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Cytochrome B (cytochrome + b)
Kinds of Cytochrome B Terms modified by Cytochrome B Selected AbstractsForced cytochrome B gene mutation expression induces mitochondrial proliferation and prevents apoptosis in human uroepithelial SV-HUC-1 cells,,INTERNATIONAL JOURNAL OF CANCER, Issue 12 2009Santanu Dasgupta Abstract Mitochondria encoded Cytochrome B (CYTB) gene mutations were reported in tumors of different anatomic origin but the functional significance of these mutations are not well studied. Earlier, we found a 7-amino acid deletion mutation in the CYTB gene in a primary bladder cancer patient. In the present study, we overexpressed this 7-amino acid deletion mutation of CYTB gene in SV-40 transformed human uroepithelial HUC-1 cells. The nuclear transcribed mitochondrial CYTB (mtCYTB) was targeted into the mitochondria and generated increased copies of mitochondria and mitochondrial COX-I protein in the transfected HUC-1 cells. The proapoptotic protein Bax largely remained confined to the cytoplasm of the mtCYTB transfected HUC-1 cells without release of Cytochrome C. The downstream apoptotic proteins PARP also remained uncleaved along with increased Lamin B1 in the mtCYTB transfected cells. Our results demonstrate that forced overexpression of mtCYTB in transformed human uroepithelial HUC-1 cells triggered mitochondrial proliferation and induction of an antiapoptotic signaling cascade favoring sustained cellular growth. Coding mitochondrial DNA mutations appear to have significant functional contribution in tumor progression. Published 2009 UICC. [source] Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flowINSECT MOLECULAR BIOLOGY, Issue 5 2002J. Martin Abstract Phylogenetic analysis of DNA sequences from mitochondrial (mt) genes (Cytochrome b and Cytochrome oxidase I) and one nuclear gene (globin 2b) was used for the investigation of Nearctic and Palearctic populations representing four Chironomus species of the subgenus Camptochironomus, namely C. biwaprimus, C. pallidivittatus, C. tentans sensu stricto and C. dilutus (the last two species constitute Holarctic C. tentans sensu lato). Phenograms constructed on the basis of mt sequences were not congruent with trees based on nuclear genes, or with morphological and cytological data. The mt tree divided the populations by continental region, rather than by the species groupings recognized by the other data sets. The incongruence is explained by mt gene flow resulting from hybridization between the sympatric species on each continent. Calculation of divergence times, based on the sequence data, suggest that C. tentans (s.l.) and C. pallidivittatus have both been in North America for about 2.5 My. [source] No 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] Population structure in the South American tern Sterna hirundinacea in the South Atlantic: two populations with distinct breeding phenologiesJOURNAL OF AVIAN BIOLOGY, Issue 4 2010Patrícia J. Faria The South American tern Sterna hirundinacea is a migratory species for which dispersal, site fidelity and migratory routes are largely unknown. Here, we used five microsatellite loci and 799,bp partial mitochondrial DNA sequences (Cytochrome b and ND2) to investigate the genetic structure of South American terns from the South Atlantic Ocean (Brazilian and Patagonian colonies). Brazilian and Patagonian colonies have two distinct breeding phenologies (austral winter and austral summer, respectively) and are under the influence of different oceanographic features (e.g. Brazil and Falklands/Malvinas ocean currents, respectively), that may promote genetic isolation between populations. Results show that the Atlantic populations are not completely panmictic, nevertheless, contrary to our expectations, low levels of genetic structure were detected between Brazilian and Patagonian colonies. Such low differentiation (despite temporal isolation of the colonies) could be explained by demographic history of these populations coupled with ongoing levels of gene flow. Interestingly, estimations of gene flow through Maximum likelihood and Bayesian approaches has indicated asymmetrical long term and contemporary gene flow from Brazilian to Patagonian colonies, approaching a source,sink metapopulation dynamic. Genetic analysis of other South American tern populations (especially those from the Pacific coast and Falklands,Malvinas Islands) and other seabird species showing similar geographical distribution (e.g. royal tern Thalasseus maximus), are fundamental in gaining a better understanding of the main processes involved in the diversification of seabirds in the southern hemisphere. [source] Glacial refugia and the phylogeography of Steller's sea lion (Eumatopias jubatus) in the North PacificJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2006A. HARLIN-COGNATO Abstract Mitochondrial DNA sequence data were used to examine the phylogeographic history of Steller's sea lions (Eumetopias jubatus) in relation to the presence of Plio-Pleistocene insular refugia. Cytochrome b and control region sequences from 336 Steller's sea lions reveal phylogenetic lineages associated with continental refugia south of the ice sheets in North America and Eurasia. Phylogenetic analysis suggests the genetic structure of E. jubatus is the result of Pleistocene glacial geology, which caused the elimination and subsequent reappearance of suitable rookery habitat during glacial and interglacial periods. The cyclic nature of geological change produced a series of independent population expansions, contractions and isolations