系統発生の

関: phylogenesis、phylogenetic、phylogeny

WordNet

of or relating to the evolutionary development of organisms; "phylogenetic development" (同)phyletic

PrepTutorEJDIC

(生物の)系統発生[学]

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2017/11/08 17:37:47」(JST)

wiki en

[Wiki en表示]

In biology, phylogenetics /ˌfaɪloʊdʒəˈnɛtɪks, -lə-/^[1]^[2] (Greek: φυλή, φῦλον - phylé, phylon = tribe, clan, race + γενετικός - genetikós = origin, source, birth)^[3] is the study of the evolutionary history and relationships among individuals or groups of organisms (e.g. species, or populations). These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny (also known as a phylogenetic tree) – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms.^[4] The tips of a phylogenetic tree can be living organisms or fossils, and represent the "end," or the present, in an evolutionary lineage. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.

Taxonomy is the identification, naming and classification of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline.^[5] The degree to which taxonomies depend on phylogenies (or classification depends on evolutionary development) differs depending on the school of taxonomy: phenetics ignores phylogeny altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them.

Construction of a phylogenetic tree

Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed.

Phenetics, popular in the mid-20th century but now largely obsolete, used distance matrix-based methods to construct trees based on overall similarity in morphology or other observable traits (i.e. in the phenotype, not the DNA), which was often assumed to approximate phylogenetic relationships.

Prior to 1990, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses.^[6]^[7]^[8]

History

The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866,^[9] and the Darwinian approach to classification became known as the "phyletic" approach.^[10]

Ernst Haeckel's recapitulation theory

During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was widely accepted. It was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs. But this theory has long been rejected.^[11]^[12] Instead, ontogeny evolves – the phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share.

Timeline of key events

Branching tree diagram from Heinrich Georg Bronn's work (1858)

Phylogenetic tree suggested by Haeckel (1866)

