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Volumn 112, Issue 41, 2015, Pages 12764-12769

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(22)  Hinchliff, Cody E a   Smith, Stephen A a   Allman, James F b   Burleigh, J Gordon c   Chaudhary, Ruchi c   Coghill, Lyndon M d   Crandall, Keith A e   Deng, Jiabin c   Drew, Bryan T f   Gazis, Romina g   Gude, Karl h   Hibbett, David S g   Katz, Laura A i   Dail Laughinghouse, H i   McTavish, Emily Jane j   Midford, Peter E d   Owen, Christopher L c   Ree, Richard H d   Rees, Jonathan A k   Soltisc, Douglas E l   more..


Author keywords

Biodiversity; Phylogeny; Synthesis; Taxonomy; Tree of life

Indexed keywords

BIODIVERSITY; CONFERENCE PAPER; DATA BASE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; SYNTHESIS; TAXONOMY; TREE OF LIFE; ANIMAL; CLASSIFICATION; HUMAN; PROCEDURES;

EID: 84944262980     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1423041112     Document Type: Article
Times cited : (545)

References (55)
  • 3
    • 84865221758 scopus 로고    scopus 로고
    • Predicting total global species richness using rates of species description and estimates of taxonomic effort
    • Costello MJ, Wilson S, Houlding B (2012) Predicting total global species richness using rates of species description and estimates of taxonomic effort Syst Biol 61(5):871-883.
    • (2012) Syst Biol , vol.61 , Issue.5 , pp. 871-883
    • Costello, M.J.1    Wilson, S.2    Houlding, B.3
  • 4
    • 43849111915 scopus 로고    scopus 로고
    • Species numbers in bacteria
    • Dykhuizen D (2005) Species numbers in bacteria Proc Calif Acad Sci 56(6, Suppl 1): 62-71.
    • (2005) Proc Calif Acad Sci , vol.56 , Issue.6 , pp. 62-71
    • Dykhuizen, D.1
  • 5
    • 46849087728 scopus 로고    scopus 로고
    • Phylogenetic signal in the eukaryotic tree of life
    • Sanderson MJ (2008) Phylogenetic signal in the eukaryotic tree of life Science 321(5885):121-123.
    • (2008) Science , vol.321 , Issue.5885 , pp. 121-123
    • Sanderson, M.J.1
  • 6
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage: The limits to inference
    • Sanderson MJ, McMahon MM, Steel M (2010) Phylogenomics with incomplete taxon coverage: The limits to inference BMC Evol Biol 10(1):155.
    • (2010) BMC Evol Biol , vol.10 , Issue.1 , pp. 155
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 7
    • 84867641403 scopus 로고    scopus 로고
    • Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis
    • Stoltzfus A, et al (2012) Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis BMC Res Notes 5:574.
    • (2012) BMC Res Notes , vol.5 , pp. 574
    • Stoltzfus, A.1
  • 8
    • 84908432176 scopus 로고    scopus 로고
    • The dawn of open access to phylogenetic data
    • Magee AF, May MR, Moore BR (2014) The dawn of open access to phylogenetic data PLoS One 9(10):e110268.
    • (2014) PLoS One , vol.9 , Issue.10 , pp. e110268
    • Magee, A.F.1    May, M.R.2    Moore, B.R.3
  • 9
    • 84884549736 scopus 로고    scopus 로고
    • Lost branches on the tree of life
    • Drew BT, et al (2013) Lost branches on the tree of life PLoS Biol 11(9):e1001636.
    • (2013) PLoS Biol , vol.11 , Issue.9 , pp. e1001636
    • Drew, B.T.1
  • 11
    • 84869088692 scopus 로고    scopus 로고
    • The global diversity of birds in space and time
    • Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time Nature 491(7424):444-448.
    • (2012) Nature , vol.491 , Issue.7424 , pp. 444-448
    • Jetz, W.1    Thomas, G.H.2    Joy, J.B.3    Hartmann, K.4    Mooers, A.O.5
  • 12
    • 0035527411 scopus 로고    scopus 로고
    • Assessment of the accuracy of matrix representation with parsimony analysis supertree construction
    • Bininda-Emonds OR, Sanderson MJ (2001) Assessment of the accuracy of matrix representation with parsimony analysis supertree construction Syst Biol 50(4):565-579.
    • (2001) Syst Biol , vol.50 , Issue.4 , pp. 565-579
    • Bininda-Emonds, O.R.1    Sanderson, M.J.2
  • 14
    • 84884681647 scopus 로고    scopus 로고
