메뉴 건너뛰기




Volumn 9, Issue 10, 2014, Pages

Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; GENETIC MARKER;

EID: 84908377778     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0111011     Document Type: Article
Times cited : (16)

References (50)
  • 1
    • 0842322955 scopus 로고    scopus 로고
    • Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA
    • Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:397-423.
    • (2003) Annu Rev Ecol Evol Syst , vol.34 , pp. 397-423
    • Funk, D.J.1    Omland, K.E.2
  • 2
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging?
    • Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1-19.
    • (2009) Evolution , vol.63 , pp. 1-19
    • Edwards, S.V.1
  • 3
    • 84888626247 scopus 로고    scopus 로고
    • High-throughput genomic data in systematics and phylogenetics
    • Lemmon EM, Lemmon AR (2013) High-throughput genomic data in systematics and phylogenetics. Annu Rev Ecol Evol Syst 44:99-121.
    • (2013) Annu Rev Ecol Evol Syst , vol.44 , pp. 99-121
    • Lemmon, E.M.1    Lemmon, A.R.2
  • 4
    • 84865248393 scopus 로고    scopus 로고
    • The promises and pitfalls of next-generation sequencing data in phylogeography
    • Carstens B, Lemmon AR, Lemmon EM (2012) The promises and pitfalls of next-generation sequencing data in phylogeography. Syst Biol 61:713-715.
    • (2012) Syst Biol , vol.61 , pp. 713-715
    • Carstens, B.1    Lemmon, A.R.2    Lemmon, E.M.3
  • 5
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56:17-24.
    • (2007) Syst Biol , vol.56 , pp. 17-24
    • Kubatko, L.S.1    Degnan, J.H.2
  • 6
    • 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 USA 104:5936-5941.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 5936-5941
    • Edwards, S.V.1    Liu, L.2    Pearl, D.K.3
  • 7
    • 84861373817 scopus 로고    scopus 로고
    • Concatenation and concordance in the reconstruction of mouse lemur phylogeny: An empirical demonstration of the effect of allele sampling in phylogenetics
    • Weisrock DW, Smith SD, Chan LM, Biebouw K, Kappeler PM, et al.. (2012) Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. Mol Biol Evol 29:1615-1630.
    • (2012) Mol Biol Evol , vol.29 , pp. 1615-1630
    • Weisrock, D.W.1    Smith, S.D.2    Chan, L.M.3    Biebouw, K.4    Kappeler, P.M.5
  • 8
    • 84897908606 scopus 로고    scopus 로고
    • Ignoring heterozygous sites biases phylogenomic estimates of divergence times: Implications for the evolutionary history of Microtus voles
    • Lischer H e L, Excoffier L, Heckel G (2014) Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of Microtus voles. Mol Biol Evol 31:817-831.
    • (2014) Mol Biol Evol , vol.31 , pp. 817-831
    • Lischer, H.E.L.1    Excoffier, L.2    Heckel, G.3
  • 10
    • 33846839295 scopus 로고    scopus 로고
    • Concordance trees, concordance factors, and the exploration of reticulate genealogy
    • Baum DA (2007) Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon 56:417-426.
    • (2007) Taxon , vol.56 , pp. 417-426
    • Baum, D.A.1
  • 11
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24:332-340.
    • (2009) Trends Ecol Evol , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 12
    • 84888140829 scopus 로고    scopus 로고
    • How low can you go? The effects of mutation rate on the accuracy of species-tree estimation
    • Lanier HC, Huang H, Knowles LL (2014) How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. Mol Phylogenet Evol 70:112-119.
    • (2014) Mol Phylogenet Evol , vol.70 , pp. 112-119
    • Lanier, H.C.1    Huang, H.2    Knowles, L.L.3
  • 13
    • 79951561454 scopus 로고    scopus 로고
    • The accuracy of species tree estimation under simulation: A comparison of methods
    • Leaché AD, Rannala B (2011) The accuracy of species tree estimation under simulation: a comparison of methods. Syst Biol 60:126-137.
    • (2011) Syst Biol , vol.60 , pp. 126-137
    • Leaché, A.D.1    Rannala, B.2
  • 14
    • 84887319003 scopus 로고    scopus 로고
    • The influence of gene flow on species tree estimation: A simulation study
    • Leaché AD, Harris RB, Rannala B, Yang Z (2014) The influence of gene flow on species tree estimation: a simulation study. Syst Biol 63:17-30.
    • (2014) Syst Biol , vol.63 , pp. 17-30
    • Leaché, A.D.1    Harris, R.B.2    Rannala, B.3    Yang, Z.4
  • 15
    • 84904966117 scopus 로고    scopus 로고
    • Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow
    • Kutschera VE, Bidon T, Hailer F, Rodi JL, Fain SR, et al.. (2014) Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow. Mol Biol Evol 31:2004-2017.