that had analogous results on Steller's sea lions and other marine and terrestrial species. Our data show evidence of four glacial refugia in which populations of Steller's sea lions diverged. These events occurred from approximately 60 000 to 180 000 years BP and thus preceded the last glacial maximum. [source] Study of the Cytochrome b Gene Sequence in Populations of TaiwanJOURNAL OF FORENSIC SCIENCES, Issue 1 2010Hsiao-Lin Hwa M.D., Ph.D. Abstract:, The cytochrome b gene (MTCYB) has been widely used in taxonomic research. In this study, the sequence polymorphism of the MTCYB gene was determined in 417 subjects of eight populations living in Taiwan (Taiwanese Han, indigenous Taiwanese, Tao, mainland Chinese, Filipino, Thai, Vietnamese, and Caucasian). Sequence variation from the revised Cambridge Reference Sequence and genetic distance between these populations were analyzed. There were 108 variable positions with a total of 99 haplotypes. Population-specific positions of MTCYB gene were noted in Tao and Caucasian populations. There were statistically significant differences of genetic distance between Taiwanese Han and Caucasian, between Taiwanese Han and Tao, and between Taiwanese Han and Filipino. A phylogenetic tree presents the genetic distances between these populations. In conclusion, there are sufficient sequence polymorphisms of the MTCYB gene in individuals of different populations, which may be used in the analyses of human ethnic groups in forensic casework. [source] Iberian origin of Brazilian local pig breeds based on Cytochrome b (MT-CYB) sequenceANIMAL GENETICS, Issue 5 2009C. A. Souza Summary The aim of this work was to investigate the possible origin of local Brazilian pig breeds through Cytochrome b (MT-CYB) mitochondrial analyses. The results indicated that the main local pig breeds descended from two different European maternal lineages, both Iberian varieties. The haplotype relationship analysis showed that Monteiro, Nilo, Piau and Tatu breeds share haplotypes only with Iberian varieties, while the Moura breed presented a different maternal lineage. The Moura appears to share a high frequency of haplotypes with the Black Hairy Iberian variety and Hungarian Mangalica breed. [source] Inferring historical introduction pathways with mitochondrial DNA: the case of introduced Argentine ants (Linepithema humile) into New ZealandDIVERSITY AND DISTRIBUTIONS, Issue 5 2007Steve E. Corin ABSTRACT The threat imposed by invasive species and difficulties associated with control and management places more impetus on trying to prevent their introduction. The identification of introduction pathways is a vital component towards this goal. In this study, we use a genetic marker-based approach to retrospectively investigate the pathway of origin of the invasive Argentine ant (Linepithema humile) into New Zealand. We intensively sample the mitochondrial gene cytochrome b, from the entire known range of Argentine ants in New Zealand. No genetic variation was found in New Zealand. In order to identify likely introduction pathways, we use two alternative genetic analyses and suggest that a tcs approach that collapses identical haplotypes and calculates the probability of parsimony is superior to standard phylogenetic tree-building algorithms. A minimum spanning network allowed relationships to be examined among sequences collated from previous international studies. The cytochrome b sequence, when compared to a global database, matched that from an Australian population. That Australia is the potential source of Argentine ants is in agreement with the New Zealand interception record, as goods from Australia have the highest number of interception records of Argentine ants. Our approach can easily be duplicated for other organisms and the methodology can be more widely applied to help aid further efforts to identify the routes of transmission for other invasive species and allow us to efficiently direct our biosecurity monitoring effort. [source] Identification of shrimp species in raw and processed food products by means of a polymerase chain reaction-restriction fragment length polymorphism method targeted to cytochrome b mitochondrial sequencesELECTROPHORESIS, Issue 15 2008Ananías Pascoal Abstract A novel PCR-RFLP method has been developed for the identification of six commercially relevant penaeid shrimp species in raw and processed food products. The method can be completed within 8,h. To implement the method, PCR amplification with the crustF/crustR primers, targeted to the amplification of a ca. 181,bp region of the cytochrome b (cytb) mitochondrial gene in penaeid shrimps, was coupled to restriction analysis with CviJI, DdeI and NlaIV. The method was also applied successfully to the identification of shrimp species in complex processed foods, including this type of shellfish as an added-value food ingredient. The small size of this molecular target facilitates amplification from fresh, frozen, or precooked samples, where DNA fragmentation may be relevant and fragment size critical. We also report the first cytb mitochondrial sequences described to date for the species Farfantepenaeus notialis, Parapenaeus longirostris and Pleoticus muelleri, and these nearly triplicate current knowledge of reference nucleotide sequences in this mitochondrial region for this group of species. The cytb mitochondrial gene may also be considered as a molecular marker for identification and phylogenetic purposes in penaeid shrimp species. [source] Recent evolutionary diversification of a protist lineageENVIRONMENTAL MICROBIOLOGY, Issue 5 2008Ramiro