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Volumn 57, Issue 2, 2010, Pages 888-898

Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling

Author keywords

Coalescent; Phylogeography; Species tree estimation; Subsampling

Indexed keywords

ARTICLE; CLASSIFICATION; COMPUTER PROGRAM; GENETICS; PHYLOGEOGRAPHY; SPECIES DIFFERENTIATION; TREE;

EID: 78049390225     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.08.006     Document Type: Article
Times cited : (25)

References (40)
  • 3
    • 52149099649 scopus 로고    scopus 로고
    • Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)
    • Belfiore N.M., Liu L., Moritz C. Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst. Biol. 2008, 57:294-310.
    • (2008) Syst. Biol. , vol.57 , pp. 294-310
    • Belfiore, N.M.1    Liu, L.2    Moritz, C.3
  • 4
    • 0035089776 scopus 로고    scopus 로고
    • The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation
    • Bernatchez L. The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation. Evolution 2001, 55:351-379.
    • (2001) Evolution , vol.55 , pp. 351-379
    • Bernatchez, L.1
  • 5
    • 0037687926 scopus 로고    scopus 로고
    • The utility of single nucleotide polymorphism in inferences of population history
    • Brumfield R.T., Beerli P., Nickerson D.A., Edwards S.V. The utility of single nucleotide polymorphism in inferences of population history. Trends Ecol. Evol. 2003, 18:249-256.
    • (2003) Trends Ecol. Evol. , vol.18 , pp. 249-256
    • Brumfield, R.T.1    Beerli, P.2    Nickerson, D.A.3    Edwards, S.V.4
  • 6
    • 40849120246 scopus 로고    scopus 로고
    • Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina Buntings
    • Carling M.D., Brumfield R.T. Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina Buntings. Genetics 2008, 178:363-377.
    • (2008) Genetics , vol.178 , pp. 363-377
    • Carling, M.D.1    Brumfield, R.T.2
  • 7
    • 77953729511 scopus 로고    scopus 로고
    • Species delimitation using a combined coalescent and information-theoretic approach: An example from North American Myotis bats
    • Carstens B.C., Dewey T.A. Species delimitation using a combined coalescent and information-theoretic approach: An example from North American Myotis bats. Syst. Biol. 2010, 59:400-414.
    • (2010) Syst. Biol. , vol.59 , pp. 400-414
    • Carstens, B.C.1    Dewey, T.A.2
  • 8
    • 34249700809 scopus 로고    scopus 로고
    • Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers
    • Carstens B.C., Knowles L.L. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst. Biol. 2007, 56:400-411.
    • (2007) Syst. Biol. , vol.56 , pp. 400-411
    • Carstens, B.C.1    Knowles, L.L.2
  • 9
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan J.H., Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Genet. 2006, 2:e68.
    • (2006) PLoS Genet. , vol.2
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 10
    • 33646904026 scopus 로고    scopus 로고
    • A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia)
    • Dolman G., Moritz C. A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 2006, 60:573-582.
    • (2006) Evolution , vol.60 , pp. 573-582
    • Dolman, G.1    Moritz, C.2
  • 11
    • 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
  • 12
    • 78049367307 scopus 로고    scopus 로고
    • PHYLIP (Phylogenetic Inference Package) Version 3.06. Distributed by the author. Department of Genome Sciences, University of Washington
    • Felsenstein, J., 2005. PHYLIP (Phylogenetic Inference Package) Version 3.06. Distributed by the author. Department of Genome Sciences, University of Washington.
    • (2005)
    • Felsenstein, J.1
  • 14
    • 43049085952 scopus 로고    scopus 로고
    • Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saproxylic springtails
    • Garrick R.G., Rowell D.M., Simmons C.S., Hillis D.M., Sunnucks P. Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saproxylic springtails. Evolution 2008, 62:1103-1118.
    • (2008) Evolution , vol.62 , pp. 1103-1118
    • Garrick, R.G.1    Rowell, D.M.2    Simmons, C.S.3    Hillis, D.M.4    Sunnucks, P.5
