In cladistics or phylogenetics, an outgroup[1] is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny.[2]
A simple cladogram showing the evolutionary relationships between four species: A, B, C, and D. Here, Species A is the outgroup, and Species B, C, and D form the ingroup.
Although the concept of outgroups has been in use from the earliest days of cladistics, the term "outgroup" is thought to have been coined in the early 1970s at the American Museum of Natural History.[3] Prior to the advent of the term, various other terms were used by evolutionary biologists, including "exgroup", "related group", and "outside groups".[3]
Choice of outgroupedit
The chosen outgroup is hypothesized to be less closely related to the ingroup than the ingroup is related to itself. The evolutionary conclusion from these relationships is that the outgroup species has a common ancestor with the ingroup that is older than the common ancestor of the ingroup. Choice of outgroup can change the topology of a phylogeny.[4] Therefore, phylogeneticists typically use more than one outgroup in cladistic analysis. The use of multiple outgroups is preferable because it provides a more robust phylogeny, buffering against poor outgroup candidates and testing the ingroup's hypothesized monophyly.[3][5][6]
To qualify as an outgroup, a taxon must satisfy the following two characteristics:
It must not be a member of the ingroup.
It must be related to the ingroup, closely enough for meaningful comparisons to the ingroup.
Therefore, an appropriate outgroup must be unambiguously outside the clade of interest in the phylogenetic study. An outgroup that is nested within the ingroup will, when used to root the phylogeny, result in incorrect conclusions about phylogenetic relationships and trait evolution.[7] However, the optimal level of relatedness of the outgroup to the ingroup depends on the depth of phylogenetic analysis. Choosing a closely related outgroup relative to the ingroup is more useful when looking at subtle differences, while choosing an unduly distant outgroup can result in mistaking convergent evolution for a direct evolutionary relationship due to a common ancestor.[8][9] For shallow phylogenetics—for example, resolving the evolutionary relationships of a clade within a genus—an appropriate outgroup would be a member of the sister clade.[10] However, for deeper phylogenetic analysis, less closely related taxa can be used. For example, Jarvis et al. (2014) used humans and crocodiles as outgroups while resolving the early branches of the avian phylogeny.[11] In molecular phylogenetics, satisfying the second requirement typically means that DNA or protein sequences from the outgroup can be successfully aligned to sequences from the ingroup. Although there are algorithmic approaches to identify the outgroups with maximum global parsimony, they are often limited by failing to reflect the continuous, quantitative nature of certain character states.[12] Character states are traits, either ancestral or derived, that affect the construction of branching patterns in a phylogenetic tree.[13]
^Giribet, G.; Ribera, C. (June 1998). "The position of arthropods in the animal kingdom: a search for a reliable outgroup for internal arthropod phylogeny". Molecular Phylogenetics and Evolution. 9 (3): 481–488. doi:10.1006/mpev.1998.0494. PMID 9667996.
^Barriel, V.; Tassy, P. (June 1998). "Rooting with Multiple Outgroups: Consensus Versus Parsimony". Cladistics. 14 (2): 193–200. doi:10.1111/j.1096-0031.1998.tb00332.x. S2CID 84759858.
^de la Torre-Barcena, Jose Eduardo; Kolokotronis, S.O.; Lee, Ernest; Stevenson, Dennis; Brenner, Eric; Katari, Manpreet; Coruzzi, Gloria; DeSalle, Rob (2009). "The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data". PLOS ONE. 4 (6): e5764. Bibcode:2009PLoSO...4.5764D. doi:10.1371/journal.pone.0005764. PMC2685480. PMID 19503618.
^Maddison, Wayne; et al. (1984). "Outgroup Analysis and Parsimony" (PDF). Systematic Zoology. 33 (1): 83–103. doi:10.2307/2413134. JSTOR 2413134.
^Wilberg, Eric W. (2015-07-01). "What's in an Outgroup? The Impact of Outgroup Choice on the Phylogenetic Position of Thalattosuchia (Crocodylomorpha) and the Origin of Crocodyliformes". Systematic Biology. 64 (4): 621–637. doi:10.1093/sysbio/syv020. ISSN 1063-5157. PMID 25840332.
^O'BRIEN, MICHAEL J.; LYMAN, R.LEE; SAAB, YOUSSEF; SAAB, ELIAS; DARWENT, JOHN; GLOVER, DANIEL S. (2002). "Two Issues in Archaeological Phylogenetics: Taxon Construction and Outgroup Selection". Journal of Theoretical Biology. 215 (2): 133–150. doi:10.1006/jtbi.2002.2548. PMID 12051970.
