title: The impact of accelerating faster than exponential population growth on genetic variation.
abstract: Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models' effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times.
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109.
authors.forename: Mark
authors.initials: M
authors.lastname: Reppell
authors.forename: Michael
authors.initials: M
authors.lastname: Boehnke
authors.forename: Sebastian
authors.initials: S
authors.lastname: Zöllner
mesh_terms: D003198:Computer Simulation; D014644:Genetic Variation; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D011156:Population Density; D011158:Population Growth; D012984:Software
keywords: coalescent; faster than exponential; population growth; rare variation