Frontiers in Genetics
Frontiers in Genetics
4 years ago

The Empirical Distribution of Singletons for Geographic Samples of DNA Sequences.

Yves Vigouroux, Philippe Cubry, Olivier François
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.

Publisher URL: http://doi.org/10.3389/fgene.2017.00139

DOI: 10.3389/fgene.2017.00139

You might also like
Discover & Discuss Important Research

Keeping up-to-date with research can feel impossible, with papers being published faster than you'll ever be able to read them. That's where Researcher comes in: we're simplifying discovery and making important discussions happen. With over 19,000 sources, including peer-reviewed journals, preprints, blogs, universities, podcasts and Live events across 10 research areas, you'll never miss what's important to you. It's like social media, but better. Oh, and we should mention - it's free.

  • Download from Google Play
  • Download from App Store
  • Download from AppInChina

Researcher displays publicly available abstracts and doesn’t host any full article content. If the content is open access, we will direct clicks from the abstracts to the publisher website and display the PDF copy on our platform. Clicks to view the full text will be directed to the publisher website, where only users with subscriptions or access through their institution are able to view the full article.