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Mitochondrial Genes (mitochondrial + gene)
Selected AbstractsRice Mitochondrial Genes Are Transcribed by Multiple Promoters That Are Highly DivergedJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 12 2006Qun-Yu Zhang Abstract Plant mitochondrial genes are often transcribed into complex sets of mRNA. To characterize the transcription initiation and promoter structure, the transcript termini of four mitochondrial genes, atp1, atp6, cob, rps7, in rice (Oryza sativa L.), were determined by using a modified circularized RNA reverse transcription-polymerase chain reaction method. The results revealed that three genes (atp1, atp6, rps7) were transcribed from multiple initiation sites, indicating the presence of multiple promoters. Two transcription termination sites were detected in three genes (atp6, cob, rps7), respectively. Analysis on the promoter architecture showed that the YRTA (Y=T or C, R=A or G) motifs that are widely present in the mitochondrial promoters of other monocotand dicot plant species were detected only in two of the 12 analyzed promoters. Our data suggest that the promoter sequences in the rice mitochondrial genome are highly diverged in comparison to those in other plants, and the YRTA motif is not an essential element for the promoter activity. (Managing editor: Li-Hui Zhao) [source] Mitochondrial genes leave homeNEW PHYTOLOGIST, Issue 3 2006Linda BonenArticle first published online: 18 OCT 200 No abstract is available for this article. [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] Detection of hazelnut DNA traces in chocolate by PCRINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 6 2003Lieve Herman Summary By use of the DneasyTM Plant Tissue kit (Qiagen Inc.) plant DNA could be extracted from chocolate and related matrices. The polymerase chain reaction (PCR) detection of mitochondrial plant DNA is directly correlated with the length of the amplified fragment indicating shearing of DNA during chocolate production. Hazelnut DNA could be specifically detected in chocolate matrices with primers derived from the intron between exon B and C of the mitochondrial gene nad1. Specificity was confirmed towards individual chocolate ingredients and in 20 hazelnut negative chocolates. From taxonomically closely related plant species, only Carpinus turczaninovii, Ostrya carpinifolia and Corylus americana showed cross reaction, this was because of the identical sequence of the nad1 fragment. Application of extra MgCl2 throughout the DNA extraction procedure and of a specially designed Mg2+ buffered PCR, increased the detection sensitivity of co-processed hazelnut in chocolate to 0.001% or 10 ppm. [source] Ethanol-Induced Oxidative Stress and Mitochondrial Dysfunction in Rat Placenta: Relevance to Pregnancy LossALCOHOLISM, Issue 3 2010Fusun Gundogan Background:, Ethanol consumption during pregnancy increases the risk of early pregnancy loss and causes intrauterine growth restriction. We previously showed that chronic gestational exposure to ethanol impairs placentation, and that this effect is associated with inhibition of insulin and insulin growth factor signaling. Since ethanol also causes oxidative stress and DNA damage, we extended our investigations to assess the role of these pathological processes on placentation and placental gene expression. Methods:, Pregnant Long Evans rats were pair-fed liquid diets containing 0% or 24% ethanol by caloric content. Placentas harvested on gestation day 16 were used to examine DNA damage, lipid peroxidation, apoptosis, mitochondrial gene/protein and hormonal gene expression in relation to ethanol exposure. Results:, Gestational exposure to ethanol increased fetal resorption, and trophoblast apoptosis/necrosis, oxidative stress, DNA damage, and lipid peroxidation. These adverse effects of ethanol were associated with increased expression of pro-apoptotic (Bax and Bak) and reduced levels of the anti-apoptotic Bcl-2 protein. In addition, increased trophoblast apoptosis proneness was associated with p53-independent activation of p21, reduced mitochondrial gene and protein expression, and dysregulated expression of prolactin (PRL) family hormones that are required for implantation and pregnancy-related adaptations. Conclusions:, Chronic gestational exposure to ethanol increases fetal demise due to impaired survival and mitochondrial function, increased oxidative stress, DNA damage and lipid peroxidation, and dysregulated expression of prolactin family hormones in placental trophoblasts. [source] Phylogeny and phylogeography of the Lozekia,Kovacsia species group (Gastropoda: Hygromiidae)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2009Zoltán Fehér Abstract The Lozekia,Kovacsia species group comprises three species of high conservation concern, Lozekia transsilvanica (Westerlund, 1876), Lozekia deubeli (M. Kimakowicz, 1890) and Kovacsia kovacsi (Varga and L. Pintér, 1972), which occupy relatively small ranges in the Carpathian-Pannonian region. Despite their conservation concern, the phylogeny and biogeographical history of these species have not been studied by molecular methods up to now. This study, based on mitochondrial cytochrome oxidase subunit I gene sequences, has two main objectives: (i) to infer the phylogenetic relationships within the group in order to test the latest morphology-based system, proposed by Nordsieck [1993, Das System der paläarktischen Hygromiidae (Gastropoda: Stylommatophora: Helicoidea). Arch Molluskenkunde 122:1] and (ii) to reconstruct the distribution history of the three species. The monophyly and thus the systematic distinctness of the three species was confirmed, but our findings do not support the monophyly of the Lozekia genus and therefore contradict the current system of the species group. Genetic diversity was found to be much higher within L. deubeli than within the other two species, a possible explanation of this phenomenon is that L. transsilvanica and K. kovacsi are more recently evolved, younger species. Nested clade phylogeographycal analysis showed that the three species evolved by fragmentation events; probably L. deubeli and the ancestor of the other two species split first. At the intraspecific level, fragmentation events, as well as range expansion, played a significant role in the biogeographical history of this species group. As our findings are based on a single mitochondrial gene, we feel premature to propose changes in the generally accepted system