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We describe sequence variation in the mitochondrial control region and its nuclear homolog in three species and seven subspecies of guillemots (Cepphus spp.). Nuclear homologs of the 5' end of the control region were found in all individuals. Nuclear sequences were approximately 50% divergent from their mitochondrial counterparts and formed a distinct phylogenetic clade; the mitochondrial-nuclear introgression event must have predated the radiation of Cepphus. As in other vertebrates, the guillemot control region has a relatively conserved central block flanked by hypervariable 5' and 3' ends. Mean pairwise interspecific divergence values among control regions were lower than those in other birds. All individuals were heteroplasmic for the number of simple tandem nucleotide repeats (A(n)C) at the 3' end of the control region. Phylogenetic analyses suggest that black guillemots are basal to pigeon and spectacled guillemots, but evolutionary relationships among subspecies remain unresolved, possibly due to incomplete lineage sorting. Describing molecular variation in nuclear homologs of mitochondrial genes is of general interest in phylogenetics because, if undetected, the homologs may confound interpretations of mitochondrial phylogenies.

Abstract.-Although phylogenetic hypotheses can provide insights into mechanisms of evolution, their utility is limited by our inability to differentiate simultaneous speciation events (hard polytomies) from rapid cladogenesis (soft polytomies). In the present paper, we tested the potential for statistical power analysis to differentiate between hard and soft polytomies in molecular phylogenies. Classical power analysis typically is used a priori to determine the sample size required to detect a particular effect size at a particular level of significance («) with a certain power (1 -~). A posteriori, power analysis is used to infer whether failure to reject a null hypothesis results from lack of an effect or from insufficient data (i.e., low power). We adapted this approach to molecular data to infer whether polytomies result from simultaneous branching events or from insufficient sequence information. We then used this approach to determine the amount of sequence data (sample size) required to detect a positive branch length (effect size). A worked example is provided based on the auklets (Charadriiformes: Alcidae), a group of seabirds among which relationships are represented by a polytomy, despite analyses of over 3000 bp of sequence data. We demonstrate the calculation of effect sizes and sample sizes from sequence data using a normal curve test for difference of a proportion from an expected value and a t-test for a difference of a mean from an expected value. Power analyses indicated that the data for the auklets should be sufficient to differentiate speciation events that occurred at least 100,000 yr apart (the duration of the shortest glacial and interglacial events of the Pleistocene), 2.6 million years ago.

We surveyed population-level sequence variation in part of the mitochondrial control region for three species including eight subspecies of Cepphus guillemots (Charadriiformes: Alcidae) to test specific predictions about mechanisms of population differentiation. We found that sequences of spectacled guillemots (C. carbo) were more closely related to those of pigeon guillemots (C. columba; both found in the Pacific Ocean) than to those of black guillemots (C. grylle; Arctic and Atlantic Oceans), despite dissimilarities in plumage between spectacled guillemots and the other species. Distributions of species and timing of divergence events suggest that speciation involved allopatric and microallopatric populations isolated by Pleistocene glaciers. Control region sequences were significantly differentiated among populations within species and suggest that gene flow is low; however, populations are probably not in genetic equilibrium, so these results probably reflect historical isolation of colonies. In contrast, phylogenetic relationships among sequences within species were poorly resolved, probably because of a combination of incomplete lineage sorting and contemporary gene flow. Indices of genetic diversity provided no suggestion of recent bottlenecks in most populations, although two populations apparently underwent recent severe bottlenecks. Genetic divergence among populations was not correlated with geographic distance, which argues against isolation by distance. Results of these analyses, combined with breeding distributions and timing of divergence events, suggest that populations diverged during isolation in glacial refugia. Our results are consistent with earlier hypotheses posed by Storer and Udvardy.