메뉴 건너뛰기




Volumn 69, Issue 2, 2015, Pages 492-507

Bayesian species delimitation combining multiple genes and traits in a unified framework

Author keywords

Bayesian phylogenetic analysis; BPP; Brownian motion; Gene flow; Speciation; Species delineation

Indexed keywords

ACCURACY ASSESSMENT; BAYESIAN ANALYSIS; BROWNIAN MOTION; DIVERGENCE; GENE FLOW; GENETIC ANALYSIS; PHENOTYPE; SPECIATION (BIOLOGY);

EID: 84922511431     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12582     Document Type: Article
Times cited : (147)

References (53)
  • 1
    • 84894248423 scopus 로고    scopus 로고
    • Ecological niche models in phylogeographic studies: applications, advances and precautions
    • Alvarado-Serrano, D. F., and L. L. Knowles. 2013. Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol. Ecol. R 14:233-248.
    • (2013) Mol. Ecol. R , vol.14 , pp. 233-248
    • Alvarado-Serrano, D.F.1    Knowles, L.L.2
  • 4
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis
    • Bryant, D., R. Bouckaert, J. Felsenstein, N. A. Rosenberg, and A. RoyChoudhury. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29:1917-1932.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1917-1932
    • Bryant, D.1    Bouckaert, R.2    Felsenstein, J.3    Rosenberg, N.A.4    Roy Choudhury, A.5
  • 5
    • 79959642957 scopus 로고    scopus 로고
    • Speciation at the mogollon rim in the arizona mountain kingsnake (Lampropeltis pyromelana)
    • Burbrink, F., H. Yao, M. Ingrasci, R. J. Bryson, T. Guiher, and S. Ruane. 2011. Speciation at the mogollon rim in the arizona mountain kingsnake (Lampropeltis pyromelana). Mol. Phylogenet. Evol. 60:445-454.
    • (2011) Mol. Phylogenet. Evol. , vol.60 , pp. 445-454
    • Burbrink, F.1    Yao, H.2    Ingrasci, M.3    Bryson, R.J.4    Guiher, T.5    Ruane, S.6
  • 6
    • 11944264347 scopus 로고    scopus 로고
    • Phylogenetic comparative analysis: a modeling approach for adaptive evolution
    • Butler, M. A., and A. A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164:683-695.
    • (2004) Am. Nat. , vol.164 , pp. 683-695
    • Butler, M.A.1    King, A.A.2
  • 7
    • 84865736697 scopus 로고    scopus 로고
    • Species delimitation with abc and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae)
    • Camargo, A., M. Morando, L. J. Avila, and J. W. Sites. 2012. Species delimitation with abc and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution 66:2834-2849.
    • (2012) Evolution , vol.66 , pp. 2834-2849
    • Camargo, A.1    Morando, M.2    Avila, L.J.3    Sites, J.W.4
  • 9
    • 84902457782 scopus 로고    scopus 로고
    • The impact of the rate prior on Bayesian estimation of divergence times with multiple loci
    • Dos Reis, M., T. Zhu, and Z. Yang. 2014. The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Syst. Biol. 63:555-565.
    • (2014) Syst. Biol. , vol.63 , pp. 555-565
    • Dos Reis, M.1    Zhu, T.2    Yang, Z.3
  • 10
    • 84891888928 scopus 로고    scopus 로고
    • Species detection and individual assignment in species delimitation: can integrative data increase efficacy?
    • Edwards, D. L., and L. L. Knowles. 2014. Species detection and individual assignment in species delimitation: can integrative data increase efficacy? Proc. R. Soc. B Biol. Sci. 281:20132765.
    • (2014) Proc. R. Soc. B Biol. Sci. , vol.281 , pp. 20132765
    • Edwards, D.L.1    Knowles, L.L.2
  • 11
    • 79954549463 scopus 로고    scopus 로고
    • SpedeSTEM: a rapid and accurate method for species delimitation
    • Ence, D., and B. Carstens. 2011. SpedeSTEM: a rapid and accurate method for species delimitation. Mol. Ecol. Res. 11:473-480.
    • (2011) Mol. Ecol. Res. , vol.11 , pp. 473-480
    • Ence, D.1    Carstens, B.2
  • 12
    • 43949115169 scopus 로고    scopus 로고
    • Comparative methods with sampling error and within-species variation: contrasts revisited and revised
    • Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am. Nat. 171:713-725.
    • (2008) Am. Nat. , vol.171 , pp. 713-725
    • Felsenstein, J.1
  • 13