and nomenclature. Further molecular phylogenetic analyses, also involving nuclear DNA sequences, should clarify if the evolutionary scenario suggested by our data is valid, and the three species can indeed be placed within the same genus, Lozekia. Zusammenfassung Die Lozekia,Kovacsia Artengruppe umfasst drei endemische Arten, Lozekia transsilvanica (Westerlund, 1876), Lozekia deubeli (M. Kimakowicz, 1890) und Kovacsia kovacsi (Varga and L. Pintér, 1972), die relativ kleine Verbreitungsgebiete in der karpatisch-pannonischen Region besitzen. Trotz ihrer naturschutzfachlichen Bedeutung wurde die Phylogenie ind biogeographische Historie dieser Arten bisher nicht mit molekularen Methoden untersucht. In dieser Studie werden, basierend auf mitochondrialen COI-Sequenzen, zwei Hauptziele verfolgt: (i) Ermittlung der phylogenetischen Beziehungen in der Gruppe um das aktuelle morphologie.basierte System von Nordsieck (1993) zu testen, und (ii) Rekonstruktion der Verbreitungsgeschichte der drei Arten. In Übereinstimmung mit morphologischen Merkmalsausprägungen wurde die Monophylie und somit die systematische Eigenständigkeit der drei Arten bestätigt, im Gegensatz zur Monophylie der Gattung Lozekia. Die genetische Diversität in L. deubeli war viel höher als in den anderen beiden Arten. Eine mögliche Erklärung dieses Befundes ist, dass L. transsilvanica und K. kovacsi rezenter evolvierte, junge Arten sind. Eine Nested clade phylogeographical analysis (NCPA) zeigte, dass die drei Arten durch Fragmentierungsereignisse entstanden, wahrscheinlich teilten sich L. deubeli und der Vorläufer der anderen beiden Arten zuerst. Auf dem intraspezifischen Niveau spielten Fragmentierungsereignisse und ebenso Arealausdehnungen eine signifikante Rolle in der biogeographischen Geschichte der Artengruppe. Da unsere Ergebnisse auf einem einzigen mitochondrialen Gen basieren, ist es zu früh für Veränderungen am generell akzeptierten System und der Nomenklatur. Weitere molekular-phylogenetische Analysen, die auch nukleäre DNA sequenzen involvieren, müssen das auf unseren Daten basierende evolutionäre Szenario bestätigen und die Fragen klären, ob die drei Arten tatsächlich zur gleichen Gattung, Lozekia, gehören. [source] Species in the genus Turritopsis (Cnidaria, Hydrozoa): a molecular evaluationJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2007M. P. Miglietta Abstract Mitochondrial ribosomal gene sequences were used to investigate the status of several populations of hydromedusae belonging to the genus Turritopsis (family Oceaniidae). Several nominal species have been described for this genus, but most of them had been synonymized and attributed to one cosmopolitan species, Turritopsis nutricula. A recent revision based on morphological and reproductive characters, however, has shown that many different populations can be distinguished and that several of the nominal Turritopsis species are likely valid biological species. Our investigation using molecular sequence data of 16S mitochondrial gene confirms these results. The Mediterranean Turritopsis must be attributed to Turritopsis dohrnii and the Turritopsis of New Zealand must be referred to Turritopsis rubra. The situation of the Japanese Turritopsis is more complex, though all sampled populations are clearly distinct from T. nutricula, a species likely confined to the Western Atlantic. The Japanese Turritopsis fall into three widely separated lineages. One of them, corresponding likely to Turritopsis pacifica, is closely related to T. rubra. A second clade, which potentially represents an as yet undescribed species, produces smaller medusae than T. pacifica and is morphologically distinguishable from it. Finally, a third group was distinguished by a single haplotype sequence that is identical with a Mediterranean sample of T. dohrnii. It is postulated that the last group of Japanese Turritopsis is likely a recent introduction, most probably by human activity. A survey of all known and potentially valid Turritopsis species is given in table format to facilitate identifications and future revisory work. Sommario Sequenze del gene mitocondriale 16S sono state utilizzate per studiare lo stato tassonomico di idroidi appartenenti al genere Turritopsis (Famiglia Oceaniidae). In letteratura, tra le numerose specie nominali di TurritoSPSis descritte, molte di queste sono state successivamente messe in sinonimia e attribuite ad un'unica specie cosmopolita, Turritopsis nutricula. Una recente revisione, basata su dati morfologici e caratteri riproduttivi, ha comunque mostrato che diverse popolazioni di Turritopsis possono essere distinte in numerose specie nominali e probabilmente rappresentano valide specie biologiche. Il presente studio conferma questa recente interpretazione, mediante lo studio di sequenze molecolari del gene 16S. La popolazione mediterranea di Turritopsisè ora attribuita a T. dohrnii, mentre la popolazione neozelandese va ascritta alla specie T. rubra. La situazione nei mari giapponesi si presenta piu' complessa, sebbene tutte le popolazioni ivi campionate siano chiaramente distinte da T. nutricula, la quale risulta confinata unicamente all'Atlantico Orientale. Le sequenze ottenute da esemplari di Turritopsis provenienti dal Giappone formano tre cladi ben distinti. Uno di essi corrisponde a Turritopsis pacifica. Un secondo clade è costituito da popolazioni che producono meduse piu' piccole rispetto a Turritopsis pacifica ed e' dunque anche morfologicamente separato. Un terzo gruppo e' rappresentato da un solo aplotipo identico alle popolazioni mediterranee di T. dohrnii. La presenza di quest'ultimo gruppo di Turritopsis in Giappone e' molto probabilmente il risultato di un'introduzione recente, in seguito ad attività umana. Per facilitare futuri lavori di revisione, è inoltre presentata tavola che riassume le caratteristiche di tutte le specie di Turritopsis conosciute e potenzialmente valide. La tavola cerca di integrare i dati morfologici e riproduttivi già noti e dei dati molecolari ottenuti con questo studio. [source] Phylogenetic inference regarding Parergodrilidae and Hrabeiella periglandulata (,Polychaeta', Annelida) based on 18S rDNA, 28S rDNA and COI sequencesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2004J. Jördens Abstract Parergodrilidae and Hrabeiella periglandulata are Annelida showing different combinations of clitellate-like and aclitellate characters. Similarities between both of these taxa and Clitellata have widely been regarded as the result of convergent