Intercoalescence Time Distribution of Incomplete Gene Genealogies in Temporally Varying Populations, and Applications in Population Genetic Inference

摘要: Summary Tracing back to a specific time T in the past, genealogy of sample haplotypes may not have reached their common ancestor and leave m lineages extant. For such an incomplete truncated at distribution expectation intercoalescence times conditional on are derived exact form this paper for populations deterministically time-varying sizes, specifically, growing exponentially. The can be integrated coalescent-based joint allele frequency spectrum (JAFS) theory, is useful population genetic inference from large-scale genomic data, without relying computationally intensive approaches, as importance sampling Markov Chain Monte Carlo (MCMC) methods. several important parameters demonstrated: quantifying growth rate onset time, estimating number ancestral ancient time. Simulation studies confirm validity derivation statistical efficiency methods using distribution. Two examples real data given show European NIEHS Environmental Genome Project, 31 mitochondrial genomes Tibetan populations.