Back to Search
Start Over
Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny
- Source :
- Molecular Biology and Evolution.
- Publication Year :
- 1994
- Publisher :
- Oxford University Press (OUP), 1994.
-
Abstract
- 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.
- Subjects :
- Mitochondrial DNA
Nuclear gene
Pseudogene
Carnivora
Molecular Sequence Data
Biology
DNA, Mitochondrial
HLA-DQ alpha-Chains
Histones
Molecular evolution
Phylogenetics
Fructose-Bisphosphate Aldolase
HLA-DQ Antigens
Sequence Homology, Nucleic Acid
Genetics
Animals
Humans
Molecular Biology
Gene
Phylogeny
Ecology, Evolution, Behavior and Systematics
Cell Nucleus
mtDNA control region
Polymorphism, Genetic
Base Sequence
Phylogenetic tree
Genetic Variation
DNA
Introns
Caniformia
Genes
Pseudogenes
Subjects
Details
- ISSN :
- 15371719
- Database :
- OpenAIRE
- Journal :
- Molecular Biology and Evolution
- Accession number :
- edsair.doi.dedup.....6b04b79d543cbe466495677b9bc242d4