Molecular Biology and Evolution, Vol 11, 341-356, Copyright © 1994 by Society for Molecular Biology and Evolution
RW Slade, C Moritz and A Heideman
Phylogenetic analyses of closely related species should use information
from multiple, independent genes with relatively high rates of sequence
evolution. To investigate species for which there are few prior sequence
data for single-copy nuclear (scnDNA) genes, primers for gene amplification
can be designed to highly conserved regions of exons in order to amplify
both coding (exons) and noncoding (introns) sequences. We have explored
this approach in a phylogenetic analysis of six species of pinnipeds that,
together with terrestrial carnivore outgroups, encompass divergence times
< or = 40-50 Mya. We sequenced one intron from each of the aldolase A
(ALD-A), aldolase C (ALD-C), and histone H2AF genes; one exon from the
major-histocompatibility-complex DQA gene; a H2AF processed pseudogene (psi
H2AF); and, for comparison with the nuclear genes, the 5' portion of the
mitochondrial DNA (mtDNA) control region. The pinniped psi H2AF genes were
found to be of limited use because they were paralogous with the gene in
the outgroup. The rate of silent substitution in scnDNA (primarily introns)
was 5-10-fold lower than that for mtDNA control region I, and scnDNA
sequence divergence increased linearly with time < or = 40-50 Mya.
Alleles at three polymorphic scnDNA loci (ALD-A, H2AF, and DQA) in the
southern elephant seal were paraphyletic with respect to the allele from
the closely related northern elephant seal, while the more numerous mtDNA
alleles were monophyletic. This we attribute to the consequences of a
higher mutation rate rather than to a lower effective population size of
mtDNA compared with scnDNA. Within the short (i.e., < 500-bp) sequences
of individual scnDNA sequences, phylogenetically informative variation was
insufficient to obtain robust phylogenies. However, the combined scnDNA
sequences produced a well-supported phylogeny congruent with that derived
from mtDNA. This analysis illustrates the high resolution of mtDNA
sequences compared with a similar length of scnDNA sequence, but it also
demonstrates the utility of combining information from multiple short
scnDNA sequences obtained using broadly applicable primers.
ORIGINAL ARTICLE
Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny
Department of Zoology, University of Queensland.
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