    • (2014) Mol Biol Evol , vol.31 , pp. 2004-2017
    • Kutschera, V.E.1    Bidon, T.2    Hailer, F.3    Rodi, J.L.4    Fain, S.R.5
  • 16
    • 40549084970 scopus 로고    scopus 로고
    • The phylogeny of crested newts (Triturus cristatus superspecies): Nuclear and mitochondrial genetic characters suggest a hard polytomy, in line with the paleogeography of the centre of origin
    • Arntzen JW, Espregueira Themudo G, Wielstra B (2007) The phylogeny of crested newts (Triturus cristatus superspecies): nuclear and mitochondrial genetic characters suggest a hard polytomy, in line with the paleogeography of the centre of origin. Contrib Zool 76:261-278.
    • (2007) Contrib Zool , vol.76 , pp. 261-278
    • Arntzen, J.W.1    Espregueira Themudo, G.2    Wielstra, B.3
  • 17
    • 77954722261 scopus 로고    scopus 로고
    • Where to draw the line? A nuclear genetic perspective on proposed range boundaries of the crested newts Triturus karelinii and T. Arntzeni
    • Arntzen JW, Wielstra B (2010) Where to draw the line? A nuclear genetic perspective on proposed range boundaries of the crested newts Triturus karelinii and T. arntzeni. Amphibia-Reptilia 31:311-322.
    • (2010) Amphibia-reptilia , vol.31 , pp. 311-322
    • Arntzen, J.W.1    Wielstra, B.2
  • 18
    • 53249153509 scopus 로고    scopus 로고
    • Triturus cristatus Superspecies - Kammolch-Artenkreis (Triturus cristatus (Laurenti, 1768) - Nördlicher Kammolch, Triturus carnifex (Laurenti, 1768) - Italienischer Kammolch, Triturus dobrogicus (Kiritzescu, 1903) - Donau-Kammolch, Triturus karelinii (Strauch, 1870) - Südlicher Kammolch)
    • Grossenbacher K, Thiesmeier B, editors, Wiebelsheim: Aula-Verlag
    • Arntzen JW (2003) Triturus cristatus Superspecies - Kammolch-Artenkreis (Triturus cristatus (Laurenti, 1768) - Nördlicher Kammolch, Triturus carnifex (Laurenti, 1768) - Italienischer Kammolch, Triturus dobrogicus (Kiritzescu, 1903) - Donau-Kammolch, Triturus karelinii (Strauch, 1870) - Südlicher Kammolch). In: Grossenbacher K, Thiesmeier B, editors. Handbuch der Reptilien und Amphibien Europas Schwanzlurche IIA. Wiebelsheim: Aula-Verlag. pp. 421-514.
    • (2003) Handbuch der Reptilien und Amphibien Europas Schwanzlurche IIA , pp. 421-514
    • Arntzen, J.W.1
  • 19
    • 79958285525 scopus 로고    scopus 로고
    • Unraveling the rapid radiation of crested newts (Triturus cristatus superspecies) using complete mitogenomic sequences
    • Wielstra B, Arntzen JW (2011) Unraveling the rapid radiation of crested newts (Triturus cristatus superspecies) using complete mitogenomic sequences. BMC Evol Biol 11:162.
    • (2011) BMC Evol Biol , vol.11 , pp. 162
    • Wielstra, B.1    Arntzen, J.W.2
  • 20
    • 84873718216 scopus 로고    scopus 로고
    • A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species
    • Wielstra B, Baird AB, Arntzen JW (2013) A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species. Mol Phylogenet Evol 67:167-175.
    • (2013) Mol Phylogenet Evol , vol.67 , pp. 167-175
    • Wielstra, B.1    Baird, A.B.2    Arntzen, J.W.3
  • 21
    • 65649096520 scopus 로고    scopus 로고
    • Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus, Salamandridae)
    • Espregueira Themudo G, Wielstra B, Arntzen JW (2009) Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus, Salamandridae). Mol Phylogenet Evol 52:321-328.
    • (2009) Mol Phylogenet Evol , vol.52 , pp. 321-328
    • Espregueira Themudo, G.1    Wielstra, B.2    Arntzen, J.W.3
  • 22
    • 1642285792 scopus 로고    scopus 로고
    • The incomplete natural history of mitochondria
    • Ballard J W O, Whitlock MC (2004) The incomplete natural history of mitochondria. Mol Ecol 13:729-744.
    • (2004) Mol Ecol , vol.13 , pp. 729-744
    • Ballard, J.W.O.1    Whitlock, M.C.2
  • 23
    • 77958059433 scopus 로고    scopus 로고
    • Sources of error inherent in species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods
    • Huang H, He Q, Kubatko LS, Knowles LL (2010) Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Syst Biol 59:573-583.
