系統的に、系統学的に

関: phylogenetic、phylogenic、phylogenically、systematic、systematically

WordNet

with regard to phylogeny; "a phylogenetically primitive part of the brain"
of or relating to the evolutionary development of organisms; "phylogenetic development" (同)phyletic
in a systematic or consistent manner; "they systematically excluded women" (同)consistently
characterized by order and planning; "the investigation was very systematic"; "a systematic administrator"

PrepTutorEJDIC

系統的に,体系的に,組織的に

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2017/06/19 10:36:54」(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 classification, identification and naming 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 1st 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, 1st attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza^[25]
1965
- Camin-Sokal parsimony, 1st parsimony (optimization) criterion and 1st 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), 1st 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, 1st 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, 1st software package for phylogenetic analysis, Felsenstein
1981
- majority consensus, Margush and MacMorris^[43]
- strict consensus, Sokal and Rohlf^[44]
- 1st computationally efficient ML algorithm, Felsenstein^[45]
1982
- PHYSIS, Mikevich and Farris
- branch and bound, Hendy and Penny^[46]
1985
- 1st cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb^[47]
- 1st issue of Cladistics
- 1st phylogenetic application of bootstrap, Felsenstein^[48]
- 1st 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]
- 1st 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, 1st 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
^ 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.

UpToDate Contents

全文を閲覧するには購読必要です。 To read the full text you will need to subscribe.

1. ノカルジア症の微生物学、疫学、および病因 microbiology epidemiology and pathogenesis of nocardiosis
2. ムンプスウイルスワクチン mumps virus vaccine
3. 一般的ではないカンピロバクター種および関連細菌の感染 infection with less common campylobacter species and related bacteria
4. 輸血によるHIV感染およびAIDS transfusion transmitted hiv infection and aids
5. 乳アレルギー：管理 milk allergy management

English Journal

Identification, characterization and immunological analysis of Ras related C3 botulinum toxin substrate 1 (Rac1) from grass carp Ctenopharyngodon idella.

Hu MY1, Shen YB1, Xu XY1, Yu HY1, Zhang M1, Dang YF1, Li JL2.
Developmental and comparative immunology.Dev Comp Immunol.2016 Jan;54(1):20-31. doi: 10.1016/j.dci.2015.08.010. Epub 2015 Aug 24.
Rac1, a Rho GTPase, serves critical immunological functions in mammals. Here, a Rac1 homolog (gcRac1) was identified in grass carp (Ctenopharyngodon idella). The full-length 2023-base pair gcRac1 cDNA contained a 579-bp open reading frame encoding a 192-residue protein, including a conserved RHO dom
PMID 26315145

Comparative mitochondrial genome analysis of Pythium insidiosum and related oomycete species provides new insights into genetic variation and phylogenetic relationships.

Tangphatsornruang S1, Ruang-Areerate P1, Sangsrakru D1, Rujirawat T2, Lohnoo T3, Kittichotirat W4, Patumcharoenpol P4, Grenville-Briggs LJ5, Krajaejun T6.
Gene.Gene.2016 Jan 1;575(1):34-41. doi: 10.1016/j.gene.2015.08.036. Epub 2015 Aug 21.
Oomycetes are eukaryotic microorganisms, which are phylogenetically distinct from the true-fungi, which they resemble morphologically. While many oomycetes are pathogenic to plants, Pythium insidiosum is capable of infecting humans and animals. Mitochondrial (mt) genomes are valuable genetic resourc
PMID 26299654

Particular Distribution of Enterobacter cloacae Strains Isolated from Urinary Tract Infection within Clonal Complexes.

Akbari M1, Bakhshi B1, Najar Peerayeh S1.
Iranian biomedical journal.Iran Biomed J.2016 Jan;20(1):49-55. Epub 2015 Oct 25.
BACKGROUND: Based on biochemical properties, Enterobacter cloacae represents a large complex of at least 13 variant species, subspecies, and genotypes that progressively identified as the most species causing hospital-acquired infections. The aim of this study was to determine the relevance between
PMID 26498349

Japanese Journal

Reciprocal Symbiont Sharing in the Lodging Mutualism between Walking Corals and Sipunculans

PLOS ONE 12(1), 2017-01-10
NAID 120005953994

Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages

Ｍｉｃｒｏｂｅｓ　ａｎｄ　ｅｎｖｉｒｏｎｍｅｎｔｓ, 2017
NAID 130005439582

2,4-Dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading gene cluster in the soybean root-nodulating bacterium Bradyrhizobium elkanii USDA94

Microbiological Research 188, 62-71, 2016-07
NAID 120005844157

Related Pictures

★リンクテーブル★

リンク元	「phylogenetic」「系統的」「systematic」「系統学的」「systematically」

「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

「系統的」

　　[★]

英: systematic、phylogenetic、systematically、phylogenetically
関: 系統学、系統学的、系統発生、組織的、システマティック、体系的

「systematic」

　　[★]

系統的な、体系的な、組織的な、システマティックな

関: phylogenetic、phylogenetically、systematically

「系統学的」

　　[★]

英: phylogenetic、phylogenic、phylogenetically、phylogenically
関: 系統学、系統的、系統発生

「systematically」

　　[★]

系統的に、体系的に

関: phylogenetic、phylogenetically、systematic

[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

[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 Convergence Divergence Evidence of common descent Extinction Event Gene-centered view Homology Last universal common ancestor Macroevolution Microevolution Origin of life Panspermia Parallel evolution 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 humans lemurs sea cows 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 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 Darwinism Catastrophism Lamarckism Orthogenesis Mutationism 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

phylogenetically