MULTIPLE NUCLEAR-GENE PHYLOGENIES - APPLICATION TO PINNIPEDS AND COMPARISON WITH A MITOCHONDRIAL-DNA GENE PHYLOGENY

Phylogenetic analyses of closely related species should use informatio n from multiple, independent genes with relatively high rates of seque nce evolution. To investigate species for which there are few prior se quence data for single-copy nuclear (scnDNA) genes, primers for gene a mplification can be designed to highly conserved regions of exons in o rder to amplify both coding (exons) and noncoding (introns) sequences. We have explored this approach in a phylogenetic analysis of six spec ies of pinnipeds that, together with terrestrial carnivore outgroups, encompass divergence times less than or equal to 40-50 Mya. We sequenc ed one intron from each of the aldolase A (ALD-A), aldolase C (ALD-C), and histone H2AF genes; one exon from the major-histocompatibility-co mplex DQA gene; a H2AF processed pseudogene (psi H2AF); and, for compa rison with the nuclear genes, the 5' portion of the mitochondrial DNA (mtDNA) control region. The pinniped psi H2AF genes were found to be o f limited use because they were paralogous with the gene in the outgro up. The rate of silent substitution in scnDNA (primarily introns) was 5-10-fold lower than that for mtDNA control region I, and scnDNA seque nce divergence increased linearly with time less than or equal to 40-5 0 Mya. Alleles at three polymorphic scnDNA loci (ALD-A, H2AF, and DQA) in the southern elephant seal were paraphyletic with respect to the a llele from the closely related northern elephant seal, while the more numerous mtDNA alleles were monophyletic. This we attribute to the con sequences of a higher mutation rate rather than to a lower effective p opulation size of mtDNA compared with scnDNA. Within the short (i.e., <500-bp) sequences of individual scnDNA sequences, phylogenetically in formative variation was insufficient to obtain robust phylogenies. How ever, the combined scnDNA sequences produced a well-supported phylogen y congruent with that derived from mtDNA. This analysis illustrates th e high resolution of mtDNA sequences compared with a similar length of scnDNA sequence, but it also demonstrates the utility of combining in formation from multiple short scnDNA sequences obtained using broadly applicable primers.