When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA.

Abstract:

:Onuphid polychaetes are tubicolous marine worms commonly reported worldwide from intertidal areas to hadal depths. They often dominate in benthic communities and have economic importance in aquaculture and recreational fishing. Here we report the phylogeny of the family Onuphidae based on the combined analyses of nuclear (18S rDNA) and mitochondrial (16S rDNA) genes. Results of Bayesian and Maximum Likelihood analyses supported the monophyly of Onuphidae and its traditional subdivision into two monophyletic subfamilies: Onuphinae and Hyalinoeciinae. Ten of 22 recognized genera were monophyletic with strong node support; four more genera included in this study were either monotypic or represented by a single species. None of the genera appeared para- or polyphyletic and this indicates a strong congruence between the traditional morphology-based systematics of the family and the newly obtained molecular-based phylogenetic reconstructions. Intergeneric relationships within Hyalinoeciinae were not resolved. Two strongly supported monophyletic groups of genera were recovered within Onuphinae: ((Onuphis, Aponuphis), Diopatra, Paradiopatra) and (Hirsutonuphis, (Paxtonia, (Kinbergonuphis, Mooreonuphis))). A previously accepted hypothesis on the subdivision of Onuphinae into the Onuphis group of genera and the Diopatra group of genera was largely rejected.

journal_name

Mol Phylogenet Evol

authors

Budaeva N,Schepetov D,Zanol J,Neretina T,Willassen E

doi

10.1016/j.ympev.2015.10.011

subject

Has Abstract

pub_date

2016-01-01 00:00:00

pages

791-801

issue

Pt B

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(15)00314-0

journal_volume

94

pub_type

杂志文章
  • Systematics, biogeography and evolution of the Saharo-Arabian naked-toed geckos genus Tropiocolotes.

    abstract::Plate tectonics constitute one of the main mechanisms of biological diversification on Earth, often being associated with cladogenetic events at different phylogenetic levels, as well as with exchange of faunas and floras across previously isolated biogeographic regions. North Africa and Arabia share a complex geologi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2020.106969

    authors: Machado L,Salvi D,James Harris D,Brito JC,Crochet PA,Geniez P,Ahmadzadeh F,Carranza S

    更新日期:2021-02-01 00:00:00

  • Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support.

    abstract::Drosophilidae (Diptera) is a diverse, cosmopolitan family of flies. Here, we present a combined analysis phylogeny of Drosophilinae, one of the two subfamilies of Drosophilidae, based on data from six different data partitions, including both molecular and morphological characters. Although our data show support for t...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(02)00226-9

    authors: Remsen J,O'Grady P

    更新日期:2002-08-01 00:00:00

  • A hairy case: The evolution of filtering carnivorous Drusinae (Limnephilidae, Trichoptera).

    abstract::The caddisfly subfamily Drusinae BANKS comprises roughly 100 species inhabiting mountain ranges in Europe, Asia Minor and the Caucasus. A 3-gene phylogeny of the subfamily previously identified three major clades that were corroborated by larval morphology and feeding ecologies: scraping grazers, omnivorous shredders ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2015.07.019

    authors: Vitecek S,Graf W,Kučinić M,Oláh J,Bálint M,Previšić A,Keresztes L,Pauls SU,Waringer J

    更新日期:2015-12-01 00:00:00

  • Molecular systematics and biodiversity of oniscidean isopods in the groundwater calcretes of central Western Australia.

    abstract::Groundwater calcrete aquifers of central Western Australia have been shown to contain a high diversity of stygobiont (subterranean aquatic) invertebrates, with each species confined to an individual calcrete and the entire system resembling a 'subterranean archipelago' containing hundreds of isolated calcretes. Here, ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.07.026

    authors: Javidkar M,Cooper SJB,King RA,Humphreys WF,Bertozzi T,Stevens MI,Austin AD

    更新日期:2016-11-01 00:00:00

  • Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants.

    abstract::We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2003.09.018

    authors: Schneider H,Smith AR,Cranfill R,Hildebrand TJ,Haufler CH,Ranker TA

    更新日期:2004-06-01 00:00:00

  • Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida).

