메뉴 건너뛰기




Volumn 57, Issue 1-2, 2009, Pages 187-199

Evidence, content and corroboration and the tree of life

Author keywords

Corroboration; Darwin; Evolution; Genomics; HGT; Karl Popper; Philosophy of science; Systematics; ToL; Tree of life; Vantage points

Indexed keywords

GENOMICS; MOLECULAR ANALYSIS; TAXONOMY; TESTING METHOD;

EID: 67651146722     PISSN: 00015342     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10441-008-9066-5     Document Type: Article
Times cited : (29)

References (48)
  • 1
    • 0030308089 scopus 로고    scopus 로고
    • On combining protein sequences and nucleic acid sequences in phylogenetic analysis: The homeobox protein case
    • DOI 10.1006/clad.1996.0005
    • D Agosti D Jacobs R Desalle 1996 On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case Cladistics 12 1 65 82 (Pubitemid 126400317)
    • (1996) Cladistics , vol.12 , Issue.1 , pp. 65-82
    • Agosti, D.1    Jacobs, D.2    DeSalle, R.3
  • 2
    • 38349128272 scopus 로고    scopus 로고
    • Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny
    • E Bapteste E Susko J Leigh I Ruiz-Trillo J Bucknam WF Doolittle 2008 Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny Mol Biol Evol 25 83 91
    • (2008) Mol Biol Evol , vol.25 , pp. 83-91
    • Bapteste, E.1    Susko, E.2    Leigh, J.3    Ruiz-Trillo, I.4    Bucknam, J.5    Doolittle, W.F.6
  • 3
    • 33645568886 scopus 로고    scopus 로고
    • Phylogenetic identification of lateral genetic transfer events
    • RG Beiko N Hamilton 2006 Phylogenetic identification of lateral genetic transfer events BMC Evol Biol 6 15
    • (2006) BMC Evol Biol , vol.6 , pp. 15
    • Beiko, R.G.1    Hamilton, N.2
  • 4
    • 84934441460 scopus 로고    scopus 로고
    • Detecting lateral genetic transfer: A phylogenetic approach
    • RG Beiko MA Ragan 2008 Detecting lateral genetic transfer: a phylogenetic approach Methods Mol Biol 452 457 469
    • (2008) Methods Mol Biol , vol.452 , pp. 457-469
    • Beiko, R.G.1    Ragan, M.A.2
  • 5
    • 0035527411 scopus 로고    scopus 로고
    • Assessment of the accuracy of matrix representation with parsimony analysis supertree construction
    • ORP Bininda-Emonds MJ Sanderson 2001 Assessment of the accuracy of matrix representation with parsimony analysis supertree construction Syst Biol 50 565 579
    • (2001) Syst Biol , vol.50 , pp. 565-579
    • Bininda-Emonds, O.R.P.1    Sanderson, M.J.2
  • 6
    • 0000443251 scopus 로고    scopus 로고
    • PTP is Meaningless, T-PTP is Contradictory: A Reply to Trueman
    • JM Carpenter PA Goloboff JS Farris 1998 PTP is meaningless, T-PTP is contradictory: a reply to trueman Cladistics 14 105 116 (Pubitemid 128403326)
    • (1998) Cladistics , vol.14 , Issue.1 , pp. 105-116
    • Carpenter, J.M.1    Goloboff, P.A.2    Farris, J.S.3
  • 7
    • 67651185356 scopus 로고    scopus 로고
    • Barnes and Noble New York (1st publication, 1859)
    • Darwin C (2004) The origin of species by means of natural selection. Barnes and Noble, New York (1st publication, 1859)
    • (2004)
    • Darwin, C.1
  • 8
    • 0026313665 scopus 로고
    • Concepts and tests of homology in the cladistic paradigm
    • MC de Pinna 1991 Concepts and tests of homology in the cladistic paradigm Cladistics 7 367 394
    • (1991) Cladistics , vol.7 , pp. 367-394
    • De Pinna, M.C.1
  • 9
    • 0038487291 scopus 로고    scopus 로고
    • Failed refutations: Further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration
    • DOI 10.1080/10635150309324
    • K de Queiroz S Poe 2003 Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration Syst Biol 52 352 367 (Pubitemid 36844324)
    • (2003) Systematic Biology , vol.52 , Issue.3 , pp. 352-367
    • De Queiroz, K.1    Poe, S.2
  • 11
    • 38249008767 scopus 로고
