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1.
J Med Entomol ; 52(5): 819-28, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26336215

ABSTRACT

Recently, there has been growing interest in analysis of the geographical variation between populations of different Phlebotomus spp. and American sand flies by comparing the sequences of various genes. However, little is known about the genetic structure of the genus Sergentomyia França & Parrot. No study has been carried out on Sergentomyia minuta Rondani. Most authors recognize this as a species with a high degree of morphological polymorphism, and some suspect that there are two subspecies: Se. minuta minuta Rondani in Europe, having about 40 horizontal cibarial teeth (sticks aligned along a straight line in the cibarial cavity), and Se. minuta parroti Adler & Theodor in North Africa, having about 70 cibarial teeth. Here we analyzed phylogeographic patterns using cytochrome b (Cytb) and cytochrome C oxidase I mtDNA for 29 populations from 10 countries: Algeria, Cyprus, France (continental and Corsica), Greece (continental and Crete), Malta, Montenegro, Morocco, Portugal (continental and Atlantic Savage Islands), Spain, and Tunisia. We analyzed intra- and interpopulation patterns of genetic diversity. Our results from Bayesian inference showed a complex genetic structure of Se. minuta with four haplogroups including many different haplotypes. One haplogroup includes all the specimens from North Africa. A second haplogroup includes a few specimens from the south of France, Spain, and one from Portugal. The third includes many specimens from southern France, all the specimens from Corsica, one from Spain, and all specimen from Portugal except one. A fourth branch includes specimens from the Balkans, Malta, Crete, Cyprus, and curiously some from the Atlantic Savage Islands; settlement of the latter population remains unexplained. However, our results suggest that the settlement of the Mediterranean basin could have occurred at the same time for Se. minuta and both Phlebotomus perniciosus Newstead and Phlebotomus ariasi Tonnoir. The spatial distribution of haplotypes was congruent with phylogenetic findings.


Subject(s)
Cytochromes b/genetics , DNA, Mitochondrial/genetics , Electron Transport Complex IV/genetics , Insect Proteins/genetics , Psychodidae/genetics , Animals , Bayes Theorem , Cytochromes b/metabolism , DNA, Mitochondrial/metabolism , Electron Transport Complex IV/metabolism , Female , Genetic Variation , Haplotypes , Insect Proteins/metabolism , Male , Molecular Sequence Data , Phylogeny , Psychodidae/metabolism , Sequence Analysis, DNA
2.
Prenat Diagn ; 35(5): 471-6, 2015 May.
Article in English | MEDLINE | ID: mdl-25643828

ABSTRACT

OBJECTIVE: By-the-book implementation of non-invasive prenatal test and clinical validation for trisomy 21. STUDY DESIGN: Publicly funded prospective study of 225 cases. Women at risk for trisomy 21 > 1/250 based on combined ultrasound and serum markers during first or second trimester were eligible following an informed consent. The technique was established from the available literature and performed on 10 mL of venous blood collected prior to chorionic villus sampling or amniocentesis. Investigators were blinded to the fetal karyotype. Results were expressed in Z-scores of the percentage of each chromosome. RESULTS: Among 976 eligible cases, 225 were processed: 8 were used for pretesting phase and 23 to build a reference set. One hundred thirty six euploid cases and 47 with trisomy 21 were then run randomly. Eleven cases yielded no result (4.8%). Z-scores were above 3 (7.58+/-2.41) for chromosome 21 in all 47 trisomies and in none of the euploid cases (0.11+/-1.0). Z-scores were within normal range for the other chromosomes in both groups. Using a cut-off of 3, sensitivity and specificity were of 100% 95% CI [94.1, 100] and 100% 95% CI [98, 100], respectively. CONCLUSION: Non-invasive prenatal test for trisomy 21 is a robust strategy that can be translated from seminal publications. Publicly funded studies should refine its indications and cost-effectiveness in prenatal screening and diagnosis. © 2015 John Wiley & Sons, Ltd.