evolution due to similar selection pressures. The position of the three taxa in the phylogenetic system of Annelida is still in debate. However, in analyses based on 18S rDNA sequences a close relationship of Parergodrilidae with Orbiniidae and Questidae was suggested. To infer their phylogeny the sequences of the 28S rDNA and of the cytochrome oxidase I (COI) gene of Stygocapitella subterranea, Parergodrilus heideri and H. periglandulata were determined. The data were extended by sequences of various species including species from Clitellata and Orbiniidae. Prior to tree reconstruction the dataset was analysed in detail for phylogenetic content by applying a sliding window analysis, a likelihood mapping and Modeltest V.3.04. Subsequently, generalized parsimony and maximum likelihood methods were employed. Clade robustness was estimated by bootstrapping. In addition, combined analyses of the sequences of 18S rDNA and 28S rDNA as well as of 18S rDNA, 28S rDNA and COI were performed. The combination of the data of the two structure genes and a mitochondrial gene improved the resolution obtained with the single datasets slightly. These analyses support a close relationship of Parergodrilidae and Orbiniidae but cannot resolve the position of H. periglandulata. In every analysis Clitellata cluster within ,Polychaeta', confirming previous investigations. Zusammenfassung Die Parergodrilidae und Hrabeiella periglandulata sind Annelida, die unterschiedliche Kombinationen von Clitellaten- und Nicht-Clitellaten-Merkmalen aufweisen. Die Übereinstimmungen zwischen Parergodrilidae, H. periglandulata und Clitellata sind jedoch meistens als Ergebnis konvergenter Evolution auf Grund ähnlicher Selektionsdrücke gedeutet worden. Die Stellung der drei Taxa im phylogenetischen System der Annelida ist noch immer in Diskussion. Analysen, die auf 18S rDNA Sequenzen basieren, weisen jedoch auf eine wahrscheinliche engere Verwandtschaft der Parergodrilidae mit den Orbiniidae und Questidae hin. Um die Phylogenie dieser Taxa aufzuklären, wurden die Sequenzen der 28S rDNA und des COI Gens von Stygocapitella subterranea, P. heideri and H. periglandulata bestimmt. Die Daten wurden durch Sequenzen verschiedener weiterer Arten erweitert, die auch Arten der Clitellata und Orbiniidae umfassen. Vor der phylogenetischen Rekonstruktion wurde der Datensatz im Detail auf das enthaltene phylogenetische Signal durch eine Sliding Window Analyse, ein Likelihood Mapping und Modeltest V.3.04 getestet. Anschließend wurden generalisierte Parsimonie und Maximum Likelihood Methoden angewendet. Die Robustheit der Bäume wurde durch Parsimonie-Bootstrapping abgeschätzt. Zusätzlich wurden kombinierte Analysen der Sequenzen von 18S rDNA und 28S rDNA als auch von 18S rDNA, 28S rDNA und COI durchgeführt. Die Kombination der Daten der beiden Strukturgene und eines mitochondrialen Gens verbesserten geringfügig die Auflösung verglichen mit den Einzelanalysen. Diese Analysen unterstützen eine nahe Verwandtschaft der Parergodrilidae mit den Orbiniidae aber die Stellung von H. periglandulata kann nicht angegeben werden. In jeder Analyse bilden die Clitellata ein Cluster innerhalb der ,Polychaeta', eine Bestätigung früherer Untersuchungen. [source] Molecular phylogeny of the freshwater sponges in Lake BaikalJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2003H. C. Schröder Abstract The phylogenetic relationship of the freshwater sponges (Porifera) in Lake Baikal is not well understood. A polyphyletic and/or monophyletic origin have been proposed. The (endemic) Baikalian sponges have been subdivided into two families: endemic Lubomirskiidae and cosmopolitan Spongillidae. In the present study, two new approaches have been made to resolve the phylogenetic relationship of Baikalian sponges; analysis of (1) nucleotide sequences from one mitochondrial gene, the cytochrome oxidase subunit I (COI) and of (2) one selected intron from the tubulin gene. Specimens from the following endemic Baikalian sponge species have been studied; Lubomirskia baicalensis , Baikalospongia intermedia, Baikalospongia recta , Baikalospongia bacillifera and Swartschewskia papyracea . They are all grouped to the family of Lubomirskiidae. Sequence comparisons were performed with the ubiquitously distributed freshwater sponge Spongilla lacustris (family Spongillidae) as well as with one marine sponge, Suberites domuncula . A sequence comparison, of the mitochondrial COI gene revealed a monophyletic grouping of the endemic Baikalian sponges with S. lacustris as the most related species to the common ancestor. The sequences of the COI gene from B. recta , B. intermedia , B. bacillifera and L. baicalensis were found to be identical and separated from those of S. lacustris and S. papyracea . In a second approach, the exon/intron sequences framing the intron-2 of the sponge tubulin gene were chosen for the phylogenetic analysis. The intron sequences were aligned and used for construction of a phylogenetic tree. This analysis revealed again a monophyletic grouping with S. lacustris as the closest related species to the common ancestor. It is concluded that the Baikalian sponges, which have been studied here, are of monophyletic origin. Furthermore, the data suggest that the endemic species S. papyracea is the phylogenetically oldest, extant, endemic Baikalian sponge species. Zusammenfassung Die phylogenetischen Beziehungen der Süßwasserschwämme [Porifera] des Baikalsees sind nur wenig verstanden; sowohl ein polyphyletischer als auch monophyletischer Urspung werden vermutet. Die Baikalschwämme werden in zwei Familien, Lubomirskiidae und Spongillidae, eingeteilt. In der vorliegenden Arbeit wird versucht, die phylogenetischen Beziehungen der Baikalschwämme über zwei Wege aufzuklären: über (i) eine Analyse der Nukleotidsequenzen eines Teils des mitochondrialen Gens der Cytochromoxidase-Untereinheit I (COI) und (ii) eines ausgewählten Introns des Tubulingens. Folgende endemischen Spezies wurden untersucht: Lubomirskia baicalensis , Baikalospongia intermedia , Baikalospongia recta , Baikalospongia bacillifera und Swartschewskia papyracea . Sie werden alle der Familie der Lubomirskiidae zugerechnet. Die Sequenzen wurden mit den entsprechenden Sequenzen des ubiquitär vorkommenden Süßwasserschwammes Spongilla lacustris sowie des Meeresschwammes Suberites domuncula verglichen. Die Sequenzvergleiche der mitochondrialen COI-Gene zeigten, daß die Baikalschwämme monophyletischen Ursprungs sind und zusammen mit S. lacustris von einem gemeinsamen