14th century, lex parsimoniae (parsimony principle), William of Ockam, English philosopher, theologian, and Franciscan monk, but the idea actually goes back to Aristotle, precursor concept
1763, Bayesian probability, Rev. Thomas Bayes,^[13] precursor concept
18th century, Pierre Simon (Marquis de Laplace), perhaps first to use ML (maximum likelihood), precursor concept
1809, evolutionary theory, Philosophie Zoologique, Jean-Baptiste de Lamarck, precursor concept, foreshadowed in the 17th century and 18th century by Voltaire, Descartes, and Leibniz, with Leibniz even proposing evolutionary changes to account for observed gaps suggesting that many species had become extinct, others transformed, and different species that share common traits may have at one time been a single race,^[14] also foreshadowed by some early Greek philosophers such as Anaximander in the 6th century BC and the atomists of the 5th century BC, who proposed rudimentary theories of evolution^[15]
1837, Darwin's notebooks show an evolutionary tree^[16]
1843, distinction between homology and analogy (the latter now referred to as homoplasy), Richard Owen, precursor concept
1858, Paleontologist Heinrich Georg Bronn (1800–1862) published a hypothetical tree to illustrating the paleontological "arrival" of new, similar species following the extinction of an older species. Bronn did not propose a mechanism responsible for such phenomena, precursor concept.^[17]
1858, elaboration of evolutionary theory, Darwin and Wallace,^[18] also in Origin of Species by Darwin the following year, precursor concept
1866, Ernst Haeckel, first publishes his phylogeny-based evolutionary tree, precursor concept
1893, Dollo's Law of Character State Irreversibility,^[19] precursor concept
1912, ML recommended, analyzed, and popularized by Ronald Fisher, precursor concept
1921, Tillyard uses term "phylogenetic" and distinguishes between archaic and specialized characters in his classification system^[20]
1940, term "clade" coined by Lucien Cuénot
1949, Jackknife resampling, Maurice Quenouille (foreshadowed in '46 by Mahalanobis and extended in '58 by Tukey), precursor concept
1950, Willi Hennig's classic formalization^[21]
1952, William Wagner's groundplan divergence method^[22]
1953, "cladogenesis" coined^[23]
1960, "cladistic" coined by Cain and Harrison^[24]
1963, first attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza^[25]
1965
- Camin-Sokal parsimony, first parsimony (optimization) criterion and first computer program/algorithm for cladistic analysis both by Camin and Sokal^[26]
- character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E. O. Wilson^[27]
1966
- English translation of Hennig^[28]
- "cladistics" and "cladogram" coined (Webster's, loc. cit.)
1969
- dynamic and successive weighting, James Farris^[29]
- Wagner parsimony, Kluge and Farris^[30]
- CI (consistency index), Kluge and Farris^[30]
- introduction of pairwise compatibility for clique analysis, Le Quesne^[31]
1970, Wagner parsimony generalized by Farris^[32]
1971
- Fitch parsimony, Fitch^[33]
- NNI (nearest neighbour interchange), first branch-swapping search strategy, developed independently by Robinson^[34] and Moore et al.
- ME (minimum evolution), Kidd and Sgaramella-Zonta^[35] (it is unclear if this is the pairwise distance method or related to ML as Edwards and Cavalli-Sforza call ML "minimum evolution".)
1972, Adams consensus, Adams^[36]
1974, first successful application of ML to phylogenetics (for nucleotide sequences), Neyman^[37]
1976, prefix system for ranks, Farris^[38]
1977, Dollo parsimony, Farris^[39]
1979
- Nelson consensus, Nelson^[40]
- MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon ^[41]
- bootstrap, Bradley Efron, precursor concept^[42]
1980, PHYLIP, first software package for phylogenetic analysis, Felsenstein
1981
- majority consensus, Margush and MacMorris^[43]
- strict consensus, Sokal and Rohlf^[44]
- first computationally efficient ML algorithm, Felsenstein^[45]
1982
- PHYSIS, Mikevich and Farris
- branch and bound, Hendy and Penny^[46]
1985
- first cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb^[47]
- first issue of Cladistics
- first phylogenetic application of bootstrap, Felsenstein^[48]
- first phylogenetic application of jackknife, Scott Lanyon^[49]
1986, MacClade, Maddison and Maddison
1987, neighbor-joining method Saitou and Nei^[50]
1988, Hennig86 (version 1.5), Farris
- Bremer support (decay index), Bremer ^[51]
1989
- RI (retention index), RCI (rescaled consistency index), Farris^[52]
- HER (homoplasy excess ratio), Archie^[53]
1990
- combinable components (semi-strict) consensus, Bremer^[54]
- SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and Olsen^[55]
1991
- DDI (data decisiveness index), Goloboff^[56]^[57]
- first cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb
1993, implied weighting Goloboff^[58]
1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, Wilkinson^[59]
1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, Wilkinson^[60]
1996, first working methods for BI (Bayesian Inference)independently developed by Li,^[61] Mau,^[62] and Rannala and Yang^[63] and all using MCMC (Markov chain-Monte Carlo)
1998, TNT (Tree Analysis Using New Technology), Goloboff, Farris, and Nixon
1999, Winclada, Nixon
2003, symmetrical resampling, Goloboff^[64]

