Divergence time and population size in the lineage leading to modern humans (Q1903092)

When DNA sequences are available for unlinked, orthologous regions of the genomes in related species, it is possible to estimate the species divergence time and the effective size of ancestral populations simultaneously. We derive several likelihood functions and apply them to DNA sequences that have been determined for humans, chimpanzees, and gorillas. Our maximum likelihood (ML) models are based on three premises. One is the molecular clock of silent substitutions -- the assumption that for a given time span, the number of substitutions along an evolutionary lineage of DNA sequence has the Poisson distribution, and that the intrinsic rate of silent substitutions \((\mu)\) is constant over the genome. The second is no intragenic recombination -- the assumption that a gene or a particular region of the genome is a non-recombined entity. The third is neutrality of silent substitutions -- the assumption that the genealogy of DNA sequences within a population is shaped solely by random sampling drift. We apply four ML models to three situations in which a set of DNA sequences is available for one, two, or three related species.