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Evolutionary genetics of Death Valley pupfish populations: mitochondrial DNA sequence variation and population structure

The pupfishes of Death Valley (genus: Cyprinodon) are a classic example of rapid (postPleistocene) allopatric divergence with several populations exhibiting striking morphological, physiological, and behavioural differences. However, genetic changes accompanying or causing this divergence have been poorly resolved and/or difficult to detect. In order to investigate the phylogeography of the system and infer historical effective population sizes, mtDNA sequence variation was assessed within and among populations. In total, mtDNA D-loop sequences revealed 11 haplotypes among 278 individuals from 16 populations. Genetic diversity within populations was generally low (1–3 haplotypes per population) suggesting relatively small effective population sizes. Most variation occurred among populations, resulting in extensive genetic structure. The genealogical relationships of mtDNA haplotypes were determined by a combined phylogenetic analysis of both D-loop and ND2 sequences. These relationships revealed that the present distribution of haplotypes in Death Valley has probably resulted from stochastic, and in some cases, incomplete sorting of ancestral variation. The presence of highly divergent haplotypes in some populations may indicate that ancestral population sizes were substantially larger, perhaps rivalling population sizes observed in contemporary coastal pupfish species. In contrast, other Death Valley populations of equal contemporary size appeared monomorphic suggesting historical genetic bottleneck events. The Death Valley pupfishes provide an important example of the limitations inherent in defining evolutionarily significant units (ESUs) for conservation purposes based on mtDNA sequence variation alone.