References

^ "phylogenetic". Dictionary.com Unabridged. Random House.
^ "phylogenetic". Merriam-Webster Dictionary.
^ Liddell, Henry George; Scott, Robert; Jones, Henry Stuart (1968). A Greek-English lexicon (9 ed.). Oxford: Clarendon Press. p. 1961.
^ "phylogeny". Biology online. Retrieved 2013-02-15.
^ Edwards AWF; Cavalli-Sforza LL (1964). "Reconstruction of evolutionary trees". In Heywood, Vernon Hilton; McNeill, J. Phenetic and Phylogenetic Classification. pp. 67–76. OCLC 733025912. Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary relationships among groups of organisms.
^ Richard C. Brusca & Gary J. Brusca (2003). Invertebrates (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. ISBN 978-0-87893-097-5.
^ Bock, W.J. (2004). Explanations in systematics. Pp. 49-56. In Williams, D.M. and Forey, P.L. (eds) Milestones in Systematics. London: Systematics Association Special Volume Series 67. CRC Press, Boca Raton, Florida.
^ Auyang, Sunny Y. (1998). Narratives and Theories in Natural History. In: Foundations of complex-system theories: in economics, evolutionary biology, and statistical physics. Cambridge, U.K.; New York: Cambridge University Press.
^ Harper, Douglas (2010). "Phylogeny". Online Etymology Dictionary. Retrieved March 18, 2013.
^ Stuessy 2009.
^ Blechschmidt, Erich (1977) The Beginnings of Human Life. Springer-Verlag Inc., p. 32: "The so-called basic law of biogenetics is wrong. No buts or ifs can mitigate this fact. It is not even a tiny bit correct or correct in a different form, making it valid in a certain percentage. It is totally wrong."
^ Ehrlich, Paul; Richard Holm; Dennis Parnell (1963) The Process of Evolution. New York: McGraw–Hill, p. 66: "Its shortcomings have been almost universally pointed out by modern authors, but the idea still has a prominent place in biological mythology. The resemblance of early vertebrate embryos is readily explained without resort to mysterious forces compelling each individual to reclimb its phylogenetic tree."
^ Bayes, T. 1763. An Essay towards solving a Problem in the Doctrine of Chances. Phil. Trans. 53: 370–418.
^ Strickberger, Monroe. 1996. Evolution, 2nd. ed. Jones & Bartlett.
^ The Theory of Evolution, Teaching Company course, Lecture 1
^ Darwin's Tree of Life^{[dead link]}
^ J. David Archibald (2009) 'Edward Hitchcock’s Pre-Darwinian (1840) 'Tree of Life'.', Journal of the History of Biology (2009) page 568.
^ Darwin, C. R. and A. R. Wallace. 1858. On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. Journal of the Proceedings of the Linnean Society of London. Zoology 3: 45-50.
^ Dollo, Louis. 1893. Les lois de l'évolution. Bull. Soc. Belge Géol. Paléont. Hydrol. 7: 164-66.
^ Tillyard R. J. 1921. A new classification of the order Perlaria. Canadian Entomologist 53: 35-43
^ Hennig. W. (1950). Grundzuge einer theorie der phylogenetischen systematik. Deutscher Zentralverlag, Berlin.
^ Wagner, W.H. Jr. 1952. The fern genus Diellia: structure, affinities, and taxonomy. Univ. Calif. Publ. Botany 26: 1–212.
^ Webster's 9th New Collegiate Dictionary
^ Cain, A. J., Harrison, G. A. 1960. "Phyletic weighting". Proceedings of the Zoological Society of London 35: 1–31.
^ Edwards, A.W.F, Cavalli-Sforza, L.L. (1963). The reconstruction of evolution. Ann. Hum. Genet. 27: 105–106.
^ Camin J.H, Sokal R.R. (1965). A method for deducing branching sequences in phylogeny.Evolution 19: 311–326.
^ Wilson, E. O. 1965. A consistency test for phylogenies based on contemporaneous species. Systematic Zoology 14: 214-220.
^ Hennig. W. (1966). Phylogenetic systematics. Illinois University Press, Urbana.
^ Farris, J.S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18: 374-85.
^ ^a ^b Kluge, A.G, Farris, J.S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1–32.
^ Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18: 201-205.
^ Farris, J.S. (1970). Methods of computing Wagner trees. Syst. Zool. 19: 83–92.
^ Fitch, W.M. (1971). Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20: 406–416.
^ Robinson. D.F. 1971. Comparison of labeled trees with valency three. Journal of Combinatorial Theory 11:105–119.
^ Kidd, K.K. and Laura Sgaramella-Zonta (1971). Phylogenetic analysis: concepts and methods. Am. J. Human Genet. 23, 235-252.
^ Adams, E. (1972). Consensus techniques and the comparison of taxonomic trees. Syst. Zool. 21: 390–397.
^ Neyman, J. (1974). Molecular studies: A source of novel statistical problems. In: Gupta SS, Yackel J. (eds), Statistical Decision Theory and Related Topics, pp. 1–27. Academic Press, New York.
^ Farris, J.S. (1976). Phylogenetic classification of fossils with recent species. Syst. Zool. 25: 271-282.
^ Farris, J.S. (1977). Phylogenetic analysis under Dollo’s Law. Syst. Zool. 26: 77–88.
^ Nelson, G.J. 1979. Cladsitic analysis and synthesis: pronciples and definitions with a historical noteon Adanson's Famille des plantes (1763-1764). Syst. Zool. 28: 1-21.
^ Gordon, Aé<.D. 1979. A measure of the agreement between rankings. Biometrika 66: 7-15.
^ Efron B. (1979). Bootstrap methods: another look at the jackknife. Ann. Stat. 7: 1–26.
^ Margush T, McMorris FR. 1981. Consensus n-trees. Bull. Math .Biol. 43, 239–244.
^ Sokal, R. R., F. J. Rohlf. 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Syst. Zool. 30:309-325.
^ Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368–376.
^ Hendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Math Biosci 59: 277–290.
^ Lipscomb, Diana. 1985. The Eukaryotic Kingdoms. Cladistics 1: 127-40.
^ Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
^ Lanyon, S.M. (1985). Detecting internal inconsistencies in distance data. Syst. Zool. 34: 397-403.
^ Saitou N, Nei M (1987) The Neighbor-joining Method: A New Method for Constructing Phylogenetic Trees. Mol. Biol. Evol. 4:406-425.
^ Bremer, K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795–803
^ Farris, J.S. (1989). The retention index and rescaled consistency index. Cladistics 5: 417–419.
^ Archie, J.W. 1989. Homoplasy Excess Ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the Consistency Index. Syst. Zool. 38: 253-69.
^ Bremer. Kåre. 1990. Combinable Component Consensus. Cladistics 6: 369–372.
^ D.L. Swofford and G.J. Olsen. 1990. Phylogeny reconstruction. In D.M. Hillis andG. Moritz, editors, Molecular Systematics, pages 411–501. Sinauer Associates, Sunderland, Mass.
^ Goloboff, P. A. (1991). Homoplasy and the choice among cladograms. Cladistics 7:215–232.
^ Goloboff, P. A. (1991b). Random data, homoplasy and information.Cladistics 7:395–406.
^ Goloboff, P. A. 1993. Estimating character weights during tree search. Cladistics 9: 83–91.
^ Wilkinson, Mark. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43:343-368.
^ Wilkinson, Mark. 1995. More on reduced consensus methods. Syst. Biol. 44:436-440.
^ Li, S. (1996). Phylogenetic tree construction using Markov Chain Monte Carlo. Ph.D. disseration, Ohio State University, Columbus.
^ Mau B (1996) Bayesian phylogenetic inference via Markov chain Monte Carlo Methods. Ph.D. dissertation, University of Wisconsin, Madison (abstract).
^ Rannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43: 304–311.
^ Goloboff, Pablo; Farris, James; Källersjö, Mari; Oxelman, Bengt; Ramiacuterez, Maria; Szumik, Claudia. 2003. Improvements to resampling measures of group support. Cladistics 19: 324–332.