    • (2010) Syst Biol , vol.59 , pp. 573-583
    • Huang, H.1    He, Q.2    Kubatko, L.S.3    Knowles, L.L.4
  • 24
    • 84875063013 scopus 로고    scopus 로고
    • Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling
    • Wielstra B, Crnobrnja-Isailović J, Litvinchuk SN, Reijnen BT, Skidmore AK, et al.. (2013) Tracing glacial refugia of Triturus newts based on mitochondrial DNA phylogeography and species distribution modeling. Front Zool 10:13.
    • (2013) Front Zool , vol.10 , pp. 13
    • Wielstra, B.1    Crnobrnja-Isailović, J.2    Litvinchuk, S.N.3    Reijnen, B.T.4    Skidmore, A.K.5
  • 25
    • 0032805966 scopus 로고    scopus 로고
    • Marking and tissue sampling effects on body condition and survival in the newt Triturus cristatus
    • Arntzen JW, Smithson A, Oldham RS (1999) Marking and tissue sampling effects on body condition and survival in the newt Triturus cristatus. Journal of Herpetology 33:567-576.
    • (1999) Journal of Herpetology , vol.33 , pp. 567-576
    • Arntzen, J.W.1    Smithson, A.2    Oldham, R.S.3
  • 26
    • 84879774396 scopus 로고    scopus 로고
    • A revised taxonomy of crested newts in the Triturus karelinii group (Amphibia: Caudata: Salamandridae), with the description of a new species
    • Wielstra B, Litvinchuk SN, Naumov B, Tzankov N, Arntzen JW (2013) A revised taxonomy of crested newts in the Triturus karelinii group (Amphibia: Caudata: Salamandridae), with the description of a new species. Zootaxa 3682:441-453.
    • (2013) Zootaxa , vol.3682 , pp. 441-453
    • Wielstra, B.1    Litvinchuk, S.N.2    Naumov, B.3    Tzankov, N.4    Arntzen, J.W.5
  • 27
    • 84899701187 scopus 로고    scopus 로고
    • Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species
    • Wielstra B, Arntzen JW (2014) Exploring the effect of asymmetric mitochondrial DNA introgression on estimating niche divergence in morphologically cryptic species. PLoS ONE 9:e95504.
    • (2014) PLoS ONE , vol.9 , pp. e95504
    • Wielstra, B.1    Arntzen, J.W.2
  • 28
    • 84905974425 scopus 로고    scopus 로고
    • Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform
    • Wielstra B, Duijm E, Lagler P, Lammers Y, Meilink W R M, et al.. (2014) Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform. Mol Ecol Resour 14:1080-1089.
    • (2014) Mol Ecol Resour , vol.14 , pp. 1080-1089
    • Wielstra, B.1    Duijm, E.2    Lagler, P.3    Lammers, Y.4    Meilink, W.R.M.5
  • 29
    • 84897654018 scopus 로고    scopus 로고
    • Alternative reproductive tactics and sexbiased gene expression: The study of the bulb mite transcriptome
    • Stuglik MT, Babik W, Radwan J (2014) Alternative reproductive tactics and sexbiased gene expression: the study of the bulb mite transcriptome. Ecology and Evolution 4:623-632.
    • (2014) Ecology and Evolution , vol.4 , pp. 623-632
    • Stuglik, M.T.1    Babik, W.2    Radwan, J.3
  • 30
    • 84894283962 scopus 로고    scopus 로고
    • Development, validation and high throughput analysis of sequence markers in non-model species
    • Zieliń Ski P, Stuglik MT, Dudek K, Konczal M, Babik W (2014) Development, validation and high throughput analysis of sequence markers in non-model species. Mol Ecol Resour 14:352-360.
    • (2014) Mol Ecol Resour , vol.14 , pp. 352-360
    • Ski, P.Z.1    Stuglik, M.T.2    Dudek, K.3    Konczal, M.4    Babik, W.5
  • 31
    • 46049108350 scopus 로고    scopus 로고
    • BatchPrimer3: A high throughput web application for PCR and sequencing primer design
    • You F, Huo N, Gu Y, Luo M-c, Ma Y, et al.. (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253.
    • (2008) BMC Bioinformatics , vol.9 , pp. 253
    • You, F.1    Huo, N.2    Gu, Y.3    Luo, M.-C.4    Ma, Y.5
  • 33
    • 67449163699 scopus 로고    scopus 로고
    • The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
    • Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM (2009) The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol 58:130-145.
