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Volumn 62, Issue 3, 2013, Pages 424-438

Phylogenetic signal variation in the genomes of medicago (Fabaceae)

Author keywords

Medicago; phylogenomics; whole genome resequencing

Indexed keywords

ARTICLE; BAYES THEOREM; CELL NUCLEUS; CHLOROPLAST; CYTOLOGY; DNA SEQUENCE; GENE LIBRARY; GENETICS; MEDICAGO; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PLANT GENOME; SEQUENCE ALIGNMENT;

EID: 84876258655     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syt009     Document Type: Article
Times cited : (50)

References (64)
  • 3
    • 51249174506 scopus 로고
    • Medicago truncatula, a model plant for studying the molecular genetics of the rhizobium-legume symbiosis
    • Barker D., Bianchi S., Blondon F. 1990. Medicago truncatula, a model plant for studying the molecular genetics of the rhizobium-legume symbiosis. Plant Mol. Biol. Rep. 8:40-49.
    • (1990) Plant Mol. Biol. Rep. , vol.8 , pp. 40-49
    • Barker, D.1    Bianchi, S.2    Blondon, F.3
  • 7
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers:bypassing gene trees in a full coalescent analysis
    • Bryant D., Bouckaert R. 2009. Inferring species trees directly from biallelic genetic markers:bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29:1917-1732.
    • (2009) Mol. Biol. Evol. , vol.29 , pp. 1917-1732
    • Bryant, D.1    Bouckaert, R.2
  • 8
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers:bypassing gene trees in a full coalescent analysis
    • Bryant D., BouckaertR., FelsensteinJ., Rosenberg N.A., RoyChoudhury A. 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    Roychoudhury, A.5
  • 11
    • 34249700809 scopus 로고    scopus 로고
    • Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting:an example from Melanoplus grasshoppers
    • Carstens B., Knowles L. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting:an example from Melanoplus grasshoppers. Syst. Biol. 56:400-411.
    • (2007) Syst. Biol. , vol.56 , pp. 400-411
    • Carstens, B.1    Knowles, L.2
  • 15
    • 77956552648 scopus 로고    scopus 로고
    • Phylogenomic analysis of BAC-end sequencelibraries in Oryza (Poaceae)
    • Cranston K., Hurwitz B., Sanderson M. 2010. Phylogenomic analysis of BAC-end sequencelibraries in Oryza (Poaceae). Syst. Bot. 35:512-523.
    • (2010) Syst. Bot. , vol.35 , pp. 512-523
    • Cranston, K.1    Hurwitz, B.2    Sanderson, M.3
  • 18
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference and the multispecies coalescent
    • Degnan J.H., 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
  • 19
    • 79959300621 scopus 로고    scopus 로고
    • Applications of next generation sequencing in molecular ecology of non-model organisms
    • Ekblom R., Galindo J. 2010. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1-15.
    • (2010) Heredity , vol.107 , pp. 1-15
    • Ekblom, R.1    Galindo, J.2
  • 22
    • 0000122573 scopus 로고
    • PHYLIP\-Phylogeny Inference Package (Version 3.2)
    • Felsenstein J. 1989. PHYLIP\-Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 24
    • 0003437302 scopus 로고    scopus 로고
    • last accessed December 7, 2011
    • Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package). Available from:URL http://evolution.genetics.washington.edu/phylip.html (last accessed December 7, 2011).
    • (2005) PHYLIP (Phylogeny Inference Package)
    • Felsenstein, J.1
  • 25
    • 34447286481 scopus 로고    scopus 로고
    • How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence
    • Gatesy J., DeSalle R., Wahlberg N. 2007. How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Syst. Biol. 56:355-363.
    • (2007) Syst. Biol. , vol.56 , pp. 355-363
    • Gatesy, J.1    Desalle, R.2    Wahlberg, N.3
  • 28
    • 46449135061 scopus 로고    scopus 로고
    • A phylogenomic study of birds reveals their evolutionary history
    • Hackett S., Kimball R., Reddy S. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763-1768.
    • (2008) Science , vol.320 , pp. 1763-1768
    • Hackett, S.1    Kimball, R.2    Reddy, S.3
  • 30
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes:Bayesian inference of phylogenetic trees
    • Huelsenbeck J., Ronquist F. 2001. MrBayes:Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.1    Ronquist, F.2
  • 31
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson D.H., Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 33
    • 25644452054 scopus 로고    scopus 로고
    • Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees
    • Jennings W. 2005. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59:2033-2047
    • (2005) Evolution , vol.59 , pp. 2033-2047
    • Jennings, W.1
  • 35
    • 70450233546 scopus 로고    scopus 로고
    • Estimating species trees:methods of phylogenetic analysis when there is incongruence across genes
    • Knowles L.L. 2009. Estimating species trees:methods of phylogenetic analysis when there is incongruence across genes. Syst. Biol. 58:463-467
    • (2009) Syst. Biol. , vol.58 , pp. 463-467
    • Knowles, L.L.1
  • 36
    • 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. 2009. STEM:species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971-973.
    • (2009) Bioinformatics , vol.25 , pp. 971-973
    • Kubatko, L.S.1    Carstens, B.C.2    Knowles, L.L.3
  • 37
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • Kubatko L.S., Degnan J.H. 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
  • 38
    • 25144446148 scopus 로고    scopus 로고
    • Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary
    • Lavin M., Herendeen P.S., Wojciechowski M.F. 2005. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. Syst. Biol. 54:575-594.
