Distinguishing migration from isolation using the variance of pairwise differences (Q1918060)

In a recent study of mitochondrial DNA in the threespine stickleback, \textit{G. Ortí} et al. [Evolution 48, 608-622 (1994)] sequenced 747 base pairs of the cytochrome \(b\) gene in 36 individuals from samples covering much of the range of this widespread species. This revealed the existence of two major clades, one comprising mainly western Pacific samples (Japan) and the other comprising mainly northeastern Pacific samples (Alaska and British Columbia). Nested within the northeastern Pacific clade was a group containing samples from the northern Atlantic and one haplotype from Los Angeles, California. The western and northeastern Pacific clades were separated by a minimum of 18 substitutions, yet one haplotype from British Columbia was identical to a common Japanese haplotype and two Alaskan samples clustered with the western Pacific clade. From this pattern, Ortí et al. inferred two major demographic events: a recent origin of Atlantic stickleback populations from a lineage resembling the Los Angeles samples, and an ancient isolation and divergence between western and northeastern Pacific sticklebacks followed by secondary contact. The present analysis focuses only on the latter comparison; the sample from Los Angeles and those from the Atlantic are omitted. Specifically, the hypothesis that the patterns of divergence within the Pacific are due solely to the isolation and subsequent divergence of western and eastern populations is tested. Under this hypothesis, haplotypes found in both areas represent retained ancestral lineages. Ortí et al. did not consider this hypothesis, but the result of the test is interesting. It illustrates the application of the method developed here and contributes something to our understanding of stickleback historical biogeography in that one hypothesis, at least, can be rejected with statistical confidence.