메뉴 건너뛰기




Volumn 31, Issue 12, 2014, Pages 3206-3215

A transcriptomic approach to ribbon worm systematics (nemertea): Resolving the pilidiophora problem

Author keywords

Concatenation; Illumina; Neonemertea; Palaeonemertea; Phylogeny; Pilidiophora; Supermatrix

Indexed keywords

FEASIBILITY STUDY; MONOPHYLY; NEMERTEA; NONHUMAN; TAXONOMY; ANIMAL; CLUSTER ANALYSIS; DNA SEQUENCE; GENE; GENETICS; INVERTEBRATE; METABOLISM; PHYLOGENY;

EID: 84919809422     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu253     Document Type: Article
Times cited : (63)

References (64)
  • 2
    • 84894596325 scopus 로고    scopus 로고
    • Conserved genes, sampling error, and phylogenomic inference
    • Betancur-R. R, Naylor G, Ortí G. 2014. Conserved genes, sampling error, and phylogenomic inference. Syst Biol. 63:257-262.
    • (2014) Syst Biol. , vol.63 , pp. 257-262
    • Betancur, R.R.1    Naylor, G.2    Ortí, G.3
  • 4
    • 67650757433 scopus 로고    scopus 로고
    • TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973.
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 5
    • 84859752085 scopus 로고    scopus 로고
    • A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. Mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea
    • Chen H-X, Sun S-C, Sundberg P, Ren W-C, Norenburg JL. 2012. A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea. BMC Genomics 13:139.
    • (2012) BMC Genomics , vol.13 , pp. 139
    • Chen, H.-X.1    Sun, S.-C.2    Sundberg, P.3    Ren, W.-C.4    Norenburg, J.L.5
  • 6
    • 84887411307 scopus 로고    scopus 로고
    • Morphology of the proboscis of Hubrechtella juliae (Nemertea, Pilidiophora): Implications for pilidiophoran monophyly
    • Chernyshev AV, Magarlamov TY, Turbeville JM. 2013. Morphology of the proboscis of Hubrechtella juliae (Nemertea, Pilidiophora): implications for pilidiophoran monophyly. J Morphol. 274: 1397-1414.
    • (2013) J Morphol. , vol.274 , pp. 1397-1414
    • Chernyshev, A.V.1    Magarlamov, T.Y.2    Turbeville, J.M.3
  • 7
    • 79954529507 scopus 로고    scopus 로고
    • ProtTest 3: Fast selection of best-fit models of protein evolution
    • Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27: 1164-1165.
    • (2011) Bioinformatics , vol.27 , pp. 1164-1165
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 8
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:e68.
    • (2006) PLoS Genet. , vol.2 , pp. e68
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 9
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375.
    • (2005) Nat Rev Genet. , vol.6 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 11
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species trees without concatenation
    • Edwards SV, Liu L, Pearl DK. 2007. High-resolution species trees without concatenation. Proc Natl Acad Sci U S A. 104:5936-5941.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 5936-5941
    • Edwards, S.V.1    Liu, L.2    Pearl, D.K.3
  • 14
    • 0029527107 scopus 로고
    • Nemertean genera and species of the world: An annotated checklist of original names and description citations, synonyms, current taxonomic status, habitats and recorded zoogeographic distribution
    • Gibson R. 1995. Nemertean genera and species of the world: an annotated checklist of original names and description citations, synonyms, current taxonomic status, habitats and recorded zoogeographic distribution. J Nat Hist. 29:271-562.
    • (1995) J Nat Hist. , vol.29 , pp. 271-562
    • Gibson, R.1
  • 18
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data. Mol Biol Evol. 27:570-580.
    • (2010) Mol Biol Evol. , vol.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 19
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254-267.
    • (2006) Mol Biol Evol. , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 22
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 23
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298.
