User:Ngilbert202/sandbox

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Article Evaluation[edit]

I'm going to evaluate the article for Coalescent theory.

There are lot of appropriate sources listed, and the links do indeed work, though some of them are to journal articles that require registration to view.

It is rated as C-Class on the project's quality scale.

It is part of the following WikiProjects: Genetics, Evolutionary biology, and Statistics.

Outgroup Stub plan[edit]

I have selected the Outgroup (cladistics) stub to edit for Evolution class.

A few immediate ideas for improvement:

1. A couple figures. Particularly with concepts like evolutionary trees, figures are very important! The stub currently has no figures. I will find (or create) at least one or two to add.

2. More internal links to biology-ish terms like "monophyletic" and "taxa".

3. More sources!

4. More content -- essentially, there is just the intro, a section on the choice of outgroup, and an example table.

Potential sources:

1) My good ole biology textbook (Freeman et al., I've got the fourth edition) 2) Our Evoultionary Analysis textbook (Herron and Freeman) 3) Nixon, K. C., and J. M. Carpenter (1993). On Outgroups. Cladistics 9:413-426. Good for history of term, for saying that outgroup doesn't have to contain sister group, need not be monophyletic, do not to be primitive relative to ingroup.

4) Maddison, W. P., Donoghue, M. J., and D. R. Maddison (1984). Outgroup Analysis and Parsimony. Systematic Biology 33:83-103. 5) Roy, S. W (2009). Phylogenomics: Gene Duplication, Unrecognized Paralogy and OUtgroup Choice. PLOS ONE http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004568

Hey friendly reviewer! Read this! =[edit]

What I've added[edit]

  • Four new references: Nixon, Giribet, Barriel, and Jarvis.
  • Figure (which I created) illustrating what an outgroup is
  • New section on history of term
  • Edited and added content, esp. in the outgroup choice section


LINK to original article

Make a note of which articles you reviewed in your sandbox.[edit]

This is that note. I reviewed Rachael Hopp and Reilly Carr.[edit]

Outgroup (cladistics)[edit]

In cladistics or phylogenetics, an outgroup is a 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.[1]

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.

History[edit]

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 1970's at the American Museum of Natural History.[2] Prior to the advent of the term, various other terms were used by evolutionary biologists, including "exgroup", "related group", and "outside groups".[2]

Choice of outgroup[edit]

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.[3] 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.[2][4][5]

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, close 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.[6] 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.[7][8] 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.[9] 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.[10] 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.[11] Character states are traits, either primitive or derived, that affect the construction of branching patterns in a phylogenetic tree.[12]

Examples[edit]

Ingroup Outgroup
Great Apes[13] New world monkeys
Placental mammals[14] Marsupials
Chordates[15] Echinoderms
Angiosperms[16] 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[edit]

References[edit]

  1. ^ Farris, J. S. (1982). "Outgroups and Parsimony". Systematic Biology. 31 (3): 328–334. doi:10.1093/sysbio/31.3.328. ISSN 1063-5157.
  2. ^ 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.
  3. ^ 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.
  4. ^ 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.
  5. ^ de la Torre-Barcena, Jose Eduardo; Kolokotronis, S.O.; Lee, Ernest; Stevenson, Dennis; Brenner, Eric; Katari, Manpreet; Coruzzi, Gloria; DeSalle, Rob. "The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data". PLOS ONE. doi:10.1371/journal.pone.0005764.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  6. ^ Maddison, Wayne; et al. (1984). "Outgroup Analysis and Parsimony" (PDF). Systemic Zoology. 33 (1): 83–103.
  7. ^ 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.
  8. ^ O'BRIEN, MICHAEL J.; LYMAN, R.LEE; SAAB, YOUSSEF; SAAB, ELIAS; DARWENT, JOHN; GLOVER, DANIEL S. "Two Issues in Archaeological Phylogenetics: Taxon Construction and Outgroup Selection". Journal of Theoretical Biology. 215 (2): 133–150. doi:10.1006/jtbi.2002.2548.
  9. ^ David A. Baum; Stacey D. Smith (2013). Tree Thinking: An Introduction to Phylogenetic Biology. Roberts. p. 175. ISBN 978-1-936221-16-5.
  10. ^ 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. doi:10.1126/science.1253451. {{cite journal}}: Explicit use of et al. in: |first1= (help)
  11. ^ Stevens, P. F. (1991). "Character States, Morphological Variation, and Phylogenetic Analysis: A Review". Systematic Botany. 16 (3): 553–583. doi:10.2307/2419343.
  12. ^ 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 – via EBSCOhost.
  13. ^ Prado-Martinez, Javier; Marques-Bonet, Tomas (2013). "Great ape genetic diversity and population history". Nature. doi:10.1038/nature12228.
  14. ^ 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. doi:10.1101/gr.5918807.
  15. ^ Cameron, Chris; Garey, James; Swalla, Billie (2000). "Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla". PNAS. doi:10.1073/pnas.97.9.4469.
  16. ^ Matthews, Sarah; Donoghue, Michael (1999). "The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes". Science. doi:10.1126/science.286.5441.947.
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