Subject(s)
DNA/blood , Down Syndrome/blood , Adult , Amniocentesis , Chorionic Villi Sampling , Cohort Studies , Down Syndrome/diagnosis , Female , Humans , Karyotyping , Pregnancy , Pregnancy Trimester, First , Pregnancy Trimester, Second , Prenatal Diagnosis , Prospective Studies , Real-Time Polymerase Chain Reaction , Risk Assessment
3.
Infect Genet Evol ; 21: 41-53, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24177594

ABSTRACT

In the Phlebotomine sandflies, a few molecular studies related on the genus Sergentomyia have been published. The present study explored the genetic variability within Sergentomyia (Sintonius) clydei (Diptera, Psychodidae). The sampling included 15 populations originating from 12 countries. A morphological approach was coupled to the sequencing of two molecular markers (cytochrome b mtDNA and cacophony nuclear DNA). The most variable morphological characters resided in the cibarium of the females, especially (i) the pigment patch pattern and (ii) the number of cibarial teeth and denticles in the armature. However this morphological approach was unable to individualize any population within S. clydei. The NJ trees based on both molecular markers individualized the specimens from the Aldabra group of islands in the Seychelles. Surprisingly, cyt b variability was not compatible with the known data about the complete submersion of Aldabra occurring relatively recently some 125,000 years ago. The settlement of these islands by S. clydei from continental Africa, the Middle East or Asia, and the value of mtDNA markers are discussed.


Subject(s)
Psychodidae/classification , Psychodidae/physiology , Sequence Analysis, DNA/methods , Animals , Female , Genetic Markers , Genetic Variation , Genome, Insect , Phylogeny , Phylogeography , Psychodidae/genetics , Seychelles
4.
Plant Mol Biol ; 83(6): 591-606, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23877482

ABSTRACT

Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91% of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67%). Non-LTR retrotransposons represent 0.75%, DNA transposons 0.99%, whereas small RNA, simple repeats and low-complexity sequences account for 1.38% of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1% of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6% of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family.


Subject(s)
Chromosomes, Artificial, Bacterial/genetics , Genome, Plant/genetics , Poaceae/genetics , Salt-Tolerant Plants/genetics , Conserved Sequence/genetics , DNA, Plant/genetics , Genome, Plant/physiology , Microsatellite Repeats/genetics , Phylogeny , Poaceae/physiology , Retroelements/genetics , Salt-Tolerant Plants/physiology , Sequence Analysis, DNA/methods , Sequence Homology, Nucleic Acid , Synteny/genetics , Terminal Repeat Sequences/genetics
5.
Mol Ecol ; 22(2): 495-507, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23171163

ABSTRACT

Macaronesia (north-east Atlantic archipelagos) has been host to complex patterns of colonization and differentiation in many groups of organisms including seabirds such as gadfly petrels (genus Pterodroma). Considering the subspecies of widely distributed soft-plumaged petrel for many years, the taxonomic status of the three gadfly petrel taxa breeding in Macaronesia is not yet settled, some authors advocating the presence of three, two or one species. These birds have already been the subject of genetic studies with only one mtDNA gene and relatively modest sample sizes. In this study, using a total of five genes (two mitochondrial genes and three nuclear introns), we investigated the population and phylogeographical histories of petrel populations breeding on Madeira and Cape Verde archipelagos. Despite confirming complete lineage sorting with mtDNA, analyses with nucDNA failed to reveal any population structuring and Isolation with Migration analysis revealed the absence of gene flow during the differentiation process of these populations. It appears that the three populations diverged in the late Pleistocene in the last 150 000 years, that is 10 times more recently than previous estimates based solely on one mtDNA gene. Finally, our results suggest that the Madeira petrel population is ancestral rather than that from Cape Verde. This study strongly advocates the use of nuclear loci in addition to mtDNA in demographical and phylogeographical history studies.


