메뉴 건너뛰기




Volumn 12, Issue 2, 2015, Pages 422-432

Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method

Author keywords

distance methods; incomplete lineage sorting; molecular clock; multispecies coalescent; phylogenetic inference; sample complexity

Indexed keywords

BIOLOGY; FORESTRY; GENES;

EID: 84927663403     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2014.2361685     Document Type: Article
Times cited : (43)

References (25)
  • 1
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • W. P. Maddison, "Gene trees in species trees," Syst. Biol., vol. 46, no. 3, pp. 523-536, 1997.
    • (1997) Syst. Biol. , vol.46 , Issue.3 , pp. 523-536
    • Maddison, W.P.1
  • 2
    • 0035400648 scopus 로고    scopus 로고
    • Gene trees and species trees are not the same
    • R. Nichols, "Gene trees and species trees are not the same," Trends Ecol. Evol., vol. 16, no. 7, pp. 358-364, 2001.
    • (2001) Trends Ecol. Evol. , vol.16 , Issue.7 , pp. 358-364
    • Nichols, R.1
  • 3
  • 4
    • 0003991673 scopus 로고    scopus 로고
    • Sunderland, MA, USA: Sinauer Assoc.
    • J. Felsenstein, Inferring Phylogenies, vol. 2, Sunderland, MA, USA: Sinauer Assoc., 2004.
    • (2004) Inferring Phylogenies , vol.2
    • Felsenstein, J.1
  • 5
    • 84972539388 scopus 로고
    • Ancestral inference in population genetics
    • R. Griffiths and S. Tavaré, "Ancestral inference in population genetics," Statist. Sci., vol. 9, pp. 307-319, 1994.
    • (1994) Statist. Sci. , vol.9 , pp. 307-319
    • Griffiths, R.1    Tavaré, S.2
  • 6
    • 0042601470 scopus 로고    scopus 로고
    • London, U.K.: Oxford Univ. Press
    • C. Semple and M. A. Steel, Phylogenetics, vol. 24, London, U.K.: Oxford Univ. Press, 2003.
    • (2003) Phylogenetics , vol.24
    • Semple, C.1    Steel, M.A.2
  • 7
    • 79951561454 scopus 로고    scopus 로고
    • The accuracy of species tree estimation under simulation: A comparison of methods
    • A. D. Leaché and B. Rannala, "The accuracy of species tree estimation under simulation: A comparison of methods," Syst. Biol., vol. 60, no. 2, pp. 126-137, 2011.
    • (2011) Syst. Biol. , vol.60 , Issue.2 , pp. 126-137
    • Leaché, A.D.1    Rannala, B.2
  • 8
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • L. Liu, L. Yu, D. K. Pearl, and S. V. Edwards, "Estimating species phylogenies using coalescence times among sequences," Syst. Biol., vol. 58, no. 5, pp. 468-477, 2009.
    • (2009) Syst. Biol. , vol.58 , Issue.5 , pp. 468-477
    • Liu, L.1    Yu, L.2    Pearl, D.K.3    Edwards, S.V.4
  • 9
    • 67449167484 scopus 로고    scopus 로고
    • Properties of consensus methods for inferring species trees from gene trees
    • abstract
    • J. H. Degnan, M. DeGiorgio, D. Bryant, and N. A. Rosenberg. (2009). Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. [Online]. 58(1), pp. 35-54. Available: http://sysbio.oxfordjournals.org/content/58/1/35.abstract
    • (2009) Syst. Biol.[Online] , vol.58 , Issue.1 , pp. 35-54
    • Degnan, J.H.1    DeGiorgio, M.2    Bryant, D.3    Rosenberg, N.A.4
  • 10
    • 76849102326 scopus 로고    scopus 로고
    • Incomplete lineage sorting: Consistent phylogeny estimation from multiple loci
    • Jan-Mar.
    • E. Mossel and S. Roch, "Incomplete lineage sorting: Consistent phylogeny estimation from multiple loci," IEEE/ACM Trans. Comput. Biol. Bioinformat., vol. 7, no. 1, pp. 166-171, Jan-Mar. 2010.
    • (2010) IEEE/ACM Trans.Comput. Biol. Bioinformat. , vol.7 , Issue.1 , pp. 166-171
    • Mossel, E.1    Roch, S.2
  • 11
    • 70350247510 scopus 로고    scopus 로고
    • Maximum tree: A consistent estimator of the species tree
    • Available
    • L. Liu, L. Yu, and D. Pearl. (2010). Maximum tree: A consistent estimator of the species tree. J. Math. Biol. [Online]. 60(1), pp. 95-106. Available: http://dx.doi.org/10.1007/s00285-009-0260-0
    • (2010) J. Math. Biol.[Online] , vol.60 , Issue.1 , pp. 95-106
    • Liu, L.1    Yu, L.2    Pearl, D.3
  • 12
    • 84891365689 scopus 로고    scopus 로고
    • An analytical comparison of multilocus methods under the multispecies coalescent: The three-taxon case
