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Volumn 64, Issue 3, 2012, Pages 685-689

Resolution of the laurasiatherian phylogeny: Evidence from genomic data

Author keywords

Laurasiatheria; Mammalian phylogeny; Molecular phylogeny; Phylogenomics

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETICS; GENOMICS; MAMMAL; PHYLOGENY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

EID: 84863086549     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.04.012     Document Type: Article
Times cited : (40)

References (36)
  • 1
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • Altenhoff A.M., Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol. 2009, 5:e10000262.
    • (2009) PLoS Comput. Biol. , vol.5
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 3
    • 48349115697 scopus 로고    scopus 로고
    • Mitogenomic relationships of placental mammals and molecular estimates of their divergences
    • Arnason U., Adegoke J.A., Gullberg A., Harley E.H., Janke A., Kullberg M. Mitogenomic relationships of placental mammals and molecular estimates of their divergences. Gene 2008, 421:37-51.
    • (2008) Gene , vol.421 , pp. 37-51
    • Arnason, U.1    Adegoke, J.A.2    Gullberg, A.3    Harley, E.H.4    Janke, A.5    Kullberg, M.6
  • 4
    • 79951577664 scopus 로고    scopus 로고
    • Retrieving a mitogenomic mammal tree using composite taxa
    • Campbell V., Lapointe J.F. Retrieving a mitogenomic mammal tree using composite taxa. Mol. Phylogenet. Evol. 2011, 58:149-156.
    • (2011) Mol. Phylogenet. Evol. , vol.58 , pp. 149-156
    • Campbell, V.1    Lapointe, J.F.2
  • 5
    • 33646152743 scopus 로고    scopus 로고
    • OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: introduction and first achievements
    • Dessimoz C., Cannarozzi G., Gil M., Margadant D., Roth A., Schneider A., Gonnet G.H. OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: introduction and first achievements. Lect. Notes Comput. Sci. 2005, 3678:61-72.
    • (2005) Lect. Notes Comput. Sci. , vol.3678 , pp. 61-72
    • Dessimoz, C.1    Cannarozzi, G.2    Gil, M.3    Margadant, D.4    Roth, A.5    Schneider, A.6    Gonnet, G.H.7
  • 6
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32:1792-1797.
    • (2004) Nucl. Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 7
    • 14844313275 scopus 로고    scopus 로고
    • Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree
    • Gadagkar S.R., Rosenberg M.S., Kumar S. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J. Exp. Zool. 2005, 304B:64-74.
    • (2005) J. Exp. Zool. , vol.304 B , pp. 64-74
    • Gadagkar, S.R.1    Rosenberg, M.S.2    Kumar, S.3
  • 8
    • 22844438847 scopus 로고    scopus 로고
    • Hidden likelihood support in genomic data: can forty-five wrongs make a right?
    • Gatesy J., Baker R. Hidden likelihood support in genomic data: can forty-five wrongs make a right?. Syst. Biol. 2005, 54:483-492.
    • (2005) Syst. Biol. , vol.54 , pp. 483-492
    • Gatesy, J.1    Baker, R.2
  • 9
    • 0032805771 scopus 로고    scopus 로고
    • Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level Artiodactyl taxa
    • Gatesy J., O'Grady P., Baker R.H. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level Artiodactyl taxa. Cladistics 1999, 15:271-313.
    • (1999) Cladistics , vol.15 , pp. 271-313
    • Gatesy, J.1    O'Grady, P.2    Baker, R.H.3
  • 10
    • 47349109604 scopus 로고    scopus 로고
    • Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations
    • Hallström B.M., Janke A. Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations. BMC Evol. Biol. 2008, 8:162.
    • (2008) BMC Evol. Biol. , vol.8 , pp. 162
    • Hallström, B.M.1    Janke, A.2
  • 11
    • 78649382339 scopus 로고    scopus 로고
    • Mammalian evolution may not be strictly bifurcating
    • Hallström B.M., Janke A. Mammalian evolution may not be strictly bifurcating. Mol. Biol. Evol. 2010, 27:2804-2816.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 2804-2816
    • Hallström, B.M.1    Janke, A.2
  • 12
    • 34548448442 scopus 로고    scopus 로고
    • Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups
    • Hallström B.M., Kullberg M., Nilsson M.A., Janke A. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Mol. Biol. Evol. 2007, 24:2059-2068.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 2059-2068
    • Hallström, B.M.1    Kullberg, M.2    Nilsson, M.A.3    Janke, A.4
  • 13
    • 82555187427 scopus 로고    scopus 로고
    • A genomic approach to examine the complex evolution of Laurasiatherian mammals
    • Hallström B.M., Schneider A., Zoller S., Janke A. A genomic approach to examine the complex evolution of Laurasiatherian mammals. PLoS 2011, 6:e28199.
    • (2011) PLoS , vol.6
    • Hallström, B.M.1    Schneider, A.2    Zoller, S.3    Janke, A.4
  • 14
    • 67649658023 scopus 로고    scopus 로고
    • Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data
    • Hou Z.-C., Romero R., Wildman D.E. Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data. Mol. Phylogenet. Evol. 2009, 52:660-664.
    • (2009) Mol. Phylogenet. Evol. , vol.52 , pp. 660-664
    • Hou, Z.-C.1    Romero, R.2    Wildman, D.E.3
  • 15
    • 13444259388 scopus 로고    scopus 로고
    • TREEFINDER a powerful graphical analysis environment for molecular phylogenetics
    • Jobb G., Von Haeseler A., Strimmer K. TREEFINDER a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4:18.
    • (2004) BMC Evol. Biol. , vol.4 , pp. 18
    • Jobb, G.1    Von Haeseler, A.2    Strimmer, K.3
  • 16
