메뉴 건너뛰기




Volumn 65, Issue 2, 2012, Pages 631-641

Eight independent nuclear genes support monophyly of the plovers: The role of mutational variance in gene trees

Author keywords

Gene trees; Mutational variance; Nuclear genes; Plover paraphyly; Pluvialis; Species tree

Indexed keywords

MITOCHONDRIAL DNA;

EID: 84866183242     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.07.018     Document Type: Article
Times cited : (13)

References (52)
  • 1
    • 79951920324 scopus 로고    scopus 로고
    • Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae
    • Alström P., Fregin S., Norman J.A., Ericson P.G.P., Christidis L., Olsson U. Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae. Mol. Phylogenet. Evol. 2011, 58:513-526.
    • (2011) Mol. Phylogenet. Evol. , vol.58 , pp. 513-526
    • Alström, P.1    Fregin, S.2    Norman, J.A.3    Ericson, P.G.P.4    Christidis, L.5    Olsson, U.6
  • 2
    • 82655183796 scopus 로고    scopus 로고
    • Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset
    • Alström P., Höhna S., Gelang M., Ericson P.G.P., Olsson A.Y. Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset. BMC Evol. Biol. 2011, 11:352.
    • (2011) BMC Evol. Biol. , vol.11 , pp. 352
    • Alström, P.1    Höhna, S.2    Gelang, M.3    Ericson, P.G.P.4    Olsson, A.Y.5
  • 3
    • 34548499987 scopus 로고    scopus 로고
    • Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds
    • Baker A.J., Pereira S.L., Paton T.P. Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biol. Lett. 2007, 3:205-209.
    • (2007) Biol. Lett. , vol.3 , pp. 205-209
    • Baker, A.J.1    Pereira, S.L.2    Paton, T.P.3
  • 4
    • 53849128215 scopus 로고    scopus 로고
    • Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data
    • Brumfield R.T., Liu L., Lum D.E., Edwards S. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Syst. Biol. 2008, 57:719-731.
    • (2008) Syst. Biol. , vol.57 , pp. 719-731
    • Brumfield, R.T.1    Liu, L.2    Lum, D.E.3    Edwards, S.4
  • 5
    • 34547662977 scopus 로고    scopus 로고
    • Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird
    • Dawson D.A., Akesson M., Burke T., Pemberton J.M., Slate J., Hansson B. Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird. Mol. Biol. Evol. 2007, 24:1537-1552.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1537-1552
    • Dawson, D.A.1    Akesson, M.2    Burke, T.3    Pemberton, J.M.4    Slate, J.5    Hansson, B.6
  • 6
    • 0028999003 scopus 로고
    • Use of filtered pipet tips to elute DNA from agarose gels
    • Dean A.D., Greenwald J.E. Use of filtered pipet tips to elute DNA from agarose gels. Biotechniques 1995, 18:980.
    • (1995) Biotechniques , vol.18 , pp. 980
    • Dean, A.D.1    Greenwald, J.E.2
  • 7
    • 77249139678 scopus 로고    scopus 로고
    • Fast and consistent estimation of species trees using supermatrix rooted triples
    • DeGiorgio M., Degnan J.H. Fast and consistent estimation of species trees using supermatrix rooted triples. Mol. Biol. Evol. 2010, 27:552-569.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 552-569
    • DeGiorgio, M.1    Degnan, J.H.2
  • 8
    • 67449167484 scopus 로고    scopus 로고
    • Properties of consensus methods for inferring species trees from gene trees
    • Degnan J.H., DeGiorgio M., Bryant D., Rosenberg N.A. Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 2009, 58:35-54.
    • (2009) Syst. Biol. , vol.58 , pp. 35-54
    • Degnan, J.H.1    DeGiorgio, M.2    Bryant, D.3    Rosenberg, N.A.4
  • 9
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
    • (2009) Trends Ecol. Evol. , vol.24 , pp. 332-340
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 11
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 12
    • 77956488734 scopus 로고    scopus 로고
    • Bayesian local clocks, or one rate to rule them all
    • Drummond A.J., Suchard M.A. Bayesian local clocks, or one rate to rule them all. BMC Biol. 2010, 8:114.
    • (2010) BMC Biol. , vol.8 , pp. 114
    • Drummond, A.J.1    Suchard, M.A.2
  • 13
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species trees without concatenation
    • Edwards S.V., Liu L., Pearl D.K. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 2007, 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
  • 14
    • 84866164918 scopus 로고    scopus 로고
    • COI Barcoding of the Shorebirds: Rates of Evolution and the Identification of Species
    • Elbourne, R., 2011. COI Barcoding of the Shorebirds: Rates of Evolution and the Identification of Species. M.Sc. thesis, University of Toronto, 154 pp.
    • (2011) M.Sc. thesis, University of Toronto. , pp. 154
    • Elbourne, R.1
  • 15
