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Mariana Cabral De Oliveira - One of the best experts on this subject based on the ideXlab platform.

Charles Lydeard - One of the best experts on this subject based on the ideXlab platform.

  • Lydeard C: A Molecular Phylogeny of Physidae (Gastropoda: Basommatophora) based on mitochondrial DNA sequences
    2015
    Co-Authors: Amy R Wethington, Charles Lydeard
    Abstract:

    The family Physidae (Pulmonata: Basommatophora) is a group of freshwater hermaphroditic snails that have a Holarctic distribution with extension into Central and South America. Despite considerable literature justifying various taxonomic schemes and groupings, no classification has been proposed using modern phylogenetic methods. In an effort to expand what is known concerning the evolutionary relationships of Physidae, we examined a portion of the mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes among 66 specimens representing 28 taxa. The Molecular Phylogeny based on mitochondrial sequences supports the monophyly of the family Physidae. Six major clades were uncovered in the analysis, corresponding to differences in penial morphology. These six groups include the following recommended phylogenetic species and species groups: Aplexa elongata (Say), Aplexa 1 group; Physa marmorata Guilding, Aplexa 3 group; P. fontinalis (Linneaus), P. jennessi Dall and P. vernalis Taylor & Jokinen, type a group; P. gyrina Say and P. ‘ancillaria ’ Say, type b group; P. acuta Draparnaud, P. spelunca Turner & Clench, P. species A and P. zionis Pilsbry, type c group; and P. pomilia Conrad and P. hendersoni Clench, type bc group

  • a Molecular Phylogeny of physidae gastropoda basommatophora based on mitochondrial dna sequences
    Journal of Molluscan Studies, 2007
    Co-Authors: Amy R Wethington, Charles Lydeard
    Abstract:

    The family Physidae (Pulmonata: Basommatophora) is a group of freshwater hermaphroditic snails that have a Holarctic distribution with extension into Central and South America. Despite considerable literature justifying various taxonomic schemes and groupings, no classification has been proposed using modern phylogenetic methods. In an effort to expand what is known concerning the evolutionary relationships of Physidae, we examined a portion of the mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes among 66 specimens representing 28 taxa. The Molecular Phylogeny based on mitochondrial sequences supports the monophyly of the family Physidae. Six major clades were uncovered in the analysis, corresponding to differences in penial morphology. These six groups include the following recommended phylogenetic species and species groups: Aplexa elongata (Say), Aplexa 1 group; Physa marmorata Guilding, Aplexa 3 group; P. fontinalis (Linneaus), P. jennessi Dall and P. vernalis Taylor & Jokinen, type a group; P. gyrina Say and P .‘ ancillaria’ Say, type b group; P. acuta Draparnaud, P. spelunca Turner & Clench, P. species A and P. zionis Pilsbry, type c group; and P. pomilia Conrad and P. hendersoni Clench, type bc group.

  • a Molecular Phylogeny of mobile river drainage basin pleurocerid snails caenogastropoda cerithioidea
    Molecular Phylogenetics and Evolution, 1997
    Co-Authors: Charles Lydeard, Wallace E Holznagel, Jeff Garner, Paul D Hartfield, Malcolm J Pierson
    Abstract:

    Abstract Sequences from the mitochondrial 16S rRNA gene were obtained to construct a Molecular Phylogeny for Mobile River drainage basin pleurocerid snails. Data from 876 aligned positions generated a single most-parsimonious tree for each of three analytical approaches: (1) equal weighting, (2) transversions weighted 2× transitions; and (3) transversions weighted 4× transitions. Identical topologies for the resulting trees depict the generaElimiaandPleuroceraas monophyletic sister taxa. The genusLeptoxisis paraphyletic withLeptoxis plicatasister to theElimia+Pleuroceraclade.L. taeniataandL. amplaare sister taxa andL. pictais the most basal pleurocerid examined. When transversions were weighted 10× transitions a single most-parsimonious tree was obtained with the only topological difference beingL. pictadepicted as sister toL. taeniataandL. amplaandL. plicatais now the most basal pleurocerid examined. Many of theElimiaspecies are closely related, but we await further data before making any taxonomic recommendations.L. pictaandL. plicataare quite distinct from each other and all other pleurocerid species examined. These data serves as an important foundation for future studies examining conservation genetics and systematics of this diverse and imperiled family.

Fabrice Not - One of the best experts on this subject based on the ideXlab platform.