    • (2008) Brief Bioinform. , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 25
    • 84903637222 scopus 로고    scopus 로고
    • New insights into the phylogeny, systematics and DNA barcoding of Nemertea
    • Kvist S, Laumer CE, Junoy J, Giribet G. 2014. New insights into the phylogeny, systematics and DNA barcoding of Nemertea. Invertebr Syst. 28:287-308.
    • (2014) Invertebr Syst. , vol.28 , pp. 287-308
    • Kvist, S.1    Laumer, C.E.2    Junoy, J.3    Giribet, G.4
  • 26
    • 40549115956 scopus 로고    scopus 로고
    • Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
    • Lartillot N, Philippe H. 2008. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci. 363:1463-1472.
    • (2008) Philos Trans R Soc Lond B Biol Sci. , vol.363 , pp. 1463-1472
    • Lartillot, N.1    Philippe, H.2
  • 27
    • 84866924443 scopus 로고    scopus 로고
    • Modeling protein evolution with several amino acid replacement matrices depending on site rates
    • Le SQ, Dang CC, Gascuel O. 2012. Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol. 29:2921-2936.
    • (2012) Mol Biol Evol. , vol.29 , pp. 2921-2936
    • Le Dang, S.Q.C.C.1    Gascuel, O.2
  • 28
    • 80051792622 scopus 로고    scopus 로고
    • Let them fall where they may: Congruence analysis in massive phylogenetically messy data sets
    • Leigh JW, Schliep K, Lopez P, Bapteste E. 2011. Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol. 28:2773-2785.
    • (2011) Mol Biol Evol. , vol.28 , pp. 2773-2785
    • Leigh, J.W.1    Schliep, K.2    Lopez, P.3    Bapteste, E.4
  • 29
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189.
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 30
    • 47749093183 scopus 로고    scopus 로고
    • Estimating species trees using multiple-allele DNA sequence data
    • Liu L, Pearl DK, Brumfield RT, Edwards SV. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62:2080-2091.
    • (2008) Evolution , vol.62 , pp. 2080-2091
    • Liu, L.1    Pearl, D.K.2    Brumfield, R.T.3    Edwards, S.V.4
  • 31
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • Liu L, Yu LL, Pearl DK, Edwards SV. 2009. Estimating species phylogenies using coalescence times among sequences. Syst Biol. 58:468-477.
    • (2009) Syst Biol. , vol.58 , pp. 468-477
    • Liu, L.1    Yu, L.L.2    Pearl, D.K.3    Edwards, S.V.4
  • 32
    • 78649571941 scopus 로고    scopus 로고
    • Development to metamorphosis of the nemertean pilidium larva
    • Maslakova SA. 2010a. Development to metamorphosis of the nemertean pilidium larva. Front Zool. 7:30.
    • (2010) Front Zool. , vol.7 , pp. 30
    • Maslakova, S.A.1
  • 33
    • 78650835592 scopus 로고    scopus 로고
    • The invention of the pilidium larva in an otherwise perfectly good spiralian phylum Nemertea
    • Maslakova SA. 2010b. The invention of the pilidium larva in an otherwise perfectly good spiralian phylum Nemertea. Int Comp Biol. 50: 734-743.
    • (2010) Int Comp Biol. , vol.50 , pp. 734-743
    • Maslakova, S.A.1
  • 34
    • 78650931246 scopus 로고    scopus 로고
    • Calibrating divergence times on species trees versus gene trees: Implications for speciation history of Aphelocoma jays
    • McCormack JE, Heled J, Delaney KS, Peterson AT, Knowles LL. 2011. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution 65: 184-202.
    • (2011) Evolution , vol.65 , pp. 184-202
    • McCormack, J.E.1    Heled, J.2    Delaney, K.S.3    Peterson, A.T.4    Knowles, L.L.5
  • 42
    • 84856735827 scopus 로고    scopus 로고
    • Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing
    • Riesgo A, Pérez-Porro AR, Carmona S, Leys SP, Giribet G. 2012. Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing. Mol Ecol Resour. 12:312-322.
    • (2012) Mol Ecol Resour. , vol.12 , pp. 312-322
    • Riesgo, A.1    Pérez-Porro, A.R.2    Carmona, S.3    Leys, S.P.4    Giribet, G.5
  • 44
    • 84871842306 scopus 로고    scopus 로고
    • Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
    • Roure B, Baurain D, Philippe H. 2013. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 30:197-214.
    • (2013) Mol Biol Evol. , vol.30 , pp. 197-214
    • Roure, B.1    Baurain, D.2    Philippe, H.3
  • 45
    • 79954579960 scopus 로고    scopus 로고
    • Evaluating ortholog prediction algorithms in a yeast model clade
    • Salichos L, Rokas A. 2011. Evaluating ortholog prediction algorithms in a yeast model clade. PLoS One 6:e18755.
    • (2011) PLoS One , vol.6 , pp. e18755
    • Salichos, L.1    Rokas, A.2
  • 46
    • 84878113118 scopus 로고    scopus 로고
    • Inferring ancient divergences requires genes with strong phylogenetic signals
    • Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327-331.
    • (2013) Nature , vol.497 , pp. 327-331
    • Salichos, L.1    Rokas, A.2
  • 47
    • 84898641369 scopus 로고    scopus 로고
    • Novel information theory-based measures for quantifying incongruence among phylogenetic trees
    • Salichos L, Stamatakis A, Rokas A. 2014. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol. 31:1261-1271.
    • (2014) Mol Biol Evol. , vol.31 , pp. 1261-1271
    • Salichos, L.1    Stamatakis, A.2    Rokas, A.3
  • 48
    • 80053148534 scopus 로고    scopus 로고
    • Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus)
    • Satler JD, Starrett J, Hayashi CY, Hedin M. 2011. Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus). PLoS One 6:e25355.
    • (2011) PLoS One , vol.6 , pp. e25355
    • Satler, J.D.1    Starrett, J.2    Hayashi, C.Y.3    Hedin, M.4
  • 50
    • 84859768479 scopus 로고    scopus 로고
    • Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz MH, Zerbino DR, Vingron M, Birney E. 2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28:1086-1092.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 53
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 54
    • 0002585075 scopus 로고
    • Die Polystilifera der Siboga-Expedition
    • Stiasny-Wijnhoff G. 1936. Die Polystilifera der Siboga-Expedition. Siboga Exped. 22:1-214.
    • (1936) Siboga Exped. , vol.22 , pp. 1-214
    • Stiasny-Wijnhoff, G.1
  • 57
    • 35549004491 scopus 로고    scopus 로고
    • Annulonemertes (phylum Nemertea): When segments do not count
    • Sundberg P, Strand M. 2007. Annulonemertes (phylum Nemertea): when segments do not count. Biol Lett. 3:570-573.
    • (2007) Biol Lett. , vol.3 , pp. 570-573
    • Sundberg, P.1    Strand, M.2
  • 58
    • 0034854012 scopus 로고    scopus 로고
    • Phylogenetic relationships among higher nemertean (Nemertea) taxa inferred from 18S rDNA sequences
    • Sundberg P, Turbeville JM, Lindh S. 2001. Phylogenetic relationships among higher nemertean (Nemertea) taxa inferred from 18S rDNA sequences. Mol Phylogenet Evol. 20:327-334.
    • (2001) Mol Phylogenet Evol. , vol.20 , pp. 327-334
    • Sundberg, P.1    Turbeville, J.M.2    Lindh, S.3
  • 59
    • 0037460766 scopus 로고    scopus 로고
    • Ribbon worm relationships: A phylogeny of the phylum Nemertea
    • Thollesson M, Norenburg JL. 2003. Ribbon worm relationships: a phylogeny of the phylum Nemertea. Proc R Soc B Biol Sci. 270: 407-415.
    • (2003) Proc R Soc B Biol Sci. , vol.270 , pp. 407-415
    • Thollesson, M.1    Norenburg, J.L.2
  • 60
    • 0036625772 scopus 로고    scopus 로고
    • Progress in nemertean biology: Development and phylogeny
    • Turbeville JM. 2002. Progress in nemertean biology: development and phylogeny. Integr Comp Biol. 42:692-703.
    • (2002) Integr Comp Biol. , vol.42 , pp. 692-703
    • Turbeville, J.M.1
  • 62
    • 13244256972 scopus 로고    scopus 로고
    • Prot4EST: Translating expressed sequence tags from neglected genomes
    • Wasmuth JD, Blaxter ML. 2004. prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 5:187.
    • (2004) BMC Bioinformatics , vol.5 , pp. 187
    • Wasmuth, J.D.1    Blaxter, M.L.2
  • 64
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.