    abstract::Newly emerging molecular phylogenetic hypotheses involving the sponge Order Haplosclerida (Class Demospongiae) are far removed from traditional views on their classification using morphology. In the new grouping of marine haplosclerid taxa by molecular data all members of one highly supported clade were found to have ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2008.02.018

    authors: Redmond NE,McCormack GP

    更新日期:2008-06-01 00:00:00

  • New patellogastropod mitogenomes help counteracting long-branch attraction in the deep phylogeny of gastropod mollusks.

    abstract::Long-branch attraction (LBA) is a well-known artifact in phylogenetic reconstruction. Sparse taxon sampling and extreme heterogeneity of evolutionary rates among lineages generate propitious situations for LBA, even defying probabilistic methods of phylogenetic inference. A clear example illustrating LBA challenges is...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.12.019

    authors: Uribe JE,Irisarri I,Templado J,Zardoya R

    更新日期:2019-04-01 00:00:00

  • Modeling nucleotide evolution at the mesoscale: the phylogeny of the neotropical pitvipers of the Porthidium group (viperidae: crotalinae).

    abstract::We analyzed the phylogeny of the Neotropical pitvipers within the Porthidium group (including intra-specific through inter-generic relationships) using 1.4 kb of DNA sequences from two mitochondrial protein-coding genes (ND4 and cyt-b). We investigated how Bayesian Markov chain Monte-Carlo (MCMC) phylogenetic hypothes...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2005.05.013

    authors: Castoe TA,Sasa MM,Parkinson CL

    更新日期:2005-12-01 00:00:00

  • Aquatic long-distance dispersal and vicariance shape the evolution of an ostracod species complex (Crustacea) in four major Brazilian floodplains.

    abstract::Cladogenesis is often driven by the interplay of dispersal and vicariance. The importance of long-distance dispersal in biogeography and speciation is increasingly recognised, but still ill-understood. Here, we study faunal interconnectivity between four large Brazilian floodplains, namely the Amazon, Araguaia, Pantan...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2017.12.019

    authors: Schön I,Higuti J,Patel T,Martens K

    更新日期:2018-04-01 00:00:00

  • Molecular phylogeny and biogeography of the spider ants, genus Leptomyrmex Mayr (Hymenoptera: Formicidae).

    abstract::This study provides the first phylogenetic reconstruction of the ant genus Leptomyrmex Mayr, a prominent endemic component of rain forest and wet sclerophyll forest in Australia, New Guinea and New Caledonia. Five genes are used to reconstruct phylogeny and estimate of ages of diversification in order to test congruen...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.03.004

    authors: Lucky A

    更新日期:2011-05-01 00:00:00

  • Molecular systematics and origin of sociality in mongooses (Herpestidae, Carnivora).

    abstract::The Herpestidae are small terrestrial carnivores comprising 18 African and Asian genera, currently split into two subfamilies, the Herpestinae and the Galidiinae. The aim of this work was to resolve intra-familial relationships and to test the origin of sociality in the group. For this purpose we analysed sequences of...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/S1055-7903(03)00229-X

    authors: Veron G,Colyn M,Dunham AE,Taylor P,Gaubert P

    更新日期:2004-03-01 00:00:00

  • A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics.

    abstract::Austropurcellia, a genus of dispersal-limited arachnids endemic to isolated patches of coastal rainforest in Queensland, Australia, has a remarkable biogeographic history. The genus is a member of the family Pettalidae, which has a classical temperate Gondwanan distribution; previous work has suggested that Austropurc...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2018.06.029

    authors: Oberski JT,Sharma PP,Jay KR,Coblens MJ,Lemon KA,Johnson JE,Boyer SL

    更新日期:2018-10-01 00:00:00

  • Discrepancies between subgeneric classification and molecular phylogeny of Ceratitis (Diptera: Tephritidae), can the evolution of host use provide some clues?

    abstract::Using molecular data from three protein encoding genes and 49 taxa (98 specimens from 20 African countries), we provide an extended phylogeny of Ceratitis and investigate the evolution of stenophagy across clades. Bayesian tree reconstructions support previously proposed monophyletic lineages (Pardalaspis, Pterandrus ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.04.004

    authors: Erbout N,Virgilio M,Lens L,Barr N,De Meyer M

    更新日期:2011-08-01 00:00:00

  • High male incidence and evolutionary implications of triploid form in northeast Asia Carassius auratus complex.

