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Mitochondrial Cytochrome C Oxidase Subunit I (mitochondrial + cytochrome_c_oxidase_subunit_i)
Selected AbstractsBIODIVERSITY RESEARCH: Genetic diversity in two introduced biofouling amphipods (Ampithoe valida & Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversityDIVERSITY AND DISTRIBUTIONS, Issue 5 2010Erik M. Pilgrim Abstract Aim, We investigated patterns of genetic diversity among invasive populations of Ampithoe valida and Jassa marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute to the contemporary distribution of these species in the region. Location, Native range: Atlantic North American coast; Invaded range: Pacific North American coast. Methods, We assessed indices of genetic diversity based on DNA sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) gene, determined the distribution of COI haplotypes among populations in both the invasive and putative native ranges of A. valida and J. marmorata and reconstructed phylogenetic relationships among COI haplotypes using both maximum parsimony and Bayesian approaches. Results, Phylogenetic inference indicates that inaccurate species-level identifications by morphological criteria are common among Jassa specimens. In addition, our data reveal the presence of three well supported but previously unrecognized clades of A. valida among specimens in the north-eastern Pacific. Different species of Jassa and different genetic lineages of Ampithoe exhibit striking disparity in geographic distribution across the region as well as substantial differences in genetic diversity indices. Main conclusions, Molecular genetic methods greatly improve the accuracy and resolution of identifications for invasive benthic marine amphipods at the species level and below. Our data suggest that multiple cryptic introductions of Ampithoe have occurred in the north-eastern Pacific and highlight uncertainty regarding the origin and invasion histories of both Jassa and Ampithoe species. Additional morphological and genetic analyses are necessary to clarify the taxonomy and native biogeography of both amphipod genera. [source] Incipient speciation of Catostylus mosaicus (Scyphozoa, Rhizostomeae, Catostylidae), comparative phylogeography and biogeography in south-east AustraliaJOURNAL OF BIOGEOGRAPHY, Issue 3 2005Michael N Dawson Abstract Aim, Phylogeography provides a framework to explain and integrate patterns of marine biodiversity at infra- and supra-specific levels. As originally expounded, the phylogeographic hypotheses are generalities that have limited discriminatory power; the goal of this study is to generate and test specific instances of the hypotheses, thereby better elucidating both local patterns of evolution and the conditions under which the generalities do or do not apply. Location, Coastal south-east Australia (New South Wales, Tasmania and Victoria), and south-west North America (California and Baja California). Methods, Phylogeographic hypotheses specific to coastal south-east Australia were generated a priori, principally from existing detailed distributional analyses of echinoderms and decapods. The hypotheses are tested using mitochondrial cytochrome c oxidase subunit I (COI) and nuclear internal transcribed spacer 1 (ITS1) DNA sequence data describing population variation in the jellyfish Catostylus mosaicus, integrated with comparable data from the literature. Results, Mitochondrial COI distinguished two reciprocally monophyletic clades of C. mosaicus (mean ± SD: 3.61 ± 0.40% pairwise sequence divergence) that were also differentiated by ITS1 haplotype frequency differences; the boundary between the clades was geographically proximate to a provincial zoogeographic boundary in the vicinity of Bass Strait. There was also limited evidence of another genetic inhomogeneity, of considerably smaller magnitude, in close proximity to a second hypothesized zoogeographic discontinuity near Sydney. Other coastal marine species also show genetic divergences in the vicinity of Bass Strait, although they are not closely concordant with each other or with reported biogeographic discontinuities in the region, being up to several hundreds of kilometres apart. None of the species studied to date show a strong phylogeographic discontinuity across the biogeographic transition zone near Sydney. Main conclusions, Patterns of evolution in the Bass Strait and coastal New South Wales regions differ fundamentally because of long-term differences in extrinsic factors. Since the late Pliocene, periods of cold climate and low sea-level segregated warm temperate organisms east or west of an emergent Bassian Isthmus resulting in population divergence and speciation; during subsequent periods of warmer and higher seas, sister taxa expanded into the Bass Strait region leading to weakly correlated phylogeographic and biogeographic patterns. The Sydney region, by contrast, has been more consistently favourable to shifts in species' ranges and long-distance movement, resulting in a lack of intra-specific and species-level diversification. Comparisons between the Sydney and Bass Strait regions and prior studies in North America suggest that vicariance plays a key role in generating coastal biodiversity and that dispersal explains many of the deviations from the phylogeographic hypotheses. [source] Phylogeographic analysis of Pimoidae (Arachnida: Araneae) inferred from mitochondrial cytochrome c oxidase subunit I and nuclear 28S rRNA gene regionsJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2008Q. Wang Abstract Using mitochondrial DNA cytochrome c oxidase subunit I and nuclear DNA 28S rRNA data, we explored the phylogenetic relationships of the family Pimoidae (Arachnida: Araneae) and tested the North America to Asia dispersal hypothesis. Sequence data were analysed using maximum parsimony and Bayesian inference. A phylogenetic analysis suggested that vicariance, instead of dispersal, better explained the present distribution pattern of Pimoidae. Times of divergence events were estimated using penalized likelihood method. The dating analysis suggested that the emergence time of Pimoidae was approximately 140 million years ago (Ma). The divergence time of the North American and Asian species of Pimoa was approximately 110 Ma. Our phylogenetic hypothesis supports