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Mitochondrial Cytochrome B (mitochondrial + cytochrome_b)
Terms modified by Mitochondrial Cytochrome B Selected AbstractsNo genetic differentiation between geographically isolated populations of Clarias macrocephalus Günther in Malaysia revealed by sequences of mtDNA Cytochrome b and D-loop gene regionsJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2010A. K. Nazia Summary In the present study, we assessed the genetic variation of three Clarias macrocephalus Günther populations collected from Kedah, Perlis and Kelantan (Peninsular Malaysia) using sequences of partial mitochondrial cytochrome b (Cyt b) and D-loop genes. A total of 57 individuals were sequenced and 1470 bp were obtained (1053 bp Cyt-b; 417 bp D-loop). The analysis revealed 21 haplotypes based on 81 polymorphic sites. Nucleotide diversity (,) was 0.003 in all populations while haplotype diversity ranged from 0.657 to 0.765. No significant genetic differentiation among the three populations was observed. Nevertheless, a number of private haplotypes was discovered, providing valuable information for selective breeding programs. [source] Adaptive radiation in African weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and morphological approachJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2007P. G. D. FEULNER Abstract We combined multiple molecular markers and geometric morphometrics to revise the current taxonomy and to build a phylogenetic hypothesis for the African weakly electric fish genus Campylomormyrus. Genetic data (2039 bp DNA sequence of mitochondrial cytochrome b and nuclear S7 genes) on 106 specimens support the existence of at least six species occurring in sympatry. We were able to further confirm these species by microsatellite analysis at 16 unlinked nuclear loci and landmark-based morphometrics. We assigned them to nominal taxa by comparisons to type specimens of all Campylomormyrus species recognized so far. Additionally, we showed that the shape of the elongated trunk-like snout is the major source of morphological differentiation among them. This finding suggests that the radiation of this speciose genus might have been driven by adaptation to different food sources. [source] Phylogenetic relationships of the newly described species Chondrostoma olisiponensis (Teleostei: Cyprinidae)JOURNAL OF FISH BIOLOGY, Issue 4 2010H. F. Gante Phylogenies were generated using mitochondrial cytochrome b and nuclear ß-actin gene DNA sequences to infer the phylogenetic relationships of the newly described Chondrostoma olisiponensis. Results indicate that the species is monophyletic with species of the lemmingii -group in mtDNA phylogenies, while it is monophyletic with species of the arcasii -group in the nuclear ß-actin trees. This is in agreement with the morphological resemblance of C. olisiponensis to both species groups. Results from nuclear but not mitochondrial DNA indicate that one population could be currently hybridizing with sympatric Chondrostoma lusitanicum. Based on a relaxed clock calibration of cytochrome b, it is estimated that C. olisiponensis split 12·5,7·9 million years ago (middle,upper Miocene) from its most recent ancestor, which coincides with a period of endorrheism in the Iberian Peninsula. [source] Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographical breaks congruent with fish community boundaries?MOLECULAR ECOLOGY, Issue 19 2009JARED B. LEE Abstract One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to determine if phylogeographical breaks in this species were congruent with previously defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we might find four clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographical regions. We generated DNA sequence data (mitochondrial cytochrome b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analysed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow and effective population size. Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographical community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not predicted by community province boundaries. [source] Phylogeography of the North American red fox: vicariance in Pleistocene forest refugiaMOLECULAR ECOLOGY, Issue 12 2009KEITH B. AUBRY Abstract Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome b (354 bp) gene and D-loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome b gene produced two clades that diverged c. 400 000 years before present (bp): a Holarctic and a Nearctic clade. D-loop analyses of the Nearctic clade indicated three distinct subclades (, 99% Bayesian posterior probability); two that were more recently derived (rho estimate c. 20 000 bp) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate c. 45 000 bp) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300 000,130 000 bp), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100 000,10 000 bp). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long-term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct. [source] Testing models of diversification in mice in the Abrothrix olivaceus/xanthorhinus complex in Chile and ArgentinaMOLECULAR ECOLOGY, Issue 2 2001M. F. Smith Abstract Samples of the forest-dwelling mouse Abrothrix olivaceus and the steppe-dwelling A. xanthorhinus across a transect between 45 and 47° S in southern Chile were analysed using the mitochondrial cytochrome b (cyt b) sequence, substantially adding to the data presented previously for these taxa from Argentina and Chile. The level of variation in the cyt b sequence throughout the entire olivaceus/xanthorhinus complex is comparable to that seen within a single species in many South American sigmodontine rodents, consistent with a previous conclusion that both taxa are sub-species of A. olivaceus. Haplotypes of xanthorhinus have not yet achieved reciprocal monophyly relative to those of olivaceus. We evaluate competing hypotheses for the morphological divergence of xanthorhinus and olivaceus by allopatry in Pleistocene refuges versus postglacial diversification across ecological gradients. Two contrasting patterns are predicted for plots of the distribution of pairwise genetic differences, depending on whether the taxa diverged in allopatric refuges or through selection across a gradient. Examples of both modes of diversification are found in this complex. [source] Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genesMOLECULAR ECOLOGY RESOURCES, Issue 5 2007RAFAEL G. SEVILLA Abstract This report describes a set of 21 polymerase chain reaction primers and amplification conditions developed to barcode practically any teleost fish species according to their mitochondrial cytochrome b and nuclear rhodopsin gene sequences. The method was successfully tested in more than 200 marine fish species comprising the main Actinopterygii family groups. When used in phylogenetic analyses, its combination of two genes with different evolutionary rates serves to identify fish at the species level. We provide a flow diagram indicating our validated polymerase chain reaction amplification conditions for barcoding and species identification applications as well as population structure or haplotyping analyses, adaptable to high-throughput analyses. [source] Mechanisms influencing the evolution of resistance to Qo inhibitor fungicides,,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 9 2002Ulrich Gisi Abstract Fungicides inhibiting the mitochondrial respiration of plant pathogens by binding to the cytochrome bc1 enzyme complex (complex III) at the Qo site (Qo inhibitors, QoIs) were first introduced to the market in 1996. After a short time period, isolates resistant to QoIs were detected in field populations of a range of important plant pathogens including Blumeria graminis Speer f sp tritici, Sphaerotheca fuliginea (Schlecht ex Fr) Poll, Plasmopara viticola (Berk & MA Curtis ex de Bary) Berl & de Toni, Pseudoperonospora cubensis (Berk & MA Curtis) Rost, Mycosphaerella fijiensis Morelet and Venturia inaequalis (Cooke) Wint. In most cases, resistance was conferred by a point mutation in the mitochondrial cytochrome b (cyt b) gene leading to an amino-acid change from glycine to alanine at position 143 (G143A), although additional mutations and mechanisms have been claimed in a number of organisms. Transformation of sensitive protoplasts of M fijiensis with a DNA fragment of a resistant M fijiensis isolate containing the mutation yielded fully resistant transformants, demonstrating that the G143A substitution may be the most powerful transversion in the cyt b gene conferring resistance. The G143A substitution is claimed not to affect the activity of the enzyme, suggesting that resistant individuals may not suffer from a significant fitness penalty, as was demonstrated in B graminis f sp tritici. It is not known whether this observation applies also for other pathogen species expressing the G143A substitution. Since fungal cells contain a large number of mitochondria, early mitotic events in the evolution of resistance to QoIs have to be considered, such as mutation frequency (claimed to be higher in mitochondrial than nuclear DNA), intracellular proliferation of mitochondria in the heteroplasmatic cell stage, and cell to cell donation of mutated mitochondria. Since the cyt b gene is located in the mitochondrial genome, inheritance of resistance in filamentous fungi is expected to be non-Mendelian and, therefore, in most species uniparental. In the isogamous fungus B graminis f sp tritici, crosses of sensitive and resistant parents yielded cleistothecia containing either sensitive or resistant ascospores and the segregation pattern for resistance in the F1 progeny population was 1:1. In the anisogamous fungus V inaequalis, donation of resistance was maternal and the segregation ratio 1:0. In random mating populations, the sex ratio (mating type distribution) is generally assumed to be 1:1. Therefore, the overall proportion of sensitive and resistant individuals in unselected populations is expected to be 1:1. Evolution of resistance to QoIs will depend mainly on early mitotic events; the selection process for resistant mutants in populations exposed to QoI treatments may follow mechanisms similar to those described for resistance controlled by single nuclear genes in other fungicide classes. It will remain important to understand how the mitochondrial nature of QoI resistance and factors such as mutation, recombination, selection and migration might influence the evolution of QoI resistance in different