    • S. Roch, "An analytical comparison of multilocus methods under the multispecies coalescent: The three-taxon case," in Proc. Pac. Symp. Biocomput., 2013, pp. 297-306.
    • (2013) Proc.Pac. Symp. Biocomput. , pp. 297-306
    • Roch, S.1
  • 13
    • 84888137812 scopus 로고    scopus 로고
    • Computational approaches to species phylogeny inference and gene tree reconciliation
    • L. Nakhleh, "Computational approaches to species phylogeny inference and gene tree reconciliation," Trends Ecol. Evol., vol. 28, no. 12, pp. 719-728, 2013.
    • (2013) Trends Ecol. Evol. , vol.28 , Issue.12 , pp. 719-728
    • Nakhleh, L.1
  • 14
    • 80053547401 scopus 로고    scopus 로고
    • Fast and accurate methods for phylogenomic analyses
    • J. Yang and T. Warnow, "Fast and accurate methods for phylogenomic analyses," BMC Bioinformat., vol. 12, no. Suppl 9, p. S4, 2011.
    • (2011) BMC Bioinformat. , vol.12 , pp. S4
    • Yang, J.1    Warnow, T.2
  • 15
    • 37249034790 scopus 로고    scopus 로고
    • Bias in phylogenetic tree reconciliation methods: Implications for vertebrate genome evolution
    • M. W. Hahn, "Bias in phylogenetic tree reconciliation methods: Implications for vertebrate genome evolution," Genome Biol., vol. 8, no. 7, p. R141, 2007.
    • (2007) Genome Biol. , vol.8 , Issue.7 , pp. R141
    • Hahn, M.W.1
  • 16
    • 0036662360 scopus 로고    scopus 로고
    • Inverting random functions II: Explicit bounds for discrete maximum likelihood estimation, with applications
    • M. A. Steel and L. A. Székely, "Inverting random functions II: Explicit bounds for discrete maximum likelihood estimation, with applications," SIAM J. Discrete Math., vol. 15, no. 4, pp. 562-575, 2002.
    • (2002) SIAM J. Discrete Math. , vol.15 , Issue.4 , pp. 562-575
    • Steel, M.A.1    Székely, L.A.2
  • 18
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • B. Rannala and Z. Yang, "Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci," Genetics, vol. 164, no. 4, pp. 1645-1656, 2003.
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 19
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of dna sequences
    • S. Tavaré, "Some probabilistic and statistical problems in the analysis of dna sequences," Lectures Math. Life Sci., vol. 17, pp. 57-86, 1986.
    • (1986) Lectures Math. Life Sci. , vol.17 , pp. 57-86
    • Tavaré, S.1
  • 20
    • 77949341703 scopus 로고    scopus 로고
    • Toward extracting all phylogenetic information from matrices of evolutionary distances
    • S. Roch, "Toward extracting all phylogenetic information from matrices of evolutionary distances," Science, vol. 327, no. 5971, pp. 1376-1379, 2010.
    • (2010) Science , vol.327 , Issue.5971 , pp. 1376-1379
    • Roch, S.1
  • 21
    • 1842550501 scopus 로고    scopus 로고
    • Information flow on trees
    • E. Mossel and Y. Peres, "Information flow on trees," Ann. Appl. Probability, vol. 13, no. 3, pp. 817-844, 2003.
    • (2003) Ann. Appl. Probability , vol.13 , Issue.3 , pp. 817-844
    • Mossel, E.1    Peres, Y.2
  • 22
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • R. R. Sokal and C. D. Michener, "A statistical method for evaluating systematic relationships," Univ. Kansas Sci. Bull., vol. 38, pp. 1409-1438, 1958.
    • (1958) Univ. Kansas Sci. Bull. , vol.38 , pp. 1409-1438
    • Sokal, R.R.1    Michener, C.D.2
  • 23
    • 58149120871 scopus 로고    scopus 로고
    • A basic limitation on inferring phylogenies by pairwise sequence comparisons
    • Available
    • M. Steel. (2009). A basic limitation on inferring phylogenies by pairwise sequence comparisons. J. Theoretical Biol. [Online]. 256 (3), pp. 467-472. Available: http://www.sciencedirect.com/science/article/pii/S0022519308005390
    • (2009) J. Theoretical Biol.[Online] , vol.256 , Issue.3 , pp. 467-472
    • Steel, M.1
  • 24
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • N. Saitou and M. Nei, "The neighbor-joining method: A new method for reconstructing phylogenetic trees," Mol. Biol. Evol., vol. 4, no. 4, pp. 406-425, 1987.
    • (1987) Mol. Biol. Evol. , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.