메뉴 건너뛰기




Volumn 100, Issue , 2016, Pages 160-169

Phylogenomic analyses reveal novel relationships among snake families

Author keywords

Phylogenomics; Reptiles; Serpentes; Snakes; Species tree methods; UCE

Indexed keywords

DNA;

EID: 84963575813     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2016.04.015     Document Type: Article
Times cited : (49)

References (53)
  • 3
    • 84929193081 scopus 로고    scopus 로고
    • Temperate snake community in South America: is diet determined by phylogeny or ecology?
    • Bellini G.P., Giraudo A.R., Arzamendia V., Etchepare E.G. Temperate snake community in South America: is diet determined by phylogeny or ecology?. PLoS ONE 2015, 10:e0123237.
    • (2015) PLoS ONE , vol.10 , pp. e0123237
    • Bellini, G.P.1    Giraudo, A.R.2    Arzamendia, V.3    Etchepare, E.G.4
  • 4
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for Illumina sequence data
    • Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30:2114-2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 5
    • 84921484907 scopus 로고    scopus 로고
    • Gripping during climbing of arboreal snakes may be safe but not economical
    • Byrnes G., Jayne B.C. Gripping during climbing of arboreal snakes may be safe but not economical. Biol. Lett. 2014, 10:20140434.
    • (2014) Biol. Lett. , vol.10 , pp. 20140434
    • Byrnes, G.1    Jayne, B.C.2
  • 9
    • 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
  • 10
    • 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
  • 11
    • 84960093575 scopus 로고    scopus 로고
    • PHYLUCE is a software package for the analysis of conserved genomic loci
    • Faircloth B.C. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 2016, 32:786-788.
    • (2016) Bioinformatics , vol.32 , pp. 786-788
    • Faircloth, B.C.1
  • 12
  • 13
    • 84879162598 scopus 로고    scopus 로고
    • A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)
    • Faircloth B.C., Sorenson L., Santini F., Alfaro M.E. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS ONE 2013, 8:e54848.
    • (2013) PLoS ONE , vol.8 , pp. e54848
    • Faircloth, B.C.1    Sorenson, L.2    Santini, F.3    Alfaro, M.E.4
  • 14
    • 84926468506 scopus 로고    scopus 로고
    • Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
    • Faircloth B.C., Branstetter M.G., White N.D., Brady S.G. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol. Ecol. Res. 2014, 15:489-501.
    • (2014) Mol. Ecol. Res. , vol.15 , pp. 489-501
    • Faircloth, B.C.1    Branstetter, M.G.2    White, N.D.3    Brady, S.G.4
  • 15
    • 38449110166 scopus 로고    scopus 로고
    • Approaching the golden age of natural product pharmaceuticals from venom libraries: an overview of toxins and toxin-derivatives currently involved in therapeutic or diagnostic applications
    • Fox J.W., Serrano S.M.T. Approaching the golden age of natural product pharmaceuticals from venom libraries: an overview of toxins and toxin-derivatives currently involved in therapeutic or diagnostic applications. Curr. Pharm. Des. 2007, 13:2927-2934.
    • (2007) Curr. Pharm. Des. , vol.13 , pp. 2927-2934
    • Fox, J.W.1    Serrano, S.M.T.2
  • 16
    • 1942533494 scopus 로고    scopus 로고
    • Assembling an arsenal: origin and evolution of the snake venom proteome inferred from phylogenetic analysis of toxin sequences
    • Fry B.G., Wüster W. Assembling an arsenal: origin and evolution of the snake venom proteome inferred from phylogenetic analysis of toxin sequences. Mol. Biol. Evol. 2004, 21:870-883.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 870-883
    • Fry, B.G.1    Wüster, W.2
  • 18
    • 28444454462 scopus 로고    scopus 로고
    • The phylogenetic position of Anomochilidae (Reptilia: Serpentes): first evidence from DNA sequences
    • Gower D.J., Vidal N., Spinks J.N., McCarthy C.J. The phylogenetic position of Anomochilidae (Reptilia: Serpentes): first evidence from DNA sequences. J. Zool. Syst. Evol. Res. 2005, 43:315-320.
    • (2005) J. Zool. Syst. Evol. Res. , vol.43 , pp. 315-320
    • Gower, D.J.1    Vidal, N.2    Spinks, J.N.3    McCarthy, C.J.4
  • 19
    • 84928358919 scopus 로고    scopus 로고
    • Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences
    • syu046
    • Huang H., Knowles L.L. Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences. Syst. Biol. 2014, syu046.
    • (2014) Syst. Biol.
    • Huang, H.1    Knowles, L.L.2
  • 20
    • 84929622531 scopus 로고    scopus 로고