Logares Summary Here, we have identified a protist (dinoflagellate) lineage that has diversified recently in evolutionary terms. The species members of this lineage inhabit cold-water marine and lacustrine habitats, which are distributed along a broad range of salinities (0,32) and geographic distances (0,18 000 km). Moreover, the species present different degrees of morphological and sometimes physiological variability. Altogether, we analysed 30 strains, generating 55 new DNA sequences. The nuclear ribosomal DNA (nrDNA) sequences (including rapidly evolving introns) were very similar or identical among all the analysed isolates. This very low nrDNA differentiation was contrasted by a relatively high cytochrome b (COB) mitochondrial DNA (mtDNA) polymorphism, even though the COB evolves very slowly in dinoflagellates. The 16 Maximum Likelihood and Bayesian phylogenies constructed using nr/mtDNA indicated that the studied cold-water dinoflagellates constitute a monophyletic group (supported also by the morphological analyses), which appears to be evolutionary related to marine-brackish and sometimes toxic Pfiesteria species. We conclude that the studied dinoflagellates belong to a lineage which has diversified recently and spread, sometimes over long distances, across low-temperature environments which differ markedly in ecology (marine versus lacustrine communities) and salinity. Probably, this evolutionary diversification was promoted by the variety of natural selection regimes encountered in the different environments. [source] RIVER CAPTURE, RANGE EXPANSION, AND CLADOGENESIS: THE GENETIC SIGNATURE OF FRESHWATER VICARIANCEEVOLUTION, Issue 5 2006C. P. Burridge Abstract River capture is potentially a key geomorphological driver of range expansion and cladogenesis in freshwater-limited taxa. While previous studies of freshwater fish, in particular, have indicated strong relationships between historical river connections and phylogeographic pattern, their analyses have been restricted to single taxa and geological hypotheses were typically constructed a posteriori. Here we assess the broader significance of river capture among taxa by testing multiple species for the genetic signature of a recent river capture event in New Zealand. During the Quaternary an upper tributary of the Clarence River system was diverted into the headwaters of the Wairau River catchment. Mitochondrial DNA (control region and cytochrome b) sequencing of two native galaxiid fishes (Galaxias vulgaris and Galaxias divergens) supports headwater exchange: populations from the Clarence and Wairau Rivers are closely related sister-groups, whereas samples from the geographically intermediate Awatere River are genetically divergent. The upland bully Gobiomorphus breviceps (Eleotridae), in contrast, lacks a genetic signature of the capture event. We hypothesize that there is an increased likelihood of observing genetic signatures from river capture events when they facilitate range expansion, as is inferred for the two galaxiid taxa studied here. When river capture merely translocates genetic lineages among established populations, by contrast, we suggest that the genetic signature of capture is less likely to be retained, as might be inferred for G. breviceps. Rates of molecular evolution calibrated against this recent event were elevated relative to traditional estimates, consistent with the contribution of polymorphisms to branch lengths at shallow phylogenetic levels prior to fixation by purifying selection and drift. [source] Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen speciesFEBS JOURNAL, Issue 13 2008Hideki Sumimoto NADPH oxidases of the Nox family exist in various supergroups of eukaryotes but not in prokaryotes, and play crucial roles in a variety of biological processes, such as host defense, signal transduction, and hormone synthesis. In conjunction with NADPH oxidation, Nox enzymes reduce molecular oxygen to superoxide as a primary product, and this is further converted to various reactive oxygen species. The electron-transferring system in Nox is composed of the C-terminal cytoplasmic region homologous to the prokaryotic (and organelle) enzyme ferredoxin reductase and the N-terminal six transmembrane segments containing two hemes, a structure similar to that of cytochrome b of the mitochondrial bc1 complex. During the course of eukaryote evolution, Nox enzymes have developed regulatory mechanisms, depending on their functions, by inserting a regulatory domain (or motif) into their own sequences or by obtaining a tightly associated protein as a regulatory subunit. For example, one to four Ca2+ -binding EF-hand motifs are present at the N-termini in several subfamilies, such as the respiratory burst oxidase homolog (Rboh) subfamily in land plants (the supergroup Plantae), the NoxC subfamily in social amoebae (the Amoebozoa), and the Nox5 and dual oxidase (Duox) subfamilies in animals (the Opisthokonta), whereas an SH3 domain is inserted into the ferredoxin,NADP+ reductase region of two Nox enzymes in Naegleria gruberi, a unicellular organism that belongs to the supergroup Excavata. Members of the Nox1,4 subfamily in animals form a stable heterodimer with the membrane protein p22phox, which functions as a docking site for the SH3 domain-containing regulatory proteins p47phox, p67phox, and p40phox; the small GTPase Rac binds to p67phox (or its homologous protein), which serves as a switch for Nox activation. Similarly, Rac activates the fungal NoxA via binding to the p67phox -like protein Nox regulator (NoxR). In plants, on the other hand, this GTPase directly