Bibliography

Schuh, Randall T.; Brower, Andrew V.Z. (2009). Biological Systematics: principles and applications (2nd ed.). Ithaca: Comstock Pub. Associates/Cornell University Press. ISBN 978-0-8014-4799-0. OCLC 312728177.
Forster, Peter; Renfrew, Colin, eds. (2006). Phylogenetic Methods and the Prehistory of Languages. McDonald Institute Press, University of Cambridge. ISBN 978-1-902937-33-5. OCLC 69733654.
Baum, David A.; Smith, Stacey D. (2013). Tree Thinking: an introduction to phylogenetic biology. Greenwood Village, CO: Roberts and Company. ISBN 978-1-936221-16-5. OCLC 767565978.
Stuessy, Tod F. (2009). Plant Taxonomy: The Systematic Evaluation of Comparative Data. Columbia University Press. ISBN 0-231-14712-0. Retrieved 6 February 2014.

External links

The Tree of Life
Interactive Tree of Life
PhyloCode
ExploreTree
UCMP Exhibit Halls: Phylogeny Wing
Willi Hennig Society
Filogenetica.org in Spanish
PhyloPat, Phylogenetic Patterns
SplitsTree, program for computing phylogenetic trees and unrooted phylogenetic networks
Dendroscope, program for drawing phylogenetic trees and rooted phylogenetic networks
Phylogenetic inferring on the T-REX server
Mesquite
NCBI – Systematics and Molecular Phylogenetics
Sydney Brenner's seminars: "What Genomes Can Tell Us About the Past"
Mikko's Phylogeny Archive
Who is Who in Phylogenetic Networks research papers related to the phylogenetic network
Phylogenetic Reconstruction from Gene-Order Data
ETE: A Python Environment for Tree Exploration This is a programming library to analyze, manipulate and visualize phylogenetic trees. See: Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni (2010). "ETE: A python Environment for Tree Exploration". BMC Bioinformatics. 11: 24. PMC 2820433 . PMID 20070885. doi:10.1186/1471-2105-11-24.
PhylomeDB: A public database hosting thousands of gene phylogenies ranging many different species. See: Huerta-Cepas, J.; Capella-Gutierrez, S.; Pryszcz, L. P.; Denisov, I.; Kormes, D.; Marcet-Houben, M.; Gabaldón, T. (2010). "PhylomeDB v3.0: An expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions". Nucleic Acids Research. 39 (Database issue): D556–60. PMC 3013701 . PMID 21075798. doi:10.1093/nar/gkq1109.
Lents, N. H.; Cifuentes, O. E.; Carpi, A. (2010). "Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise". Cell Biology Education. 9 (4): 513. doi:10.1187/cbe.09-10-0076.