    • 84875271870 scopus 로고    scopus 로고
    • Fast likelihood calculations for comparative analyses
    • Freckleton, R. 2012. Fast likelihood calculations for comparative analyses. Methods Ecol. Evol. 3:940-947.
    • (2012) Methods Ecol. Evol. , vol.3 , pp. 940-947
    • Freckleton, R.1
  • 14
    • 0036920097 scopus 로고    scopus 로고
    • Phylogenetic analysis and comparative data: a test and review of evidence
    • Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. Am. Nat. 160:712-726.
    • (2002) Am. Nat. , vol.160 , pp. 712-726
    • Freckleton, R.P.1    Harvey, P.H.2    Pagel, M.3
  • 16
    • 28344432025 scopus 로고    scopus 로고
    • Geneland: a program for landscape genetics
    • Guillot, G., F. Mortier, and A. Estoup. 2005. Geneland: a program for landscape genetics. Mol. Ecol. Notes 5:712-715.
    • (2005) Mol. Ecol. Notes , vol.5 , pp. 712-715
    • Guillot, G.1    Mortier, F.2    Estoup, A.3
  • 17
    • 84868012824 scopus 로고    scopus 로고
    • A unifying model for the analysis of phenotypic, genetic and geographic data
    • Guillot, G., S. Renaud, R. Ledevin, J. Michaux, and J. Claude. 2012. A unifying model for the analysis of phenotypic, genetic and geographic data. Syst. Biol. 61:897-911.
    • (2012) Syst. Biol. , vol.61 , pp. 897-911
    • Guillot, G.1    Renaud, S.2    Ledevin, R.3    Michaux, J.4    Claude, J.5
  • 18
    • 84555177821 scopus 로고    scopus 로고
    • Phylogenetic and coalescent strategies of species delimitation in snubnose darters (Percidae: Etheostoma)
    • Harrington, R. C., and T. J. Near. 2012. Phylogenetic and coalescent strategies of species delimitation in snubnose darters (Percidae: Etheostoma). Syst. Biol. 61:63-79.
    • (2012) Syst. Biol. , vol.61 , pp. 63-79
    • Harrington, R.C.1    Near, T.J.2
  • 19
    • 77958071783 scopus 로고    scopus 로고
    • Species delimitation using dominant and codominant multilocus markers
    • Hausdorf, B., and C. Hennig. 2010. Species delimitation using dominant and codominant multilocus markers. Syst. Biol. 59:491-503.
    • (2010) Syst. Biol. , vol.59 , pp. 491-503
    • Hausdorf, B.1    Hennig, C.2
  • 20
    • 84888854912 scopus 로고    scopus 로고
    • Integrative testing of how environments from the past to the present shape genetic structure across landscapes
    • He, Q., D. L. Edwards, and L. L. Knowles. 2013. Integrative testing of how environments from the past to the present shape genetic structure across landscapes. Evolution 67:3386-3402.
    • (2013) Evolution , vol.67 , pp. 3386-3402
    • He, Q.1    Edwards, D.L.2    Knowles, L.L.3
  • 21
    • 84860124330 scopus 로고    scopus 로고
    • Population genetics and objectivity in species diagnosis
    • Hey, J., and C. Pinho. 2012. Population genetics and objectivity in species diagnosis. Evolution 66:1413-1429.
    • (2012) Evolution , vol.66 , pp. 1413-1429
    • Hey, J.1    Pinho, C.2
  • 22
    • 84898959182 scopus 로고    scopus 로고
    • A linear-time algorithm for gaussian and non-gaussian trait evolution models
    • R package: phylolm.
    • Ho, L. S. T., and C. Ané. 2014. A linear-time algorithm for gaussian and non-gaussian trait evolution models. Syst. Biol. 63:397-408. R package: phylolm.
    • (2014) Syst. Biol. , vol.63 , pp. 397-408
    • Ho, L.S.T.1    Ané, C.2
  • 23
    • 68949103876 scopus 로고    scopus 로고
    • Inferring weak population structure with the assistance of sample group information
    • Hubisz, M. J., D. Falush, M. Stephens, and J. K. Pritchard. 2009. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Res. 9:1322-1332.
    • (2009) Mol. Ecol. Res. , vol.9 , pp. 1322-1332
    • Hubisz, M.J.1    Falush, D.2    Stephens, M.3    Pritchard, J.K.4
  • 24
    • 34249066206 scopus 로고    scopus 로고
    • Inference of population structure under a Dirichlet process model
    • Huelsenbeck, J. P., and P. Andolfatto. 2007. Inference of population structure under a Dirichlet process model. Genetics 175:1787-1802.
    • (2007) Genetics , vol.175 , pp. 1787-1802
    • Huelsenbeck, J.P.1    Andolfatto, P.2
  • 26