Subject(s)
Biological Evolution , Birds/classification , Genetics, Population , Phylogeography , Animals , Birds/genetics , Cabo Verde , Cell Nucleus/genetics , DNA, Mitochondrial/genetics , Gene Flow , Genetic Variation , Introns , Portugal , Sequence Analysis, DNA
6.
Mar Genomics ; 8: 49-58, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23199880

ABSTRACT

Since the first molecular study of the suborder Notothenioidei in 1994, many phylogenetic studies have been published. Among these, those with a sufficient number of taxa have all suggested that the Nototheniidae, as currently defined, is monophyletic only with the inclusion of the Channichthyidae, Artedidraconidae, Bathydraconidae and Harpagiferidae. This is corroborated by more recent studies including more taxa, but in these studies either the number of nuclear markers or the number of taxa included remained low. We obtained sequences for a large sampling covering most nototheniid genera for five markers described previously for other samplings (COI, Rhodopsin retrogene, Pkd1, HECW2, and SSRP1) and one nuclear marker never used before in phylogenetic inference (PPM1d). The topology for the combined analysis of the nuclear coding genes, as well as the topology for SSRP1 (non-coding) and the combined analysis for all markers all support the paraphyly of Nototheniidae, the genus Notothenia (including Paranotothenia) is the sister group of the clade Channichthyidae, Artedidraconidae, Bathydraconidae and Harpagiferidae, and genus Gobionotothen is a sister group to both. As in previous studies, Trematomus, Lepidonotothen and Patagonotothen form a clade that also includes Indonotothenia cyanobrancha. The position of Pleuragramma antarctica, Dissostichus species and Aethotaxis mitopteryx remains unstable and dependant on markers and analyses. We therefore propose the inclusion of the four families of the High Antarctic clade in the Nototheniidae, and their transformation into subfamilies. We transfer Paranotothenia magellanica to the genus Notothenia, as Notothenia magellanica.


Subject(s)
DNA, Mitochondrial/genetics , Genetic Markers/genetics , Perciformes/classification , Perciformes/genetics , Phylogeny , Animals , Genetic Variation , Molecular Sequence Data
7.
Mol Ecol ; 21(10): 2502-18, 2012 May.
Article in English | MEDLINE | ID: mdl-22469156

ABSTRACT

Sampling at appropriate spatial scales in the Southern Ocean is logistically challenging and may influence estimates of diversity by missing intermediate representatives. With the assistance of sampling efforts especially influenced by the International Polar Year 2007-2008, we gathered nearly 1500 specimens of the crinoid species Promachocrinus kerguelensis from around Antarctica. We used phylogeographic and phylogenetic tools to assess its genetic diversity, demographic history and evolutionary relationships. Six phylogroups (A-F) identified in an earlier study are corroborated here, with the addition of one new phylogroup (E2). All phylogroups are circumpolar, sympatric and eurybathic. The phylogeny of Promachocrinus phylogroups reveals two principal clades that may represent two different cryptic species with contrasting demographic histories. Genetic diversity indices vary dramatically within phylogroups, and within populations, suggesting multiple glacial refugia in the Southern Ocean: on the Kerguelen Plateau, in the East Weddell Sea and the South Shetland Islands (Atlantic sector), and on the East Antarctic continental shelf in the Dumont d'Urville Sea and Ross Sea. The inferences of gene flow vary among the phylogroups, showing discordant spatial patterns. Phylogroup A is the only one found in the Sub-Antarctic region, although without evident connectivity between Bouvet and Kerguelen populations. The Scotia Arc region shows high levels of connectivity between populations in most of the phylogroups, and barriers to gene flow are evident in East Antarctica.