English Journal

The evolutionary history of the genes involved in the biosynthesis of the antioxidant ergothioneine.

Jones GW1, Doyle S2, Fitzpatrick DA3.
Gene.Gene.2014 Oct 1;549(1):161-70. doi: 10.1016/j.gene.2014.07.065. Epub 2014 Jul 26.
Ergothioneine (EGT) is a histidine betaine derivative that exhibits antioxidant action in humans. EGT is primarily synthesized by fungal species and a number of bacterial species. A five-gene cluster (egtA, egtB, egtC, egtD &egtE) responsible for EGT production in Mycobacteria smegmatis has rece
PMID 25068406

Flavimarina pacifica gen. nov., sp. nov., a new marine bacterium of the family Flavobacteriaceae, and emended descriptions of the genus Leeuwenhoekiella, Leeuwenhoekiella aequorea and Leeuwenhoekiella marinoflava.

Nedashkovskaya OI1, Kukhlevskiy AD, Zhukova NV, Kim SB.
Antonie van Leeuwenhoek.Antonie Van Leeuwenhoek.2014 Sep;106(3):421-9. doi: 10.1007/s10482-014-0210-8. Epub 2014 Jun 15.
A facultatively anaerobic, Gram-stain negative, rod-shaped and yellow pigmented bacterium, designated strain IDSW-73(T), was isolated from a seawater sample and subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain formed a d
PMID 24929933

Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.

Hameed A1, Shahina M1, Lin SY1, Lai WA1, Liu YC1, Hsu YH1, Young CC2.
International journal of systematic and evolutionary microbiology.Int J Syst Evol Microbiol.2014 Sep 1. pii: ijs.0.066142-0. doi: 10.1099/ijs.0.066142-0. [Epub ahead of print]
A Gram-stain-negative, strictly aerobic, rod- or oval-shaped, motile, non-spore-forming bacterium, designated strain CC-AMHB-3T, was isolated from coastal surface seawater off Hualien, Taiwan. The novel strain showed high pairwise 16S rRNA gene sequence similarities to Ruegeria mobilis NBRC 101030T
PMID 25180090

Japanese Journal

核リボソームDNA, internal transcribed spacer 2 region (ITS2)領域の塩基配列によるEphedra sinica関連Ephedra属植物の系統解析

垣内信子,樋口真理,田中沙織,西川佳奈美,上川翔平,大塚功,フライタークヘルムート
九州保健福祉大学研究紀要 14, 169-172, 2013-03-00
古来よりマオウ属植物は、日本及び中国で生薬として用いられており、中国のEphedra 属植物の系統は3つの大きなグループに分かれている。現在、Ephedra sinica が日本及び中国市場で優位を占めている。E.sinica は、東および中央アジアに分布するE. dahurica やE. pseudodistachya と、形態的に類似している。一方西アジア及びヨーロッパに分布するマオウ属植物で …
NAID 110009596035

貝形虫の殻のMg/Ca比, Sr/Ca比による古環境推定の現状と問題点

森下知晃,山口龍彦,眞柴久和,神谷隆宏
地質学雑誌 116(10), 523-543, 2010-00-00
… (2) The partition coefficients of Mg/Ca and Sr/Ca ratios vary with the taxa, habitat, and phyletic group. … The Mg/Ca partition coefficient of marine ostracodes is clearly dependent on the phyletic group at the family level. …
NAID 120005344013

Phyletic Diversity in the Frog Rana rugosa (Anura: Ranidae) with Special Reference to a Unique Morphotype Found from Sado Island, Japan