    • Analyzing and synthesizing phylogenies using tree alignment graphs
    • Smith SA, Brown JW, Hinchliff CE (2013) Analyzing and synthesizing phylogenies using tree alignment graphs PLOS Comput Biol 9(9):e1003223.
    • (2013) PLOS Comput Biol , vol.9 , Issue.9 , pp. e1003223
    • Smith, S.A.1    Brown, J.W.2    Hinchliff, C.E.3
  • 15
    • 84873599883 scopus 로고    scopus 로고
    • Amalgamating source trees with different taxonomic levels
    • Berry V, Bininda-Emonds ORP, Semple C (2013) Amalgamating source trees with different taxonomic levels Syst Biol 62(2):231-249.
    • (2013) Syst Biol , vol.62 , Issue.2 , pp. 231-249
    • Berry, V.1    Bininda-Emonds, O.R.P.2    Semple, C.3
  • 16
    • 78649687580 scopus 로고    scopus 로고
    • Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
    • Kupczok A, Schmidt HA, von Haeseler A (2010) Accuracy of phylogeny reconstruction methods combining overlapping gene data sets Algorithms Mol Biol 5:37.
    • (2010) Algorithms Mol Biol , vol.5 , pp. 37
    • Kupczok, A.1    Schmidt, H.A.2    Von Haeseler, A.3
  • 17
    • 0001354740 scopus 로고
    • Treebase: A prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life
    • Sanderson MJ, Donoghue MJ, Piel W, Eriksson T (1994) TreeBASE: A prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life Am J Bot 81(6):183.
    • (1994) Am J Bot , vol.81 , Issue.6 , pp. 183
    • Sanderson, M.J.1    Donoghue, M.J.2    Piel, W.3    Eriksson, T.4
  • 19
    • 0039861672 scopus 로고
    • Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes
    • Lake JA, Henderson E, Oakes M, Clark MW (1984) Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes Proc Natl Acad Sci USA 81(12):3786-3790.
    • (1984) Proc Natl Acad Sci USA , vol.81 , Issue.12 , pp. 3786-3790
    • Lake, J.A.1    Henderson, E.2    Oakes, M.3    Clark, M.W.4
  • 20
    • 42149157760 scopus 로고    scopus 로고
    • Broad phylogenomic sampling improves resolution of the animal tree of life
    • Dunn CW, et al (2008) Broad phylogenomic sampling improves resolution of the animal tree of life Nature 452(7188):745-749.
    • (2008) Nature , vol.452 , Issue.7188 , pp. 745-749
    • Dunn, C.W.1
  • 21
    • 84890056203 scopus 로고    scopus 로고
    • The genome of the ctenophore mnemiopsis leidyi and its implications for cell type evolution
    • NISC Comparative Sequencing Program
    • Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution Science 342(6164):1242592.
    • (2013) Science , vol.342 , Issue.6164 , pp. 1242592
    • Ryan, J.F.1
  • 22
    • 77955497041 scopus 로고    scopus 로고
    • Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships
    • Pick KS, et al (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships Mol Biol Evol 27(9):1983-1987.
    • (2010) Mol Biol Evol , vol.27 , Issue.9 , pp. 1983-1987
    • Pick, K.S.1
  • 23
    • 65249099546 scopus 로고    scopus 로고
    • Phylogenomics revives traditional views on deep animal relationships
    • Philippe H, et al (2009) Phylogenomics revives traditional views on deep animal relationships Curr Biol 19(8):706-712.
    • (2009) Curr Biol , vol.19 , Issue.8 , pp. 706-712
    • Philippe, H.1
  • 24
    • 40749116835 scopus 로고    scopus 로고
    • Phylogenomics reshuffles the eukaryotic supergroups
    • Burki F, et al (2007) Phylogenomics reshuffles the eukaryotic supergroups PLoS One 2(8):e790.
    • (2007) PLoS One , vol.2 , Issue.8 , pp. e790
    • Burki, F.1
  • 25
    • 80052019696 scopus 로고    scopus 로고
    • Estimating the timing of early eukaryotic diversification with multigene molecular clocks
    • Parfrey LW, Lahr DJG, Knoll AH, Katz LA (2011) Estimating the timing of early eukaryotic diversification with multigene molecular clocks Proc Natl Acad Sci USA 108(33):13624-13629.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.33 , pp. 13624-13629
    • Parfrey, L.W.1    Lahr, D.J.G.2    Knoll, A.H.3    Katz, L.A.4
  • 26
    • 84862884930 scopus 로고    scopus 로고
    • Turning the crown upside down: Gene tree parsimony roots the eukaryotic tree of life
