Evolution of the cytochrome b gene of mammals.
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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ABSTRACT: Perccottus glenii (also called the Amur sleeper) is a freshwater invasive fish species which has rapidly spread during the last two decades in many European countries. On Romanian territory it has been registered since 2001, when it was identified in Suceava River from the Siret basin. Since very little genetic data has been obtained so far for the invasive populations of Perccottus glenii, this study addresses this issue, and is based on a case study for the Siret River. 25 individuals from this area were subjected to genetic analysis, aiming to describe the nucleotide sequence for the entire cytochrome b gene, and to identify the haplotypes diversity within the sampled population. The DNA was isolated using the phenol: chloroform: isoamyl alcohol (25:24:1) protocol (Sambrook et al., 1989), followed by a target DNA fragment multiplication through the PCR reaction. The PCR products were purified and sequenced. For the 25 analysed samples only 2 haplotypes were identified. The results showed a low level of genetic variability for the Perccottus glenii population from the Siret River, which sustains the