  • Molecular Phylogeny and Morphological Evolution of the Acantharia (Radiolaria)
    2020
    Co-Authors: Johan Decelle, Noritoshi Suzuki, Frederic Mahe, Colomban De Vargas, Fabrice Not
    Abstract:

    Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W.T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive Molecular Phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This Molecular Phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference Phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia. © 2011 Elsevier GmbH. All rights reserved. Key words: Acantharia; strontium sulfate; Molecular Phylogeny; Radiolaria; Rhizaria; single-cells. Introduction Acantharia are marine protists taxonomically affiliated to the super-group Rhizaria, the phylum Retaria and to the first rank taxon Radiolaria (Adl et al. 2005; Moreira et al. 2007). Their characteristic star-shaped morphology consists of a skeleton of 10 or 20 spicules made of celestite (strontium sulphate; Odum 1951; Suzuki and Aita, 2011), arranged according to the geometric law of Müller 1 Corresponding author; fax +33 2 98 29 23 23 e-mail decelle@sb-roscoff.fr (J. Decelle). (1859). The skeleton supports a typical rhizarian amoeboid cell whose shape and motility are controlled by-characteristic axopods and myonemes (Febvre, 1981). The Acantharia are the only known organisms able to biomineralize strontium sulfate as the principal component of the skeleton. In surface waters of marine ecosystems, Acantharia consistently outnumber their rhizarian counterparts, such as Foraminifera and Polycystinea (Caron and Swanberg 1990; Michaels et al. 1995; Stoecker et al. 2009 Andreoli 1982), and they can form blooms at certain periods of the year, reaching densities up to 500 000 individuals.m -2 (Massera Bottazzi and Andreoli 1978, 1981). Acantharian cells have also been found hundreds and even thousands of meters deep in the water column (Antia et al. 1993; Bernstein et al. 1987; Martin et al. 2010). Within the marine food web, the Acantharia are active predators (Swanberg and Caron 1991), and they significantly contribute to carbon flux and biogeochemical cycles of strontium and barium in the oceans (Bernstein et al., 1987; Martin et al. 2010). Furthermore, they indirectly contribute to primary production through endosymbiotic relationships with tens to hundreds of microalgae per cell (Michaels 1988(Michaels , 1991. Despite holding a key position in marine ecosystems, the Acantharia have been largely overlooked in ecological studies, essentially due to dissolution of the skeleton in classical fixatives (Beers and Stewart 1970) and the lack of success in culturing them. Our knowledge of their biology and diversity is therefore still in its infancy. The first classification of Acantharia was initiated by Johannes Müller (1856Müller ( , 1859, and completed by his student Ernst Haeckel (1887, 1888). This classification initially comprised 372 species, and further studies added around 80 more (Mielck 1907; Popofsky 1904a Popofsky , b, 1906. All of the diagnostic characters used by these authors were exclusively based on the morphology of the skeleton, such as the length, form and central junction of the spicules. Working on living specimens, W.T. Schewiakoff emended this classification in 1926 by taking into account various features of the cell body (e.g. structure and colour of the cytoplasm, absence or presence of the central capsule, myonemes). In his remarkable monograph based on accurate observations of 500 living cells, he confirmed a total of 130 species, and erected the main taxonomic framework for the Acantharia (Schewiakoff 1926). Minor modifications have since been made to this classification (Bernstein et al. 1999; Febvre et al. 2000; Reshetnyak 1981; Tan 1998; Trégouboff 1953). The class Acantharia currently comprises around 50 genera and 150 species, which are grouped into 18 families distributed in 4 orders: Holacanthida, Chaunacanthida, Symphiacanthida and Arthracanthida (Bernstein et al. 1999). The distinction between the four orders is mainly based on the way the spicules cross the cytoplasm. In the Holacanthida, which was considered by Schewiakoff to be the most basal order, 10 diametral spicules loosely cross the centre of the cell, where they tangle to form