    • 79955399641 scopus 로고    scopus 로고
    • Phylogenetics, species boundaries and timing of resource tracking in a highlyspecialized group of seed beetles (Coleoptera: Chrysomelidae: Bruchinae)
    • Kergoat, G., B. P. L. Ru, G. Genson, C. Cruaud, A. Couloux, and A. Delobel. 2011. Phylogenetics, species boundaries and timing of resource tracking in a highlyspecialized group of seed beetles (Coleoptera: Chrysomelidae: Bruchinae). Mol. Phylogenet. Evol. 59:746-760.
    • (2011) Mol. Phylogenet. Evol. , vol.59 , pp. 746-760
    • Kergoat, G.1    Ru, B.P.L.2    Genson, G.3    Cruaud, C.4    Couloux, A.5    Delobel, A.6
  • 27
    • 34447620474 scopus 로고    scopus 로고
    • Delimiting species without monophyletic gene trees
    • Knowles, L. L., and B. Carstens. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56:887-895.
    • (2007) Syst. Biol. , vol.56 , pp. 887-895
    • Knowles, L.L.1    Carstens, B.2
  • 28
    • 77956935937 scopus 로고    scopus 로고
    • Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)
    • Leaché, A., and M. Fujita. 2010. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc. R. Soc. B Biol. Sci. 277:3071-3077.
    • (2010) Proc. R. Soc. B Biol. Sci. , vol.277 , pp. 3071-3077
    • Leaché, A.1    Fujita, M.2
  • 30
    • 0034616970 scopus 로고    scopus 로고
    • Removing allometric effects of body size in morphological analysis
    • Lleonart, J., J. Salat, and G. Torres. 2000. Removing allometric effects of body size in morphological analysis. J. Theor. Biol. 205:85-93.
    • (2000) J. Theor. Biol. , vol.205 , pp. 85-93
    • Lleonart, J.1    Salat, J.2    Torres, G.3
  • 31
    • 0026293261 scopus 로고
    • Methods for the analysis of comparative data in evolutionary biology
    • Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45:1065-1080.
    • (1991) Evolution , vol.45 , pp. 1065-1080
    • Lynch, M.1
  • 32
    • 0001199482 scopus 로고
    • Phenotypic evolution by neutral mutation
    • Lynch, M., and W. G. Hill. 1986. Phenotypic evolution by neutral mutation. Evolution 40:915-935.
    • (1986) Evolution , vol.40 , pp. 915-935
    • Lynch, M.1    Hill, W.G.2
  • 33
    • 77953763337 scopus 로고    scopus 로고
    • Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation?: insights from tests with niche models
    • McCormack, J. E., A. J. Zellmer, and L. L. Knowles. 2010. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation?: insights from tests with niche models. Evolution 64:1231-1244.
    • (2010) Evolution , vol.64 , pp. 1231-1244
    • McCormack, J.E.1    Zellmer, A.J.2    Knowles, L.L.3
  • 34
    • 84884838878 scopus 로고    scopus 로고
    • An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex
    • McKay, B. D., H. L. Mays, Y. Wu, H. Li, C.-t. Yao, I. Nishiumi, and F. Zou. 2013. An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex. Mol. Ecol. 22:4943-4957.
    • (2013) Mol. Ecol. , vol.22 , pp. 4943-4957
    • McKay, B.D.1    Mays, H.L.2    Wu, Y.3    Li, H.4    Yao, C.-t.5    Nishiumi, I.6    Zou, F.7
  • 36
    • 84857687461 scopus 로고    scopus 로고
    • Delimiting species using multilocus data: diagnosing cryptic diveristy in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae)
    • Niemiller, M. L., T. J. Near, and B. M. Fitzpatrick. 2012. Delimiting species using multilocus data: diagnosing cryptic diveristy in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution 66:846-866.
    • (2012) Evolution , vol.66 , pp. 846-866
    • Niemiller, M.L.1    Near, T.J.2    Fitzpatrick, B.M.3
  • 37
    • 84891842622 scopus 로고    scopus 로고
    • Upstream analyses create problems with dna-based species delimitation
    • Olave, M., E. Solà, and L. L. Knowles. 2013. Upstream analyses create problems with dna-based species delimitation. Syst. Biol. 63:263-271.
    • (2013) Syst. Biol. , vol.63 , pp. 263-271
    • Olave, M.1    Solà, E.2    Knowles, L.L.3
  • 38
    • 72049107504 scopus 로고    scopus 로고
    • New heuristic methods for joint species delimitation and species tree inference