Subject(s)
DNA, Mitochondrial/genetics , Echinodermata/genetics , Genetic Variation , Phylogeny , Sympatry , Animals , Antarctic Regions , Echinodermata/classification , Gene Flow , Genetics, Population , Haplotypes , Molecular Sequence Data , Oceans and Seas , Phylogeography , Sequence Analysis, DNA
8.
Infect Genet Evol ; 12(5): 966-77, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22386852

ABSTRACT

Several populations of the series Guyanensis (Diptera, Psychodidae, Psychodopygus) were collected from the Yasuní National Park in the Ecuadorian Amazon region. The specimens comprised the species Psychodopygus geniculatus, Psychodopygus luisleoni and Psychodopygus corossoniensis. Within Ps. geniculatus, we observed two populations, one with a narrow paramere and relatively short genital filaments and the other characterized by a wider coxite and longer genital filaments. A multiple approach combining morphology, morphometry and DNA sequencing of the ribosomal internal transcribed spacer 2 (ITS2) and the mitochondrial cytochrome b gene was carried out. Morphological, morphometric and molecular data strongly suggested the presence of two populations within Ps. geniculatus. The lack of intermediate forms within these populations supported the proposal of two sympatric species. This report describes Psychodopygus francoisleponti n. sp.


Subject(s)
Psychodidae/classification , Animals , Arthropod Antennae/anatomy & histology , Base Sequence , Cluster Analysis , Cytochromes b/genetics , DNA, Intergenic/genetics , Discriminant Analysis , Ecuador , Female , Genitalia, Male/anatomy & histology , Head/anatomy & histology , Male , Molecular Sequence Data , Polymerase Chain Reaction , Principal Component Analysis , Psychodidae/anatomy & histology , Psychodidae/genetics , Sequence Alignment , Sympatry , Wings, Animal/anatomy & histology
9.
Ann Bot ; 107(8): 1259-77, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21610209

ABSTRACT

BACKGROUND AND AIMS: The Spathelia-Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia-Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. METHODS: A species-level phylogenetic analysis of the Spathelia-Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL-trnF, rps16 and psbA-trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. KEY RESULTS: With the exception of Spathelia, all genera of the Spathelila-Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. CONCLUSIONS: The Spathelia-Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities and oil cells, haplostemonous flowers with appendaged staminal filaments, and a tracheidal tegmen.


Subject(s)
DNA, Plant/chemistry , Evolution, Molecular , Genetic Markers/genetics , Genome, Plastid/genetics , Phylogeny , Rutaceae/classification , Bayes Theorem , DNA, Plant/genetics , Genes, Plant/genetics , Microscopy, Electron, Scanning , Molecular Sequence Data , Plant Leaves/anatomy & histology , Plant Leaves/ultrastructure , Rutaceae/anatomy & histology , Rutaceae/genetics , Seeds/anatomy & histology , Seeds/ultrastructure , Sequence Alignment
10.
Mycologia ; 103(5): 1037-46, 2011.
Article in English | MEDLINE | ID: mdl-21558500

ABSTRACT

This contribution to the genus Cantharellus in North America deals with the smaller, reddish pink species from the Gulf of Mexico states and eastern United States. C. texensis sp. nov. is presented as a new southern lookalike of C. cinnabarinus. The morphological species concepts are supported by newly generated molecular sequence data from the protein coding gene tef1. Similarities to C. persicinus, a third pinkish taxon, are discussed. The very different microscopic features for the three taxa are illustrated in detail. C. cinnabarinus is neotypified. C. minor forma intensissima is considered to be possibly unrelated not only to the discussed taxa in this paper but also to typical C. minor.