a central body (Acanthocollidae) or do not join at all (Acantochiasmidae and Acanthoplegmidae). The Chaunacanthida are characterized by having 20 spicules that are more or less joined at the cell centre and that can be easily dissociated. The Symphiacanthida and the Arthracanthida have 20 tightly joined spicules. The spicules in the Symphiacanthida are attached to each other at the centre by their basal parts, forming a uniform central body. The Arthracanthida, which are characterized by the presence of a thick central capsule, were suggested to represent the most derived forms of Acantharia (Schewiakoff 1926), and are divided into two suborders, the Sphaenacantha and the Phyllacantha. Hitherto, there has been little effort to validate this morphology-based acantharian taxonomy using Molecular phylogenetics. Because of the elusive nature of Acantharia and the difficulty to perform accurate morphological identification on living specimens, very few cells have been isolated, morphologically identified and sequenced (about 20 18S rDNA sequences are publicly available to date). For instance, only 4 of the 30 genera of Arthracanthida are represented in GenBank from isolated specimens (Gilg et al. 2009; Oka et al. 2005; Zettler et al. 1997). Molecular phylogenies including these sequences have nevertheless highlighted inconsistencies within the existing morphological classification. The orders Symphiacanthida and Arthracanthida are mixed, the Chaunacanthida includes specimens identified as Symphiacanthida, and the Holacanthida is simply missing in these analyses (Gilg et al. 2009; Oka et al. 2005). Yet, together with more recent investigations (Krabberød et al. 2011), these studies demonstrated the monophyly of the Acantharia among the Radiolaria. In addition to sequences from isolates, numerous sequences assigned to Acantharia have been retrieved from environmental surveys of genetic diversity in various environments, including coastal López-García et al. 2003 and Edgcomb et al. 2002 respectively). This considerable diversity of environmental 18S rDNA sequences from Acantharia has no associated morphological information. This phenomenon will undoubtedly be further amplified with the advent of environmental surveys using high-throughput DNA sequencing technologies. As for many protist groups, reference sequences (from Molecular Phylogeny of Acantharia 437 morphologically identified organisms) are fundamental anchors to taxonomically characterize the coming profusion of environmental data. The current vision of the systematics of Acantharia is very obscure. Molecular tools can be helpful to examine the relationships among Acantharia, for which morphology-based classification is unstable (Febvre, 1989). The present study aims at producing a comprehensive Molecular Phylogeny of Acantharia, and shedding light on the morphological evolution of this ecologically key group of marine protists. To do so, we isolated, morphologically identified and sequenced ribosomal DNA markers (18S rDNA and partial 28S rDNA) for more than 100 acantharian specimens collected worldwide. This morpho-Molecular approach on single-cells allowed to assess the validity of the current morphological taxonomy, and to explore the evolution of the group. Results Molecular Phylogeny of the Acantharia The entire 18S rDNA and the D1 and D2 regions of the 28S rDNA were sequenced from acantharian cells isolated in the Mediterranean sea, the Red sea, the English Channel and the West Pacific ocean. In total, 107 partial 28S rDNA and 78 18S rDNA sequences were obtained From the 28S rDNA Phylogeny Comparison between Molecular Phylogeny and Morphological Taxonomy Our sampling included representatives of the 4 orders of Acantharia, including the first sequence data for Holacanthida. Based on morphological criteria, we identified 24 (of the 49 described) genera and 14 (of 18) families. Clades A, B, C and D encompass the two acantharian orders Holacanthida and Chaunacanthida, except for Phyllostaurus echinoides (Ei 68) and Acanthostaurus purpurascens (Vil 45) in clade B Clades E and F mainly contain representatives from the Arthracanthida, and a few from the Symphiacanthida. The specimens forming clade E are easier to identify compared to other Acantharia, due to the presence of a shel

