Apr 24, 2013

Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach

Genetics
Sara SheehanYun S Song

Abstract

Throughout history, the population size of modern humans has varied considerably due to changes in environment, culture, and technology. More accurate estimates of population size changes, and when they occurred, should provide a clearer picture of human colonization history and help remove confounding effects from natural selection inference. Demography influences the pattern of genetic variation in a population, and thus genomic data of multiple individuals sampled from one or more present-day populations contain valuable information about the past demographic history. Recently, Li and Durbin developed a coalescent-based hidden Markov model, called the pairwise sequentially Markovian coalescent (PSMC), for a pair of chromosomes (or one diploid individual) to estimate past population sizes. This is an efficient, useful approach, but its accuracy in the very recent past is hampered by the fact that, because of the small sample size, only few coalescence events occur in that period. Multiple genomes from the same population contain more information about the recent past, but are also more computationally challenging to study jointly in a coalescent framework. Here, we present a new coalescent-based method that can efficiently in...Continue Reading

Mentioned in this Paper

In Silico
Genome
Genetics, Population
Genomics
Underpopulation
Chromosomes
Probability
Markov Chains
Genome, Human
Sampling - Surgical Action

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