    • O'Meara, B. 2010. New heuristic methods for joint species delimitation and species tree inference. Syst. Biol. 59:59-73.
    • (2010) Syst. Biol. , vol.59 , pp. 59-73
    • O'Meara, B.1
  • 39
    • 0033613376 scopus 로고    scopus 로고
    • Inferring the historical patterns of biological evolution
    • Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
    • (1999) Nature , vol.401 , pp. 877-884
    • Pagel, M.1
  • 41
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 42
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala, B., and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656.
    • (2003) Genetics , vol.164 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 43
    • 84877090539 scopus 로고    scopus 로고
    • Improved reversible jump algorithms for Bayesian species delimitation
    • Rannala, B., and Z. Yang. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics 194:245-253.
    • (2013) Genetics , vol.194 , pp. 245-253
    • Rannala, B.1    Yang, Z.2
  • 44
    • 84859893546 scopus 로고    scopus 로고
    • Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference
    • Rannala, B., T. Zhu, and Z. Yang. 2012. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 325-335
    • Rannala, B.1    Zhu, T.2    Yang, Z.3
  • 45
    • 36248992880 scopus 로고    scopus 로고
    • Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus)
    • Rissler, L. J., and J. J. Apodaca. 2007. Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Syst. Biol. 56:924-942.
    • (2007) Syst. Biol. , vol.56 , pp. 924-942
    • Rissler, L.J.1    Apodaca, J.J.2
  • 46
    • 84866167805 scopus 로고    scopus 로고
    • The effects of sampling on delimiting species from multi-locus sequence data
    • Rittmeyer, E., and C. Austin. 2012. The effects of sampling on delimiting species from multi-locus sequence data. Mol. Phylogenet. Evol. 65:451-463.
    • (2012) Mol. Phylogenet. Evol. , vol.65 , pp. 451-463
    • Rittmeyer, E.1    Austin, C.2
  • 47
    • 84885964273 scopus 로고    scopus 로고
    • Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)
    • Satler, J. D., B. C. Carstens, and M. Hedin. 2013. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus). Syst. Biol. 62:805-823.
    • (2013) Syst. Biol. , vol.62 , pp. 805-823
    • Satler, J.D.1    Carstens, B.C.2    Hedin, M.3
  • 48
    • 54849427082 scopus 로고    scopus 로고
    • Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution
    • Warren, D. L., R. E. Glor, and M. Turelli. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62:2868-2883.
    • (2008) Evolution , vol.62 , pp. 2868-2883
    • Warren, D.L.1    Glor, R.E.2    Turelli, M.3
  • 49
    • 77955243011 scopus 로고    scopus 로고
    • ENMTools: a toolbox for comparative studies of environmental niche models
    • Warren, D. L., R. E. Glor, and M. Turelli. 2010. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33:607-611.
    • (2010) Ecography , vol.33 , pp. 607-611
    • Warren, D.L.1    Glor, R.E.2    Turelli, M.3
  • 50
    • 0036005519 scopus 로고    scopus 로고
    • Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (sceloporus)
    • Wiens, J. J., and T. A. Penkrot. 2002. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (sceloporus). Syst. Biol. 51:69-91.
    • (2002) Syst. Biol. , vol.51 , pp. 69-91
    • Wiens, J.J.1    Penkrot, T.A.2
  • 51
    • 77952703002 scopus 로고    scopus 로고
    • Bayesian species delimitation using multilocus sequence data
    • Yang, Z., and B. Rannala. 2010. Bayesian species delimitation using multilocus sequence data. Proc. Natl. Acad. Sci. USA 107:9264-9269.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 9264-9269
    • Yang, Z.1    Rannala, B.2
  • 53
    • 80054890844 scopus 로고    scopus 로고
    • Evaluation of a Bayesian coalescent method of species delimitation
    • Zhang, C., D.-X. Zhang, T. Zhu, and Z. Yang. 2011. Evaluation of a Bayesian coalescent method of species delimitation. Syst. Biol. 60:747-761.
    • (2011) Syst. Biol. , vol.60 , pp. 747-761
    • Zhang, C.1    Zhang, D.-X.2    Zhu, T.3    Yang, Z.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.