Subject(s)
Basidiomycota/classification , Basidiomycota/genetics , Fungal Proteins/genetics , Genes, Fungal , Transcriptional Elongation Factors/genetics , Base Sequence , Basidiomycota/cytology , DNA, Fungal/analysis , Phylogeny , Polymerase Chain Reaction , Sequence Analysis, DNA , Spores, Fungal/classification , Texas , United States
11.
Infect Genet Evol ; 11(2): 334-42, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21093612

ABSTRACT

Stomoxys calcitrans (Diptera: Muscidae: Stomoxyini), a synanthropic fly with a worldwide distribution, is recognized to have an important medical and veterinary impact. We conducted a phylogeographic analysis based on several populations from five major zoogeographic regions of the world in order to analyse population genetic structure of S. calcitrans and to trace its global dispersion. Results from mitochondrial (COI, Cyt-b and ND1-16S) and nuclear (ITS2) DNA show a substantial differentiation of Oriental populations (first lineage) from the Afrotropical, Palearctic, Nearctic, Neotropical and Oceanian populations (second lineage). The divergence time analyses suggest the separation between the two lineages approximately in mid-Pleistocene. Oriental populations are isolated and would not have participated in the colonization of other regions, unlike the Afrotropical one which seems to be the source of S. calcitrans dispersion towards other regions. Demographic analyses indicate that Oriental, Afrotropical and Palearctic regions have undergone a population expansion during late Pleistocene-early Holocene. The expansion time of this cosmopolitan species could have been influenced by continental human expansions and by animal domestication.


Subject(s)
DNA, Mitochondrial/genetics , DNA, Ribosomal Spacer/genetics , Muscidae/genetics , Animals , Base Sequence , Cell Nucleus/genetics , Demography , Genes, Insect , Genes, rRNA , Genetic Markers , Genetic Variation , Haplotypes , Humans , Mitochondria/genetics , Molecular Sequence Data , Phylogeography , Sequence Analysis, DNA
12.
Fungal Genet Biol ; 47(8): 693-706, 2010 Aug.
Article in English | MEDLINE | ID: mdl-20460164

ABSTRACT

We studied the mode of reproduction and its evolution in the fungal subgenus Penicillium Biverticillium using phylogenetic and experimental approaches. We sequenced mating type (MAT) genes and nuclear DNA fragments in sexual and putatively asexual species. Examination of the concordance between individual trees supported the recognition of the morphological species. MAT genes were detected in two putatively asexual species and were found to evolve mostly under purifying selection, although high substitution rates were detected at some sites in some clades. The first steps of sexual reproduction could be induced under controlled conditions in one of the two species, although no mature cleistothecia were produced. Altogether, these findings suggest that the asexual Penicillium species may have lost sex only very recently and/or that the MAT genes are involved in other functions. An ancestral state reconstruction analysis indicated several events of putative sex loss in the genus. Alternatively, it is possible that the supposedly asexual Penicillium species may have retained a cryptic sexual stage.


Subject(s)
Cell Division , Genes, Mating Type, Fungal , Penicillium/growth & development , Penicillium/genetics , Phylogeny , Recombination, Genetic , Cluster Analysis , DNA, Fungal/chemistry , DNA, Fungal/genetics , Evolution, Molecular , Molecular Sequence Data , Sequence Analysis, DNA
13.
Proc Natl Acad Sci U S A ; 107(17): 7680-5, 2010 Apr 27.
Article in English | MEDLINE | ID: mdl-20388903

ABSTRACT

The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera. We sequenced BACs from two major pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, corresponding to 15 regions distributed on 11 B. mori chromosomes, each BAC/region being anchored by known orthologous gene(s) to analyze syntenic relationships and genome rearrangements among the three species. Nearly 300 genes and numerous transposable elements were identified, with long interspersed nuclear elements and terminal inverted repeats the most abundant transposable element classes. There was a high degree of synteny conservation between B. mori and the two noctuid species. Conserved syntenic blocks of identified genes were very small, however, approximately 1.3 genes per block between B. mori and the two noctuid species and 2.0 genes per block between S. frugiperda and H. armigera. This corresponds to approximately two chromosome breaks per Mb DNA per My. This is a much higher evolution rate than among species of the Drosophila genus and may be related to the holocentric nature of the lepidopteran genomes. We report a large cluster of eight members of the aminopeptidase N gene family that we estimate to have been present since the Jurassic. In contrast, several clusters of cytochrome P450 genes showed multiple lineage-specific duplication events, in particular in the lepidopteran CYP9A subfamily. Our study highlights the value of the silkworm genome as a reference in lepidopteran comparative genomics.


