Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate
| Autor: | Benjamin C. Jackson, Henry J Barton, Kai Zeng |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
Mutation rate mutation rate X Chromosome comparing sex chromosomes and autosomes Population inferring demography Locus (genetics) Biology 010603 evolutionary biology 01 natural sciences Statistical power 03 medical and health sciences Effective population size Methods Genetics Animals education Molecular Biology Ecology Evolution Behavior and Systematics 030304 developmental biology Population Density 0303 health sciences education.field_of_study Genome Autosome Models Genetic Population size Genetic Techniques sex ratio evolution Drosophila simulans effective population size Sex ratio Demography |
| Zdroj: | Molecular Biology and Evolution |
| ISSN: | 1537-1719 0737-4038 |
| DOI: | 10.1093/molbev/msy212 |
| Popis: | It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variation in Ne and u between loci. These methods rely on either polymorphism data alone or both polymorphism and divergence data. In addition to inferring demography, we can use the methods to study a variety of questions: 1) comparing sex chromosomes with autosomes (for finding evidence for male-driven evolution, an unequal sex ratio, or sex-biased demographic changes) and 2) analyzing multilocus data from within autosomes or sex chromosomes (for studying determinants of variability in Ne and u). Simulations suggest that the methods can provide accurate parameter estimates and have substantial statistical power for detecting difference in Ne and u. As an example, we use the methods to analyze a polymorphism data set from Drosophila simulans. We find clear evidence for rapid population expansion. The results also indicate that the autosomes have a higher mutation rate than the X chromosome and that the sex ratio is probably female-biased. The new methods have been implemented in a user-friendly package. |
| Databáze: | OpenAIRE |
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