    • 2942532721 scopus 로고    scopus 로고
    • Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data
    • Ericson P.G.P., Envall I., Irestedt M., Norman J.A. Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data. BMC Evol. Biol. 2003, 3:16.
    • (2003) BMC Evol. Biol. , vol.3 , pp. 16
    • Ericson, P.G.P.1    Envall, I.2    Irestedt, M.3    Norman, J.A.4
  • 16
    • 33947639977 scopus 로고    scopus 로고
    • Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves)
    • Fain M.G., Houde P. Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves). BMC Evol. Biol. 2007, 7:35.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 35
    • Fain, M.G.1    Houde, P.2
  • 17
    • 0033004743 scopus 로고    scopus 로고
    • Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
    • Foster P.G., Hickey D.A. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 1999, 48:284-290.
    • (1999) J. Mol. Evol. , vol.48 , pp. 284-290
    • Foster, P.G.1    Hickey, D.A.2
  • 18
    • 0842322955 scopus 로고    scopus 로고
    • Species-level paraphyly and polyphyly: frequencies, causes, and consequences, with insights from animal mitochondrial DNA
    • Funk D.J., Omland K.E. Species-level paraphyly and polyphyly: frequencies, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 2003, 34:397-423.
    • (2003) Annu. Rev. Ecol. Evol. Syst. , vol.34 , pp. 397-423
    • Funk, D.J.1    Omland, K.E.2
  • 19
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 22
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 24
    • 70450237691 scopus 로고    scopus 로고
    • What is the danger of the anomaly zone for empirical phylogenetics?
    • Huang H., Knowles L.L. What is the danger of the anomaly zone for empirical phylogenetics?. Syst. Biol. 2009, 58:527-536.
    • (2009) Syst. Biol. , vol.58 , pp. 527-536
    • Huang, H.1    Knowles, L.L.2
  • 25
    • 0022211482 scopus 로고
    • Statistical proprieties of the number of recombination events in the history of a sample of DNA sequences
    • Hudson R.R., Kaplan N.L. Statistical proprieties of the number of recombination events in the history of a sample of DNA sequences. Genetics 1985, 111:147-164.
    • (1985) Genetics , vol.111 , pp. 147-164
    • Hudson, R.R.1    Kaplan, N.L.2
  • 26
    • 18544366082 scopus 로고    scopus 로고
    • Chromosomal polymorphism and comparative painting analysis in the zebra finch
    • Itoh Y., Arnold A.P. Chromosomal polymorphism and comparative painting analysis in the zebra finch. Chromosome Res. 2005, 13:47-56.
    • (2005) Chromosome Res. , vol.13 , pp. 47-56
    • Itoh, Y.1    Arnold, A.P.2
  • 27
    • 80052751970 scopus 로고    scopus 로고
    • Species tree inference in a recent radiation of orioles (Genus Icterus): multiple markers and methods reveal cytonuclear discordance in the northern oriole group
    • Jacobsen F., Omland K.E. Species tree inference in a recent radiation of orioles (Genus Icterus): multiple markers and methods reveal cytonuclear discordance in the northern oriole group. Mol. Phylogenet. Evol. 2011, 61:460-469.
    • (2011) Mol. Phylogenet. Evol. , vol.61 , pp. 460-469
    • Jacobsen, F.1    Omland, K.E.2
  • 28
    • 70450233546 scopus 로고    scopus 로고
    • Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes
    • Knowles L.L. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 2009, 58:463-467.
    • (2009) Syst. Biol. , vol.58 , pp. 463-467
    • Knowles, L.L.1
  • 29
    • 45849088450 scopus 로고    scopus 로고
    • Resolving species phylogenies of recent evolutionary radiations
    • Knowles L.L., Chan Y. Resolving species phylogenies of recent evolutionary radiations. Ann. MO Bot. Gard. 2008, 95:224-231.
    • (2008) Ann. MO Bot. Gard. , vol.95 , pp. 224-231
    • Knowles, L.L.1    Chan, Y.2
  • 30
    • 79951561454 scopus 로고    scopus 로고
    • The accuracy of species tree estimation under simulation: a comparison of methods
    • Leaché A.D., Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Syst. Biol. 2011, 60:126-137.
    • (2011) Syst. Biol. , vol.60 , pp. 126-137
    • Leaché, A.D.1    Rannala, B.2
  • 31
    • 84863115972 scopus 로고    scopus 로고
    • A species tree for the Australo-Papuan fairy-wrens and allies (Aves: Maluridae)
    • Lee J.Y., Joseph L., Edwards S.V. A species tree for the Australo-Papuan fairy-wrens and allies (Aves: Maluridae). Syst. Biol. 2012, 61:253-271.
    • (2012) Syst. Biol. , vol.61 , pp. 253-271
    • Lee, J.Y.1    Joseph, L.2    Edwards, S.V.3
  • 32
    • 65649117685 scopus 로고    scopus 로고
    • DNASP v5: a software for comprehensive analysis of DNA polymorphism data
    • Librado P., Rozas J. DNASP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452.
