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Evolution Paper Topics

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  1. Eocyte Hypothesis
  2. Homoplasy
  3. Clonal Interference
  4. Punctuated Gradualism
  5. Semantides

Citation Exercise

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The classification of crocodiles known as gharials are made up of two different species: Gavialis gangeticus and Tomistoma schlegelii. [1]


Homoplasy, in biology and phylogenetics, is when a trait has been gained or lost independently in separate lineages over the course of evolution. This is different from homology, which is the similarity of traits due to common ancestry [2]. Homoplasy can arise from both similar selection pressures acting on adapting species, and the effects of genetic drift [3][4].

Homoplasy is the similarity in trait that is not due to a common ancestor.

Most often, homoplasy is viewed as a similarity in morphological traits. However, homoplasy may also appear in other trait types, such as similarity in the genetic sequence [5][6], life cycle types [7] or even behavioral traits [8][6].

Etymology

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The term homoplasy was first used by Ray Lankester in 1870 [9]. The corresponding adjective is either homoplasic or homoplastic. It is derived from the two ancient greek words ὁμός (homós), meaning "similar, alike, the same", and πλάσσω (plássō), meaning "to shape, to mold".[10][11][12][5]

Parallelism and convergence

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Parallel and convergent evolution lead to homoplasy when different species independently evolve or gain a comparable trait, which diverges from the trait inferred to have been present in their common ancestor. When the similar traits are caused by an equivalent developmental mechanism, the process is referred to as parallel evolution[13][14]. The process is called convergent evolution when the similarity arises from different developmental mechanisms [14][15]. These types of homoplasy may occur when different lineages live in comparable ecological niches that require similar adaptations for an increase in fitness. An interesting example is that of the marsupial moles (Notoryctidae), golden moles (Chrysochloridae) and northern moles (Talpidae). These are mammals from different geographical regions and lineages, and have all independently evolved very similar burrowing characteristics (such as a cone-shaped heads and flat frontal claws) to live in a subterranean ecological niche [16].

Reversion

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In contrast, reversal (a.k.a. vestigialization) leads to homoplasy through the disappearance of previously gained traits [17]. This process may result from changes in the environment in which certain gained traits are no longer relevant, or have even become costly [18][4]. This can be observed in subterranean and cave-dwelling animals by their loss of sight [16][19], in cave-dwelling animals through their loss of pigmentation [19], and in both snakes and legless lizards through their loss of limbs [20][21].

Distinguishing homology from homoplasy

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Homoplasy, especially the type that occurs in more closely related phylogenetic groups, can make phylogenetic analysis more challenging. Phylogenetic trees are created by means of parsimony analysis [22][23]. These analyses can be done with phenotypic, as well as genetic traits (DNA sequences) [24]. Using parsimony analysis, the hypothesis that requires the fewest evolutionary changes is preferred over alternative hypotheses. Construction of these trees may become a challenge when clouded by the occurrence of homoplasy in the traits used for the analysis. The most important approach in overcoming these challenges, is by increasing the amount of independent (non-pleiotropic, non-linked) characteristics used in the construction of these phylogenic trees. Along with parsimony analysis, one could perform a likelihood analysis, where the probability of a tree being true is calculated and branch lengths are measured; and bootstrapping, in which trees are constructed for each characteristic separately to estimate the confidence of a tree [6].

According to cladistic interpretation, homoplasy can be identified when a given similarity in trait cannot be explained by relation through a common ancestor on a preferred phylogenetic hypothesis - that is, the feature in question arises (or disappears) at more than one point on the tree [17].

In the case of DNA sequences, homoplasy cannot be avoided due to its four-state nature. An observed homoplasy may simply be the result of random nucleotide substitutions accumulating over time, and thus may not need an adaptationist evolutionary explanation [6].

