Evolution of the cytochrome b gene of mammals.

Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720.
Journal of Molecular Evolution (Impact Factor: 1.86). 03/1991; 32(2):128-44. DOI: 10.1007/BF02515385
Source: PubMed

ABSTRACT With the polymerase chain reaction (PCR) and versatile primers that amplify the whole cytochrome b gene (approximately 1140 bp), we obtained 17 complete gene sequences representing three orders of hoofed mammals (ungulates) and dolphins (cetaceans). The fossil record of some ungulate lineages allowed estimation of the evolutionary rates for various components of the cytochrome b DNA and amino acid sequences. The relative rates of substitution at first, second, and third positions within codons are in the ratio 10 to 1 to at least 33. For deep divergences (greater than 5 million years) it appears that both replacements and silent transversions in this mitochondrial gene can be used for phylogenetic inference. Phylogenetic findings include the association of (1) cetaceans, artiodactyls, and perissodactyls to the exclusion of elephants and humans, (2) pronghorn and fallow deer to the exclusion of bovids (i.e., cow, sheep, and goat), (3) sheep and goat to the exclusion of other pecorans (i.e., cow, giraffe, deer, and pronghorn), and (4) advanced ruminants to the exclusion of the chevrotain and other artiodactyls. Comparisons of these cytochrome b sequences support current structure-function models for this membrane-spanning protein. That part of the outer surface which includes the Qo redox center is more constrained than the remainder of the molecule, namely, the transmembrane segments and the surface that protrudes into the mitochondrial matrix. Many of the amino acid replacements within the transmembrane segments are exchanges between hydrophobic residues (especially leucine, isoleucine, and valine). Replacement changes at first and second positions of codons approximate a negative binomial distribution, similar to other protein-coding sequences. At four-fold degenerate positions of codons, the nucleotide substitutions approximate a Poisson distribution, implying that the underlying mutational spectrum is random with respect to position.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The systematics of the recent capromyids were studied with phenetics and phylogenetic methods of external and cranial characters and nucleotide sequence of cytochrome b. Analyses of morphological variation and similarity indicate the validity of Mysateles garridoi as a valid species and separate Capromys pilorides from the rest of the species of capromyids. Cranial volume discriminated the taxa and demonstrated low encephalization coefficients that could be interpreted as evolution without selective pressures and/or a primitive character state. Analysis of sequence divergence identified Plagiodontia aedium as the most basal species and discovered a new taxon (a cryptic species). Mysateles was paraphyletic and the new combination Mesocapromys melanurus was proposed. Molecular and morphologic data support the return of M. gundlachi to subspecific level (=M. prehensilis gundlachi) and the validity of five genera, with Mysateles and Mesocapromys being very similar. Divergence times were estimated to be 23 My for Plagiodontia from Geocapromys and between 17 and 19 My for the divergence among Capromys, Mysateles and Mesocapromys. The subspecies of Capromys and Mysateles were estimated to have diverged 2,4 My and 0,8 My, respectively. Morphologic and molecular analyses established phenetics and phylogene-tics relationships that justify the taxonomic arrangement.
    Proceedings of the International Symposium “Insular Vertebrate Evolution: the Palaeontological Approach”, Mallorca; 01/2005
  • [Show abstract] [Hide abstract]
    ABSTRACT: A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of bats from the 4 great desert regions of North America. We inferred a phylogeny of the regional species pool to calculate PCS metrics using community membership data delimited using 3 different methods. We also randomized our phylogeny to determine how reasonable changes to the tree affect PCS metrics. Overall, PCS metrics are quite robust to moderate changes in the phylogeny from which they are calculated. These metrics also are fairly insensitive to our 3 methods of delimiting communities. Additionally, we found that in general, communities are significantly phylogenetically clustered, suggesting habitat filtering has been important in community assembly.
    Journal of Mammalogy 12/2014; 95(6):1240-1253. DOI:10.1644/14-MAMM-A-007 · 2.23 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The Blind Mole Rats of Anatolia (Nannospalax xanthodon (Nordmann, 1840)) are characterised by prolific chromosomal diversification. While the geographic distribution of various cytotypes is well documented, opinions on their taxonomic ranking varies amongst authorities. A partial sequence (630 bp) of mitochondrial cytochrome b gene in 13 Blind Mole Rats from the Konya basin, central Anatolia, which represented three distinct cytotypes (2n = 40, 58, and 60) yielded nine cyt b haplotypes. Phylogenetic reconstructions recognized three well supported lineages which matched diploid number counts. Genetic divergences between cytotypes were high (K2P between 8.16% ± 1.19 and 11.33% ± 1.42) and application of the 2% divergence rate to the net divergence estimates suggests their divergence about 3.84 and 5.43 Mya (95% confidence interval = 1.53-8.19 Mya). If one would rely on genetic operational criteria in species delimitation, there would be little doubt that the three Nannospalax cytotypes analysed in this study belong to distinct allopatric species. Before translating the results into formal taxonomy, more genetic information should be acquired on different Nannospalax cytotypes occupying the eastern Mediterranean.
    Zoology in the Middle East 01/2010; 50:27-34. · 0.52 Impact Factor