Vorfahren abstammen. Die Sequenzen des COI-Gens von B. recta , B. intermedia , B. bacillifera und L. baicalensis sind identisch und trennen sich phylogenetisch von S. lacustris und S. papyracea ab. Bei dem zweiten von uns gewählten Weg wurden die Sequenzen des zweiten Introns des Schwamm-Tubulingens zur phylogenetischen Analyse herangezogen. Auch dabei konnte gezeigt werden, daß die Baikalschwämme , zusammen mit S. lacustris als dem nächsten verwandten gemeinsamen Vorfahren , einen monophyletischen Ursprung haben. S. papyracea stellt den phylogenetisch ältesten endemischen Baikalschwamm dar. [source] Recent evolution of host-associated divergence in the seabird tick Ixodes uriaeMOLECULAR ECOLOGY, Issue 21 2009FLORENT KEMPF Abstract Ecological interactions are an important source of rapid evolutionary change and thus may generate a significant portion of novel biodiversity. Such changes may be particularly prevalent in parasites, where hosts can induce strong selection for adaptation. To understand the relative frequency at which host-associated divergences occur, it is essential to examine the evolutionary history of the divergence process, particularly when it is occurring over large geographical scales where both geographical and host-associated isolation may playa part. In this study, we use population genetics and phylogeography to study the evolutionary history of host-associated divergence in the seabird tick Ixodes uriae (Acari, Ixodidae). We compare results from microsatellite markers that reflect more ecological timescales with a conserved mitochondrial gene (COIII) that reflects more ancient divergence events. Population structure based on microsatellites showed clear evidence of host-associated divergence in all colonies examined. However, isolated populations of the same host type did not always group together in overall analyses and the genetic differentiation among sympatric host races was highly variable. In contrast, little host or geographical structure was found for the mitochondrial gene fragment. These results suggest that host race formation in I. uriae is a recent phenomenon, that it may have occurred several times and that local interactions are at different points in the divergence process. Rapid divergence in I. uriae implies a strong interaction with its local host species, an interaction that will alter the ecological dynamics of the system and modify the epidemiological landscape of circulating micropathogens. [source] Spatial and temporal population genetic structure of four northeastern Pacific littorinid gastropods: the effect of mode of larval development on variation at one mitochondrial and two nuclear DNA markersMOLECULAR ECOLOGY, Issue 10 2009HYUK JE LEE Abstract We investigated the effect of development mode on the spatial and temporal population genetic structure of four littorinid gastropod species. Snails were collected from the same three sites on the west coast of Vancouver Island, Canada in 1997 and again in 2007. DNA sequences were obtained for one mitochondrial gene, cytochrome b (Cyt b), and for up to two nuclear genes, heat shock cognate 70 (HSC70) and aminopeptidase N intron (APN54). We found that the mean level of genetic diversity and long-term effective population sizes (Ne) were significantly greater for two species, Littorina scutulata and L. plena, that had a planktotrophic larval stage than for two species, Littorina sitkana and L. subrotundata, that laid benthic egg masses which hatched directly into crawl-away juveniles. Predictably, two poorly dispersing species, L. sitkana and L. subrotundata, showed significant spatial genetic structure at an 11- to 65-km geographical scale that was not observed in the two planktotrophic species. Conversely, the two planktotrophic species had more temporal genetic structure over a 10-year interval than did the two direct-developing species and showed highly significant temporal structure for spatially pooled samples. The greater temporal genetic variation of the two planktotrophic species may have been caused by their high fecundity, high larval dispersal, and low but spatially correlated early survivorship. The sweepstakes-like reproductive success of the planktotrophic species could allow a few related females to populate hundreds of kilometres of coastline and may explain their substantially larger temporal genetic variance but lower spatial genetic variance relative to the direct-developing species. [source] Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species groupMOLECULAR ECOLOGY, Issue 5 2005DAVID G. CHAPPLE Abstract Palaeoclimatic events and biogeographical processes since the mid-Tertiary are believed to have strongly influenced the evolution and distribution of the terrestrial vertebrate fauna of southeastern Australia. We examined the phylogeography of the temperate-adapted members of the Egernia whitii species group, a group of skinks that comprise both widespread low- to mid-elevation (E. whitii) and montane-restricted species (Egernia guthega, Egernia montana), in order to obtain important insights into the influence of past biogeographical processes on the herpetofauna of southeastern Australia. Sequence data were obtained from all six temperate-adapted species within the E. whitii species group, and specifically from across the distributional ranges of E. whitii, E. guthega and E. montana. We targeted a fragment of the ND4 mitochondrial gene (696 bp) and analysed the data using maximum likelihood and Bayesian methods. Our data reveal a deep phylogeographical break in the east Gippsland region of Victoria between ,northern' (Queensland, New South Wales, Australian Capital Territory) and ,southern' (Victoria, Tasmania, South Australia) populations of E. whitii. This divergence appears to have occurred during the late Miocene,Pliocene, with the Gippsland basin possibly forming a geographical barrier to dispersal. Substantial structuring within both the ,northern' and the ,southern' clades is consistent with the effects of Plio,Pleistocene glacial-interglacial cycles. Pleistocene glacial cycles also appear to have shaped the phylogeographical patterns observed in the alpine species, E. guthega and E. montana. We used our results to examine the biogeographical process that led to the origin and subsequent diversification of the lowland and alpine herpetofauna of southeastern Australia. [source] Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigasterMOLECULAR ECOLOGY, Issue 10 2004I. TARJUELO Abstract Variation