Sekiya Kunio,Ohtani Hiromi,Ogata Mitsuaki [他],MIURA Ikuo
Current Herpetology 29(2), 69-78, 2010
We investigated a sample of apparently unique frogs from Sado Island, Japan. While being tentatively identified to Rana rugosa on the basis of general morphological resemblance, this form (yellow type …
NAID 130000415072

Related Pictures

★リンクテーブル★

リンク元	「phylogenetic」「phylogeny」「系統発生」「phylogenesis」
拡張検索	「phyletic tree」「interphyletic」「monophyletic」

「phylogenetic」

　　[★]

系統発生の、系統学の、系統学的な、系統的な

関: genealogical、genealogy、phyletic、phylogenesis、phylogenetically、phylogenic、phylogenically、phylogeny、systematic、systematically

「phylogeny」

　　[★]

系統発生、系統樹、系統発生学、系統学

関: genealogical、genealogical tree、genealogy、phyletic、phyletic tree、phylogenesis、phylogenetic、phylogenetic tree、phylogram

「系統発生」

　　[★]

英: phylogenesis、phylogeny、phylogenetic、phyletic
関: 系統学、系統学的、系統樹、系統的、系統発生学; 発生

「phylogenesis」

　　[★]

系統発生

関: phyletic、phylogenetic、phylogeny

「phyletic tree」

　　[★]

系統樹

関: genealogical tree、phylogenetic tree、phylogeny、phylogram

「interphyletic」

　　[★]

移行型の

関: transitional

「monophyletic」

　　[★]

単系統性の

関: monophyly

[1] "phylogenetic". Dictionary.com Unabridged. Random House.

[2] "phylogenetic". Merriam-Webster Dictionary.

[3] Liddell, Henry George; Scott, Robert; Jones, Henry Stuart (1968). A Greek-English lexicon (9 ed.). Oxford: Clarendon Press. p. 1961.

[4] "phylogeny". Biology online. Retrieved 2013-02-15.

[5] Edwards AWF; Cavalli-Sforza LL (1964). "Reconstruction of evolutionary trees". In Heywood, Vernon Hilton; McNeill, J. Phenetic and Phylogenetic Classification. pp. 67–76. OCLC 733025912. Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary relationships among groups of organisms.

[6] Richard C. Brusca & Gary J. Brusca (2003). Invertebrates (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. ISBN 978-0-87893-097-5.

[7] Bock, W.J. (2004). Explanations in systematics. Pp. 49-56. In Williams, D.M. and Forey, P.L. (eds) Milestones in Systematics. London: Systematics Association Special Volume Series 67. CRC Press, Boca Raton, Florida.

[8] Auyang, Sunny Y. (1998). Narratives and Theories in Natural History. In: Foundations of complex-system theories: in economics, evolutionary biology, and statistical physics. Cambridge, U.K.; New York: Cambridge University Press.

[9] Harper, Douglas (2010). "Phylogeny". Online Etymology Dictionary. Retrieved March 18, 2013.

[FOOTNOTEStuessy2009-10] Stuessy 2009.

[11] Blechschmidt, Erich (1977) The Beginnings of Human Life. Springer-Verlag Inc., p. 32: "The so-called basic law of biogenetics is wrong. No buts or ifs can mitigate this fact. It is not even a tiny bit correct or correct in a different form, making it valid in a certain percentage. It is totally wrong."

[12] Ehrlich, Paul; Richard Holm; Dennis Parnell (1963) The Process of Evolution. New York: McGraw–Hill, p. 66: "Its shortcomings have been almost universally pointed out by modern authors, but the idea still has a prominent place in biological mythology. The resemblance of early vertebrate embryos is readily explained without resort to mysterious forces compelling each individual to reclimb its phylogenetic tree."

[13] Bayes, T. 1763. An Essay towards solving a Problem in the Doctrine of Chances. Phil. Trans. 53: 370–418.

[14] Strickberger, Monroe. 1996. Evolution, 2nd. ed. Jones & Bartlett.

[15] The Theory of Evolution, Teaching Company course, Lecture 1

[16] Darwin's Tree of Life^{[dead link]}

[17] J. David Archibald (2009) 'Edward Hitchcock’s Pre-Darwinian (1840) 'Tree of Life'.', Journal of the History of Biology (2009) page 568.

[18] Darwin, C. R. and A. R. Wallace. 1858. On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. Journal of the Proceedings of the Linnean Society of London. Zoology 3: 45-50.