^David A. Baum; Stacey D. Smith (2013). Tree Thinking: An Introduction to Phylogenetic Biology. Roberts. p. 175. ISBN978-1-936221-16-5.
^Jarvis, E.; et al. (December 2014). "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science. 346 (6215): 1320–1331. Bibcode:2014Sci...346.1320J. doi:10.1126/science.1253451. PMC4405904. PMID 25504713.
^Stevens, P. F. (1991). "Character States, Morphological Variation, and Phylogenetic Analysis: A Review". Systematic Botany. 16 (3): 553–583. doi:10.2307/2419343. JSTOR 2419343.
^Rineau, Valentin; Grand, Anaïs; Zaragüeta, René; Laurin, Michel (May 1, 2015). "Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes". Contributions to Zoology. 84 (2): 129–148. doi:10.1163/18759866-08402003.
^Prado-Martinez, Javier; Marques-Bonet, Tomas (2013). "Great ape genetic diversity and population history". Nature. 499 (7459): 471–475. Bibcode:2013Natur.499..471P. doi:10.1038/nature12228. PMC3822165. PMID 23823723.
^Murphy, William; Pringle, Thomas; Crider, Tess; Springer, Mark; Miller, Webb (2007). "Using genomic data to unravel the root of the placental mammal phylogeny". Genome Research. 17 (4): 413–421. doi:10.1101/gr.5918807. PMC1832088. PMID 17322288.
^Cameron, Chris; Garey, James; Swalla, Billie (2000). "Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla". PNAS. 97 (9): 4469–4474. doi:10.1073/pnas.97.9.4469. PMC18258. PMID 10781046.
^Matthews, Sarah; Donoghue, Michael (1999). "The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes". Science. 286 (5441): 947–950. doi:10.1126/science.286.5441.947. PMID 10542147.
October 27, 2023
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In cladistics or phylogenetics an outgroup 1 is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup the set of organisms under study and is distinct from sociological outgroups The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted Because the polarity direction of character change can be determined only on a rooted phylogeny the choice of outgroup is essential for understanding the evolution of traits along a phylogeny 2 A simple cladogram showing the evolutionary relationships between four species A B C and D Here Species A is the outgroup and Species B C and D form the ingroup Contents 1 History 2 Choice of outgroup 3 Examples 4 See also 5 ReferencesHistory editAlthough the concept of outgroups has been in use from the earliest days of cladistics the term outgroup is thought to have been coined in the early 1970s at the American Museum of Natural History 3 Prior to the advent of the term various other terms were used by evolutionary biologists including exgroup related group and outside groups 3 Choice of outgroup editThe chosen outgroup is hypothesized to be less closely related to the ingroup than the ingroup is related to itself The evolutionary conclusion from these relationships is that the outgroup species has a common ancestor with the ingroup that is older than the common ancestor of the ingroup Choice of outgroup can change the topology of a phylogeny 4 Therefore phylogeneticists typically use more than one outgroup in cladistic analysis The use of multiple outgroups is preferable because it provides a more robust phylogeny buffering against poor outgroup candidates and testing the ingroup s hypothesized monophyly 3 5 6 To qualify as an outgroup a taxon must satisfy the following two characteristics It must not be a member of the ingroup It must be related to the ingroup closely enough for meaningful comparisons to the ingroup Therefore an appropriate outgroup must be unambiguously outside the clade of interest in the phylogenetic study An outgroup that is nested within the ingroup will when used to root the phylogeny result in incorrect conclusions about phylogenetic relationships and trait evolution 7 However the optimal level of relatedness of the outgroup to the ingroup depends on the depth of phylogenetic analysis Choosing a closely related outgroup relative to the ingroup is more useful when looking at subtle differences while choosing an unduly distant outgroup can result in mistaking convergent evolution for a direct evolutionary relationship due to a common ancestor 8 9 For shallow phylogenetics for example resolving the evolutionary relationships of a clade within a genus an appropriate outgroup would be a member of the sister clade 10 However for deeper phylogenetic analysis less closely related taxa can be used For example Jarvis et al 2014 used humans and crocodiles as