plant pathogens. © 2002 Society of Chemical Industry [source] A molecular diagnostic for identifying central African forest artiodactyls from faecal pelletsANIMAL CONSERVATION, Issue 1 2010S. Ntie Abstract Small to medium-sized central African forest artiodactyls constitute a diverse yet heavily hunted group composed primarily of species within the genera Cephalophus, Neotragus, Tragelaphus and Hyemoschus. Of these genera, Cephalophus is the richest with as many as seven sympatric species known to occur in central African forests. However, differentiating species from their faeces or from tissue where the whole carcass is unavailable is very difficult. In order to develop a robust molecular diagnostic for species identification, a database of mitochondrial cytochrome b (553 bp) and control region (,675 bp) sequences was compiled from all forest Cephalophus species and other similarly sized, sympatric Tragelaphus, Neotragus and Hyemoschus species. Reference phylogenies from each marker were then used to recover the identity of sequences obtained from unknown faecal samples collected in the field. Results were then compared to determine which region best recovered species identity with the highest statistical support. Restriction fragment length polymorphisms (RFLPs) were also assessed as an alternative method for rapid species identification. Of the methods examined, tree-based analyses built on a geographically comprehensive database of control region sequences was the best means of reliably recovering species identity from central African duikers. However, three sister taxa appear indistinguishable (Cephalophus callipygus, Cephalophus ogilbyi and Cephalophus weynsi) and not all species were monophyletic. This lack of monophyly may be due to incomplete lineage sorting commonly observed in recently derived taxa, hybridization or the presence of nuclear translocated copies of mitochondrial DNA. The high level of intra-specific variation and lack of robust species-specific diagnostic sites made an RFLP-based approach to duiker species identification difficult to implement. The tree-based control region diagnostic presented here has many important applications including fine-scale mapping of species distributions, identification of confiscated tissue and environmental impact assessments. [source] Combining genetic and ecological data to assess the conservation status of the endangered Ethiopian walia ibexANIMAL CONSERVATION, Issue 2 2009B. Gebremedhin Abstract Knowledge about the phylogenetic history, genetic variation and ecological requirements of a species is important for its conservation and management. Unfortunately, for many species this information is lacking. Here we use multiple approaches (phylogenetics, population genetics and ecological modelling) to evaluate the evolutionary history and conservation status of Capra walie, an endangered flagship species of wild goat endemic to Ethiopia. The analysis of mitochondrial cytochrome b and Y-chromosome DNA sequences suggests that C. walie forms a monophyletic clade with Capra nubiana, but potentially has been isolated for up to 0.8 million years from this closely related species. Microsatellite DNA analyses show that C. walie has very low genetic variation (mean heterozygosity=0.35) compared with other endangered mammals. This reduced variation likely derives from a prolonged demographic decline and small effective population size. Ecological niche modelling using the bioclimatic features of habitats occupied by C. walie, suggests ecological differences between C. walie and C. nubiana, and identifies the areas most suitable for future reintroductions of C. walie. The genetic and bioclimatic data suggest that C. walie is distinct and requires immediate conservation actions including genetic monitoring and reintroductions to establish independent populations. This study illustrates how combining noninvasive sampling along with genetic and ecological (bioclimatic) approaches can help assess conservation status of poorly known species. [source] Genetic relationships of the western Mediterranean painted frogs based on allozymes and mitochondrial markers: evolutionary and taxonomic inferences (Amphibia, Anura, Discoglossidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2006ZANGARI FRANCESCA Allozymes and sequencing of mitochondrial cytochrome b (cyt b) and 12S genes were used to reconstruct the genetic structure and phylogenetic relationships of all Discoglossus taxa described so far (except the probably extinct D. nigriventer). This is the first time that a comprehensive study on the Discoglossus painted frogs has used nuclear and mitochondrial markers, evidencing a discordant pattern between the two datasets. Comparison of these discrepancies suggests a role of stochastic sorting of ancestral polymorphisms, possibly associated with male-biased dispersal and present or past secondary contact. The genetic relationships between taxa with intermediate levels of divergence were well defined by allozyme data, but showed short internodes and low bootstrap values for mitochondrial data, suggesting a rapid radiation of their lineages during the Messinian Lago Mare phase. The results provide information about the taxonomic status of D. galganoi and D. jeanneae, considered as subspecies, and indicate D. pictus as nonmonophyletic, confirming D. scovazzi as a distinct species. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87, 515,536. [source] A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behavioursBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2001REBECCA T. KIMBALL The South-east Asian pheasant genus Polyplectron is comprised of six or seven species which are characterized by ocelli (ornamental eye-spots) in all but one species, though the sizes and distribution of ocelli vary among species. All Polyplectron species have lateral displays, but species with ocelli also display frontally to females, with feathers held erect and spread to clearly display the ocelli. The two least ornamented Polyplectron species, one of which completely lacks ocelli, have been considered the primitive members of the genus, implying that ocelli are derived. We examined this hypothesis phylogenetically using complete mitochondrial cytochrome b and control region sequences, as well as sequences from intron G in the nuclear ovomucoid gene, and found that the two least ornamented species are in fact the most recently evolved. Thus, the absence and reduction of ocelli and other ornamental traits in Polyplectronare recent losses. The only variable that may correlate with the reduction in ornamentation is habitat, as the two less-ornamented species inhabit montane regions, while the ornamented species inhabit lowland regions. The implications of these findings are discussed in light of models of sexual selection. The phylogeny is not congruent with current geographical distributions, and there is little evidence that Pleistocene sea level changes promoted speciation in this genus. Maximum likelihood and maximum parsimony analyses of cytochrome b sequences suggest that the closest relatives of Polyplectron are probably the peafowl and the argus pheasants. [source] Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing dataCLADISTICS, Issue 6 2006Timothy M. Crowe The phylogenetic relationships, biogeography and classification of, and morpho-behavioral (M/B) evolution in, gamebirds (Aves: Galliformes) are investigated. In-group taxa (rooted on representatives of the Anseriformes) include 158 species representing all suprageneric galliform taxa and 65 genera. The characters include 102 M/B attributes and 4452 nucleic acid base pairs from mitochondrial cytochrome b (CYT B), NADH dehydrogenase subunit 2 (ND2), 12S ribosomal DNA (12S) and control region (CR), and nuclear ovomucoid intron G (OVO-G). Analysis of the combined character data set yielded a single, completely resolved cladogram that had the highest levels of jackknife support, which suggests a need for a revised classification for the phasianine galliforms. Adding 102 M/B characters to the combined CYT B and ND2 partitions (2184 characters) decisively overturns the topology suggested by analysis of the two mtDNA partitions alone, refuting the view that M/B characters should be excluded from phylogenetic analyses because of their relatively small number and putative character state ambiguity. Exclusion of the OVO-G partition (with >,70% missing data) from the combined data set had no effect on cladistic structure, but slightly lowered jackknife support at several nodes. Exclusion of third positions of codons in an analysis of a CYT B + ND2 partition resulted in a massive loss of resolution and support, and even failed to recover the monophyly of the Galliformes with jackknife support. A combined analysis of putatively less informative, "non-coding" characters (CYT B/ND2 third position sites + CR +12S + OVO-G sequences) yielded a highly resolved consensus cladogram congruent with the combined-evidence cladogram. Traditionally recognized suprageneric galliform taxa emerging in the combined cladogram are: the families Megapodiidae (megapodes), Cracidae (cracids), Numididae (guineafowls), Odontophoridae (New World quails) and Phasianidae (pheasants, pavonines, partridges, quails, francolins, spurfowls and grouse) and the subfamilies Cracinae (curassows, chachalacas and the horned guan), Penelopinae (remaining guans), Pavoninae sensu lato (peafowls, peacock pheasants and argus pheasants), Tetraoninae (grouse) and Phasianinae (pheasants minus Gallus). The monophyly of some traditional groupings (e.g., the perdicinae: partridges/quails/francolins) is rejected decisively, contrasted by the emergence of other unexpected groupings. The most remarkable phylogenetic results are the placement of endemic African galliforms as sisters to geographically far-distant taxa in Asia and the Americas. Biogeographically, the combined-data cladogram supports the hypothesis that basal lineages of galliforms diverged prior to the Cretaceous/Tertiary (K-T) Event and that the subsequent cladogenesis was influenced by the break-up of Gondwana. The evolution of gamebirds in Africa, Asia and the Americas has a far more complicated historical biogeography than suggested to date. With regard to character evolution: spurs appear to have evolved at least twice within the Galliformes; a relatively large number of tail feathers (, 14) at least three times; polygyny at least twice; and sexual dimorphism many times. © The Willi Hennig Society 2006. [source] | |||||||||||||