interacts with the N-terminus of Rboh, leading to superoxide production. Here I describe the regulation of Nox-family oxidases on the basis of three-dimensional structures and evolutionary conservation. [source] Identification and characterization of cytochrome bc1 subcomplexes in mitochondria from yeast with single and double deletions of genes encoding cytochrome bc1 subunitsFEBS JOURNAL, Issue 17 2007Vincenzo Zara We have examined the status of the cytochrome bc1 complex in mitochondrial membranes from yeast mutants in which genes for one or more of the cytochrome bc1 complex subunits were deleted. When membranes from wild-type yeast were resolved by native gel electrophoresis and analyzed by immunodecoration, the cytochrome bc1 complex was detected as a mixed population of enzymes, consisting of cytochrome bc1 dimers, and ternary complexes of cytochrome bc1 dimers associated with one and two copies of the cytochrome c oxidase complex. When membranes from the deletion mutants were resolved and analyzed, the cytochrome bc1 dimer was not associated with the cytochrome c oxidase complex in many of the mutant membranes, and membranes from some of the mutants contained a common set of cytochrome bc1 subcomplexes. When these subcomplexes were fractionated by SDS/PAGE and analyzed with subunit-specific antibodies, it was possible to recognize a subcomplex consisting of cytochrome b, subunit 7 and subunit 8 that is apparently associated with cytochrome c oxidase early in the assembly process, prior to acquisition of the remaining cytochrome bc1 subunits. It was also possible to identify a subcomplex consisting of subunit 9 and the Rieske protein, and two subcomplexes containing cytochrome c1 associated with core protein 1 and core protein 2, respectively. The analysis of all the cytochrome bc1 subcomplexes with monospecific antibodies directed against Bcs1p revealed that this chaperone protein is involved in a late stage of cytochrome bc1 complex assembly. [source] Three mammalian cytochromes b561 are ascorbate-dependent ferrireductasesFEBS JOURNAL, Issue 16 2006Dan Su Cytochromes b561 are a family of transmembrane proteins found in most eukaryotic cells. Three evolutionarily closely related mammalian cytochromes b561 (chromaffin granule cytochrome b, duodenal cytochrome b, and lysosomal cytochrome b) were expressed in a Saccharomyces cerevisiae,fre1,fre2 mutant, which lacks almost all of its plasma membrane ferrireductase activity, to study their ability to reduce ferric iron (Fe3+). The expression of each of these cytochromes b561 was able to rescue the growth defect of the ,fre1,fre2 mutant cells in iron-deficient conditions, suggesting their involvement in iron metabolism. Plasma membrane ferrireductase activities were measured using intact yeast cells. Each cytochrome b561 showed significant FeCN and Fe3+ -EDTA reductase activities that were dependent on the presence of intracellular ascorbate. Site-directed mutagenesis of lysosomal cytochrome b was conducted to identify amino acids that are indispensable for its activity. Among more than 20 conserved or partially conserved amino acids that were investigated, mutations of four His residues (H47, H83, H117 and H156), one Tyr (Y66) and one Arg (R67) completely abrogated the FeCN reductase activity, whereas mutations of Arg (R149), Phe (F44), Ser (S115), Trp (W119), Glu (E196), and Gln (Q131) affected the ferrireductase activity to some degree. These mutations may affect the heme coordination, ascorbate binding, and/or ferric substrate binding. Possible roles of these residues in lysosomal cytochrome b are discussed. This study demonstrates the ascorbate-dependent transmembrane ferrireductase activities of members of the mammalian cytochrome b561 family of proteins. [source] Modeling the Qo site of crop pathogens in Saccharomyces cerevisiae cytochrome bFEBS JOURNAL, Issue 11 2004Nicholas Fisher Saccharomyces cerevisiae has been used as a model system to characterize the effect of cytochrome b mutations found in fungal and oomycete plant pathogens resistant to Qo inhibitors (QoIs), including the strobilurins, now widely employed in agriculture to control such diseases. Specific residues in the Qo site of yeast cytochrome b were modified to obtain four new forms mimicking the Qo binding site of Erysiphe graminis, Venturia inaequalis, Sphaerotheca fuliginea and Phytophthora megasperma. These modified versions of cytochrome b were then used to study the impact of the introduction of the G143A mutation on bc1 complex activity. In addition, the effects of two other mutations F129L and L275F, which also confer levels of QoI insensitivity, were also studied. The G143A mutation caused a high level of resistance to QoI compounds such as myxothiazol, axoxystrobin and pyraclostrobin, but not to stigmatellin. The pattern of resistance conferred by F129L and L275F was different. Interestingly G143A had a slightly deleterious effect on the bc1 function in V. inaequalis, S. fuliginea and P. megasperma Qo site mimics but not in that for E. graminis. Thus small variations in the Qo site seem to affect the impact of the G143A mutation on bc1 activity. Based on this observation in the yeast model, it might be anticipated that the G143A mutation might affect the fitness of pathogens differentially. If so, this could contribute to observed differences in the rates of evolution of QoI resistance in fungal and oomycete pathogens. [source] Molecular basis of resistance to cytochrome bc1 inhibitorsFEMS YEAST RESEARCH, Issue 2 2008Nick Fisher Abstract Inhibitors of the mitochondrial respiratory chain enzyme cytochrome bc1 (respiratory complex III) have been developed as antimicrobial agents. They are used in agriculture to control plant pathogenic fungi and in medicine against human pathogens, such as the malaria parasite Plasmodium falciparum, or Pneumocystis jiroveci (an opportunistic pathogenic fungus life-threatening in immuno-compromised patients). These respiratory inhibitors are thus effective against a broad range of important pathogens. Unfortunately, the problem of acquired resistance has rapidly emerged. A growing number of pathogen isolates resistant to inhibitor treatment have been reported, and this resistance is often linked to mutation within cytochrome b, one of the essential catalytic subunits of the complex. Saccharomyces cerevisiae is an invaluable model in order to assess the impact of the mutations on the sensitivity to the drugs, on the respiratory capacity and the fitness of cells. In this minireview, the inhibitors, their mode of action, and the mutations implicated in resistance and studied in yeast are briefly reviewed. Four mutations that are of particular importance in medicine and in agriculture are briefly reviewed and described in more detail and the molecular basis of resistance and of evolution of the mutations is discussed succinctly. [source] No 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] Intraspecific structure within three caviar-producing sturgeons (Acipenser gueldenstaedtii, A. stellatus, and Huso huso) based on mitochondrial DNA analysisJOURNAL OF APPLIED ICHTHYOLOGY, Issue 6 2005P. Doukakis Summary A survey of three mitochondrial DNA regions (control region, NADH5, cytochrome b) and comprehensive sequencing of the control region (631,646 bps) was conducted to examine whether subspecies and geographic populations within three species of Eurasian sturgeons, Acipenser gueldenstaedtii, A. stellatus, and Huso huso, are genetically distinct. Neither subspecies nor populations exhibited diagnostic distinction or reciprocal monophyly in any gene region examined. For the control region, molecular variance analyses (amova) indicate that most of the variance is because of differences among haplotypes within subspecies (H. huso: 99.6%; A. stellatus: 95.0%; A. gueldenstaedtii: 81.0%) and populations (A. gueldenstaedtii: 76.1%). Significant pairwise F -values were found for all pairwise comparisons except for Sea of Azov and Caspian Sea A. gueldenstaedtii and Caspian Sea and Black Sea A. stellatus and H. huso. Only weak genetic differentiation is apparent between select subspecies and populations, reflective of biogeographic and management history. High genetic diversity within A. gueldenstaedtii suggests the possibility of additional population structure. Future research and management projects should consider these results. [source] Radiation of Atlantic goldcrests Regulus regulus spp.: evidence of a new taxon from the Canary IslandsJOURNAL OF AVIAN BIOLOGY, Issue 4 2006Martin Päckert Phylogenetic relationships between goldcrest populations from the Atlantic Islands (Azores and Canary Islands) were investigated by two molecular markers (mitochondrial control region and cytochrome b sequences), and partly by morphology and territorial song. The Azorean goldcrest populations are closely related to European nominate R. r. regulus. Most probably, the Azores were colonized by goldcrests in a single late-pleistocene invasion, while colonization of the Canary Islands presumably occurred in two steps: An early invasion to Tenerife and La Gomera 1.9,2.3 million years (my) ago and a more recent one to El Hierro and La Palma 1.3,1.8 my ago. Distribution of haplotypes on the Azores suggests a division of R. r. azoricus on São Miguel into an eastern population with close affinities to R. r. sanctaemariae and a western population belonging to the lineage of R. r. inermis on the central and western island group. The Canarian populations are genetically substructured into a northeastern group embracing Tenerife and La Gomera and a second, southwestern group including El Hierro and La Palma. Genetic distances between members of the two Canarian clades range at 3.1,3.4% (TrN distance, control region and cytochrome b). Differentiation between the two groups is also supported by morphology and by territorial song. Substitution rate estimates for the both genes range at approximately the same values of 0.0031 and 0.0044 substitutions per site and lineage per my which roughly corresponds 0.61,0.83% divergence between Regulus lineages per my. Highest local rates occur in island clades of the Azorean and the Canarian population and in R. r. japonensis from the Russian Far East and Japan. However, a general acceleration of a molecular clock in island populations is not evident from the Regulus data set due to extremely low local rate estimates in the Canarian clade of Tenerife and La Gomera. As a taxonomic consequence of the marked differentiation of the two Canarian goldcrest clades the populations from El Hierro and La Palma are described as a taxon new to science and are named Regulus regulus ellenthalerae n. ssp. [source] Eastern Beringian biogeography: historical and spatial genetic structure of singing voles in AlaskaJOURNAL OF BIOGEOGRAPHY, Issue 8 2010Marcelo Weksler Abstract Aim Pleistocene climatic cycles have left marked signatures in the spatial and historical genetic structure of high-latitude organisms. We examine the mitochondrial (cytochrome b) genetic structure of the singing vole, Microtus miurus (Rodentia: Cricetidae: Arvicolinae), a member of the Pleistocene Beringian fauna, and of the insular vole, Microtus abbreviatus, its