    • (2009) Syst Biol , vol.58 , pp. 130-145
    • Lemmon, A.R.1    Brown, J.M.2    Stanger-Hall, K.3    Lemmon, E.M.4
  • 34
    • 65649117685 scopus 로고    scopus 로고
    • DnaSP v5: A software for comprehensive analysis of DNA polymorphism data
    • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
    • (2009) Bioinformatics , vol.25 , pp. 1451-1452
    • Librado, P.1    Rozas, J.2
  • 35
    • 62349132559 scopus 로고    scopus 로고
    • Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
    • Corander J, Marttinen P, Siren J, Tang J (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9:539.
    • (2008) BMC Bioinformatics , vol.9 , pp. 539
    • Corander, J.1    Marttinen, P.2    Siren, J.3    Tang, J.4
  • 36
    • 1342331102 scopus 로고    scopus 로고
    • DISTRUCT: A program for the graphical display of population structure
    • Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137-138.
    • (2004) Mol Ecol Notes , vol.4 , pp. 137-138
    • Rosenberg, N.A.1
  • 37
    • 84860109324 scopus 로고    scopus 로고
    • MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space
    • Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, et al.. (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol.
    • (2012) Syst Biol
    • Ronquist, F.1    Teslenko, M.2    Van Der Mark, P.3    Ayres, D.L.4    Darling, A.5
  • 39
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
    • Larget BR, Kotha SK, Dewey CN, Ané C (2010) BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26:2910-2911.
    • (2010) Bioinformatics , vol.26 , pp. 2910-2911
    • Larget, B.R.1    Kotha, S.K.2    Dewey, C.N.3    Ané, C.4
  • 40
    • 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
  • 41
  • 42
    • 52149099649 scopus 로고    scopus 로고
    • Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)
    • Belfiore NM, Liu L, Moritz C (2008) Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst Biol 57:294-310.
    • (2008) Syst Biol , vol.57 , pp. 294-310
    • Belfiore, N.M.1    Liu, L.2    Moritz, C.3
  • 43
    • 85027956222 scopus 로고    scopus 로고
    • The modality of nine Triturus newt hybrid zones, assessed with nuclear, mitochondrial and morphological data
    • Arntzen JW, Wielstra B, Wallis GP (2014) The modality of nine Triturus newt hybrid zones, assessed with nuclear, mitochondrial and morphological data. Biol J Linn Soc 113:604-622.
    • (2014) Biol J Linn Soc , vol.113 , pp. 604-622
    • Arntzen, J.W.1    Wielstra, B.2    Wallis, G.P.3
  • 44
    • 84865514429 scopus 로고    scopus 로고
    • Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models
    • Wielstra B, Arntzen JW (2012) Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models. BMC Evol Biol 12:161.
    • (2012) BMC Evol Biol , vol.12 , pp. 161
    • Wielstra, B.1    Arntzen, J.W.2
  • 45
    • 0026311951 scopus 로고
    • Restricted gene flow in a moving hybrid zone of the newts Triturus cristatus and T. Marmoratus in western France
    • Arntzen JW, Wallis GP (1991) Restricted gene flow in a moving hybrid zone of the newts Triturus cristatus and T. marmoratus in western France. Evolution 45:805-826.
    • (1991) Evolution , vol.45 , pp. 805-826
    • Arntzen, J.W.1    Wallis, G.P.2
  • 46
    • 45249121769 scopus 로고    scopus 로고
    • Environmental parameters that determine species geographical range limits as a matter of time and space
    • Arntzen JW, Espregueira Themudo G (2008) Environmental parameters that determine species geographical range limits as a matter of time and space. J Biogeogr 35:1177-1186.
    • (2008) J Biogeogr , vol.35 , pp. 1177-1186
    • Arntzen, J.W.1    Espregueira Themudo, G.2
  • 47
    • 78149386517 scopus 로고    scopus 로고
    • Phylogenetic insights on adaptive radiation
    • Glor RE (2010) Phylogenetic insights on adaptive radiation. Annu Rev Ecol Evol Syst 41:251-270.
    • (2010) Annu Rev Ecol Evol Syst , vol.41 , pp. 251-270
    • Glor, R.E.1
  • 49
    • 84879418928 scopus 로고    scopus 로고
    • Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci
    • Williams JS, Niedzwiecki JH, Weisrock DW (2013) Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci. Mol Phylogenet Evol 68:671-682.
    • (2013) Mol Phylogenet Evol , vol.68 , pp. 671-682
    • Williams, J.S.1    Niedzwiecki, J.H.2    Weisrock, D.W.3
  • 50
    • 56549103832 scopus 로고    scopus 로고
    • Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow
    • Eckert AJ, Carstens BC (2008) Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol Phylogenet Evol 49:832-842.
    • (2008) Mol Phylogenet Evol , vol.49 , pp. 832-842
    • Eckert, A.J.1    Carstens, B.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.