    • Katz LA, Grant JR, Parfrey LW, Gordon Burleigh J (2012) Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life Syst Biol 61(4):653-660.
    • (2012) Syst Biol , vol.61 , Issue.4 , pp. 653-660
    • Katz, L.A.1    Grant, J.R.2    Parfrey, L.W.3    Gordon Burleigh, J.4
  • 27
    • 84858411861 scopus 로고    scopus 로고
    • Rooting the eukaryotic tree with mitochondrial and bacterial proteins
    • Derelle R, Lang BF (2012) Rooting the eukaryotic tree with mitochondrial and bacterial proteins Mol Biol Evol 29(4):1277-1289.
    • (2012) Mol Biol Evol , vol.29 , Issue.4 , pp. 1277-1289
    • Derelle, R.1    Lang, B.F.2
  • 28
    • 84894295410 scopus 로고    scopus 로고
    • An alternative root for the eukaryote tree of life
    • He D, et al (2014) An alternative root for the eukaryote tree of life Curr Biol 24(4): 465-470.
    • (2014) Curr Biol , vol.24 , Issue.4 , pp. 465-470
    • He, D.1
  • 29
    • 17044416291 scopus 로고    scopus 로고
    • Reconstructing patterns of reticulate evolution in plants
    • Linder CR, Rieseberg LH (2004) Reconstructing patterns of reticulate evolution in plants Am J Bot 91(10):1700-1708.
    • (2004) Am J Bot , vol.91 , Issue.10 , pp. 1700-1708
    • Linder, C.R.1    Rieseberg, L.H.2
  • 30
    • 0031466095 scopus 로고    scopus 로고
    • The role of hybridization and introgression in the diversification of animals
    • Dowling TE, Secor CL (1997) The role of hybridization and introgression in the diversification of animals Annu Rev Ecol Syst 28:593-619.
    • (1997) Annu Rev Ecol Syst , vol.28 , pp. 593-619
    • Dowling, T.E.1    Secor, C.L.2
  • 31
    • 84902675998 scopus 로고    scopus 로고
    • Reticulate evolution and the human past: An anthropological perspective
    • Winder IC, Winder NP (2014) Reticulate evolution and the human past: An anthropological perspective Ann Hum Biol 41(4):300-311.
    • (2014) Ann Hum Biol , vol.41 , Issue.4 , pp. 300-311
    • Winder, I.C.1    Winder, N.P.2
  • 32
    • 84870200615 scopus 로고    scopus 로고
    • Evolutionary implications of horizontal gene transfer
    • Syvanen M (2012) Evolutionary implications of horizontal gene transfer Annu Rev Genet 46:341-358.
    • (2012) Annu Rev Genet , vol.46 , pp. 341-358
    • Syvanen, M.1
  • 33
    • 84922775800 scopus 로고    scopus 로고
    • Origins of major archaeal clades correspond to gene acquisitions from bacteria
    • Nelson-Sathi S, et al (2015) Origins of major archaeal clades correspond to gene acquisitions from bacteria Nature 517(7532):77-80.
    • (2015) Nature , vol.517 , Issue.7532 , pp. 77-80
    • Nelson-Sathi, S.1
  • 34
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle WF (1999) Phylogenetic classification and the universal tree Science 284(5423):2124-2129.
    • (1999) Science , vol.284 , Issue.5423 , pp. 2124-2129
    • Doolittle, W.F.1
  • 35
    • 33748032715 scopus 로고    scopus 로고
    • Taking the first steps towards a standard for reporting on phylogenies: Minimum information about a phylogenetic analysis (miapa
    • Leebens-Mack J, et al (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA) OMICS 10(2):231-237.
    • (2006) OMICS , vol.10 , Issue.2 , pp. 231-237
    • Leebens-Mack, J.1
  • 36
    • 84862498268 scopus 로고    scopus 로고
    • Nexml: Rich, extensible, and verifiable representation of comparative data and metadata
    • Vos RA, et al (2012) NeXML: Rich, extensible, and verifiable representation of comparative data and metadata Syst Biol 61(4):675-689.
    • (2012) Syst Biol , vol.61 , Issue.4 , pp. 675-689
    • Vos, R.A.1
  • 37
    • 84866065801 scopus 로고    scopus 로고
    • Groundtruthing next-gen sequencing for microbial ecologybiases and errors in community structure estimates from PCR amplicon pyrosequencing
    • Lee CK, et al (2012) Groundtruthing next-gen sequencing for microbial ecologybiases and errors in community structure estimates from PCR amplicon pyrosequencing PLoS One 7(9):e44224.
    • (2012) PLoS One , vol.7 , Issue.9 , pp. e44224
    • Lee, C.K.1
  • 38
    • 79952447866 scopus 로고    scopus 로고