Real world examples and applications of homoplasy

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Tarantula morphology tends to be excessively homoplastic, which has led to many misidentifications in their phylogenetic analysis. Ortiz, Francke, and Bond conducted a study on the genus Bonnetina, whose members exhibited remarkable heterogeneity to the point that their monophyly was questioned. Additionally, previous attempts at pinpointing the phylogenetic position of Bonnetina were arguably unsuccessful. Their study aimed to address these two issues, as well as create a timeline in the evolution of Bonnetina, and determine the reliability of tarantula classification based on morphology. Due to known issues with homoplasy among tarantulas, they planned to tackle these issues with a molecular approach. They sampled DNA from numerous taxa, and created five nuclear markers and one mitochondrial marker to sequence the genes of interest. The data were analyzed using several different models, such as maximum likelihood estimates and Bayesian methods. As a result of their study, they concluded that Bonnetina was indeed monophyletic, with the exception of Bonnetina juxtantricola. The last common ancestor of all tarantulas was about 92 million years ago, with Bonnetina diverging from its sister taxa about 19 million years ago. Most importantly, they confirmed that nearly all morphological traits within the genus Bonnetina were homoplastic. Only sexual features were observed to not be homoplastic, suggesting that sexual selection may have been a driving force in the divergence of tarantulas.[25]

The phylogeny of gharials, a classification of crocodiles, is also significantly impacted by homoplasy. These endangered reptiles are made up of two different species: Gavialis gangeticus and Tomistoma schlegelii. An important distinction between the two is that under morphological analysis of extant species and fossils, Tomistoma is considered a true crocodile, while Gavialis is not, with the two species' shared characteristic of fish eating being a product of homoplasy. However, molecular data suggests that the gharials are sister taxa, with their shared fish eating trait being a result of homology. Further complicating matters is molecular and morphological data suggesting that the genus of thoracosaurs emerged within the lineage of gharials, despite the fact that the now extinct thoracosaurs actually emerged much sooner than gharials. Lee and Yates conducted a study aiming to combine molecular and morphological methods in order to address this anomaly and distinguish which traits were due to homology, and which were due to homoplasy. They checked living and fossilized crocodiles for a comprehensive list of known traits, and created a supermatrix made up of 10 nuclear genes. The resulting data were analyzed by parsimony and tip dating methods. From their research, they confirmed that the two species of gharials were indeed sister taxa, meaning that the shared traits between Tomistoma and true crocodiles were a result of homoplasy. They also concluded that the only possible explanation for the data placing thoracosaurs within the gharial lineage was a significant amount of homoplastic convergence between thoracosaurs and Gavialis.[26].

There are numerous other documented examples of homoplasy within evolutionary systems, such as within Eusiroidea (Crustaceans and Amphipoda)[27], Urticaceae [28], Asteraceae [29], Polypodioideae (Selligueoid Ferns) [30], Ants [31], and Merluccius capensis (Cape Hakes) [32].

The occurrence of homoplasy can also be used to make predictions about evolution. Recent studies have used homoplasy to predict the possibility and the path of extraterrestrial evolution. For example, Levin et al. (2017) suggest that the development of eye-like structures is highly likely, due to its numerous, independently evolved incidences on earth [17][33].

Homoplasy vs. evolutionary contingency

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In his book Wonderful Life, Stephen Jay Gould claims that repeating the evolutionary process, from any point in time onward, would not produce the same results [34]. The occurrence of homoplasy is viewed by some biologists as an argument against Gould’s theory of evolutionary contingency. Powell & Mariscal (2015) argue that this disagreement is caused by an equivocation and that both the theory of contingency as well as homoplastic occurrence can be true at the same time [35].