    • Systematics and conservation: On predicting the feature diversity of subsets of taxa
    • DP Faith 1992 Systematics and conservation: on predicting the feature diversity of subsets of taxa Cladistics 8 361 373
    • (1992) Cladistics , vol.8 , pp. 361-373
    • Faith, D.P.1
  • 12
    • 1542580018 scopus 로고    scopus 로고
    • From species to supertrees: Popperian corroboration and some current controversies in systematics
    • DOI 10.1071/SB03017
    • DP Faith 2004 From species to supertrees: Popperian corroboration and some current controversies in systematics Aust Syst Bot 17 1 16 (Pubitemid 38345383)
    • (2004) Australian Systematic Botany , vol.17 , Issue.1 , pp. 1-16
    • Faith, D.P.1
  • 13
    • 30344480828 scopus 로고    scopus 로고
    • Science and philosophy for molecular systematics: Which is the cart and which is the horse?
    • DOI 10.1016/j.ympev.2005.08.018, PII S1055790305002848
    • DP Faith 2006 Science and philosophy for molecular systematics: which is the cart and which is the horse? Mol Phylogenet Evol 38 553 557 (Pubitemid 43069396)
    • (2006) Molecular Phylogenetics and Evolution , vol.38 , Issue.2 , pp. 553-557
    • Faith, D.P.1
  • 14
    • 0035527351 scopus 로고    scopus 로고
    • Towards an inclusive philosophy for phylogenetic inference
    • DP Faith JWH Trueman 2001 Towards an inclusive philosophy for phylogenetic inference Syst Biol 50 331 350
    • (2001) Syst Biol , vol.50 , pp. 331-350
    • Faith, D.P.1    Trueman, J.W.H.2
  • 16
    • 0000375117 scopus 로고
    • Conjectures and refutations
    • JS Farris 1995 Conjectures and refutations Cladistics 11 105 118
    • (1995) Cladistics , vol.11 , pp. 105-118
    • Farris, J.S.1
  • 17
    • 0000074814 scopus 로고    scopus 로고
    • Likelihood and inconsistency
    • JS Farris 1999 Likelihood and inconsistency Cladistics 15 199 204
    • (1999) Cladistics , vol.15 , pp. 199-204
    • Farris, J.S.1
  • 18
    • 0034465971 scopus 로고    scopus 로고
    • Corroboration versus "strongest evidence"
    • JS Farris 2000 Corroboration versus "strongest evidence" Cladistics 16 385 393
    • (2000) Cladistics , vol.16 , pp. 385-393
    • Farris, J.S.1
  • 19
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • J Felsenstein 1978 Cases in which parsimony or compatibility methods will be positively misleading Syst Zool 27 401 410
    • (1978) Syst Zool , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 20
    • 0002975381 scopus 로고
    • Alternative methods of phylogenetic inference and their interrelationship
    • J Felsenstein 1979 Alternative methods of phylogenetic inference and their interrelationship Syst Zool 28 49 62
    • (1979) Syst Zool , vol.28 , pp. 49-62
    • Felsenstein, J.1
  • 21
    • 0001306645 scopus 로고
    • A likelihood approach to character weighting and what it tells us about parsimony and compatibility
    • J Felsenstein 1981 A likelihood approach to character weighting and what it tells us about parsimony and compatibility Biol J Linn Soc 16 183 196
    • (1981) Biol J Linn Soc , vol.16 , pp. 183-196
    • Felsenstein, J.1
  • 22
    • 0002245769 scopus 로고
    • Phylogenies from gene frequencies a statistical problem
    • J Felsenstein 1985 Phylogenies from gene frequencies a statistical problem Syst Zool 34 300 311
    • (1985) Syst Zool , vol.34 , pp. 300-311
    • Felsenstein, J.1
  • 24
    • 0027616543 scopus 로고
    • Alignment ambiguous nucleotide sites and the exclusion of data
    • J Gatesy W Wheeler R DeSalle 1993 Alignment ambiguous nucleotide sites and the exclusion of data Mol Phylogenet Evol 2 152 157
    • (1993) Mol Phylogenet Evol , vol.2 , pp. 152-157
    • Gatesy, J.1    Wheeler, W.2    Desalle, R.3
  • 25
    • 0032805771 scopus 로고    scopus 로고
    • Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyl taxa