    • (2009) Bioinformatics , vol.25 , pp. 1451-1452
    • Librado, P.1    Rozas, J.2
  • 33
    • 34548575126 scopus 로고    scopus 로고
    • Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
    • Liu L., Pearl D.K. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 2007, 56:504-514.
    • (2007) Syst. Biol. , vol.56 , pp. 504-514
    • Liu, L.1    Pearl, D.K.2
  • 34
    • 47749093183 scopus 로고    scopus 로고
    • Estimating species trees using multiple-allele DNA sequence data
    • Liu L., Pearl D.K., Brumfield R.T., Edwards S.V. Estimating species trees using multiple-allele DNA sequence data. Evolution 2008, 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
  • 36
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison W.P., Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55:21-30.
    • (2006) Syst. Biol. , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 37
    • 70450265498 scopus 로고    scopus 로고
    • Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design
    • McCormack J.E., Huang H., Knowles L.L. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 2009, 58:501-508.
    • (2009) Syst. Biol. , vol.58 , pp. 501-508
    • McCormack, J.E.1    Huang, H.2    Knowles, L.L.3
  • 38
    • 73149117123 scopus 로고    scopus 로고
    • The causes of mitochondrial DNA gene tree paraphyly in birds
    • McKay B.D., Zink R.M. The causes of mitochondrial DNA gene tree paraphyly in birds. Mol. Phylogenet. Evol. 2010, 54:647-650.
    • (2010) Mol. Phylogenet. Evol. , vol.54 , pp. 647-650
    • McKay, B.D.1    Zink, R.M.2
  • 39
    • 0001506399 scopus 로고    scopus 로고
    • Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds
    • Paton T., Haddrath O., Baker A.J. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. Biol. Sci. 2002, 269:839-846.
    • (2002) Proc. Biol. Sci. , vol.269 , pp. 839-846
    • Paton, T.1    Haddrath, O.2    Baker, A.J.3
  • 40
    • 33646393242 scopus 로고    scopus 로고
    • Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree
    • Paton T.A., Baker A.J. Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree. Mol. Phylogenet. Evol. 2006, 39:657-667.
    • (2006) Mol. Phylogenet. Evol. , vol.39 , pp. 657-667
    • Paton, T.A.1    Baker, A.J.2
  • 41
    • 1642322100 scopus 로고    scopus 로고
    • RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds
    • Paton T.A., Baker A.J., Groth J.G., Barrowclough G.F. RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds. Mol. Phylogenet. Evol. 2003, 29:268-278.
    • (2003) Mol. Phylogenet. Evol. , vol.29 , pp. 268-278
    • Paton, T.A.1    Baker, A.J.2    Groth, J.G.3    Barrowclough, G.F.4
  • 43
    • 23744447511 scopus 로고    scopus 로고
    • Multiple gene evidence for parallel evolution and retention of ancestral morphological states in the shanks (Charadriiformes: Scolopacidae)
    • Pereira S.L., Baker A.J. Multiple gene evidence for parallel evolution and retention of ancestral morphological states in the shanks (Charadriiformes: Scolopacidae). Condor 2005, 107:514-526.
    • (2005) Condor , vol.107 , pp. 514-526
    • Pereira, S.L.1    Baker, A.J.2
  • 44
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • Phillips M.J., Delsuc F., Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 2004, 21:1455-1458.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 45
    • 45849154165 scopus 로고    scopus 로고
    • JModelTest: phylogenetic model averaging
    • Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1253-1256
    • Posada, D.1
  • 48
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt H.A., Strimmer K., Vingron M., von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    von Haeseler, A.4
  • 51
    • 77954794504 scopus 로고    scopus 로고
    • Phylogenetic and coalescent analysis of three loci suggest that the water rail is divisible into two species, Rallus aquaticus and R. indicus
    • Tavares E.S., de Kroon G.H., Baker A.J. Phylogenetic and coalescent analysis of three loci suggest that the water rail is divisible into two species, Rallus aquaticus and R. indicus. BMC Evol. Biol. 2010, 10:226.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 226
    • Tavares, E.S.1    de Kroon, G.H.2    Baker, A.J.3
  • 52
    • 41049084425 scopus 로고    scopus 로고
    • Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles
    • Townsend T.M., Alegre E., Kelley S.T., Wiens J.J., Reeder T.W. Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Mol. Phylogenet. Evol. 2008, 47:129-142.
    • (2008) Mol. Phylogenet. Evol. , vol.47 , pp. 129-142
    • Townsend, T.M.1    Alegre, E.2    Kelley, S.T.3    Wiens, J.J.4    Reeder, T.W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.