    • Progress in molecular and morphological taxon discovery in fungi and options for formal classification of environmental sequences
    • Hibbett DS, et al (2011) Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences Fungal Biol Rev 25(1):38-47.
    • (2011) Fungal Biol Rev , vol.25 , Issue.1 , pp. 38-47
    • Hibbett, D.S.1
  • 39
    • 84885955856 scopus 로고    scopus 로고
    • Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes
    • Gilbert C, Cordaux R (2013) Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes Genome Biol Evol 5(5):822-832.
    • (2013) Genome Biol Evol , vol.5 , Issue.5 , pp. 822-832
    • Gilbert, C.1    Cordaux, R.2
  • 40
    • 84888436630 scopus 로고    scopus 로고
    • Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes
    • Qiu H, Yoon HS, Bhattacharya D (2013) Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes Front Plant Sci 4:366.
    • (2013) Front Plant Sci , vol.4 , pp. 366
    • Qiu, H.1    Yoon, H.S.2    Bhattacharya, D.3
  • 41
    • 84867493524 scopus 로고    scopus 로고
    • Available at Accessed April 1 2014
    • Index Fungorum Available at www.indexfungorum.org/ Accessed April 1, 2014.
    • Index Fungorum.
  • 42
    • 84873739311 scopus 로고    scopus 로고
    • The silva ribosomal RNA gene database project: Improved data processing and web-based tools
    • (Database issue
    • Quast C, et al (2013) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools Nucleic Acids Res 41(Database issue):D590-D596.
    • (2013) Nucleic Acids Res , vol.41 , pp. D590-D596
    • Quast, C.1
  • 43
    • 84891813947 scopus 로고    scopus 로고
    • The silva and "all-species living tree project (ltp)" taxonomic frameworks
    • (Database issue
    • Yilmaz P, et al (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks Nucleic Acids Res 42(Database issue):D643-D648.
    • (2014) Nucleic Acids Res , vol.42 , pp. D643-D648
    • Yilmaz, P.1
  • 44
    • 58149200954 scopus 로고    scopus 로고
    • Database resources of the national center for biotechnology information
    • (Database issue
    • Sayers EW, et al (2009) Database resources of the National Center for Biotechnology Information Nucleic Acids Res 37(Database issue):D5-D15.
    • (2009) Nucleic Acids Res , vol.37 , pp. D5-D15
    • Sayers, E.W.1
  • 47
    • 34250341823 scopus 로고    scopus 로고
    • A higher-level phylogenetic classification of the fungi
    • Hibbett DS, et al (2007) A higher-level phylogenetic classification of the Fungi Mycol Res 111(Pt 5):509-547.
    • (2007) Mycol Res , vol.111 , pp. 509-547
    • Hibbett, D.S.1
  • 48
    • 78149339000 scopus 로고    scopus 로고
    • Towards resolving lamiales relationships: Insights from rapidly evolving chloroplast sequences
    • Schäferhoff B, et al (2010) Towards resolving Lamiales relationships: Insights from rapidly evolving chloroplast sequences BMC Evol Biol 10:352.
    • (2010) BMC Evol Biol , vol.10 , pp. 352
    • Schäferhoff, B.1
  • 49
    • 84940737875 scopus 로고    scopus 로고
    • Phylesystem: A git-based data store for community-curated phylogenetic estimates
    • btv276
    • McTavish EJ, et al (2015) Phylesystem: A git-based data store for community-curated phylogenetic estimates Bioinformatics 2015:btv276.
    • (2015) Bioinformatics , vol.2015
    • McTavish, E.J.1
  • 52
    • 84867977644 scopus 로고    scopus 로고
    • Reconstructing minimal rooted trees
    • Semple C (2003) Reconstructing minimal rooted trees Discrete Appl Math 127(3): 489-503.
    • (2003) Discrete Appl Math , vol.127 , Issue.3 , pp. 489-503
    • Semple, C.1
  • 54
    • 31344435061 scopus 로고    scopus 로고
    • Measuring support and finding unsupported relationships in supertrees
    • Wilkinson M, Pisani D, Cotton JA, Corfe I (2005) Measuring support and finding unsupported relationships in supertrees Syst Biol 54(5):823-831.
    • (2005) Syst Biol , vol.54 , Issue.5 , pp. 823-831
    • Wilkinson, M.1    Pisani, D.2    Cotton, J.A.3    Corfe, I.4


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