[19] Dollo, Louis. 1893. Les lois de l'évolution. Bull. Soc. Belge Géol. Paléont. Hydrol. 7: 164-66.

[20] Tillyard R. J. 1921. A new classification of the order Perlaria. Canadian Entomologist 53: 35-43

[21] Hennig. W. (1950). Grundzuge einer theorie der phylogenetischen systematik. Deutscher Zentralverlag, Berlin.

[22] Wagner, W.H. Jr. 1952. The fern genus Diellia: structure, affinities, and taxonomy. Univ. Calif. Publ. Botany 26: 1–212.

[23] Webster's 9th New Collegiate Dictionary

[24] Cain, A. J., Harrison, G. A. 1960. "Phyletic weighting". Proceedings of the Zoological Society of London 35: 1–31.

[25] Edwards, A.W.F, Cavalli-Sforza, L.L. (1963). The reconstruction of evolution. Ann. Hum. Genet. 27: 105–106.

[26] Camin J.H, Sokal R.R. (1965). A method for deducing branching sequences in phylogeny.Evolution 19: 311–326.

[27] Wilson, E. O. 1965. A consistency test for phylogenies based on contemporaneous species. Systematic Zoology 14: 214-220.

[28] Hennig. W. (1966). Phylogenetic systematics. Illinois University Press, Urbana.

[29] Farris, J.S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18: 374-85.

[Kluge-30] Kluge, A.G, Farris, J.S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1–32.

[31] Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18: 201-205.

[32] Farris, J.S. (1970). Methods of computing Wagner trees. Syst. Zool. 19: 83–92.

[33] Fitch, W.M. (1971). Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20: 406–416.

[34] Robinson. D.F. 1971. Comparison of labeled trees with valency three. Journal of Combinatorial Theory 11:105–119.

[35] Kidd, K.K. and Laura Sgaramella-Zonta (1971). Phylogenetic analysis: concepts and methods. Am. J. Human Genet. 23, 235-252.

[36] Adams, E. (1972). Consensus techniques and the comparison of taxonomic trees. Syst. Zool. 21: 390–397.

[37] Neyman, J. (1974). Molecular studies: A source of novel statistical problems. In: Gupta SS, Yackel J. (eds), Statistical Decision Theory and Related Topics, pp. 1–27. Academic Press, New York.

[38] Farris, J.S. (1976). Phylogenetic classification of fossils with recent species. Syst. Zool. 25: 271-282.

[39] Farris, J.S. (1977). Phylogenetic analysis under Dollo’s Law. Syst. Zool. 26: 77–88.

[40] Nelson, G.J. 1979. Cladsitic analysis and synthesis: pronciples and definitions with a historical noteon Adanson's Famille des plantes (1763-1764). Syst. Zool. 28: 1-21.

[41] Gordon, Aé<.D. 1979. A measure of the agreement between rankings. Biometrika 66: 7-15.

[42] Efron B. (1979). Bootstrap methods: another look at the jackknife. Ann. Stat. 7: 1–26.

[43] Margush T, McMorris FR. 1981. Consensus n-trees. Bull. Math .Biol. 43, 239–244.

[44] Sokal, R. R., F. J. Rohlf. 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Syst. Zool. 30:309-325.

[45] Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368–376.

[46] Hendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Math Biosci 59: 277–290.

[47] Lipscomb, Diana. 1985. The Eukaryotic Kingdoms. Cladistics 1: 127-40.

[48] Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.

[49] Lanyon, S.M. (1985). Detecting internal inconsistencies in distance data. Syst. Zool. 34: 397-403.

[50] Saitou N, Nei M (1987) The Neighbor-joining Method: A New Method for Constructing Phylogenetic Trees. Mol. Biol. Evol. 4:406-425.

[51] Bremer, K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795–803

[52] Farris, J.S. (1989). The retention index and rescaled consistency index. Cladistics 5: 417–419.

[53] Archie, J.W. 1989. Homoplasy Excess Ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the Consistency Index. Syst. Zool. 38: 253-69.

[54] Bremer. Kåre. 1990. Combinable Component Consensus. Cladistics 6: 369–372.

[55] D.L. Swofford and G.J. Olsen. 1990. Phylogeny reconstruction. In D.M. Hillis andG. Moritz, editors, Molecular Systematics, pages 411–501. Sinauer Associates, Sunderland, Mass.