  • 15
    • 57349140938 scopus 로고    scopus 로고
    • Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes
    • Geraldes A., Basset P., Gibson B., Smith K.L., Harr B., Yu H.-T., Bulatova Y.Z., Nachman N.W. Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol. Ecol. 2008, 17:5349-5363.
    • (2008) Mol. Ecol. , vol.17 , pp. 5349-5363
    • Geraldes, A.1    Basset, P.2    Gibson, B.3    Smith, K.L.4    Harr, B.5    Yu, H.-T.6    Bulatova, Y.Z.7    Nachman, N.W.8
  • 16
    • 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
  • 17
    • 11944260381 scopus 로고
    • Approaches for assessing phylogenetic accuracy
    • Hillis D.M. Approaches for assessing phylogenetic accuracy. Syst. Biol. 1995, 44:3-16.
    • (1995) Syst. Biol. , vol.44 , pp. 3-16
    • Hillis, D.M.1
  • 18
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • Oxford University Press, New York, D. Futuyma, J. Antonovics (Eds.)
    • Hudson R.R. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 1991, 1-44. Oxford University Press, New York. D. Futuyma, J. Antonovics (Eds.).
    • (1991) Oxford Surveys in Evolutionary Biology , pp. 1-44
    • Hudson, R.R.1
  • 19
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 20
    • 34247500920 scopus 로고    scopus 로고
    • Estimating a geographically explicit model of population divergence
    • Knowles L.L., Carstens B.C. Estimating a geographically explicit model of population divergence. Evolution 2007, 61:477-493.
    • (2007) Evolution , vol.61 , pp. 477-493
    • Knowles, L.L.1    Carstens, B.C.2
  • 21
    • 63549118031 scopus 로고    scopus 로고
    • STEM: species tree estimation using maximum likelihood for gene trees under coalescence
    • Kubatko L.S., Carstens B.C., Knowles L.L. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25:971-973.
    • (2009) Bioinformatics , vol.25 , pp. 971-973
    • Kubatko, L.S.1    Carstens, B.C.2    Knowles, L.L.3
  • 22
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner M.K., Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 1994, 11:459-468.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 23
    • 57249086459 scopus 로고    scopus 로고
    • Divergence across Australia's Carpentarian barrier: statistical phylogeography of the red-backed Fairy Wren (Malurus melanocephalus)
    • Lee J.Y., Edwards S.V. Divergence across Australia's Carpentarian barrier: statistical phylogeography of the red-backed Fairy Wren (Malurus melanocephalus). Evolution 2008, 62:3117-3134.
    • (2008) Evolution , vol.62 , pp. 3117-3134
    • Lee, J.Y.1    Edwards, S.V.2
  • 24
    • 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
  • 25
    • 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
  • 26
    • 78049395010 scopus 로고    scopus 로고
    • Mesquite: A Modular System for Evolutionary Analysis. Version 1.01. Available at <>
    • Maddison, W.P., Maddison, D.R., 2004. Mesquite: A Modular System for Evolutionary Analysis. Version 1.01. Available at http://mesquiteproject.org.
    • (2004)
    • Maddison, W.P.1    Maddison, D.R.2
  • 27
    • 70450265498 scopus 로고    scopus 로고
    • Breaking them down and building them up: evaluating the accuracy of maximum-likelihood estimates of species trees
    • McCormack J.E., Huang H., Knowles L.L. Breaking them down and building them up: evaluating the accuracy of maximum-likelihood estimates of species trees. 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
  • 28
    • 57349111146 scopus 로고    scopus 로고
    • Geographic variation in adaptation at the molecular level: a case study of plant immunity genes
    • Moeller D.A., Tiffin P. Geographic variation in adaptation at the molecular level: a case study of plant immunity genes. Evolution 2008, 62:3069-3081.
    • (2008) Evolution , vol.62 , pp. 3069-3081
    • Moeller, D.A.1    Tiffin, P.2
  • 29
    • 84882454218 scopus 로고    scopus 로고
    • Coalescent theory
    • John Wiley and Sons, Ltd., West Sussex, England, D.J. Balding, M. Bishop, C. Cannings (Eds.)