the current morphology-based taxonomy and suggests that the cave dwelling might have played an important role in the speciation of pimoids in arid areas. Kurzfassung Die verwandtschaftlichen Verhältnisse der Spinnenfamilie Pimoidae (Arachnida: Araneae) wurden mit Hilfe von mtDNA COI und nuDNA 28S rRNA-Daten untersucht und die Ausbreitungshypothese von Nordamerika nach Asien getestet. Sequenzen wurden mit Maximum Parsimonie und Bayesian Inferenz analysiert. Die Analyse zeigte, dass das rezente Verbreitungsmuster der Pimoidae durch Vikarianz besser erklärt wird als durch Ausbreitung. Zeiten für Aufspaltungsereignisse wurden geschätzt mit Hilfe der Bayesischen Molekularen Analyse. Diese legt eine Abspaltung der Pimoidae vor etwa 140 Millionen Jahren nahe. Die Aufspaltung zwischen Nordamerika und Asien hat demzufolge vor 110 Millionen Jahren stattgefunden. Unsere phylogenetische Analyse unterstützt die aktuelle auf Morphologie basierende Taxonomie und zeigt, dass das Höhlenleben eine größere Rolle bei der Speziation in trockenen als in feuchten Gebieten spielte. [source] Genetic variation in the Desert Springsnail (Tryonia porrecta): implications for reproductive mode and dispersalMOLECULAR ECOLOGY, Issue 6 2005R. HERSHLER Abstract Allozymes and mitochondrial cytochrome c oxidase subunit I (mtCOI) sequences were analysed to determine whether populations of the western North American gastropod Tryonia porrecta (from California, Nevada, Utah, and northwest Mexico) are strongly differentiated in accordance with traditional interpretation of regional fauna as ancient relicts inhabiting isolated fragments of late Tertiary palaeodrainages. These data were also used to assess whether this species, for which males have not been recorded, is a rare example of a molluscan parthenogen. Both data sets strongly supported monophyly of T. porrecta populations. Five of the nine sampled populations consisted of a single monoallelic allozyme genotype while the others contained two to 10 distinct genotypes. Allozymic data for genetically diverse Utah populations provided evidence of clonal and sexual reproduction. mtCOI haplotypes of T. porrecta formed two subgroups which differed by 1.99,2.60%. The common haplotype was found in seven populations with rare haplotypes observed in single populations. Based on these results and an available mtCOI molecular clock for related hydrobiid snails, T. porrecta is interpreted as a primarily parthenogenetic species that undergoes occasional sexual reproduction and has accumulated substantial diversity following its mid-Pliocene to mid-Pleistocene origin. Our results also suggest that the distribution of present-day populations of these gill-breathing snails did not result from fragmentation of an ancient, well-integrated drainage but instead reflects overland colonization of habitats which only recently became available following desiccation of late Quaternary pluvial lakes. [source] Identification of Dictyothrips betae as the vector of Polygonum ring spot virusANNALS OF APPLIED BIOLOGY, Issue 2 2010M. Ciuffo Dictyothrips betae (Thysanoptera: Thripidae) is the predominant thrips species on Polygonum convolvulus and Polygonum dumetorum plants infected with a recently described tospovirus species, Polygonum ring spot virus (PolRSV). Laboratory transmission experiments (leaf disk assays) with adults collected directly in the field demonstrated the competence of this thrips to transmit PolRSV, although only at a rate of 4%. However, this increased to 16% using newly emerged larvae fed on infected leaves. Frankliniella occidentalis and Thrips tabaci failed to transmit PolRSV in leaf disk assays. Reverse transcription-polymerase chain reaction (RT-PCR) with specific primers for the N protein and Western blot analysis of adult thrips to detect the N protein confirmed the presence of the virus in D. betae individuals after feeding for at least 5 days on healthy plants. For molecular identification purposes partial sequences of mitochondrial cytochrome c oxidase subunit I (COI), nuclear 28S ribosomal DNA and the elongation factor-1, (EF-1,) from D. betae were cloned. COI sequence was also used for deriving a phylogenetic tree, including D. betae. The results confirmed a relationship between this species and tospovirus-transmitting insects of the genus Thrips. [source] A combined approach to the phylogeny of Cephalopoda (Mollusca)CLADISTICS, Issue 5 2004A. R. Lindgren Cephalopoda represents a highly diverse group of molluscs, ranging in habitat from coastal regions to deep benthic waters. While cephalopods remain at the forefront of modern biology, in providing insight into fields such as neurobiology and population genetics, little is known about the relationships within the group. This study provides a comprehensive phylogenetic analysis of Cephalopoda (Mollusca) using a combination of molecular and morphological data. Four loci (three nuclear 18S rRNA, fragments of 28S rRNA and histone H3 and one mitochondrial cytochrome c oxidase subunit I) were combined with 101 morphological characters to test the relationships of 60 species of cephalopods, with emphasis within Decabrachia (squids and cuttlefishes). Individual and combined data sets were analyzed using the direct optimization method, with parsimony as the optimality criterion. Analyses were repeated for 12 different parameter sets accounting for a range of indel/change and transversion/transition cost ratios. Most analyses support the monophyly of Cephalopoda, Nautiloidea, Coleoidea and Decabrachia, however, the monophyly of Octobrachia was refuted due to the lack of support for a Cirroctopoda + Octopoda group. When analyzing all molecular evidence in combination and for total evidence analyses, Vampyromorpha formed the sister group to Decabrachia under the majority of parameters, while morphological data and some individual data sets supported a sister relationship between Vampyromorpha and Octobrachia. Within Decabrachia, a relationship between the sepioids Idiosepiida, Sepiida, Sepiolida and the teuthid Loliginidae was supported. Spirulida fell within the teuthid group in most analyses, further rendering Teuthida paraphyletic. Relationships within Decabrachia and specifically Oegopsida were found to be highly parameter-dependent. © The Willi Hennig Society 2004. [source] | ||||||||||