putative sister species found only on the St Matthew Archipelago. We reconstruct the phylogenetic and phylogeographical structure of these taxa, characterize their geographical partitioning and date coalescent and cladogenetic events in these species. Finally, we compare the recovered results with the phylogenetic, coalescent and spatial genetic patterns of other eastern Beringian mammals and high-latitude arvicoline rodents. Location Continental Alaska (alpine and arctic tundra) and the St Matthew Archipelago (Bering Sea). Methods We generated and analysed cytochrome b sequences of 97 singing and insular voles (M. miurus and M. abbreviatus) from Alaska. Deep evolutionary structure was inferred by phylogenetic analysis using parsimony, maximum likelihood and Bayesian approaches; the geographical structure of genetic diversity was assessed using analysis of molecular variance and network analysis; ages of cladogenetic and coalescent events were estimated using a relaxed molecular clock model with Bayesian approximation. Results Regional nucleotide diversity in singing voles is higher than in other high-latitude arvicoline species, but intra-population diversity is within the observed range of values for arvicolines. Microtus abbreviatus specimens are phylogenetically nested within M. miurus. Molecular divergence date estimates indicate that current genetic diversity was formed in the last glacial (Wisconsinan) and previous interglacial (Sangamonian) periods, with the exception of a Middle Pleistocene split found between samples collected in the Wrangell Mountains region and all other singing vole samples. Main conclusions High levels of phylogenetic and spatial structure are observed among analysed populations. This pattern is consistent with that expected for a taxon with a long history in Beringia. The spatial genetic structure of continental singing voles differs in its northern and southern ranges, possibly reflecting differences in habitat distribution between arctic and alpine tundra. Our phylogenetic results support the taxonomic inclusion of M. miurus in its senior synonym, M. abbreviatus. [source] Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of MadagascarJOURNAL OF BIOGEOGRAPHY, Issue 3 2010Charlotte Tollenaere Abstract Aim, To describe the phylogeographic patterns of the black rat, Rattus rattus, from islands in the western Indian Ocean where the species has been introduced (Madagascar and the neighbouring islands of Réunion, Mayotte and Grande Comore), in comparison with the postulated source area (India). Location, Western Indian Ocean: India, Arabian Peninsula, East Africa and the islands of Madagascar, Réunion, Grande Comore and Mayotte. Methods, Mitochondrial DNA (cytochrome b, tRNA and D-loop, 1762 bp) was sequenced for 71 individuals from 11 countries in the western Indian Ocean. A partial D-loop (419 bp) was also sequenced for eight populations from Madagascar (97 individuals), which were analysed in addition to six previously published populations from southern Madagascar. Results, Haplotypes from India and the Arabian Peninsula occupied a basal position in the phylogenetic tree, whereas those from islands were distributed in different monophyletic clusters: Madagascar grouped with Mayotte, while Réunion and Grand Comore were present in two other separate groups. The only exception was one individual from Madagascar (out of 190) carrying a haplotype that clustered with those from Réunion and South Africa. ,Isolation with migration' simulations favoured a model with no recurrent migration between Oman and Madagascar. Mismatch distribution analyses dated the expansion of Malagasy populations on a time-scale compatible with human colonization history. Higher haplotype diversity and older expansion times were found on the east coast of Madagascar compared with the central highlands. Main conclusions, Phylogeographic patterns supported the hypothesis of human-mediated colonization of R. rattus from source populations in either the native area (India) or anciently colonized regions (the Arabian Peninsula) to islands of the western Indian Ocean. Despite their proximity, each island has a distinct colonization history. Independent colonization events may have occurred simultaneously in Madagascar and Grande Comore, whereas Mayotte would have been colonized from Madagascar. Réunion was colonized independently, presumably from Europe. Malagasy populations may have originated from a single successful colonization event, followed by rapid expansion, first in coastal zones and then in the central highlands. The congruence of the observed phylogeographic pattern with human colonization events and pathways supports the potential relevance of the black rat in tracing human history. [source] Are the Northern Andes a species pump for Neotropical birds?JOURNAL OF BIOGEOGRAPHY, Issue 2 2010Phylogenetics, biogeography of a clade of Neotropical tanagers (Aves: Thraupini) Abstract Aim, We used mitochondrial DNA sequence data to reconstruct the phylogeny of a large clade of tanagers (Aves: Thraupini). We used the phylogeny of this Neotropical bird group to identify areas of vicariance, reconstruct ancestral zoogeographical areas and elevational distributions, and to investigate the correspondence of geological events to speciation events. Location, The species investigated are found in 18 of the 22 zoogeographical regions of South America, Central America and the Caribbean islands; therefore, we were able to use the phylogeny to address the biogeographical history of the entire region. Methods, Molecular sequence data were gathered from