    abstract::Carassius auratus complex is believed to originate from East Eurasia and consist of diploid and triploid forms. Diploid form reproduces sexually, whereas triploid form possesses mixture modes of unisexual gynogenesis and sexual reproduction, which makes it a unique case to study evolutionary issues among vertebrates. ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.10.006

    authors: Jiang FF,Wang ZW,Zhou L,Jiang L,Zhang XJ,Apalikova OV,Brykov VA,Gui JF

    更新日期:2013-01-01 00:00:00

  • Phylogeography of Chinese bamboo partridge, Bambusicola thoracica thoracica (Aves: Galliformes) in south China: inference from mitochondrial DNA control-region sequences.

    abstract::Chinese bamboo partridge (Bambusicola thoracica thoracica), an endemic subspecies of south China, distributes in mountainous areas that were affected by climate changes throughout the Pleistocene. We investigated the potential impact of cyclical Pleistocene climate changes on phylogeographic patterns using 1140 nucleo...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.01.028

    authors: Huang Z,Liu N,Liang W,Zhang Y,Liao X,Ruan L,Yang Z

    更新日期:2010-07-01 00:00:00

  • A species-to-be? The genetic status and colonization history of the critically endangered Killarney shad.

    abstract::Typically anadromous, the twaite shad (Alosa fallax) can become landlocked and adapt to a fully freshwater life. The only landlocked shad population in Northwestern Europe is found in a lake in Ireland, Lough Leane. The Killarney shad, Alosa killarnensis (or Alosa fallax killarnensis, as it is mostly referred to) disp...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2013.07.029

    authors: Coscia I,McDevitt AD,King JJ,Roche WK,McLoughlin C,Mariani S

    更新日期:2013-12-01 00:00:00

  • Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution.

    abstract::Virtually no information regarding timing of deep lineage divergences within mosquito family (Culicidae) exists, which poses an important problem in the postgenomic era. To address this issue, the complete 15,354 bp mitochondrial genome of Anopheles funestus was assembled from both mtDNA and cDNA sequences generated f...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2006.01.006

    authors: Krzywinski J,Grushko OG,Besansky NJ

    更新日期:2006-05-01 00:00:00

  • Phylogeographic surveys and apomictic genetic connectivity in the North Atlantic red seaweed Mastocarpus stellatus.

    abstract::The North Atlantic red alga Mastocarpus stellatus is characterized by two life histories (sexual-type and direct-type), which correspond to two geographically isolated breeding groups. These features enable M. stellatus to be an interesting model to investigate how environmental shift and apomictic propagation have in...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2015.10.029

    authors: Li JJ,Hu ZM,Liu RY,Zhang J,Liu SL,Duan DL

    更新日期:2016-01-01 00:00:00

  • The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa.

    abstract::The ancestral genome composition in Onychophora (velvet worms) is unknown since only a single species of Peripatidae has been studied thus far, which shows a highly derived gene order with numerous translocated genes. Due to this lack of information from Onychophora, it is difficult to infer the ancestral mitochondria...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2010.05.011

    authors: Braband A,Cameron SL,Podsiadlowski L,Daniels SR,Mayer G

    更新日期:2010-10-01 00:00:00

  • Molecular genetic aspects of tetraploidy in the common carp Cyprinus carpio.

    abstract::Genome duplications are believed to have occurred on multiple occasions in vertebrate evolution. Studies of duplicate gene loci in tetraploid animals may reveal important general aspects of gene duplication, an important mode of gene evolution in metazoans. The common carp Cyprinus carpio has twice as many chromosomes...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1994.1007

    authors: Larhammar D,Risinger C

    更新日期:1994-03-01 00:00:00

  • Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae-Andropogoneae): Taxonomic implications and evidence of interspecific hybridization.

    abstract::Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, it is a challenging task for several reasons, including the low interspecies variability of markers currently used in phylogenetic reconstructions and the occurrence of reticulate evolution and polyploidy i...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2016.02.022

    authors: Welker CAD,Souza-Chies TT,Longhi-Wagner HM,Peichoto MC,McKain MR,Kellogg EA

    更新日期:2016-06-01 00:00:00

  • Isolation, phylogeny and evolution of the SymRK gene in the legume genus Lupinus L.

    abstract::SymRK is one of the key genes involved in initial steps of legume symbiotic association with fungi (mycorrhization) and nitrogen-fixing bacteria (nodulation). A large portion of the sequence encoding the extracellular domain of SYMRK was obtained for 38 lupine accessions and 2 outgroups in order to characterize this r...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.04.017

    authors: Mahé F,Markova D,Pasquet R,Misset MT,Aïnouche A

    更新日期:2011-07-01 00:00:00

  • Species trees for spiny lizards (genus Sceloporus): identifying points of concordance and conflict between nuclear and mitochondrial data.