Subject(s)
Chromosomes/genetics , Evolution, Molecular , Genes, Insect/genetics , Moths/genetics , Synteny/genetics , Animals , Base Sequence , CD13 Antigens/genetics , Chromosomes, Artificial, Bacterial/genetics , Cluster Analysis , Genomics/methods , Molecular Sequence Data , Multigene Family/genetics , Sequence Analysis, DNA
14.
Infect Genet Evol ; 10(5): 629-37, 2010 Jul.
Article in English | MEDLINE | ID: mdl-20381646

ABSTRACT

Biting midges of the Culicoides obsoletus Meigen species complex (Diptera: Ceratopogonidae) are increasingly suspected as vectors of the recent emergence of bluetongue virus in Europe. Within this complex, identification of the C. obsoletus and Culicoides scoticus females is considered as difficult or sometimes not possible while the identification of males is easy, based on genitalia observation. Nolan et al. (2007) concluded that the distinction of C. obsoletus and C. scoticus females is not possible according to morphology but require molecular analyses. In 2010, the identification of biting midges is done under a stereomicroscope without specific identification within the C. obsoletus species complex. However, such a specific identification distinguishing C. obsoletus s. str. and C. scoticus s. str. is crucial to identify the European competent vectors of the virus, their relative abundances and then accurately assess the risk. We performed morphometric analyses of head, genitalia and thorax of females combined with sequencing of the cytochrome oxidase I barcode fragment of mitochondrial DNA on 88 specimens in order to have a molecular identification of our sampled species. As we knew the actual species of individuals thanks to molecular results, we explored the discriminant power of 15 morphometric variables to distinguish the females according to their species. Multivariate analyses were performed on the morphometric measurements to identify and validate a combination of variables leading to an accurate species identification. It appears that females of C. obsoletus and C. scoticus can be accurately distinguished based on only four variables: width between chitinous plates, length and width of spermathecae1 and length of spermatheca2. This approach should improve the accuracy of morphologically-based species identification.


Subject(s)
Bluetongue/transmission , Ceratopogonidae/anatomy & histology , Ceratopogonidae/classification , Electron Transport Complex IV/genetics , Insect Vectors/anatomy & histology , Insect Vectors/classification , Mitochondria/enzymology , Protein Subunits/genetics , Animals , Bluetongue/epidemiology , Bluetongue virus , Ceratopogonidae/enzymology , Ceratopogonidae/genetics , DNA, Mitochondrial/analysis , Female , Insect Vectors/enzymology , Insect Vectors/genetics , Male , Mitochondria/genetics , Molecular Sequence Data , Phylogeny , Principal Component Analysis
15.
Mol Phylogenet Evol ; 56(3): 1025-39, 2010 Sep.
Article in English | MEDLINE | ID: mdl-20226866

ABSTRACT

With over 1600 extant described species, the Muricidae are one of the most species-rich and morphologically diverse families of molluscs. As predators of molluscs, polychaetes, anthozoans barnacles and other invertebrates, they form an important component of many benthic communities. Traditionally, the classification of muricids at specific and generic levels has been based primarily on shells, while subfamilies have been defined largely by radular morphology, although the composition and relationships of suprageneric groups have never been studied exhaustively. Here we present the phylogenetic relationships of 77 muricid species belonging to nine of the ten currently recognized subfamilies, based on Bayesian inference and Maximum Likelihood analyses of partial sequences of three mitochondrial (12S, 16S and COI) and one nuclear (28S) genes. The resulting topologies are discussed with respect to traditional subfamilial arrangements, and previous anatomical and molecular findings. We confirm monophyly of each of the subfamilies Ergalataxinae, Rapaninae, Coralliophilinae, Haustrinae, Ocenebrinae and Typhinae as previously defined, but earlier concepts of Muricinae, Trophoninae and Muricopsinae are shown to be polyphyletic. Based on our phylogenetic hypothesis, a new arrangement of these subfamilies is proposed.


