The complete mitochondrial genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis.

Abstract:

BACKGROUND:With more than 100000 living species, mollusks are the second most diverse metazoan phylum. The current taxonomic classification of mollusks recognizes eight classes (Neomeniomorpha, Chaetodermomorpha, Polyplacophora, Monoplacophora, Cephalopoda, Gastropoda, Bivalvia, and Scaphopoda) that exhibit very distinct body plans. In the past, phylogenetic relationships among mollusk classes have been contentious due to the lack of indisputable morphological synapomorphies. Fortunately, recent phylogenetic analyses based on multi-gene data sets are rendering promising results. In this regard, mitochondrial genomes have been widely used to reconstruct deep phylogenies. For mollusks, complete mitochondrial genomes are mostly available for gastropods, bivalves, and cephalopods, whereas other less-diverse lineages have few or none reported. RESULTS:The complete DNA sequence (14662 bp) of the mitochondrial genome of the chaetodermomorph Scutopus ventrolineatus Salvini-Plawen, 1968 was determined. Compared with other mollusks, the relative position of protein-coding genes in the mitochondrial genome of S. ventrolineatus is very similar to those reported for Polyplacophora, Cephalopoda and early-diverging lineages of Bivalvia and Gastropoda (Vetigastropoda and Neritimorpha; but not Patellogastropoda). The reconstructed phylogenetic tree based on combined mitochondrial and nuclear sequence data recovered monophyletic Aplacophora, Aculifera, and Conchifera. Within the latter, Cephalopoda was the sister group of Gastropoda and Bivalvia + Scaphopoda. CONCLUSIONS:Phylogenetic analyses of mitochondrial sequences showed strong among-lineage rate heterogeneity that produced long-branch attraction biases. Removal of long branches (namely those of bivalves and patellogastropods) ameliorated but not fully resolved the problem. Best results in terms of statistical support were achieved when mitochondrial and nuclear sequence data were concatenated.

journal_name

BMC Evol Biol

journal_title

BMC evolutionary biology

authors

Osca D,Irisarri I,Todt C,Grande C,Zardoya R

doi

10.1186/s12862-014-0197-9

subject

Has Abstract

pub_date

2014-09-25 00:00:00

pages

197

issn

1471-2148

pii

s12862-014-0197-9

journal_volume

14

pub_type

杂志文章
  • Genome classification by gene distribution: an overlapping subspace clustering approach.

    abstract:BACKGROUND:Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-8-116

    authors: Li J,Halgamuge SK,Tang SL

    更新日期:2008-04-23 00:00:00

  • Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders.

    abstract:BACKGROUND:The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly d...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-13-183

    authors: Zhang Y,Li S

    更新日期:2013-09-04 00:00:00

  • Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems.

    abstract:BACKGROUND:The discovery of restriction endonucleases and modification DNA methyltransferases, key instruments of genetic engineering, opened a new era of molecular biology through development of the recombinant DNA technology. Today, the number of potential proteins assigned to type II restriction enzymes alone is bey...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-35

    authors: Mokrishcheva ML,Solonin AS,Nikitin DV

    更新日期:2011-02-03 00:00:00

  • New transitional fossil snakeflies from China illuminate the early evolution of Raphidioptera.

    abstract:BACKGROUND:Raphidioptera (snakeflies) is a holometabolous order of the superorder Neuropterida characterized by the narrowly elongate adult prothorax and the long female ovipositor. Mesozoic snakeflies were markedly more diverse than the modern ones are. However, the evolutionary history of Raphidioptera is largely une...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-14-84

    authors: Liu X,Ren D,Yang D

    更新日期:2014-04-18 00:00:00

  • A genomic timescale for the origin of eukaryotes.

    abstract:BACKGROUND:Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relations...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-1-4

    authors: Hedges SB,Chen H,Kumar S,Wang DY,Thompson AS,Watanabe H

    更新日期:2001-01-01 00:00:00

  • On the potential for extinction by Muller's ratchet in Caenorhabditis elegans.

    abstract:BACKGROUND:The self-fertile hermaphrodite worm C. elegans is an important model organism for biology, yet little is known about the origin and persistence of the self-fertilizing mode of reproduction in this lineage. Recent work has demonstrated an extraordinary degree of selfing combined with a high deleterious mutati...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-8-125

    authors: Loewe L,Cutter AD

    更新日期:2008-04-30 00:00:00

  • Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales.

    abstract:BACKGROUND:The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-019-1359-6

    authors: Springer MS,Emerling CA,Gatesy J,Randall J,Collin MA,Hecker N,Hiller M,Delsuc F

    更新日期:2019-01-23 00:00:00

  • Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans.

