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Outgroup (cladistics)

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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.

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]

History

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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 outgroup

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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]

Examples

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Ingroup Outgroup
Great Apes[14] Gibbons
Placental mammals[15] Marsupials
Chordates[16] Ambulacrarians
Angiosperms[17] Gymnosperms

In 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

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References

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  1. ^ Grimaldi, David; Engel, Michael S.; Engel, Michael S. (2005-05-16). Evolution of the Insects. Cambridge University Press. ISBN 9780521821490.
  2. ^ Farris, J. S. (1982). "Outgroups and Parsimony". Systematic Biology. 31 (3): 328–334. doi:10.1093/sysbio/31.3.328. ISSN 1063-5157.
  3. ^ 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. PMID 34929985. S2CID 221577454.
  4. ^ 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.
  5. ^ 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.
  6. ^ 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.
  7. ^ Maddison, Wayne; et al. (1984). "Outgroup Analysis and Parsimony" (PDF). Systematic Zoology. 33 (1): 83–103. doi:10.2307/2413134. JSTOR 2413134.
  8. ^ 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.
  9. ^ 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.
  10. ^ David A. Baum; Stacey D. Smith (2013). Tree Thinking: An Introduction to Phylogenetic Biology. Roberts. p. 175. ISBN 978-1-936221-16-5.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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.
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