    • The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record
    • Hsiang A.Y., Field D.J., Webster T.H., Behlke A.D.B., Davis M.B., Racicot R.A., Gauthier J.A. The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record. BMC Evol. Biol. 2015, 15:87.
    • (2015) BMC Evol. Biol. , vol.15 , pp. 87
    • Hsiang, A.Y.1    Field, D.J.2    Webster, T.H.3    Behlke, A.D.B.4    Davis, M.B.5    Racicot, R.A.6    Gauthier, J.A.7
  • 21
    • 84908448749 scopus 로고    scopus 로고
    • Should genes with missing data be excluded from phylogenetic analyses?
    • Jiang W., Chen S.-Y., Wang H., Li D.-Z., Wiens J.J. Should genes with missing data be excluded from phylogenetic analyses?. Mol. Phylogenet. Evol. 2014, 80:308-318.
    • (2014) Mol. Phylogenet. Evol. , vol.80 , pp. 308-318
    • Jiang, W.1    Chen, S.-Y.2    Wang, H.3    Li, D.-Z.4    Wiens, J.J.5
  • 23
    • 84909979108 scopus 로고    scopus 로고
    • When do species tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny
    • Lambert S.M., Reeder T.W., Wiens J.J. When do species tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny. Mol. Phylogenet. Evol. 2015, 82:146-155.
    • (2015) Mol. Phylogenet. Evol. , vol.82 , pp. 146-155
    • Lambert, S.M.1    Reeder, T.W.2    Wiens, J.J.3
  • 24
    • 3142611436 scopus 로고    scopus 로고
    • A molecular approach to discerning the phylogenetic placement of the enigmatic snake Xenophidion schaeferi among the Alethinophidia
    • Lawson R., Slowinski J.B., Burbrink F.T. A molecular approach to discerning the phylogenetic placement of the enigmatic snake Xenophidion schaeferi among the Alethinophidia. J. Zool. 2004, 263:285-294.
    • (2004) J. Zool. , vol.263 , pp. 285-294
    • Lawson, R.1    Slowinski, J.B.2    Burbrink, F.T.3
  • 25
    • 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
  • 27
    • 84936771254 scopus 로고    scopus 로고
    • Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing
    • Leaché A.D., Chavez A.S., Jones L.N., Grummer J.A., Gottscho A.D., Linkem C.W. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biol. Evol. 2015, 7:706-719.
    • (2015) Genome Biol. Evol. , vol.7 , pp. 706-719
    • Leaché, A.D.1    Chavez, A.S.2    Jones, L.N.3    Grummer, J.A.4    Gottscho, A.D.5    Linkem, C.W.6
  • 28
    • 80051975928 scopus 로고    scopus 로고
    • Estimating species trees from unrooted gene trees
    • Liu L., Yu L. Estimating species trees from unrooted gene trees. Syst. Biol. 2011, 60:661-667.
    • (2011) Syst. Biol. , vol.60 , pp. 661-667
    • Liu, L.1    Yu, L.2
  • 29
    • 84876805079 scopus 로고    scopus 로고
    • A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
    • Pyron R.A., Burbrink F.T., Wiens J.J. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol. Biol. 2013, 13:93.
    • (2013) BMC Evol. Biol. , vol.13 , pp. 93
    • Pyron, R.A.1    Burbrink, F.T.2    Wiens, J.J.3
  • 30
    • 84908603912 scopus 로고    scopus 로고
    • Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)
    • Pyron R.A., Hendry C.R., Chou V.M., Lemmon E.M., Lemmon A.R., Burbrink F.T. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia). Mol. Phylogenet. Evol. 2014, 81:221-231.
    • (2014) Mol. Phylogenet. Evol. , vol.81 , pp. 221-231
    • Pyron, R.A.1    Hendry, C.R.2    Chou, V.M.3    Lemmon, E.M.4    Lemmon, A.R.5    Burbrink, F.T.6
  • 31
    • 84925424118 scopus 로고    scopus 로고
    • Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa
    • Reeder T.W., Townsend T.M., Mulcahy D.G., Noonan B.P., Wood P.L., Sites J.W., Wiens J.J. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa. PLoS ONE 2015, 10:e0118199.
    • (2015) PLoS ONE , vol.10 , pp. e0118199
    • Reeder, T.W.1    Townsend, T.M.2    Mulcahy, D.G.3    Noonan, B.P.4    Wood, P.L.5    Sites, J.W.6    Wiens, J.J.7
  • 32
    • 84860595791 scopus 로고    scopus 로고
    • Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    • Rohland N., Reich D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 2012, 22:939-946.
    • (2012) Genome Res. , vol.22 , pp. 939-946
    • Rohland, N.1    Reich, D.2
  • 34
    • 84907459397 scopus 로고    scopus 로고
    • Phylogeny of courtship and male-male combat behavior in snakes
    • Senter P., Harris S.M., Kent D.L. Phylogeny of courtship and male-male combat behavior in snakes. PLoS ONE 2014, 9:e107528.
    • (2014) PLoS ONE , vol.9 , pp. e107528
    • Senter, P.1    Harris, S.M.2    Kent, D.L.3
  • 35
    • 50949129519 scopus 로고    scopus 로고