    abstract:BACKGROUND:Representatives of Cetacea have the greatest absolute brain size among animals, and the largest relative brain size aside from humans. Despite this, genes implicated in the evolution of large brain size in primates have yet to be surveyed in cetaceans. RESULTS:We sequenced ~1240 basepairs of the brain devel...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-98

    authors: McGowen MR,Montgomery SH,Clark C,Gatesy J

    更新日期:2011-04-14 00:00:00

  • Diversification of CYCLOIDEA-like genes in Dipsacaceae (Dipsacales): implications for the evolution of capitulum inflorescences.

    abstract:BACKGROUND:CYCLOIDEA (CYC)-like genes have been implicated in the development of capitulum inflorescences (i.e. flowering heads) in Asteraceae, where many small flowers (florets) are packed tightly into an inflorescence that resembles a single flower. Several rounds of duplication of CYC-like genes have occurred in Ast...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-325

    authors: Carlson SE,Howarth DG,Donoghue MJ

    更新日期:2011-11-06 00:00:00

  • The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic.

    abstract:BACKGROUND:Glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. The glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. However, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and so...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-6-101

    authors: Stechmann A,Baumgartner M,Silberman JD,Roger AJ

    更新日期:2006-11-23 00:00:00

  • Environment-dependent microevolution in a Mediterranean pine (Pinus pinaster Aiton).

    abstract:BACKGROUND:A central question for understanding the evolutionary responses of plant species to rapidly changing environments is the assessment of their potential for short-term (in one or a few generations) genetic change. In our study, we consider the case of Pinus pinaster Aiton (maritime pine), a widespread Mediterr...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-014-0200-5

    authors: Alía R,Chambel R,Notivol E,Climent J,González-Martínez SC

    更新日期:2014-09-23 00:00:00

  • Patterns of genetic variation among geographic and host-plant associated populations of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae).

    abstract:BACKGROUND:Populations of herbivorous insects may become genetically differentiated because of local adaptation to different hosts and climates as well as historical processes, and further genetic divergence may occur following the development of reproductive isolation among populations. Here we investigate the populat...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-1116-7

    authors: Wang YZ,Li BY,Hoffmann AA,Cao LJ,Gong YJ,Song W,Zhu JY,Wei SJ

    更新日期:2017-12-20 00:00:00

  • Neutral genomic signatures of host-parasite coevolution.

    abstract:BACKGROUND:Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-019-1556-3

    authors: Živković D,John S,Verin M,Stephan W,Tellier A

    更新日期:2019-12-19 00:00:00

  • Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms.

    abstract:BACKGROUND:The chloroplast genes matK and rbcL have been proposed as a "core" DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80%) may be inflated because they may have involved comparisons among distantly related species within target genera. To ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-12-73

    authors: Clement WL,Donoghue MJ

    更新日期:2012-05-30 00:00:00

  • ADGRL4/ELTD1 is a highly conserved angiogenesis-associated orphan adhesion GPCR that emerged with the first vertebrates and comprises 3 evolutionary variants.

    abstract:BACKGROUND:Our laboratory identified ADGRL4/ELTD1, an orphan GPCR belonging to the adhesion GPCR (aGPCR) family, as a novel regulator of angiogenesis and a potential anti-cancer therapeutic target. Little is known about how ADGRL4/ELTD1 (and aGPCRs in general) function, a problem compounded by a lack of known ligands o...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-019-1445-9

    authors: Favara DM,Banham AH,Harris AL

    更新日期:2019-07-12 00:00:00

  • Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae).

    abstract:BACKGROUND:The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-016-0806-x

    authors: Arbizu CI,Ellison SL,Senalik D,Simon PW,Spooner DM

    更新日期:2016-10-28 00:00:00

  • Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes.

    abstract:BACKGROUND:Transposable elements (TE) have attracted much attention since they shape the genome and contribute to species evolution. Organisms have evolved mechanisms to control TE activity. Testis expressed 19 (Tex19) represses TE expression in mouse testis and placenta. In the human and mouse genomes, Tex19 and Secre...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-015-0506-y

    authors: Bianchetti L,Tarabay Y,Lecompte O,Stote R,Poch O,Dejaegere A,Viville S

    更新日期:2015-10-12 00:00:00

  • Selection at a genomic region of major effect is responsible for evolution of complex life histories in anadromous steelhead.

    abstract:BACKGROUND:Disparity in the timing of biological events occurs across a variety of systems, yet the understanding of genetic basis underlying diverse phenologies remains limited. Variation in maturation timing occurs in steelhead trout, which has been associated with greb1L, an oestrogen target gene. Previous technique...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-018-1255-5

    authors: Micheletti SJ,Hess JE,Zendt JS,Narum SR

    更新日期:2018-09-15 00:00:00

  • Unravelling the role of host plant expansion in the diversification of a Neotropical butterfly genus.

