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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"DNA was quantified using a spectrophotometer (NanoDrop ND-1000 Spectrophotometer, Thermo Scietific, Wilmington, DE). The cytb gene was amplified using the universal primers: L14724 (5 0 -CGAAGCTTGATATGAAAAAC CATCGTTG-3 0 ) and H15915 (5 0 -GGAATTCATCTC-TCCGGTT TACAAGAC-3 0 ) (Irwin et al., 1991). Amplifications consisted of an initial denaturation at 94 C for 5 min, 30 cycles of denaturation at 93 C for 1 min, annealing at 50 C for 1 min, extension at Figure 1. "
[Show abstract][Hide abstract] ABSTRACT: The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome b and D-loop). Populations in northern Anatolia are divided into two genetic lineages (the "eastern" and "western Black Sea" lineages) by the Kızılırmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations between Myodes populations.
Mitochondrial DNA 11/2015; DOI:10.3109/19401736.2015.1089537 · 1.21 Impact Factor
"12 , AY146613 and AY486544 ) from Trysilelva , and Gyrodactylus lavareti ( AY225306 ) as outgroup . This analysis is based on precise estimates of a molecular clock ( i . e . mutation rates ) ( Kumar , 2005 ) . We used three different mutation rates , one conservative estimate of 2·0% divergence per million years generally sug - gested for mtDNA ( Irwin et al . 1991 ; Bermingham et al . 1997 ; Bernatchez , 2001 ) , and one intermediate mutation rate of 13·7% and one high mutation rate of 20·3% divergence per million years suggested by Meinilä et al . ( 2004 ) based on studies of G . salaris and G . thymalli ."
[Show abstract][Hide abstract] ABSTRACT: The extent of geographic genetic variation is the result of several processes such as mutation, gene flow, selection and drift. Processes that structure the populations of parasite species are often directly linked to the processes that influence the host. Here, we investigate the genetic population structure of the ectoparasite
Žitňan, 1960 (Monogenea) collected from grayling (
L.) throughout the river Glomma, the largest watercourse in Norway. Parts of the mitochondrial dehydrogenase subunit 5 (NADH 5) and cytochrome oxidase I (COI) genes from 309
were analysed to study the genetic variation and investigated the geographical distribution of parasite haplotypes. Three main clusters of haplotypes dominated the three distinct geographic parts of the river system; one cluster dominated in the western main stem of the river, one in the eastern and one in the lower part. There was a positive correlation between pairwise genetic distance and hydrographic distance. The results indicate restricted gene flow between sub-populations of
, most likely due to barriers that limit upstream migration of infected grayling. More than 80% of the populations had private haplotypes, also indicating long-time isolation of sub-populations. According to a molecular clock calibration, much of the haplotype diversity of
in the river Glomma has developed after the last glaciation.
"C o n v e n t i o n a l p h y l o g e n e t i c reconstructions based on single evolutionary markers have failed to recover robust phylogenies (e.g., Irwin et al. 1991, Matthee et al. 2004), while supermatrix approaches are more informative for constructing more reliable trees (e.g., Cognato and Vogler 2001, Murphy et al. 2002). However, our phylogenetic reconstruction was similar to the one provided by a supermatrix comprising five nuclear introns and two mitochondrial genes (Robison and Matthee 2005), and to a previous report of non-Brazilian Sylvilagus based on 12S rDNA data (Halanych and Robinson 1997). "
[Show abstract][Hide abstract] ABSTRACT: A large geographic differentiation has been reported in Sylvilagus brasiliensis based on external
characters of a small number of specimens. A new karyotype with 2n = 40 and FNa = 74
from Rio de Janeiro is herein reported. Phylogenetic analyses based on cytochrome b DNA
of eight samples from the states of Paraíba, Tocantins, Goiás, Minas Gerais and Rio de
Janeiro suggested a strongly structured population. Altogether, molecular and karyotypic data
suggested that the diversity of Sylvilagus in eastern Brazil may be larger than the one reported
in the literature on the basis of external characters.