two mitochondrial markers (cytochrome b and ND2) and analysed using Bayesian and maximum-likelihood approaches. Dispersal,vicariance analysis (DIVA) was used to reconstruct zoogeographical areas and elevational distributions. A Bayesian framework was also used to address changes in elevation during the evolutionary history of the group. Results, Our phylogeny was similar to previous tanager phylogenies constructed using fewer species; however, we identified three genera that are not monophyletic and uncovered high levels of sequence divergence within some species. DIVA identified early diverging nodes as having a Northern Andean distribution, and the most recent common ancestor of the species included in this study occurred at high elevations. Most speciation events occurred either within highland areas or within lowland areas, with few exchanges occurring between the highlands and lowlands. The Northern Andes has been a source for lineages in other regions, with more dispersals out of this area relative to dispersals into this area. Most of the dispersals out of the Northern Andes were dispersals into the Central Andes; however, a few key dispersal events were identified out of the Andes and into other zoogeographical regions. Main conclusions, The timing of diversification of these tanagers correlates well with the main uplift of the Northern Andes, with the highest rate of speciation occurring during this timeframe. Central American tanagers included in this study originated from South American lineages, and the timing of their dispersal into Central America coincides with or post-dates the completion of the Panamanian isthmus. [source] Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatumJOURNAL OF BIOGEOGRAPHY, Issue 5 2008Stephanie N. J. Greaves Abstract Aim, To examine the hypothesis raised by Graham S. Hardy that Pleistocene glacial cycles suffice to explain divergence among lineages within the endemic New Zealand speckled skink, Oligosoma infrapunctatum Boulenger. Location, Populations were sampled from across the entire range of the species, on the North and South Islands of New Zealand. Methods, We sequenced the mitochondrial genes ND2 (550 bp), ND4 + tRNAs (773 bp) and cytochrome b (610 bp) of 45 individuals from 21 locations. Maximum likelihood, maximum parsimony and Bayesian methods were used for phylogenetic reconstruction. The Shimodaira,Hasegawa test was used to examine hypotheses about the taxonomic status of morphologically distinctive populations. Results, Our analysis revealed four strongly supported clades within O. infrapunctatum. Clades were largely allopatric, except on the west coast of the South Island, where representatives from all four clades were found. Divergences among lineages within the species were extremely deep, reaching over 5%. Two contrasting phylogeographical patterns are evident within O. infrapunctatum. Main conclusions, The deep genetic divisions we found suggest that O. infrapunctatum is a complex of cryptic species which diverged in the Pliocene, contrary to the existing Pleistocene-based hypothesis. Although Pleistocene glacial cycles do not underlie major divergences within this species, they may be responsible for the shallower phylogeographical patterns that are found within O. infrapunctatum, which include a radiation of haplotypes in the Nelson and Westland regions. [source] Maintenance of mitochondrial DNA copy number and expression are essential for preservation of mitochondrial function and cell growthJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 2 2008Jaan-Yeh Jeng Abstract To examine whether a reduction in the mtDNA level will compromise mitochondrial biogenesis and mitochondrial function, we created a cell model with depleted mtDNA. Stable transfection of small interfering (si)RNA of mitochondrial transcription factor A (Tfam) was used to interfere with Tfam gene expression. Selected stable clones showed 60,95% reduction in Tfam gene expression and 50,90% reduction in cytochrome b (Cyt b) gene expression. Tfam gene knockdown clones also showed decreased mtDNA-encoded cytochrome c oxidase subunit I (COX I) protein expression. However, no significant differences in protein expression were observed in nuclear DNA (nDNA)-encoded mitochondrial respiratory enzyme subunits. The cell morphology changed from a rhombus-like to a spindle-like form as determined in clones with decreased expressions of Tfam, mtRNA, and mitochondrial proteins. The mitochondrial respiratory enzyme activities and ATP production in such clones were significantly lower. The proportions of mtDNA mutations including 8-hydroxy-2,-deoxyguanosine (8-OHdG), a 4,977-bp deletion, and a 3,243-point mutation were also examined in these clones. No obvious increase in mtDNA mutations was observed in mitochondrial dysfunctional cell clones. The mitochondrial respiratory activity and ATP production ability recovered in cells with increased mtDNA levels after removal of the specific siRNA treatment. These experimental results provide direct evidence to substantiate that downregulation of mtDNA copy number and expression may compromise mitochondrial function and subsequent cell growth and morphology. J. Cell. Biochem. 