References

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  1. ^ Lee, Michael S. Y.; Yates, Adam M. (2018-06-27). "Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record". Proc. R. Soc. B. 285 (1881): 20181071. doi:10.1098/rspb.2018.1071. ISSN 0962-8452. PMC 6030529. PMID 30051855.
  2. ^ Torres-Montúfar, Alejandro; Borsch, Thomas; Ochoterena, Helga (2017-07-13). "When Homoplasy Is Not Homoplasy: Dissecting Trait Evolution by Contrasting Composite and Reductive Coding". Systematic Biology. 67 (3): 543–551. doi:10.1093/sysbio/syx053. ISSN 1063-5157. PMID 28645204.
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  7. ^ Silberfeld, T.; Leigh, J.W.; Verbruggen, H.; Cruaud, C.; de Reviers, B.; Rousseau, F. (2010). "A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the "brown algal crown radiation."". Molecular Phylogenetics and Evolution. 56 (2): 659–674. doi:10.1016/j.ympev.2010.04.020. PMID 20412862.
  8. ^ de Querioz, A.; Wimberger, P.H. (1993). "The usefulness of behavior for phylogeny estimation: levels of homoplasy in behavioral and morphological characters". Evolution. 47 (1): 46–60. doi:10.1111/j.1558-5646.1993.tb01198.x. PMID 28568085. S2CID 205778379.
  9. ^ Lankester, E.R. (1870). "On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements". Annals and Magazine of Natural History. 6 (31): 34–43. doi:10.1080/00222937008696201.
  10. ^ Bailly, Anatole (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette. ISBN 2010035283. OCLC 461974285.
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  12. ^ Holt, J.R.; Judica, C.A. (February 4, 2014). "Systematic Biology - Dictionary of Terms: Homoplasy". Retrieved September 21, 2018.
  13. ^ Archie, J.W. (1989). "Homoplasy excess ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index". Systematic Biology. 38 (3): 253–269. doi:10.2307/2992286. JSTOR 2992286.
  14. ^ a b Wake, David B. (September 1991). "Homoplasy: The Result of Natural Selection, or Evidence of Design Limitations?". The American Naturalist. 138 (3): 543–567. doi:10.1086/285234. ISSN 0003-0147. S2CID 85043463.
  15. ^ Hodin, J. (2000). "Plasticity and constraints in development and evolution". Journal of Experimental Zoology. 288 (1): 1–20. doi:10.1002/(SICI)1097-010X(20000415)288:1<1::AID-JEZ1>3.0.CO;2-7. PMID 10750048.
  16. ^ a b Nevo, E. (1979). "Adaptive convergence and divergence of subterranean mammals". Annual Review of Ecology and Systematics. 10: 269–308. doi:10.1146/annurev.es.10.110179.001413.
  17. ^ a b c Wake, D.B.; Wake, M.H.; Specht, C.D. (2011). "Homoplasy: From detecting pattern to determining process and mechanism of evolution". Science. 331 (6020): 1032–1035. doi:10.1126/science.1188545. PMID 21350170. S2CID 26845473.
  18. ^ Fong, D.W.; Kane, T.C.; Culver, D.C. (1995). "Vestigialization and loss of nonfunctional characters". Annual Review of Ecology and Systematics. 26: 249–68. doi:10.1146/annurev.es.26.110195.001341.
  19. ^ a b Jones, R.; Culver, D.C. (1989). "Evidence for selection on sensory structures in a cave population of Gammarus minus (Amphipoda)". Evolution. 43 (3): 688–693. doi:10.1111/j.1558-5646.1989.tb04267.x. PMID 28568387. S2CID 32245717.
  20. ^ Skinner, A.; Lee, M.S.Y. (2009). "Body-form evolution in the scincid lizard Lerista and the mode of macroevolutionary transitions". Evolutionary Biology. 36: 292–300. doi:10.1007/s11692-009-9064-9. S2CID 42060285.
  21. ^ Skinner, A; Lee, M.S.Y.; Hutchinson, M.N. (2008). "Rapid and repeated limb loss in a clade of scincid lizards". BMC Evolutionary Biology. 8: 310. doi:10.1186/1471-2148-8-310. PMC 2596130. PMID 19014443.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  22. ^ Wiley, E.O.; Lieberman, B.S. (2011). Phylogenetics: Theory and Practice of Phylogenetic Systematics. Hoboken, NJ: John Wiley & Sons, Inc. ISBN 9780470905968.