    • J Gatesy P O'Grady RH Baker 1999 Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa Cladistics 15 271 313
    • (1999) Cladistics , vol.15 , pp. 271-313
    • Gatesy, J.1    O'Grady, P.2    Baker, R.H.3
  • 26
    • 0036698966 scopus 로고    scopus 로고
    • Resolution of a supertree/supermatrix paradox
    • DOI 10.1080/10635150290102311
    • J Gatesy C Matthee R DeSalle C Hayashi 2002 Resolution of a supertree/supermatrix paradox Syst Biol 51 652 664 (Pubitemid 35180694)
    • (2002) Systematic Biology , vol.51 , Issue.4 , pp. 652-664
    • Gatesy, J.1    Matthee, C.2    Desalle, R.3    Hayashi, C.4
  • 27
    • 1642326753 scopus 로고    scopus 로고
    • Transformation series as an ideographic character concept
    • DOI 10.1111/j.1096-0031.2004.00003.x
    • T Grant AG Kluge 2004 Transformation series as an ideographic character concept Cladistics 20 23 31 (Pubitemid 38370664)
    • (2004) Cladistics , vol.20 , Issue.1 , pp. 23-31
    • Grant, T.1    Kluge, A.G.2
  • 28
    • 14144252565 scopus 로고    scopus 로고
    • Falsifications and corroborations: Karl Popper's influence on systematics
    • DOI 10.1016/j.ympev.2005.01.003
    • KG Helfenbein R DeSalle 2005 Falsifications and corroborations: Karl Popper's influence on systematics Mol Phylogenet Evol 35 1 271 280 (Pubitemid 40281417)
    • (2005) Molecular Phylogenetics and Evolution , vol.35 , Issue.1 , pp. 271-280
    • Helfenbein, K.G.1    DeSalle, R.2
  • 29
    • 67651192680 scopus 로고
    • University of Illinois Press Urbana
    • Hennig W (1966) Phylogenetic systematics. Translated by D. Dwight Davis and Rainer Zangerl. University of Illinois Press, Urbana
    • (1966)
    • Hennig, W.1
  • 30
    • 0002851739 scopus 로고
    • A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes)
    • AG Kluge 1989 A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes) Syst Zool 38 1 25
    • (1989) Syst Zool , vol.38 , pp. 1-25
    • Kluge, A.G.1
  • 31
    • 0031430478 scopus 로고    scopus 로고
    • Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics
    • AG Kluge 1997 Sophisticated falsification and research cycles: consequences for differential character weighting in phylogenetic systematics Zool Scr 26 4 349
    • (1997) Zool Scr , vol.26 , Issue.4 , pp. 349
    • Kluge, A.G.1
  • 32
    • 0000590136 scopus 로고    scopus 로고
    • Total Evidence Or Taxonomic Congruence: Cladistics Or Consensus Classification
    • PII S0748300797900566
    • AG Kluge 1998 Total evidence or taxonomic congruence: cladistics or consensus classification Cladistics 14 151 158 (Pubitemid 128369212)
    • (1998) Cladistics , vol.14 , Issue.2 , pp. 151-158
    • Kluge, A.G.1
  • 33
    • 0035527349 scopus 로고    scopus 로고
    • Philosophical conjectures and their refutation
    • AG Kluge 2001 Philosophical conjectures and their refutation Syst Biol 50 322 330
    • (2001) Syst Biol , vol.50 , pp. 322-330
    • Kluge, A.G.1
  • 34
    • 0041924987 scopus 로고    scopus 로고
    • On the deduction of species relationships: A precis
    • AG Kluge 2003 On the deduction of species relationships: a precis Cladistics 19 233 239
    • (2003) Cladistics , vol.19 , pp. 233-239
    • Kluge, A.G.1
  • 35
    • 84963036271 scopus 로고
    • Quantitative phyletics and the evolution of anurans
    • AG Kluge JS Farris 1969 Quantitative phyletics and the evolution of anurans Syst Zool 18 1 32
    • (1969) Syst Zool , vol.18 , pp. 1-32
    • Kluge, A.G.1    Farris, J.S.2
  • 36
    • 0001324274 scopus 로고
    • Cladistic: What's in a word?
    • AG Kluge AJ Wolf 1993 Cladistic: what's in a word? Cladistics 9 183 199
    • (1993) Cladistics , vol.9 , pp. 183-199
    • Kluge, A.G.1    Wolf, A.J.2
  • 37
    • 67651187819 scopus 로고    scopus 로고
    • New York University NewYork