Subject(s)
Evolution, Molecular , Gastropoda/genetics , Phylogeny , Animals , Bayes Theorem , Cell Nucleus/genetics , DNA, Mitochondrial/genetics , Gastropoda/classification , Likelihood Functions , Models, Genetic , Sequence Alignment , Sequence Analysis, DNA
16.
Mol Ecol ; 19(2): 292-306, 2010 Jan.
Article in English | MEDLINE | ID: mdl-20041992

ABSTRACT

Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely related pathogens specialized on different hosts. For this goal, we sequenced c. 17,000-32,000 ESTs from each of four Microbotryum species, which are fungal pathogens responsible for anther smut disease on host plants in the Caryophyllaceae. Forty-two of the 372 predicted orthologous genes showed significant signal of positive selection, which represents a good number of candidate genes for further investigation. Sequencing 16 of these genes in 9 additional Microbotryum species confirmed that they have indeed been rapidly evolving in the pathogen species specialized on different hosts. The genes showing significant signals of positive selection were putatively involved in nutrient uptake from the host, secondary metabolite synthesis and secretion, respiration under stressful conditions and stress response, hyphal growth and differentiation, and regulation of expression by other genes. Many of these genes had transmembrane domains and may therefore also be involved in pathogen recognition by the host. Our approach thus revealed fruitful and should be feasible for many non-model organisms for which candidate genes for diversifying selection are needed.


Subject(s)
Basidiomycota/genetics , Host-Pathogen Interactions/genetics , Selection, Genetic , Caryophyllaceae/microbiology , Cluster Analysis , DNA, Fungal/genetics , Expressed Sequence Tags , Gene Library , Genes, Fungal , Plant Diseases/microbiology , Sequence Alignment , Sequence Analysis, DNA , Species Specificity
17.
J Zool (1987) ; 278(3): 218-230, 2009 Jul.
Article in English | MEDLINE | ID: mdl-32336891

ABSTRACT

The masked palm civet is distributed through south-east Asia, China and the Himalayas. Because of its potential role in the severe acute respiratory syndrome (SARS) epidemic, it has become important to gather information on this species, and notably to provide a tool to determine the origin of farm and market animals. For this purpose, we studied the genetic variability and the phylogeographic pattern of the masked palm civet Paguma larvata. First, two portions of mitochondrial genes, cytochrome b and the control region, were sequenced for a total of 76 individuals sampled from China, the Indochinese region and the Sundaic region. Results indicated a low genetic variability and suggested a lack of a phylogeographic structure in this species, which do not allow inferring the geographic origin of samples of unknown origin, although it is possible to distinguish individuals from China and the Sundaic region. This low variation is in contrast to the well-marked morphological differentiation between the populations in the Sundaic and Chinese-Indochinese regions. We also used five microsatellite loci to genotype 149 samples from two wild and four farmed populations in China, where the masked palm civet is farmed and where the SARS coronavirus was isolated. These analyses also showed a reduced variability in Chinese civets and showed that farmed populations did not exhibit a lower genetic diversity than wild populations, suggesting frequent introductions of wild individuals into farms.