[56] Goloboff, P. A. (1991). Homoplasy and the choice among cladograms. Cladistics 7:215–232.

[57] Goloboff, P. A. (1991b). Random data, homoplasy and information.Cladistics 7:395–406.

[58] Goloboff, P. A. 1993. Estimating character weights during tree search. Cladistics 9: 83–91.

[59] Wilkinson, Mark. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43:343-368.

[60] Wilkinson, Mark. 1995. More on reduced consensus methods. Syst. Biol. 44:436-440.

[61] Li, S. (1996). Phylogenetic tree construction using Markov Chain Monte Carlo. Ph.D. disseration, Ohio State University, Columbus.

[62] Mau B (1996) Bayesian phylogenetic inference via Markov chain Monte Carlo Methods. Ph.D. dissertation, University of Wisconsin, Madison (abstract).

[63] Rannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43: 304–311.

[64] Goloboff, Pablo; Farris, James; Källersjö, Mari; Oxelman, Bengt; Ramiacuterez, Maria; Szumik, Claudia. 2003. Improvements to resampling measures of group support. Cladistics 19: 324–332.

v t e Topics in phylogenetics
Relevant fields	Computational phylogenetics Molecular phylogenetics Cladistics Evolutionary taxonomy
Basic concepts	Phylogenetic tree Phylogenetic network Long branch attraction Clade vs Grade Ghost lineage Ghost population
Inference methods	Maximum parsimony Probabilistic methods Maximum likelihood Bayesian inference Distance-matrix methods Neighbor-joining UPGMA Least squares Three-taxon analysis
Current topics	PhyloCode DNA barcoding Molecular phylogenetics Phylogenetic comparative methods Phylogenetic network Phylogenetic niche conservatism Phylogenetics software Phylogenomics Phylogeography
Group traits	Primitive Plesiomorphy Symplesiomorphy Derived Apomorphy Synapomorphy Autapomorphy
Group types	Monophyly Paraphyly Polyphyly
List of evolutionary biology topics Evolutionary biology

v t e Evolutionary biology
Evolutionary history of life Index of evolutionary biology articles Introduction Outline of evolution Timeline of evolution
Evolution	Abiogenesis Adaptation Adaptive radiation Cladistics Coevolution Common descent Cospeciation Convergence Divergence Earliest known life forms Evidence of common descent Extinction Event Gene-centered view Homology Last universal common ancestor Macroevolution Microevolution Origin of life Panspermia Parallel evolution Prehistoric Autopsy Speciation Taxonomy
Population genetics	Biodiversity Gene flow Genetic drift Mutation Natural selection Variation
Development	Canalisation Evolutionary developmental biology Inversion Modularity Phenotypic plasticity
Of taxa	Birds origin Brachiopods Cephalopods Dinosaurs Fish Fungi Insects butterflies Life Mammals cats dogs dolphins and whales horses primates humans lemurs sea cows wolves Molluscs Plants Reptiles Spiders Tetrapods Viruses influenza
Of organs	Cell DNA Flagella Eukaryotes symbiogenesis chromosome endomembrane system mitochondria nucleus plastids In animals eye hair auditory ossicle nervous system brain
Of processes	Aging Death Programmed cell death Avian flight Biological complexity Cooperation Color vision in primates Emotion Empathy Ethics Eusociality Immune system Metabolism Monogamy Morality Mosaic evolution Multicellularity Sexual reproduction Gamete differentiation/sexes Life cycles/nuclear phases Mating types Sex-determination Snake venom
Tempo and modes	Gradualism/Punctuated equilibrium/Saltationism Micromutation/Macromutation Uniformitarianism/Catastrophism
Speciation	Allopatric Anagenesis Catagenesis Cladogenesis Ecological Hybrid Parapatric Peripatric Reinforcement Sympatric
History	Renaissance and Enlightenment Transmutation of species Charles Darwin On the Origin of Species History of paleontology Transitional fossil The eclipse of Darwinism Modern synthesis History of molecular evolution Extended evolutionary synthesis
Philosophy	Darwinism Alternatives to evolution by natural selection Catastrophism Lamarckism Orthogenesis Mutationism Saltationism Structuralism Spandrel Theistic Vitalism
Related	Biogeography Ecological genetics Molecular evolution Phylogenetics Tree Polymorphism Protocell Systematics
Category Commons Portal WikiProject

匿名

検索

案内

案内

phyletic