  • Molecular Phylogeny and morphological evolution of the acantharia radiolaria
    Protist, 2012
    Co-Authors: Johan Decelle, Noritoshi Suzuki, Frederic Mahe, Colomban De Vargas, Fabrice Not
    Abstract:

    Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W.T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive Molecular Phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This Molecular Phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference Phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia.

Nicolas Puillandre - One of the best experts on this subject based on the ideXlab platform.

  • Molecular Phylogeny and evolution of the cone snails gastropoda conoidea
    Molecular Phylogenetics and Evolution, 2014
    Co-Authors: Nicolas Puillandre, Philippe Bouchet, Thomas F Duda, S Kauferstein, Alan J Kohn, Baldomero M Olivera, Maren Watkins, Christopher G Meyer
    Abstract:

    We present a large-scale Molecular Phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first Phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published Molecular Phylogeny of the entire group nearly a decade ago. Most of the numerous Molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using Molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of Molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the Molecular Phylogeny, is published in an accompanying paper.

  • Molecular Phylogeny taxonomy and distribution of french unio species bivalvia unionidae
    Hydrobiologia, 2014
    Co-Authors: Vincent Prie, Nicolas Puillandre
    Abstract:

    A plethora of unionid names was established in the nineteenth century by the “Nouvelle Ecole”. Although naiad morphological plasticity is well documented, the currently recognized fauna, with 17 species and subspecies included in the French checklist for the Unio genus, is still based upon morphological characters only. Insights have been provided from Molecular data elsewhere in Europe and North Africa, but the French fauna remains unstudied. We present a Molecular Phylogeny of the Unio genus in France based on COI, 16S and 28S genes; taking up all available data in Europe plus 273 specimens collected in all main French drainages. The results show that there are either three valid species in France, with U. pictorum and U. mancus synonymized, or five, with the subspecies U. crassus courtillieri elevated to species level. Subspecies were generally not recovered, which questions the evolutionary units tacitly implied by subspecific names. Although sampling topotypes is the most reliable way to evaluate the status of a nominal subspecies, major human-induced changes in aquatic hydrosystems challenge the method. Nevertheless, operational taxonomy has to rely on ground-truthed data and we propose to reduce the actual number of valid taxa in France to the seven observed operational taxonomic units.

  • the dragon tamed a Molecular Phylogeny of the conoidea gastropoda
    Journal of Molluscan Studies, 2011
    Co-Authors: Nicolas Puillandre, Yuri I Kantor, Alexander Sysoev, Arnaud Couloux, Christopher P Meyer, Timothy A Rawlings, Jonathan A Todd, Philippe Bouchet
    Abstract:

    The superfamily Conoidea constitutes one of the most diverse and taxonomically challenging groups among marine molluscs. Classifications based on shell or radular characters are highly contradictory and disputed. Whereas the monophyly of the Conidae and Terebridae has not been challenged, the other constituents of the superfamily are placed in a ‘trash’ group, the turrids, the non-monophyly of which has been demonstrated by anatomical and Molecular evidence. We present here a new Molecular Phylogeny based on a total of 102 conoidean genera (87 ‘turrids’, 5 cones and 10 terebrids) and three mitochondrial genes [cytochrome oxidase I (COI), 12S rRNA and 16S rRNA]. The resulting tree recognizes 14 clades. When the Conidae (Conus s.l.) and Terebridae are ranked as families for consistency of usage, the ‘turrids’ must be split into 12 families of comparable rank. A new genuslevel classification of the Conoidea is published in an accompanying paper.

  • starting to unravel the toxoglossan knot Molecular Phylogeny of the turrids neogastropoda conoidea
    Molecular Phylogenetics and Evolution, 2008
    Co-Authors: Nicolas Puillandre, Yuri I Kantor, Alexander Sysoev, Arnaud Couloux, Sarah Samadi, Mariecatherine Boisselier, Corinne Cruaud, Philippe Bouchet
    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.

Bhavanath Jha - One of the best experts on this subject based on the ideXlab platform.

  • Molecular Phylogeny and barcoding of caulerpa bryopsidales based on the tufa rbcl 18s rdna and its rdna genes
    PLOS ONE, 2013
    Co-Authors: Mudassar Anisoddin Kazi, C R K Reddy, Bhavanath Jha
    Abstract:

    The biodiversity assessment of different taxa of the genus Caulerpa is of interest from the context of morphological plasticity, invasive potential of some species and biotechnological and pharmacological applications. The present study investigated the identification and Molecular Phylogeny of different species of Caulerpa occurring along the Indian coast inferred from tufA, rbcL, 18S rDNA and ITS rDNA nucleotide sequences. Molecular data confirmed the identification of 10 distinct Caulerpa species: C. veravalensis, C. verticillata, C. racemosa, C. microphysa, C. taxifolia, C. sertularioides, C. scalpelliformis, C. serrulata, C. peltata and C. mexicana. All datasets significantly supported the sister relationship between C. veravalensis and C. racemosa var. cylindracea. It was also concluded from the results that the specimen identified previously as C. microphysa and C. lentillifera could not be considered as separate species. The Molecular data revealed the presence of multiple lineages for C. racemosa which can be resolved into separate species. All four markers were used to ascertain their utility for DNA barcoding. The tufA gene proved a better marker with monophyletic association as the main criteria for identification at the species level. The results also support the use of 18S rDNA insertion sequences to delineate the Caulerpa species through character-based barcoding. The ITS rDNA (5.8S-ITS2) phylogenetic analysis also served as another supporting tool. Further, more sequences from additional Caulerpa specimens will need to be analysed in order to support the role of these two markers (ITS rDNA and 18S insertion sequence) in identification of Caulerpa species. The present study revealed the Phylogeny of Caulerpa as complete as possible using the currently available data, which is the first comprehensive report illustrating the Molecular Phylogeny and barcoding of the genus Caulerpa from Indian waters.