    • (2005) Syst. Biol. , vol.54 , pp. 575-594
    • Lavin, M.1    Herendeen, P.S.2    Wojciechowski, M.F.3
  • 39
    • 57249086459 scopus 로고    scopus 로고
    • Divergence across Australia's Carpenterian barrier:statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus)
    • Lee J.Y., Edwards S.V. 2008. Divergence across Australia's Carpenterian barrier:statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution 62:3117-3134.
    • (2008) Evolution , vol.62 , pp. 3117-3134
    • Lee, J.Y.1    Edwards, S.V.2
  • 41
    • 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. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 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
  • 42
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison W., Knowles L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21-30.
    • (2006) Syst. Biol. , vol.55 , pp. 21-30
    • Maddison, W.1    Knowles, L.2
  • 43
    • 84857229990 scopus 로고    scopus 로고
    • The tree versus the forest: The fungal tree of life and the topological diversity within the yeast phylome
    • Marcet-Houben M., Gabaldón T. 2009. The tree versus the forest: The fungal tree of life and the topological diversity within the yeast phylome. PLoS One 4:e4357
    • (2009) PLoS One , vol.4
    • Marcet-Houben, M.1    Gabaldón, T.2
  • 47
    • 33745632616 scopus 로고    scopus 로고
    • Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
    • Nishihara H., Hasegawa M., Okada N. 2006. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl Acad. Sci. U S A 103:9929-9934.
    • (2006) Proc. Natl Acad. Sci. U S A , vol.103 , pp. 9929-9934
    • Nishihara, H.1    Hasegawa, M.2    Okada, N.3
  • 48
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P., Nei M. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 49
    • 1042304216 scopus 로고    scopus 로고
    • APE:analysis of phylogenetics and evolution in R language
    • Paradis E., Claude J., Strimmer K. 2004. APE:analysis of phylogenetics and evolution in R language. Bioinformatics 20:289-290.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 50
    • 0002393841 scopus 로고
    • The Use of Tree Comparison Metrics
    • Penny D., Hendy M. 1985. The Use of Tree Comparison Metrics. Syst. Zool. 34:75-82.
    • (1985) Syst. Zool. , vol.34 , pp. 75-82
    • Penny, D.1    Hendy, M.2
  • 54
    • 0041386108 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • R Core Team 2012. MrBayes 3:Bayesian phylogenetic inference under mixed models
    • R Core Team 2012. R: A language and environment for statistical computing. Available from:URL www.r-project.org. Ronquist F., Huelsenbeck J. 2003. MrBayes 3:Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.2
  • 55
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage: The limits to inference
    • Sanderson M.J., McMahon M.M., Steel M. 2010. Phylogenomics with incomplete taxon coverage: The limits to inference. BMC Evol. Biol. 10:155.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 155
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 56
    • 70350714430 scopus 로고    scopus 로고
    • Phylogenomics of primates and their ancestral populations
    • Siepel A. 2009. Phylogenomics of primates and their ancestral populations. Genome Res. 19:1929-1941.
    • (2009) Genome Res. , vol.19 , pp. 1929-1941
    • Siepel, A.1
  • 58
    • 77954629195 scopus 로고    scopus 로고
    • Phylogeny and character evolution in Medicago (Leguminosae): Evidence from analyses of plastid trnK/matK and nuclear GA3ox1 sequences
    • Steele K.P., Ickert-Bond S.M., Zarre S., Wojciechowski M.F. 2010. Phylogeny and character evolution in Medicago (Leguminosae):evidence from analyses of plastid trnK/matK and nuclear GA3ox1 sequences. Am. J. Bot. 97:1142-1155.
    • (2010) Am. J. Bot. , Issue.97 , pp. 1142-1155
    • Steele, K.P.1    Ickert-Bond, S.M.2    Zarre, S.3    Wojciechowski, M.F.4
  • 59
    • 33646878378 scopus 로고    scopus 로고
    • Novel relationships among ten fish model species revealed based on phylogenomic analysis using ESTs
    • Steinke D., Salzburger W., Meyer A. 2006. Novel relationships among ten fish model species revealed based on phylogenomic analysis using ESTs. J. Mol. Evol. 62:772-784.
    • (2006) J. Mol. Evol. , vol.62 , pp. 772-784
    • Steinke, D.1    Salzburger, W.2    Meyer, A.3
  • 60
    • 0021066244 scopus 로고
    • Evolutionary relationship of DNA sequences in finite populations
    • Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
    • (1983) Genetics , vol.105 , pp. 437-460
    • Tajima, F.1
  • 61
    • 33751073183 scopus 로고    scopus 로고
    • Molecular evolution of plant immune system genes
    • Tiffin P., Moeller D.A. 2006. Molecular evolution of plant immune system genes. Trends Genet. 22:662-670.
    • (2006) Trends Genet , vol.22 , pp. 662-670
    • Tiffin, P.1    Moeller, D.A.2
  • 62
    • 78651454774 scopus 로고    scopus 로고
    • Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: Molecular data change the placement of fossil taxa
    • Wiens J.J., Kuczynski C.A., Townsend T., Reeder T.W., Mulcahy D.G., Sites J.W. 2010. Combining phylogenomics and fossils in higher-level squamate reptile phylogeny:molecular data change the placement of fossil taxa. Syst. Biol. 59:674-688.
    • (2010) Syst. Biol. , Issue.59 , pp. 674-688
    • Wiens, J.J.1    Kuczynski, C.A.2    Townsend, T.3    Reeder, T.W.4    Mulcahy, D.G.5    Sites, J.W.6
  • 63
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu T.D., Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873-881.
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2


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