    • Lienau EK (2007) Horizontal gene transfer and the tree of life: an empirical approach to systematics in the genome age: biology. New York University, NewYork
    • (2007)
    • Lienau, E.K.1
  • 38
    • 33747341087 scopus 로고    scopus 로고
    • Reciprocal illumination in the gene content tree of life
    • EK Lienau R DeSalle JA Rosenfeld PJ Planet 2006 Reciprocal illumination in the gene content tree of life Syst Biol 55 3 441 453
    • (2006) Syst Biol , vol.55 , Issue.3 , pp. 441-453
    • Lienau, E.K.1    Desalle, R.2    Rosenfeld, J.A.3    Planet, P.J.4
  • 39
    • 0000147290 scopus 로고
    • The implications of congruence in Menidia
    • MF Mickevich JS Farris 1981 The implications of congruence in Menidia Syst Zool 30 351 370
    • (1981) Syst Zool , vol.30 , pp. 351-370
    • Mickevich, M.F.1    Farris, J.S.2
  • 40
    • 1642272011 scopus 로고    scopus 로고
    • Character distributions are phylogenetic evidence
    • MJ Novacek 2001 Character distributions are phylogenetic evidence Paleobiology 27 172 173
    • (2001) Paleobiology , vol.27 , pp. 172-173
    • Novacek, M.J.1
  • 41
    • 67651182338 scopus 로고
    • Rowman and Littlefield Totowa
    • Popper KR (1983) Realism and the aim of science. Rowman and Littlefield, Totowa
    • (1983)
    • Popper, K.R.1
  • 42
    • 67651198114 scopus 로고    scopus 로고
    • Routledge Classics London. (ISBN 0-415-27844-9. 1st publication, 1935, last modified, 1980)
    • Popper KR (2002) The logic of scientific discovery. Routledge Classics, London, p 513 (ISBN 0-415-27844-9. 1st publication, 1935, last modified, 1980)
    • (2002) , pp. 513
    • Popper, K.R.1
  • 43
    • 0038632315 scopus 로고    scopus 로고
    • Popper and systematics
    • DOI 10.1080/10635150309338
    • O Rieppel 2003 Popper and systematics Syst Biol 52 259 271 (Pubitemid 36594683)
    • (2003) Systematic Biology , vol.52 , Issue.2 , pp. 259-271
    • Rieppel, O.1
  • 44
    • 19544388952 scopus 로고    scopus 로고
    • Proper names in twin worlds: Monophyly, paraphyly, and the world around us
    • DOI 10.1016/j.ode.2004.03.003, PII S1439609205000310
    • O Rieppel 2005 Proper names in twin worlds: monophyly, paraphyly, and the world around us Org Divers Evol 5 89 100 (Pubitemid 40727967)
    • (2005) Organisms Diversity and Evolution , vol.5 , Issue.2 , pp. 89-100
    • Rieppel, O.1
  • 45
    • 0035725563 scopus 로고    scopus 로고
    • Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration
    • DOI 10.1006/clad.2001.0165
    • ME Siddall 2001 Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration Cladistics 17 395 399 (Pubitemid 34209326)
    • (2001) Cladistics , vol.17 , Issue.4 , pp. 395-399
    • Siddall, M.E.1
  • 46
    • 0036557785 scopus 로고    scopus 로고
    • Conflict between amino acid and nucleotide characters
    • DOI 10.1111/j.1096-0031.2002.tb00148.x
    • MP Simmons H Ochoterena JV Freudenstein 2002 Conflict between amino acid and nucleotide characters Cladistics 18 200 206 (Pubitemid 36264193)
    • (2002) Cladistics , vol.18 , Issue.2 , pp. 200-206
    • Simmons, M.P.1    Ochoterena, H.2    Freudenstein, J.V.3
  • 47
    • 0028878618 scopus 로고
    • Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data
    • WC Wheeler 1995 Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data Syst Biol 44 321 331
    • (1995) Syst Biol , vol.44 , pp. 321-331
    • Wheeler, W.C.1
  • 48
    • 0029265578 scopus 로고
    • Elision: A method for accommodating multiple molecular sequence alignment with alignment ambiguous sites
    • W Wheeler J Gatesy R DeSalle 1995 Elision: a method for accommodating multiple molecular sequence alignment with alignment ambiguous sites Mol Phylogenet Evol 4 1 9
    • (1995) Mol Phylogenet Evol , vol.4 , pp. 1-9
    • Wheeler, W.1    Gatesy, J.2    Desalle, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.