in pigmentation is common in marine invertebrates, although few studies have shown the existence of genetic differentiation of chromatic forms in these organisms. We studied the genetic structure of a colonial ascidian with populations of different colour morphs in the northwestern Mediterranean. A fragment of the c oxidase subunit 1 (COI) mitochondrial gene was sequenced in seven populations of Pseudodistoma crucigaster belonging to three different colour morphs (orange, yellow and grey). Maximum likelihood analyses showed two well-supported clades separating the orange morph from the yellow-grey morphotypes. Genetic divergence between these clades was 2.12%, and ,ST values between populations of the two clades were high (average 0.936), pointing to genetic isolation. Nested clade and coalescence analyses suggest that a past fragmentation event may explain the phylogeographical origin of these two clades. Non-neutral mtDNA evolution is observed in our data when comparing the two clades, showing a significant excess of nonsynonymous polymorphism within the yellow,grey morphotype using the McDonald,Kreitman test, which is interpreted as further support of reproductive isolation. We conclude that the two clades might represent separate species. We compare the population genetic differentiation found with that estimated for other colonial and solitary ascidian species, and relate it to larval dispersal capabilities and other life-history traits. [source] Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequencesMOLECULAR ECOLOGY, Issue 10 2003A. J. Crawford Abstract Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c- myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c- myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (FST) based upon mitochondrial data were always higher than nuclear-based FST estimates, even after correcting for the expected fourfold lower effective population size (Ne) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the Ne of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c- myc. Nuclear FST estimates were , 0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of Ne within localities on the order of 105. This value is two to three orders of magnitude larger than any previous Ne estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 107 years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models. [source] Characterization of single-nucleotide polymorphism markers in the Mediterranean mussel, Mytilus galloprovincialisAQUACULTURE RESEARCH, Issue 10 2010Manuel Vera Abstract The Mediterranean mussel, Mytilus galloprovincialis, is one of the most important aquaculture species in Europe. Appropriate molecular markers are required to evaluate genetic resources and to trace genealogies in breeding programmes for improving mussel culture. Microsatellites have been commonly applied to this purpose in other species. However, Mediterranean mussel microsatellites have demonstrated high frequencies of null alleles that hamper accurate estimates of population parameters and confident parentage inferences. As alternative markers, we have characterized in silico 25 potential single-nucleotide polymorphism (SNP) markers in the Mediterranean mussel from expressed sequence tag (EST) public databases. The genotyping of SNPs was performed using a single-base extension approach. Their polymorphism was evaluated in 47 individuals from an Atlantic population. Out of the 25 potential SNPs tested, 12 were technically feasible (producing a single amplicon) and polymorphic. All were biallelic and had an unbiased heterozygosity ranging from 0.160 to 0.504. One SNP was from a mitochondrial gene. The combined potential of nuclear SNPs for parentage assignment gave an exclusion probability of a false couple of parents of 0.9471. These markers will be useful for evaluating resources and tracing genealogies in genetic breeding programmes implemented to solve the main problems of mussel culture. [source] Latitudinal clines in body size, but not in thermal tolerance or heat-shock cognate 70 (HSC70), in the highly-dispersing intertidal gastropod Littorina keenae (Gastropoda: Littorinidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2010HYUK JE LEE Natural populations of widely-distributed animals often exhibit clinal variation in phenotypic traits or in allele frequencies of a particular gene over their geographical range. A planktotrophic intertidal snail, Littorina keenae is broadly distributed along the north-eastern Pacific coast through a large latitudinal range (24°50,N,43°18,N). We tested for latitudinal clines in two complex phenotypic traits , thermal tolerance and body size , and one single locus trait , heat shock cognate 70 (HSC70) , in L. keenae along almost its entire geographical range. We found only weak evidence for a latitudinal cline in the thermal tolerance and no evidence for a cline in allele frequencies at HSC70. However, as predicted by Bergmann's rule, we detected a strong latitudinal cline that accounted for 60% of the variance in body size (R2 = 0.598; P < 0.001). In contrast, body size did not significantly affect thermal tolerance. HSC70 showed no genetic differentiation among the populations, supporting our previous mitochondrial gene-based estimate of high gene flow during this snail's free-swimming larval stage. Given that L. keenae experiences panmixia along its species range, the observed size cline may be partially or entirely caused by a phenotypically plastic response to local thermal environments rather than by genetic divergence in body size among populations in response to locally optimizing natural selection. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 494,505. [source] A three-way contact zone between forms of Patella rustica (Mollusca: Patellidae) in the central Mediterranean SeaBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010ALEXANDRA SÁ-PINTO Previous studies have reported the occurrence of three differentiated mtDNA lineages within Patella rustica in the Mediterranean Sea. Two hypotheses have been proposed to explain these observations: (1) the maintenance of ancestral polymorphism within a single species; (2) the occurrence of cryptic species not identified previously. To distinguish between these hypotheses, we screened the genetic variability at nine allozyme loci, an intron from the ,-amylase gene and a mitochondrial gene for 187 individuals of P. rustica sampled from seven Mediterranean localities. Eight additional localities were screened for the last two markers to place the differentiated lineages in a clear geographic context. Our results demonstrate that the three mtDNA lineages correspond to three distinct nuclear genotype clusters and provide further details on their distribution: the cluster corresponding to the mtDNA lineage from the Atlantic and western Mediterranean extends as far as the south coast of Italy, whereas the remaining two clusters occur in sympatry in the eastern Mediterranean. One of the eastern Mediterranean clusters is highly differentiated and seems to be reproductively isolated from the codistributed form; we therefore suggest that it corresponds to a new species. The remaining two clusters are less differentiated and form a contact zone across south Italian shores. This three-way contact zone constitutes an interesting model for the study of speciation in the marine realm. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 154,169. [source] DIVERSITY IN THE WEAPONS OF SEXUAL SELECTION: HORN EVOLUTION IN THE BEETLE GENUS ONTHOPHAGUS (COLEOPTERA: SCARABAEIDAE)EVOLUTION, Issue 5 2005Douglas J. Emlen Abstract Both ornaments and weapons of sexual selection frequently exhibit prolific interspecific diversity of form. Yet, most studies of this diversity have focused on ornaments involved with female mate choice, rather than on the weapons of male competition. With few exceptions, the mechanisms of divergence in weapon morphology remain largely unexplored. Here, we characterize the evolutionary radiation of one type of weapon: beetle horns. We use partial sequences from four nuclear and three mitochondrial genes to develop a phylogenetic hypothesis for a worldwide sample of 48 species from the dung beetle genus Onthophagus (Coleoptera: Scarabaeidae). We then use these data to test for multiple evolutionary origins of horns and to characterize the evolutionary radiation of horns. Although our limited sampling of one of the world's most species-rich genera almost certainly underestimates the number of evolutionary events, our phylogeny reveals prolific evolutionary lability of these exaggerated sexually selected weapons (more than 25 separate gains and losses of five different horn types). We discuss these results in the context of the natural history of these beetles and explore ways that sexual selection and ecology may have interacted to generate this extraordinary diversity of weapon morphology. [source] EVOLUTION OF SUBTERRANEAN DIVING BEETLES (COLEOPTERA: DYTISCIDAE HYDROPORINI, BIDESSINI) IN THE ARID ZONE OF AUSTRALIAEVOLUTION, Issue 12 2003Remko Leys Abstract Calcrete aquifers in arid inland Australia have recently been found to contain the world's most diverse assemblage of subterranean diving beetles (Coleoptera: Dytiscidae). In this study we test whether the adaptive shift hypothesis (ASH) or the climatic relict hypothesis (CRH) is the most likely mode of evolution for the Australian subterranean diving beetles by using a phylogeny based on two sequenced fragments of mitochondrial genes (CO1 and 16S-tRNA-ND1) and linearized using a relaxed molecular clock method. Most individual calcrete aquifers contain an assemblage of diving beetle species of distantly related lineages and/or a single pair of sister species that significantly differ in size and morphology. Evolutionary transitions from surface to subterranean life took place in a relatively small time frame between nine and four million years ago. Most of the variation in divergence times of the sympatric sister species is explained by the variation in latitude of the localities, which correlates with the onset of aridity from the north to the south and with an aridity maximum in the Early Pliocene (five mya). We conclude that individual calcrete aquifers were colonized by several distantly related diving beetle lineages. Several lines of evidence from molecular clock analyses support the CRH, indicating that all evolutionary transitions took place during the Late Miocene and Early Pliocene as a result of aridification. [source] RECONSTRUCTING PLUMAGE EVOLUTION IN ORIOLES (ICTERUS): REPEATED CONVERGENCE AND REVERSAL IN PATTERNSEVOLUTION, Issue 6 2000Kevin E. Omland Abstract. Several empirical studies suggest that sexually selected characters, including bird plumage, may evolve rapidly and show high levels of convergence and other forms of homoplasy. However, the processes that might generate such convergence have not been explored theoretically. Furthermore, no studies have rigorously addressed this issue using a robust phylogeny and a large number of signal characters. We scored the appearance of 44 adult male plumage characters that varied across New World orioles (Icterus). We mapped the plumage characters onto a molecular phylogeny based on two mitochondrial genes. Reconstructing the evolution of these characters revealed evidence of convergence or reversal in 42 of the 44 plumage characters. No plumage character states are restricted to any groups of species higher than superspecies in the oriole phylogeny. The high frequency of convergence and reversal is reflected in the low overall retention index (RI = 0.66) and the low overall consistency index (CI = 0.28). We found similar results when we mapped plumage changes onto a total evidence tree. Our findings reveal that plumage patterns and colors are highly labile between species of orioles, but highly conserved within the oriole genus. Furthermore, there are at least two overall plumage types that have convergently evolved repeatedly in the three oriole clades. This overall convergence leads to significant conflict between the molecular and plumage data. It is not clear what evolutionary processes lead to this homoplasy in individual characters or convergence in overall pattern. However, evolutionary constraints such as developmental limitations and genetic correlations between characters are likely to play a role. Our results are consistent with the belief that avian plumage and other sexually selected characters may evolve rapidly and may exhibit high homoplasy. The overall convergence in oriole plumage patterns is an interesting evolutionary phenomenon, but it cautions against heavy reliance on plumage characters for constructing phylogenies. [source] Quantitative analysis of human mitochondrial DNA using a real-time PCR assayHIV MEDICINE, Issue 3 2003K Gourlain Objectives Known for their ability to inhibit the human DNA polymerase-,, nucleoside analogues induce toxic effects on mitochondria ranging from increased