    • Nordborg M. Coalescent theory. Handbook of Statistical Genetics 2000, 843-872. John Wiley and Sons, Ltd., West Sussex, England. third ed. D.J. Balding, M. Bishop, C. Cannings (Eds.).
    • (2000) Handbook of Statistical Genetics , pp. 843-872
    • Nordborg, M.1
  • 30
    • 72049107504 scopus 로고    scopus 로고
    • New heuristic methods for joint species delimitation and species tree estimation
    • O'Meara B.C. New heuristic methods for joint species delimitation and species tree estimation. Syst. Biol. 2010, 59:59-73.
    • (2010) Syst. Biol. , vol.59 , pp. 59-73
    • O'Meara, B.C.1
  • 31
    • 44449119051 scopus 로고    scopus 로고
    • Multilocus phylogeography of a Holarctic duck: colonization of North America from Eurasia by Gadwall (Anas strepera)
    • Peters J.L., Zhuravlev Y.N., Fefelov I., Humphries E.M., Omland K.E. Multilocus phylogeography of a Holarctic duck: colonization of North America from Eurasia by Gadwall (Anas strepera). Evolution 2008, 62:1469-1483.
    • (2008) Evolution , vol.62 , pp. 1469-1483
    • Peters, J.L.1    Zhuravlev, Y.N.2    Fefelov, I.3    Humphries, E.M.4    Omland, K.E.5
  • 32
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A., Grassly N.C. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1997, 13:235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 33
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson D.R., Foulds L.R. Comparison of phylogenetic trees. Math. Biosci. 1981, 53:131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.R.1    Foulds, L.R.2
  • 34
    • 0001085724 scopus 로고
    • On the genealogy of nested sub-samples from a haploid population
    • Saunders I.W., Tavare S., Watterson G.A. On the genealogy of nested sub-samples from a haploid population. Adv. Appl. Prob. 1984, 16:471-491.
    • (1984) Adv. Appl. Prob. , vol.16 , pp. 471-491
    • Saunders, I.W.1    Tavare, S.2    Watterson, G.A.3
  • 35
    • 78049388201 scopus 로고    scopus 로고
    • SumTrees: Summarization of Split Support on Phylogenetic Trees. Part of the: DendroPy Phylogenetic Computation Library. Available at <>
    • Sukumaran, J., 2008. SumTrees: Summarization of Split Support on Phylogenetic Trees. Part of the: DendroPy Phylogenetic Computation Library. Available at http://sourceforge.net/projects/dendropy.
    • (2008)
    • Sukumaran, J.1
  • 36
    • 78049353689 scopus 로고    scopus 로고
    • PAUP*. Phylogenetic Analysis Using Parsimony (and other methods). Version 4. Sinnauer Associates, Sunderland, MA
    • Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (and other methods). Version 4. Sinnauer Associates, Sunderland, MA.
    • (2002)
    • Swofford, D.L.1
  • 37
    • 0035544546 scopus 로고    scopus 로고
    • Phylogeography and historical ecology of the North Atlantic intertidal
    • Wares J.P., Cunningham C.W. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 2001, 55:2455-2469.
    • (2001) Evolution , vol.55 , pp. 2455-2469
    • Wares, J.P.1    Cunningham, C.W.2
  • 38
    • 12344265079 scopus 로고    scopus 로고
    • Divergence population genetics of chimpanzees
    • Won Y., Hey J. Divergence population genetics of chimpanzees. Mol. Biol. Evol. 2005, 22:297-307.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 297-307
    • Won, Y.1    Hey, J.2
  • 39
    • 0043198532 scopus 로고    scopus 로고
    • Historical isolation, range expansion, and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum)
    • Zamudio K.R., Savage W.K. Historical isolation, range expansion, and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum). Evolution 2003, 57:1631-1652.
    • (2003) Evolution , vol.57 , pp. 1631-1652
    • Zamudio, K.R.1    Savage, W.K.2
  • 40
    • 78049384377 scopus 로고    scopus 로고
    • Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Ph.D. Dissertation. The University of Texas at Austin. Available at.
    • Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. Ph.D. Dissertation. The University of Texas at Austin. Available at: http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html.
    • (2006)
    • Zwickl, D.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.