  23. ^ Schuh, R.T.; Brower, A.V.Z. (2018). Biological Systematics: Principles and Applications. Ithaca, NY: Cornell University Press. ISBN 9780801462436.
  24. ^ Felsenstein, J. (2004). Inferring phylogenies. Sinauer. ISBN 978-0878931774.
  25. ^ Ortiz, D., Francke, O. F., & Bond, J. E. (2018-10-01). "A tangle of forms and phylogeny: Extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas". Molecular Phylogenetics and Evolution. 127: 55–73. doi:10.1016/j.ympev.2018.05.013. ISSN 1055-7903. PMID 29778724. S2CID 29152043.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  26. ^ Lee, Michael S. Y.; Yates, Adam M. (2018-06-27). "Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record". Proc. R. Soc. B. 285 (1881): 20181071. doi:10.1098/rspb.2018.1071. ISSN 0962-8452. PMC 6030529. PMID 30051855.
  27. ^ Verheye, Marie L.; Martin, Patrick; Backeljau, Thierry; D'Udekem D'Acoz, Cédric (2015-12-22). "DNA analyses reveal abundant homoplasy in taxonomically important morphological characters of Eusiroidea (Crustacea, Amphipoda)". Zoologica Scripta. 45 (3): 300–321. doi:10.1111/zsc.12153. ISSN 0300-3256. S2CID 86052388.
  28. ^ Wu, Zeng-Yuan; Milne, Richard I.; Chen, Chia-Jui; Liu, Jie; Wang, Hong; Li, De-Zhu (2015-11-03). "Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae, Conflicting with Current Classification Schemes". PLOS ONE. 10 (11): e0141821. doi:10.1371/journal.pone.0141821. ISSN 1932-6203. PMC 4631448. PMID 26529598.
  29. ^ Mejías, José A.; Chambouleyron, Mathieu; Kim, Seon-Hee; Infante, M. Dolores; Kim, Seung-Chul; Léger, Jean-François (2018-07-19). "Phylogenetic and morphological analysis of a new cliff-dwelling species reveals a remnant ancestral diversity and evolutionary parallelism in Sonchus (Asteraceae)". Plant Systematics and Evolution. 304 (8): 1023–1040. doi:10.1007/s00606-018-1523-2. ISSN 0378-2697. S2CID 49873212.
  30. ^ He, Li-Juan; Schneider, Harald; Hovenkamp, Peter; Marquardt, Jeannine; Wei, Ran; Wei, Xueping; Zhang, Xian-Chun; Xiang, Qiaoping (2018-05-09). "A molecular phylogeny of selligueoid ferns (Polypodiaceae): Implications for a natural delimitation despite homoplasy and rapid radiation". Taxon. 67 (2): 237–249. doi:10.12705/672.1.
  31. ^ Schär, Sämi; Talavera, Gerard; Espadaler, Xavier; Rana, Jignasha D.; Andersen Andersen, Anne; Cover, Stefan P.; Vila, Roger (2018-06-27). "Do Holarctic ant species exist? Trans-Beringian dispersal and homoplasy in the Formicidae". Journal of Biogeography. 45 (8): 1917–1928. doi:10.1111/jbi.13380. ISSN 0305-0270. S2CID 51832848.
  32. ^ Henriques, Romina; von der Heyden, Sophie; Matthee, Conrad A. (2016-03-28). "When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensisandM. paradoxus)". PeerJ. 4: e1827. doi:10.7717/peerj.1827. ISSN 2167-8359. PMC 4824878. PMID 27069785.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  33. ^ Levin, S.R.; Scott, T.W.; Cooper, H.S.; West, S.A. (2017). "Darwin's aliens". International Journal of Astrobiology. 18: 1–9. doi:10.1017/S1473550417000362. S2CID 54216054.
  34. ^ Gould, S.J. (2000). Wonderful Life: The Burgess Shale and the Nature of History. London: Vintage Books. ISBN 9780099273455.
  35. ^ Powell, R.; Mariscal, C. (2015). "Convergent evolution as natural experiment: the tape of life reconsidered". Interface Focus. 5 (6): 20150040. doi:10.1098/rsfs.2015.0040. PMC 4633857. PMID 26640647.

Category:Biological concepts Category:Evolutionary biology Category:Phylogenetics


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