    abstract::Spiny lizards (genus Sceloporus) represent one of the most diverse and species rich clades of squamate reptiles in continental North America. Sceloporus contains 90+ species, which are partitioned into 21 species groups containing anywhere from one to 15 species. Despite substantial progress towards elucidating the ph...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2009.09.006

    authors: Leaché AD

    更新日期:2010-01-01 00:00:00

  • Molecular phylogeny of Vipera Laurenti, 1768 and the related genera Macrovipera (Reuss, 1927) and Daboia (Gray, 1842), with comments about neurotoxic Vipera aspis aspis populations.

    abstract::We used mtDNA sequences (cytochrome b and NADH dehydrogenase subunit 2) to reconstruct molecular phylogenies of Vipera sensu lato, Vipera sensu stricto, and Vipera aspis. Three major clades were identified within the Vipera s.l. group: (1) the European vipers, (2) the oriental vipers, consisting of Montivipera (Vipera...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2004.11.004

    authors: Garrigues T,Dauga C,Ferquel E,Choumet V,Failloux AB

    更新日期:2005-04-01 00:00:00

  • The effects of sampling on delimiting species from multi-locus sequence data.

    abstract::As a fundamental unit in biology, species are used in a wide variety of studies, and their delimitation impacts every subfield of the life sciences. Thus, it is of utmost importance that species are delimited in an accurate and biologically meaningful way. However, due to morphologically similar, cryptic species, and ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2012.06.031

    authors: Rittmeyer EN,Austin CC

    更新日期:2012-11-01 00:00:00

  • Critical reexamination of palynological characters used to delimit Asclepiadaceae in comparison to the molecular phylogeny obtained from plastid matK sequences.

    abstract::The family Asclepiadaceae (Dicotyledones) was created by Brown in 1810 by splitting in two the family Apocynaceae of Jussieu established in 1789. The morphological characters used to make this distinction were mainly palynological, such as presence of tetrads or pollinia and number and orientation of pollinia. Those c...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1006/mpev.1997.0510

    authors: Civeyrel L,Le Thomas A,Ferguson K,Chase MW

    更新日期:1998-06-01 00:00:00

  • Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca).

    abstract::Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five ...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2006.10.009

    authors: Colgan DJ,Ponder WF,Beacham E,Macaranas J

    更新日期:2007-03-01 00:00:00

  • Phylogeographic patterns of decapod crustaceans at the Atlantic-Mediterranean transition.

    abstract::Comparative multispecies studies allow contrasting the effect of past and present oceanographic processes on phylogeographic patterns. In the present study, a fragment of the COI gene was analyzed in seven decapod crustacean species from five families and with different bathymetric distributions. A total of 769 indivi...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2011.11.009

    authors: García-Merchán VH,Robainas-Barcia A,Abelló P,Macpherson E,Palero F,García-Rodríguez M,Gil de Sola L,Pascual M

    更新日期:2012-02-01 00:00:00

  • Molecular markers reveal genetic isolation and phylogeography of the S and F intersterility groups of the wood-decay fungus Heterobasidion annosum.

    abstract::The root-rot fungus Heterobasidion annosum (Fr.) Bref. species complex consists of three intersterility groups (S, F, and P), separated by their host affinity. The phylogenetic relationship of the species complex was studied, with the focus on the S and F groups, by comparing DNA sequences of four nuclear gene fragmen...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/s1055-7903(03)00087-3

    authors: Johannesson H,Stenlid J

    更新日期:2003-10-01 00:00:00

  • Phylogenetic comparison of metabolic capacities of organisms at genome level.

    abstract::Horizontal gene transfer (HGT) has been shown to widely spread in organisms by comparative genomic studies. However, its effect on the phylogenetic relationship of organisms, especially at a system level of different cellular functions, is still not well understood. In this work, we have constructed phylogenetic trees...

    journal_title:Molecular phylogenetics and evolution

    pub_type: 杂志文章

    doi:10.1016/j.ympev.2003.08.011

    authors: Ma HW,Zeng AP

    更新日期:2004-04-01 00:00:00