serum lactate levels to fatal lactic acidosis. DNA polymerase-, ensures the mitochondrial DNA (mtDNA) replication and, thus, its inhibition leads to the decrease of the mtDNA. We describe a real-time PCR assay for mtDNA quantification associating DNA extraction procedures applied on peripheral blood mononuclear cells (PBMCs) and subcutaneous adipose tissues and to study the antiretroviral effect on mitochondria. Methods Total DNA was extracted from PBMCs and subcutaneous adipose tissues. Nuclear and mitochondrial genes were amplified to determine the number of copies of mtDNA per cell using a cyt-b recombinant plasmid as standard control. We analysed eight HIV-infected asymptomatic patients never treated, four patients who had been treated for 6 months with highly active antiretroviral therapy (HAART) and six non-infected donors. Results The mtDNA quantification gave rise to reproducible results as the mean coefficients of variation were 1.09% for replicates of samples undertaken 10 times within the same run, and 5.78% and 3.7% for replicates tested in five different runs at 1:100 and 1:1000 dilutions, respectively. Median levels of mtDNA in PBMCs of healthy donors, naive and treated HIV-infected patients were 2.94, 2.78 and 1.93 log HIV-1 RNA copies/mL, respectively. Whereas DNA from PBMCs was shown to be devoid of inhibitors, subcutaneous adipose tissues needed an extra treatment as they were found to be highly inhibited. Conclusions The method generated consistent and reproducible results and was successfully applied to DNAs extracted from PBMCs and subcutaneous adipose tissues with adapted extraction. The mtDNA changes in PBMCs were found to be fast as they fall off after 6 months' therapy, decreasing from 2.78 to 1.93 log copies/mL. [source] Inflammatory bowel disease-associated gene expression in intestinal epithelial cells by differential cDNA screening and mRNA displayINFLAMMATORY BOWEL DISEASES, Issue 5 2003Kouhei Fukushima M.D., Ph.D. Abstract Intestinal epithelial cells are actively involved in the pathogenesis of inflammatory bowel disease resulting in an altered functional phenotype. The modulation of epithelial gene expression may occur as a consequence of proliferative, metabolic, immune, inflammatory, or genetic abnormalities. Differential screening of epithelial-cell-derived cDNA libraries (from control, ulcerative colitis, and Crohn's disease epithelial cells) and differential display of mRNA were used for investigation of disease-associated gene expression and modulation. Intestinal epithelial gene expression was successfully analyzed by both approaches. Using differential screening with clones encoding mitochondrial genes, quantitative overexpression was observed in both ulcerative colitis and Crohn's disease, while a unique expression of small RNA was noticed in Crohn's disease cells using Alu-homologous clones. Differential display demonstrated that several genes were differentially displayed among control, ulcerative colitis, and Crohn's disease epithelial cells. This was confirmed by immunohistochemical staining of pleckstrin, desmoglein 2 and voltage-dependent anion channel in control and inflammatory bowel disease mucosal samples. In summary, several inflammatory bowel disease-related associations were found. Since both differential screening and display have advantages and limitations, the combination of both techniques can generate complementary information, facilitate search for novel genes, and potentially identify genes uniquely associated with inflammatory bowel disease. [source] Nuclear mitochondrial-like sequences in ants: evidence from Atta cephalotes (Formicidae: Attini)INSECT MOLECULAR BIOLOGY, Issue 6 2007J. Martins Jr Abstract Nuclear mitochondrial-like sequences (numts) are copies of mitochondrial DNA that have migrated to the genomic DNA. We present the first characterization of numts in ants, these numts being homologues to a mitochondrial DNA fragment containing loci the 3, portion of the cytochrome oxidase I gene, an intergenic spacer, the tRNA leucine gene and the 5, portion of the cytochrome oxidase II gene. All 67 specimens of Atta cephalotes (Hymenoptera: Formicidae: Attini) investigated had these homologues, which are within two monophyletic groups that we called numt1 and numt2. Numt1 and numt2 sequences are less variable than mitochondrial sequences and released from the severe purifying selection constraining the evolution of mitochondrial genes. Their formation probably involved bottlenecks related to two distinct transfer events of ancient and fast evolving mitochondrial DNA fragments to comparative slowly evolving nuclear DNA regions. [source] Distribution of nuclear mitochondrial DNA in cattle nuclear genomeJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2007Y. Liu Summary The nuclear mitochondrial pseudogenes (numts), originated from mtDNA insertions into the nuclear genome, have been detected to exist in many species. However, the distribution of numts in cattle nuclear genome yet has not been fully reported. By referring to the whole cattle mtDNA sequence and to the recently released cattle nuclear genome by Human Genome Sequencing Center (HGSC), 303 numts were identified by BLAST with 55 numts unmapped to cattle nuclear genome. Further analysis found that the size of the numts ranges from 37 to 1932 bp, and the homologous identity between numts and their corresponding mtDNA fragments varies from 73 to 98%. Furthermore, the identified cattle numts cover nearly all the mitochondrial genes including mtDNA control region, distributing over all the chromosomes with the exception of the chromosome 23 and Y chromosome (in the latter the sequence data are not available). In the discovered numts, 29 relatively complete mitochondrial genes, which were distributed in 72 numts, were detected. Undoubtedly, this research would provide some valuable information for successive research related to mitochondrial genes and the evolution of cattle. [source] Transcriptional response to aging and caloric restriction in heart and adipose tissueAGING CELL, Issue 5 2007Nancy J. Linford Summary Sustained caloric restriction (CR) extends lifespan in animal models but the mechanism and primary tissue target(s) have not been identified. Gene expression changes with aging and CR were examined in both heart and white adipose tissue (WAT) of Fischer 344 (F344) male rats using Affymetrix® RAE 230 arrays and validated by quantitative reverse transcriptase,polymerase chain reaction (qRT-PCR) on 18 