Article

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: 1.68). 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
    • "genenames.org). MT-CYB DNA was PCR amplified with primers L14724 (Irwin et al. 1991) and citb REV (Casado et al. 2010), with a pre‑denaturation step at 94°C for 2 min; 35 cycles of denaturation at 94°C for 1 min, annealing at 50°C for 1 min, extension at 72°C for 1 min 30 s, and final extension of 72°C for 5 min. VWF was PCR amplified with e28‑vWF F104 and e28‑vWF R1141 (Voss and Jansa 2009), with a pre‑denaturation step at 94°C for 2 min; 35 cycles of denaturation at 94°C for 45 s, annealing at 55°C for 30 s, extension at 72°C for 1 min 30 s, and final extension of 72°C for 10 min. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Here we report the first record of genus Cryptonanus in the state of Rio de Janeiro, Brazil. One specimen (MZUSP35409) was captured in an Atlantic Forest fragment and was identified by morphological characters and molecular analysis using cytochrome-b (MT-CYB) and von Willebrand Factor (VWF). Phylogenetic reconstructions based on VWF sequences positioned our specimen into the genus Cryptonanus, and the shortest genetic distance of MT-CYB was estimated between our specimen and an undescribed specimen from Piauí. Our record increases the genus’ geographic range approximately 350 km from Cotia and Ibiúna municipalities, São Paulo. The genus Cryptonanus remains taxonomically poorly understood.
    Full-text · Article · Jan 2016 · Check List
  • Source
    • "genenames.org). MT-CYB DNA was PCR amplified with primers L14724 (Irwin et al. 1991) and citb REV (Casado et al. 2010), with a pre‑denaturation step at 94°C for 2 min; 35 cycles of denaturation at 94°C for 1 min, annealing at 50°C for 1 min, extension at 72°C for 1 min 30 s, and final extension of 72°C for 5 min. VWF was PCR amplified with e28‑vWF F104 and e28‑vWF R1141 (Voss and Jansa 2009), with a pre‑denaturation step at 94°C for 2 min; 35 cycles of denaturation at 94°C for 45 s, annealing at 55°C for 30 s, extension at 72°C for 1 min 30 s, and final extension of 72°C for 10 min. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Here we report the first record of genus Cryptonanus in the state of Rio de Janeiro, Brazil. One specimen (MZUSP35409) was captured in an Atlantic Forest fragment and was identified by morphological characters and molecular analysis using cytochrome-b (MT-CYB) and von Willebrand Factor (VWF). Phylogenetic reconstructions based on VWF sequences positioned our specimen into the genus Cryptonanus, and the shortest genetic distance of MT-CYB was estimated between our specimen and an undescribed specimen from Piauí. Our record increases the genus’ geographic range approximately 350 km from Cotia and Ibiúna municipalities, São Paulo. The genus Cryptonanus remains taxonomically poorly understood.
    Full-text · Article · Jan 2016 · Check List
    • "DNA of Atlantoxerus getulus (voucher PMS 19301; Supplemental Appendix 2) was extracted using a QIAamp ® DNA Mini kit (Qiagen, Valencia, CA, USA), following the manufacturer's conditions. Cytb was amplified using the trans-mammalian primers L14727-SP and H15497-SP (Irwin et al. 1991). Amplification was performed using a 20 μl reaction containing 2.5 mm MgCl 2 , 0.5 μm of forward and reverse primer, 0.2 mm of dNTPs and one unit of Fermentas Taq in the supplied ammonium buffer. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Bristly ground squirrels Xerini are a small rodent tribe of six extant species. Despite a dense fossil record the group was never diverse. Our phylogenetic reconstruction, based on the analysis of cytochrome
    No preview · Article · Dec 2015 · Mammalia
Show more