    abstract:BACKGROUND:Understanding the processes underlying diversification is a central question in evolutionary biology. For butterflies, access to new host plants provides opportunities for adaptive speciation. On the one hand, locally abundant host species can generate ecologically significant selection pressure. But a diver...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-016-0701-5

    authors: McClure M,Elias M

    更新日期:2016-06-16 00:00:00

  • Limited genomic divergence between intraspecific forms of Culex pipiens under different ecological pressures.

    abstract:BACKGROUND:Divergent selection can be a major driver of ecological speciation. In insects of medical importance, understanding the speciation process is both of academic interest and public health importance. In the West Nile virus vector Culex pipiens, intraspecific pipiens and molestus forms vary in ecological and ph...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-015-0477-z

    authors: Gomes B,Wilding CS,Weetman D,Sousa CA,Novo MT,Savage HM,Almeida AP,Pinto J,Donnelly MJ

    更新日期:2015-09-16 00:00:00

  • Genetic tests of ancient asexuality in root knot nematodes reveal recent hybrid origins.

    abstract:BACKGROUND:The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of th...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-8-194

    authors: Lunt DH

    更新日期:2008-07-07 00:00:00

  • Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara).

    abstract:BACKGROUND:Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively d...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-13-208

    authors: Jones ME,Anderson CL,Hipsley CA,Müller J,Evans SE,Schoch RR

    更新日期:2013-09-25 00:00:00

  • Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria.

    abstract:BACKGROUND:The impact of historical contingency, i.e. the past evolutionary history of a population, on further adaptation is mostly unknown at both the phenotypic and genomic levels. We addressed this question using a two-step evolution experiment. First, replicate populations of Escherichia coli were propagated in fo...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-016-0662-8

    authors: Plucain J,Suau A,Cruveiller S,Médigue C,Schneider D,Le Gac M

    更新日期:2016-04-23 00:00:00

  • Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes.

    abstract:BACKGROUND:Rh50 proteins belong to the family of ammonia permeases together with their Amt/MEP homologs. Ammonia permeases increase the permeability of NH3/NH4+ across cell membranes and are believed to be involved in excretion of toxic ammonia and in the maintenance of pH homeostasis. RH50 genes are widespread in euka...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-016-0850-6

    authors: Matassi G

    更新日期:2017-01-03 00:00:00

  • Aphid reproductive investment in response to mortality risks.

    abstract:BACKGROUND:Aphids are striking in their prodigious reproductive capacity and reliance on microbial endosymbionts, which provision their hosts with necessary amino acids and provide protection against parasites and heat stress. Perhaps as a result of this bacterial dependence, aphids have limited immune function that ma...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-10-251

    authors: Barribeau SM,Sok D,Gerardo NM

    更新日期:2010-08-17 00:00:00

  • Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam.

    abstract:BACKGROUND:Synonymous codon usage is typically biased towards translationally superior codons in many organisms. In Drosophila, genomic data indicates that translationally optimal codons and splice optimal codons are mostly mutually exclusive, and adaptation to translational efficiency is reduced in the intron-exon bou...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-9-214

    authors: Takahashi A

    更新日期:2009-08-27 00:00:00

  • SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamily.

    abstract:BACKGROUND:The CACTA (also called En/Spm) superfamily of DNA-only transposons contain the core sequence CACTA in their Terminal Inverted Repeats (TIRs) and so far have only been described in plants. Large transcriptome and genome sequence data have recently become publicly available for Schistosoma mansoni, a digenetic...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-6-89

    authors: DeMarco R,Venancio TM,Verjovski-Almeida S

    更新日期:2006-11-07 00:00:00

  • Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles.

    abstract:BACKGROUND:Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We have studied the molecular evolution of these gene families in the genomes of 48 phylogenetically div...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-014-0249-1

    authors: Greenwold MJ,Bao W,Jarvis ED,Hu H,Li C,Gilbert MT,Zhang G,Sawyer RH

    更新日期:2014-12-12 00:00:00

  • Unique genes in plants: specificities and conserved features throughout evolution.

    abstract:BACKGROUND:Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications. These duplications lead up to the formation of gene families, which are the usual material for many evolutionary studies. However, all characterized genomes include single-copy (unique...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-8-280

    authors: Armisén D,Lecharny A,Aubourg S

    更新日期:2008-10-10 00:00:00

  • Adaptive evolution in the toxicity of a spider's venom enzymes.

    abstract:BACKGROUND:Sphingomyelinase D is the main toxin present in the venom of Loxosceles spiders. Several isoforms present in these venoms can be structurally classified in two groups. Class I Sphingomyelinase D contains a single disulphide bridge and variable loop. Class II Sphingomyelinase D presents an additional intracha...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-015-0561-4

    authors: Pedroso A,Matioli SR,Murakami MT,Pidde-Queiroz G,Tambourgi DV

    更新日期:2015-12-21 00:00:00