103: 347,357, 2008. © 2007 Wiley-Liss, Inc. [source] Evolutionary acceleration in the most endangered mammal of Canada: speciation and divergence in the Vancouver Island marmot (Rodentia, Sciuridae)JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2007A. CARDINI Abstract The Vancouver Island marmot is the most endangered mammal of Canada. Factors which have brought this population to the verge of extinction have not yet been fully elucidated, but the effects of deforestation and habitat fragmentation on survival rates, as well as those of variation in rainfall, temperature, snowpack depth and snowmelt strongly suggest that marmots on the island are struggling to keep pace with environmental changes. Genetic analyses, however, seem to indicate that the Vancouver Island marmot may merely represent a melanistic population of its parental species on the mainland. Were it not for its black pelage colour, it is unlikely that it would have attracted much attention as a conservation priority. Our study uses three-dimensional coordinates of cranial landmarks to further assess phenotypic differentiation of the Vancouver Island marmot. A pattern of strong interspecific divergence and low intraspecific variation was found which is consistent with aspects of drift-driven models of speciation. However, the magnitude of shape differences relative to the putatively neutral substitutions in synonymous sites of cytochrome b is too large for being compatible with a simple neutral model. A combination of bottlenecks and selective pressures due to natural and human-induced changes in the environment may offer a parsimonious explanation for the large phenotypic differentiation observed in the species. Our study exemplifies the usefulness of a multidisciplinary approach to the study of biological diversity for a better understanding of evolutionary models and to discover aspects of diversity that may be undetected by using only a few genetic markers to characterize population divergence and uniqueness. [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] Distinguishing between two sympatric Acanthopagrus species from Dapeng Bay, Taiwan, using morphometric and genetic charactersJOURNAL OF FISH BIOLOGY, Issue 2 2009M. C. Tseng Morphometric and genetic data were used to compare two sympatric and morphologically similar species, Acanthopagrus berda and Acanthopagrus taiwanensis, in Dapeng Bay, South-western Taiwan. A principle component analysis of morphological data indicated a distinction between the two species, with pectoral fin length and eye diameter accounting for 32·27% of the variation. Interspecific sequence divergence, based on mtDNA cytochrome b (0·118 ± 0·01), was larger than intraspecific divergences between haplotypes (0·007 for A. taiwanensis and 0·003 for A. berda). Individuals of the two species clustered into different groups in three phylogenetic trees with 100% bootstrap support. The mean observed heterozygosity for eight microsatellite loci was 0·471 ± 0·202 for A. taiwanensis and 0·637 ± 0·145 for A. berda. Nei's unbiased measure of interspecific genetic distance (DS) was 1·334. FST (0·134) and RST (0·404) values indicated significant differentiation between species. An unrooted neighbour-joining tree was constructed by allele-sharing distances and the factorial correspondence analysis split all specimens into two distinct clusters. The results of morphometric, mtDNA and microsatellite analyses indicated the presence of two species, A. taiwanensis and A. berda. [source] Mitochondrial DNA in Atherina (Teleostei, Atheriniformes): differential distribution of an intergenic spacer in lagoon and marine forms of Atherina boyeriJOURNAL OF FISH BIOLOGY, Issue 5 2008V. MILANA The big-scale sand smelt Atherina boyeri lives in fresh water, brackish water and sea water of the western Atlantic Ocean and Mediterranean Sea. Previous studies concerning distribution, biometric characters and genetic molecular markers have suggested the possible existence of two or even three different groups or species of sand smelt, one ,lagoon' type and one (or two , punctuated and non-punctuated on the flanks) ,marine' type. In this study, the presence and the localization of an insertion was described, c. 200 bp in length, in the mtDNA of the lagoon and marine punctuated specimens of A. boyeri and its absence in the marine non-punctuated specimens, as well as in other two congeneric species, Atherina hepsetus and Atherina presbyter, and in the atheriniform Menidia menidia. The intergenic spacer is located between the tRNAGlu and cytochrome b (cyt b) genes and shares a c. 50% sequence similarity with cyt b. The distribution and the features of the intergenic spacer suggest that it might have originated from an event of gene duplication, which involved the cyt b gene (or, more likely, a part of it) and which took place in the common ancestor of the lagoon and the marine punctuated specimens. The data obtained therefore support the hypothesis of the existence of three cryptic and, or sibling species within the A. boyeri taxon and provide a genetic molecular marker to distinguish them. [source] Rapid PCR-RFLP Method for the Identification of 5 Billfish SpeciesJOURNAL OF FOOD SCIENCE, Issue 4 2005Hung-Sheng Hsieh ABSTRACT: A rapid and reliable polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to identify billfish species Xiphias gladius (swordfish), Makaira nigricans (blue marlin), Makaira indica (black marlin), Istiophorus platypterus (sailfish), and Tetrapturus audax (striped marlin). After DNA extraction and amplifying, the 348-bp PCR products from gene encoding of cytochrome b were subjected to restriction enzyme analysis. No single enzyme tested was able to distinguish the 5 species at the same time, but the combination of results obtained from the digests of Bsa JI and Cac 81 could be used to differentiate the 5 billfish species. This sensitive, rapid, and valid method can be used to detect fraudulent substitutes. [source] | ||||||||||||||||||||||||||||||||||||||||