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • Katoh K., Kuma K., Toh H., Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl. Acids Res. 2005, 33:511-518.
    • (2005) Nucl. Acids Res. , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 18
    • 33846906954 scopus 로고    scopus 로고
    • Site specific rates of mitochondrial genomes and the phylogeny of eutheria
    • Kjer K.M., Honeycutt R.L. Site specific rates of mitochondrial genomes and the phylogeny of eutheria. BMC Evol. Biol. 2007, 7:8.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 8
    • Kjer, K.M.1    Honeycutt, R.L.2
  • 19
    • 0036897677 scopus 로고    scopus 로고
    • Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling
    • Lin Y.-H., McLenachan P.A., Gore A.R., Phillips M.J., Ota R., Hendy M.D., Penny D. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol. Biol. Evol. 2002, 19:2060-2070.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 2060-2070
    • Lin, Y.-H.1    McLenachan, P.A.2    Gore, A.R.3    Phillips, M.J.4    Ota, R.5    Hendy, M.D.6    Penny, D.7
  • 20
    • 84859530730 scopus 로고    scopus 로고
    • Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
    • McCormack J.E., Faircloth B.C., Crawford N.G., Gowaty P.A., Brumfield R.T., Glenn T.C. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 2012, 22:746-754.
    • (2012) Genome Res. , vol.22 , pp. 746-754
    • McCormack, J.E.1    Faircloth, B.C.2    Crawford, N.G.3    Gowaty, P.A.4    Brumfield, R.T.5    Glenn, T.C.6
  • 22
    • 34147184456 scopus 로고    scopus 로고
    • Using genomic data to unravel the root of the placental mammals phylogeny
    • Murphy W.J., Pringle T.H., Crider T.A., Springer M.S., Miller W. Using genomic data to unravel the root of the placental mammals phylogeny. Genome Res. 2007, 17:413-421.
    • (2007) Genome Res. , vol.17 , pp. 413-421
    • Murphy, W.J.1    Pringle, T.H.2    Crider, T.A.3    Springer, M.S.4    Miller, W.5
  • 24
    • 33745632616 scopus 로고    scopus 로고
    • Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
    • Nishihara H., Hasegawa M., Okada N. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl. Acad. Sci. USA 2006, 103:9929-9934.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 9929-9934
    • Nishihara, H.1    Hasegawa, M.2    Okada, N.3
  • 25
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: a novel method for fast and accurate multiple sequence alignment
    • Notedrame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302:205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notedrame, C.1    Higgins, D.G.2    Heringa, J.3
  • 26
    • 49749129961 scopus 로고    scopus 로고
    • Confirming the phylogeny of mammals by use of large comparative sequence data sets
    • Prasad A.B., Allard M.W., Green E.D. Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol. Biol. Evol. 2008, 25:1795-1808.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1795-1808
    • Prasad, A.B.1    Allard, M.W.2    Green, E.D.3
  • 27
    • 1542376765 scopus 로고    scopus 로고
    • Congruent mammalian trees from mitochondrial and nuclear genes using bayesian methods
    • Reyes A., Gissi C., Catzeflis F., Nevo E., Pesole G., Saccone C. Congruent mammalian trees from mitochondrial and nuclear genes using bayesian methods. Mol. Biol. Evol. 2004, 21:397-403.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 397-403
    • Reyes, A.1    Gissi, C.2    Catzeflis, F.3    Nevo, E.4    Pesole, G.5    Saccone, C.6
  • 28
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 29
    • 0041386108 scopus 로고    scopus 로고
    • MRBAYES 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F., Huelsenbeck M. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, M.2
  • 30
    • 59149097358 scopus 로고    scopus 로고
    • Algorithm of OMA for large-scale orthology inference
    • Roth A.C.J., Gonnet G.H., Dessimoz C. Algorithm of OMA for large-scale orthology inference. BMC Bioinform. 2008, 9:518.
    • (2008) BMC Bioinform. , vol.9 , pp. 518
    • Roth, A.C.J.1    Gonnet, G.H.2    Dessimoz, C.3
  • 31
    • 34548555911 scopus 로고    scopus 로고
    • OMA Browser - exploring orthologous relations across 352 complete genomes
    • Schneider A., Dessimoz C., Gonnet G.H. OMA Browser - exploring orthologous relations across 352 complete genomes. Bioinformatics 2007, 23:2180-2182.
    • (2007) Bioinformatics , vol.23 , pp. 2180-2182
    • Schneider, A.1    Dessimoz, C.2    Gonnet, G.H.3
  • 32
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 33
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
    • Suyama M., Torrents D., Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucl. Acids Res. 2006, 34:609-612.
    • (2006) Nucl. Acids Res. , vol.34 , pp. 609-612
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 35
    • 80052730828 scopus 로고    scopus 로고
    • Phylogenomic analyses and improved resolution of Cetartiodactyla
    • Zhou X., Xu S., Yang Y., Zhou K., Yang G. Phylogenomic analyses and improved resolution of Cetartiodactyla. Mol. Phylogenet. Evol. 2011, 61:255-264.
    • (2011) Mol. Phylogenet. Evol. , vol.61 , pp. 255-264
    • Zhou, X.1    Xu, S.2    Yang, Y.3    Zhou, K.4    Yang, G.5
  • 36
    • 84555186853 scopus 로고    scopus 로고
    • Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals
    • Zhou X., Xu S., Xu J., Chen B., Zhou K., Yang G. Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals. Syst. Biol. 2011, 61:150-164.
    • (2011) Syst. Biol. , vol.61 , pp. 150-164
    • Zhou, X.1    Xu, S.2    Xu, J.3    Chen, B.4    Zhou, K.5    Yang, G.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.