genes. As expected, age had a substantial effect on transcription on both tissues, although only 21% of cardiac age-associated genes were also altered in WAT. Gene set enrichment analysis revealed coordinated small magnitude changes in ribosomal, proteasomal, and mitochondrial genes with similarities in aging between heart and WAT. CR had very different effects on these two tissues at the transcriptional level. In heart, very few age-associated expression changes were affected by CR, while in WAT, CR suppressed a substantial subset of the age-associated changes. Genes unaltered by aging but altered by CR were identified in WAT but not heart. Most interestingly, we identified a gene expression signature associated with mammalian target of rapamycin (mTOR) activity that was down-regulated with age but preserved by CR in both WAT and heart. In addition, lipid metabolism genes, particularly those associated with peroxisome proliferator-activated receptor , (PPAR,)-mediated adipogenesis were reduced with age but preserved with CR in WAT. These results highlight tissue-specific differences in the gene expression response to CR and support a role for CR-mediated preservation of mTOR activity and adipogenesis in aging WAT. [source] Mitochondrial DNA variation of an isolated population of the Adriatic brook lamprey Lampetra zanandreai (Agnatha: Petromyzontidae): phylogeographic and phylogenetic inferencesJOURNAL OF FISH BIOLOGY, Issue 9 2009V. Caputo Two mitochondrial genes were examined to compare an isolated population of the Adriatic brook lamprey Lampetra zanandreai in central Italy with other populations in the species range (Po plain) and with parasitic and freshwater lampreys. A single haplotype, identical to one in a Venetian sample, was found in 10 individuals from the isolated population. The reduced variability is consistent with a history of dispersal after the Pleistocene expansion of the Po basin. The results support the hypothesis of an origin of L. zanandreai and L. fluviatilis,L. planeri from a common anadromous ancestor. [source] Occurrence of the scalloped ribbonfish Zu cristatus(Lampridiformes) in coastal waters of the central Tyrrhenian Sea, ItalyJOURNAL OF FISH BIOLOGY, Issue A 2006P. G. Bianco The occurrence of two individuals of Zu cristatus at 2 m depth in coastal waters of the Gulf of Castellamare (Tyrrhenian Sea, Italy) together with records of this rare pan-Oceanic mesopelagic species is reported. Analyses of two mitochondrial genes (12 s and 16 s; 936 bp) revealed a 2·6% sequence divergence between Mediterranean and Pacific (Japanese) samples of the species. [source] Comparative mtDNA sequence (control region, ATPase 6 and NADH-1) divergence in Hucho taimen(Pallas) across four Siberian river basinsJOURNAL OF FISH BIOLOGY, Issue 4 2005E. Froufe Hucho taimen from eight populations spanning four drainage basins (Amur, Lena, Enisei and Khatanga) were analysed for nucleotide sequence variation across three mitochondrial genes (ATP6, NADH-1 and control region). Samples of H. hucho, Brachymystax lenok(sharp-snouted and blunt-snouted forms) and Parahucho perryi were also included for comparison. Nucleotide variation across a total of 1826 base pairs in H. taimen revealed shared haplotypes between the Amur and Lena basins, further supporting a previous hypothesis of late to post-Pleistocene hydrological exchange between these now disjunct basins. In contrast to an earlier study using the control region alone, clear phylogeographic structure was seen at a large geographic scale, reflected by two phylogroups, one corresponding to the Amur and Lena basins, and the other to the Enisei and Khatanga basins. Comparative rates of divergence revealed considerably faster and less heterogeneous substitution rates for the two coding genes, especially at interspecific levels compared to the mtDNA control region. [source] Rice Mitochondrial Genes Are Transcribed by Multiple Promoters That Are Highly DivergedJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 12 2006Qun-Yu Zhang Abstract Plant mitochondrial genes are often transcribed into complex sets of mRNA. To characterize the transcription initiation and promoter structure, the transcript termini of four mitochondrial genes, atp1, atp6, cob, rps7, in rice (Oryza sativa L.), were determined by using a modified circularized RNA reverse transcription-polymerase chain reaction method. The results revealed that three genes (atp1, atp6, rps7) were transcribed from multiple initiation sites, indicating the presence of multiple promoters. Two transcription termination sites were detected in three genes (atp6, cob, rps7), respectively. Analysis on the promoter architecture showed that the YRTA (Y=T or C, R=A or G) motifs that are widely present in the mitochondrial promoters of other monocotand dicot plant species were detected only in two of the 12 analyzed promoters. Our data suggest that the promoter sequences in the rice mitochondrial genome are highly diverged in comparison to those in other plants, and the YRTA motif is not an essential element for the promoter activity. (Managing editor: Li-Hui Zhao) [source] Lactate Detection by MRS in Mitochondrial Encephalopathy: Optimization of Technical ParametersJOURNAL OF NEUROIMAGING, Issue 1 2008Antônio José da Rocha MD ABSTRACT Mitochondriopathies are a heterogeneous group of diseases with variable phenotypic presentation, which can range from subclinical to lethal forms. They are related either to DNA mutations or nuclear-encoded mitochondrial genes that affect the integrity and function of these organelles, compromising adenosine triphosphate (ATP) synthesis. Magnetic resonance (MR) is the most important imaging technique to detect structural and metabolic brain abnormalities in mitochondriopathies, although in some cases these studies may present normal results, or the identified brain abnormalities may be nonspecific. Magnetic resonance spectroscopy (MRS) enables the detection of high cerebral lactate levels, even when the brain has normal appearance by conventional MR scans. MRS is a useful tool for the diagnosis of mitochondriopathies, but must be correlated with clinical, neurophysiological, biochemical, histological, and molecular data to corroborate the diagnosis. Our aim is to clarify the most relevant issues related to the use of MRS in order to optimize its technical parameters, improving its use in the diagnosis of mitochondriopathies, which is often a challenge. [source] | |||||||||||||||||||||||||||||||||||||||||||