Gene Genealogies within the Organismal Pedigrees of Random-Mating Populations

Using computer simulations, we generated and analyzed genetic distances among selectively neutral haplotypes transmitted through gene genealogies with random-mating organismal pedigrees.Constraints and possible biases on haplotype distances due to correlated ancestry were evaluated by comparing observed distributions of distances to those predicted from an inbreeding theory that assumes independence among haplotype pairs.Results suggest that: I) mean time to common ancestry ofneutral haplotypes can be a reasonably good predictor ofevolutionary effective population size; 2) the nonindependence ofhaplotype paths ofdescent within a given gene genealogy typically produces significant departures from the theoretical probability distributions ofhaplotype distances; 3) frequency distributions of distances between haplotypes drawn from "replicate" organismal pedigrees or from multiple unlinked loci within an organismal pedigree exhibit very close agreement with the theory for independent haplotypes.These results are relevant to interpretations ofcurrent molecular data on genetic distances among nonrecombining haplotypes at either nuclear or cytoplasmic loci.