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.

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Available from: David M Irwin, Aug 28, 2015
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    • "Eleven newly collected specimens of the Laotian rock rat were included in this study, nine from Phong Nha–Ke Bang National Park and two from Hin Nam No National Biodiversity Conservation Area, eastern Lao PDR (Fig. 1). We sequenced the complete cytochrome b for all 11 samples using five primers (Irwin et al. 1991). Additional 16 published sequences of the partial and complete cytochrome b from individuals of populations around Khammouan Limestone National Biodiversity Conser­ vation Area (Jenkins et al. 2005; Huchon et al. 2007; Rivière­Dobigny et al. 2011) and from distinct clades G and H, whose samples were collected in Laos (Nicolas et al. 2012), were also incorporated in the analyses. "
    Mammal Study 06/2015; 40(2):109-114. DOI:10.3106/041.040.0206 · 0.43 Impact Factor
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    • "Mitochondrial DNA was extracted and purified using a Wizard Miniprep kit (Promega, Madison, Wisconsin), whereas total genomic DNA was extracted from liver using DNeasy Blood and Tissue kits (Qiagen, Valencia, California) following the method of Smith and Patton (1999). The complete mitochondrial Cytb gene (1,143 bp) was amplified following methods outlined in Bradley et al. (2007) and Tiemann-Boege et al. (2000) using primers MVZ05 (Smith and Patton 1993), H15915 (Irwin et al. 1991), and CB40 (Hanson and Bradley 2008). Intron 2 of the alcohol dehydrogenase gene (Adh1-I2, 598 bp) was amplified following the methods of Amman et al. (2006) using primers 2340-I, 2340-II, Exon II-F, and Exon III-R. "
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    ABSTRACT: The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.
    Journal of Mammalogy 05/2015; DOI:10.1093/jmammal/gyv067 · 2.23 Impact Factor
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    • "Among the protein-encoding genes in mitogenomes, cytochrome b (cytb) sequences have been used extensively in the molecular phylogeny of eutherians since (Irwin et al., 1991). Agnarsson and colleagues advocated using cytb sequences in reconstructing the eutherian tree (Agnarsson and May-Collado, 2008; Agnarsson et al., 2010, 2011; Kuntner et al., 2010), and their studies showed that even a single cytb gene can perform unexpectedly well in reconstructing the eutherian tree if the taxon sampling is sufficiently dense. "
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