18.
Mol Ecol Resour ; 9(5): 1311-21, 2009 Sep.
Article in English | MEDLINE | ID: mdl-21564902

ABSTRACT

Identifying life stages of species with complex life histories is problematic as species are often only known and/or described from a single stage. DNA barcoding has been touted as an important tool for linking life-history stages of the same species. To test the current efficacy of DNA barcodes for identifying unknown mollusk life stages, 24 marine gastropod egg capsules were collected off the Philippines in deep water and sequenced for partial fragments of the COI, 16S and 12S mitochondrial genes. Two egg capsules of known shallow-water Mediterranean species were used to calibrate the method. These sequences were compared to those available in GenBank and the Barcode of Life Database (BOLD). Using COI sequences alone, only a single Mediterranean egg capsule was identified to species, and a single Philippine egg capsule was identified tentatively to genus; all other COI sequences recovered matches between 76% and 90% with sequences from BOLD and GenBank. Similarity-based identification using all three markers confirmed the Mediterranean specimens' identifications. A phylogenetic approach was also implemented to confirm similarity-based identifications and provide a higher-taxonomic identification when species-level identifications were not possible. Comparison of available GenBank sequences to the diversity curve of a well-sampled coral reef habitat in New Caledonia highlights the poor taxonomic coverage achieved at present in existing genetic databases, emphasizing the need to develop DNA barcoding projects for megadiverse and often taxonomically challenging groups such as mollusks, to fully realize its potential as an identification and discovery tool.

19.
Mol Phylogenet Evol ; 49(1): 211-26, 2008 Oct.
Article in English | MEDLINE | ID: mdl-18652904

ABSTRACT

For the first time, on the basis of nuclear, plastid and mitochondrial sequence data, the most comprehensive molecular phylogeny of the Dictyotales to date is presented, in a broad context where all brown algal orders are included (except Discosporangiales, Ascoseirales and Nemodermatales). A veto supertree approach was used here to evaluate congruency and conflicts between genes: phylogenetic signal was congruent and mainly carried by chloroplastic information. Supermatrix analyses (BI, ML and MP) revealed that Dictyotales is sister to Onslowiales, this ensemble being sister of a clade also encompassing Sphacelariales and Syringodermatales. The family Scoresbyellaceae is merged into the family Dictyotaceae. Furthermore, the current subdivision of the Dictyotaceae into two tribes was not supported. The enigmatic genus Stoechospermum was shown to belong to the same clade as Dictyota, Rugulopteryx, Scoresbyella and Canistrocarpus. Homoeostrichus and Dictyopteris did not appear monophyletic. Zonaria stipitata clustered with the Spatoglossum species; since this is consistent with its morphological features, the new combination Spatoglossum stipitatum is proposed accordingly.


Subject(s)
Phaeophyceae/classification , Phaeophyceae/genetics , Phylogeny , Bayes Theorem , Chloroplasts/genetics , DNA, Algal/genetics , DNA, Chloroplast/genetics , DNA, Mitochondrial/genetics , DNA, Ribosomal/genetics , Evolution, Molecular , Genes, Mitochondrial , Likelihood Functions , Mitochondria/genetics , Sequence Alignment , Sequence Analysis, DNA
20.
Mol Phylogenet Evol ; 47(3): 1122-34, 2008 Jun.
Article in English | MEDLINE | ID: mdl-18180170

ABSTRACT

The superfamily Conoidea is one of the most speciose groups of marine mollusks, with estimates of about 340 recent valid genera and subgenera, and 4000 named living species. Previous classifications were based on shell and anatomical characters, and clades and phylogenetic relationships are far from well assessed. Based on a dataset of ca. 100 terminal taxa belonging to 57 genera, information provided by fragments of one mitochondrial (COI) and three nuclear (28S, 18S and H3) genes is used to infer the first molecular phylogeny of this group. Analyses are performed on each gene independently as well as for a data matrix where all genes are concatenated, using Maximum Likelihood, Maximum Parsimony and Bayesian approaches. Several well-supported clades are defined and are only partly identifiable to currently recognized families and subfamilies. The nested sampling used in our study allows a discussion of the classification at various taxonomical levels, and several genera, subfamilies and families are found polyphyletic.


Subject(s)
Evolution, Molecular , Gastropoda/classification , Gastropoda/genetics , Phylogeny , Animals , Databases, Genetic
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