Sequence variation in the guillemot (Alcidae: Cepphus) mitochondrial control region and its nuclear homolog

We describe sequence variation in the mitochondrial control region and itsnuclear homolog in three species and seven subspecies of guillemots(Cepphus spp.). Nuclear homologs of the 5' end of the control region werefound in all individuals. Nuclear sequences were approximately 50%divergent from their mitochondrial counterparts and formed a distinctphylogenetic clade; the mitochondrial-nuclear introgression event must havepredated the radiation of Cepphus. As in other vertebrates, the guillemotcontrol region has a relatively conserved central block flanked byhypervariable 5' and 3' ends. Mean pairwise interspecific divergence valuesamong control regions were lower than those in other birds. All individualswere heteroplasmic for the number of simple tandem nucleotide repeats(A(n)C) at the 3' end of the control region. Phylogenetic analyses suggestthat black guillemots are basal to pigeon and spectacled guillemots, butevolutionary relationships among subspecies remain unresolved, possibly dueto incomplete lineage sorting. Describing molecular variation in nuclearhomologs of mitochondrial genes is of general interest in phylogeneticsbecause, if undetected, the homologs may confound interpretations ofmitochondrial phylogenies.