outgroups while resolving the early branches of the avian phylogeny 11 In molecular phylogenetics satisfying the second requirement typically means that DNA or protein sequences from the outgroup can be successfully aligned to sequences from the ingroup Although there are algorithmic approaches to identify the outgroups with maximum global parsimony they are often limited by failing to reflect the continuous quantitative nature of certain character states 12 Character states are traits either ancestral or derived that affect the construction of branching patterns in a phylogenetic tree 13 Examples editIngroup OutgroupGreat Apes 14 GibbonsPlacental mammals 15 MarsupialsChordates 16 EchinodermsAngiosperms 17 GymnospermsIn each example a phylogeny of organisms in the ingroup may be rooted by scoring the same character states for one or more members of the outgroup See also editApomorphy a derived trait of an organism Sister group a group that may be closely related to an ingroup Plesiomorphy an ancestral trait of an organism Primitive phylogenetics a term for ancestral traitsReferences edit Grimaldi David Engel Michael S Engel Michael S 2005 05 16 Evolution of the Insects ISBN 9780521821490 Farris J S 1982 Outgroups and Parsimony Systematic Biology 31 3 328 334 doi 10 1093 sysbio 31 3 328 ISSN 1063 5157 a b c Nixon Kevin Carpenter James December 1993 On Outgroups Cladistics 9 4 413 426 doi 10 1111 j 1096 0031 1993 tb00234 x S2CID 221577454 Giribet G Ribera C June 1998 The position of arthropods in the animal kingdom a search for a reliable outgroup for internal arthropod phylogeny Molecular Phylogenetics and Evolution 9 3 481 488 doi 10 1006 mpev 1998 0494 PMID 9667996 Barriel V Tassy P June 1998 Rooting with Multiple Outgroups Consensus Versus Parsimony Cladistics 14 2 193 200 doi 10 1111 j 1096 0031 1998 tb00332 x S2CID 84759858 de la Torre Barcena Jose Eduardo Kolokotronis S O Lee Ernest Stevenson Dennis Brenner Eric Katari Manpreet Coruzzi Gloria DeSalle Rob 2009 The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome Wide EST Data PLOS ONE 4 6 e5764 Bibcode 2009PLoSO 4 5764D doi 10 1371 journal pone 0005764 PMC 2685480 PMID 19503618 Maddison Wayne et al 1984 Outgroup Analysis and Parsimony PDF Systematic Zoology 33 1 83 103 doi 10 2307 2413134 JSTOR 2413134 Wilberg Eric W 2015 07 01 What s in an Outgroup The Impact of Outgroup Choice on the Phylogenetic Position of Thalattosuchia Crocodylomorpha and the Origin of Crocodyliformes Systematic Biology 64 4 621 637 doi 10 1093 sysbio syv020 ISSN 1063 5157 PMID 25840332 O BRIEN MICHAEL J LYMAN R LEE SAAB YOUSSEF SAAB ELIAS DARWENT JOHN GLOVER DANIEL S 2002 Two Issues in Archaeological Phylogenetics Taxon Construction and Outgroup Selection Journal of Theoretical Biology 215 2 133 150 doi 10 1006 jtbi 2002 2548 PMID 12051970 David A Baum Stacey D Smith 2013 Tree Thinking An Introduction to Phylogenetic Biology Roberts p 175 ISBN 978 1 936221 16 5 Jarvis E et al December 2014 Whole genome analyses resolve early branches in the tree of life of modern birds Science 346 6215 1320 1331 Bibcode 2014Sci 346 1320J doi 10 1126 science 1253451 PMC 4405904 PMID 25504713 Stevens P F 1991 Character States Morphological Variation and Phylogenetic Analysis A Review Systematic Botany 16 3 553 583 doi 10 2307 2419343 JSTOR 2419343 Rineau Valentin Grand Anais Zaragueta Rene Laurin Michel May 1 2015 Experimental systematics sensitivity of cladistic methods to polarization and character ordering schemes Contributions to Zoology 84 2 129 148 doi 10 1163 18759866 08402003 Prado Martinez Javier Marques Bonet Tomas 2013 Great ape genetic diversity and population history Nature 499 7459 471 475 Bibcode 2013Natur 499 471P doi 10 1038 nature12228 PMC 3822165 PMID 23823723 Murphy William Pringle Thomas Crider Tess Springer Mark Miller Webb 2007 Using genomic data to unravel the root of the placental mammal phylogeny Genome Research 17 4 413 421 doi 10 1101 gr 5918807 PMC 1832088 PMID 17322288 Cameron Chris Garey James Swalla Billie 2000 Evolution of the chordate body plan New insights from phylogenetic analyses of deuterostome phyla PNAS 97 9 4469 4474 doi 10 1073 pnas 97 9 4469 PMC 18258 PMID 10781046 Matthews Sarah Donoghue Michael 1999 The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes Science 286 5441 947 950 doi 10 1126 science 286 5441 947 PMID 10542147 Retrieved from https en wikipedia org w index php title Outgroup cladistics amp oldid 1177189650, wikipedia, wiki, book, books, library,
