Pennisetum glaucum [L.] R. Br. (pearl millet) in
Africa, and find support for range expansion having started from Northern Mali. Overall,
we report that the empirical distribution of singletons is a useful measure to analyze results
of sequencing projects based on large scale sampling of individuals across geographic
space.
Domaines
Génétique des populations [q-bio.PE]
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