    • Calculating bootstrap probabilities of phylogeny using multilocus sequence data
    • Seo T.K. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol. Biol. Evol. 2008, 25:960-971.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 960-971
    • Seo, T.K.1
  • 36
    • 84883591070 scopus 로고    scopus 로고
    • STRAW: Species TRee Analysis Web Server
    • Shaw T., Ruan Z., Glenn T., Liu L. STRAW: Species TRee Analysis Web Server. Nucleic Acids Res. 2013, 41:W230-W241.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W230-W241
    • Shaw, T.1    Ruan, Z.2    Glenn, T.3    Liu, L.4
  • 37
    • 84899553363 scopus 로고    scopus 로고
    • RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30:1312-1315.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1315
    • Stamatakis, A.1
  • 38
    • 84960362109 scopus 로고    scopus 로고
    • How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards
    • Streicher J.W., Schulte J.A., Wiens J.J. How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards. Syst. Biol. 2016, 65:128-145.
    • (2016) Syst. Biol. , vol.65 , pp. 128-145
    • Streicher, J.W.1    Schulte, J.A.2    Wiens, J.J.3
  • 40
    • 9644269182 scopus 로고    scopus 로고
    • Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree
    • Townsend T., Larson A., Louis E.J., Macey J.R. Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Syst. Biol. 2004, 53:735-757.
    • (2004) Syst. Biol. , vol.53 , pp. 735-757
    • Townsend, T.1    Larson, A.2    Louis, E.J.3    Macey, J.R.4
  • 42
    • 40949150808 scopus 로고    scopus 로고
    • Origin of tropical American burrowing reptiles by transatlantic rafting
    • Vidal N., Azvolinsky A., Cruaud C., Hedges S.B. Origin of tropical American burrowing reptiles by transatlantic rafting. Biol. Lett. 2007, 4:115-118.
    • (2007) Biol. Lett. , vol.4 , pp. 115-118
    • Vidal, N.1    Azvolinsky, A.2    Cruaud, C.3    Hedges, S.B.4
  • 43
    • 28044466648 scopus 로고    scopus 로고
    • The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes
    • Vidal N., Hedges S.B. The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. C. R. Biol. 2005, 328:1000-1008.
    • (2005) C. R. Biol. , vol.328 , pp. 1000-1008
    • Vidal, N.1    Hedges, S.B.2
  • 45
    • 84872480881 scopus 로고    scopus 로고
    • Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
    • Wagner C.E., Keller I., Wittwer S., Selz O.M., Mwaiko S., Greuter L., Sivasundar A., Seehausen O. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol. Ecol. 2013, 22:787-798.
    • (2013) Mol. Ecol. , vol.22 , pp. 787-798
    • Wagner, C.E.1    Keller, I.2    Wittwer, S.3    Selz, O.M.4    Mwaiko, S.5    Greuter, L.6    Sivasundar, A.7    Seehausen, O.8
  • 46
    • 80052006478 scopus 로고    scopus 로고
    • Missing data in phylogenetic analysis: reconciling results from simulations and empirical data
    • Wiens J.J., Morrill M.C. Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst. Biol. 2011, 60:719-731.
    • (2011) Syst. Biol. , vol.60 , pp. 719-731
    • Wiens, J.J.1    Morrill, M.C.2
  • 47
    • 84865026977 scopus 로고    scopus 로고
    • Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling
    • Wiens J.J., Tiu J. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS ONE 2012, 7:42925.
    • (2012) PLoS ONE , vol.7 , pp. 42925
    • Wiens, J.J.1    Tiu, J.2
  • 48
  • 49
    • 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. Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa. Syst. Biol. 2010, 59:674-688.
    • (2010) Syst. Biol. , vol.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
  • 51
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analysis
    • Yang Z. Among-site rate variation and its impact on phylogenetic analysis. Trends Ecol. Evol. 1996, 11:367-372.
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
    • Yang, Z.1
  • 52
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assemble using de Bruijn graphs
    • Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assemble using de Bruijn graphs. Genome Res. 2008, 18:821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 53
    • 84949033709 scopus 로고    scopus 로고
    • Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species
    • Zheng Y., Wiens J.J. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol. Phylogenet. Evol. 2016, 94:537-557.
    • (2016) Mol. Phylogenet. Evol. , vol.94 , pp. 537-557
    • Zheng, Y.1    Wiens, J.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.