Homoplasy

Last updated

Homoplasy, in biology and phylogenetics, is the term used to describe a feature that has been gained or lost independently in separate lineages over the course of evolution. This is different from homology, which is the term used to characterize the similarity of features that can be parsimoniously explained by common ancestry. [1] Homoplasy can arise from both similar selection pressures acting on adapting species, and the effects of genetic drift. [2] [3]

Contents

Homoplasy is the similarity in a feature that is not parsimoniously explained by descent from a common ancestor. Apomorphy - Homoplasy.svg
Homoplasy is the similarity in a feature that is not parsimoniously explained by descent from a common ancestor.

Most often, homoplasy is viewed as a similarity in morphological characters. However, homoplasy may also appear in other character types, such as similarity in the genetic sequence, [4] [5] life cycle types [6] or even behavioral traits. [7] [5]

Etymology

The term homoplasy was first used by Ray Lankester in 1870. [8] 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". [9] [10] [11] [4]

Parallelism and convergence

Parallel and convergent evolution lead to homoplasy when different species independently evolve or gain apparently identical features, which are different from the feature inferred to have been present in their common ancestor. When the similar features are caused by an equivalent developmental mechanism, the process is referred to as parallel evolution. [12] [13] The process is called convergent evolution when the similarity arises from different developmental mechanisms. [13] [14] 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 cone-shaped heads and flat frontal claws) to live in a subterranean ecological niche. [15]

Reversion

In contrast, reversal (a.k.a. vestigialization) leads to homoplasy through the disappearance of previously gained features. [16] This process may result from changes in the environment in which certain gained characteristics are no longer relevant, or have even become costly. [17] [3] This can be observed in subterranean and cave-dwelling animals by their loss of sight, [15] [18] in cave-dwelling animals through their loss of pigmentation, [18] and in both snakes and legless lizards through their loss of limbs. [19] [20]

Distinguishing homology from homoplasy

Homoplasy, especially the type that occurs in more closely related phylogenetic groups, can make phylogenetic analysis more challenging. Phylogenetic trees are often selected by means of parsimony analysis. [21] [22] These analyses can be done with phenotypic characters, as well as DNA sequences. [23] Using parsimony analysis, the hypothesis of relationships that requires the fewest (or least costly) character state transformations is preferred over alternative hypotheses. Evaluation of these trees may become a challenge when clouded by the occurrence of homoplasy in the characters used for the analysis. The most important approach to overcoming these challenges is to increase the number of independent (non-pleiotropic, non-linked) characteristics used in the phylogenetic analysis. Along with parsimony analysis, one could perform a likelihood analysis, where the most likely tree, given a particular model of evolution, is selected, and branch lengths are inferred.

According to the cladistic interpretation, homoplasy is invoked when the distribution of a character state cannot be explained parsimoniously (without extra inferred character state transformations between the terminals and their ancestral node) on a preferred phylogenetic hypothesis - that is, the feature in question arises (or disappears) at more than one point on the tree. [16]

In the case of DNA sequences, homoplasy is very common due to the redundancy of the genetic code. An observed homoplasy may simply be the result of random nucleotide substitutions accumulating over time, and thus may not need an adaptationist evolutionary explanation. [5]

Examples and applications of homoplasy

There are numerous documented examples of homoplasy within the following taxa:

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. [16] [32]

Homoplasy vs. evolutionary contingency

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. [33] 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 and homoplastic occurrence can be true at the same time. [34]

See also

Related Research Articles

Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.

In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference, methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.

<span class="mw-page-title-main">Cladogram</span> Diagram used to show relations among groups of organisms with common origins

A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.

<span class="mw-page-title-main">Convergent evolution</span> Independent evolution of similar features

Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions.

A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.

<span class="mw-page-title-main">Gnetophyta</span> Division of plants containing three genera of gymnosperms

Gnetophyta is a division of plants, grouped within the gymnosperms, that consists of some 70 species across the three relict genera: Gnetum, Welwitschia, and Ephedra. The earliest unambiguous records of the group date to the Jurassic, and they achieved their highest diversity during the Early Cretaceous. The primary difference between gnetophytes and other gymnosperms is the presence of vessel elements, a system of small tubes (xylem) that transport water within the plant, similar to those found in flowering plants. Because of this, gnetophytes were once thought to be the closest gymnosperm relatives to flowering plants, but more recent molecular studies have brought this hypothesis into question, with many recent phylogenies finding them to be nested within the conifers.

<span class="mw-page-title-main">Outgroup (cladistics)</span>

In cladistics or phylogenetics, an outgroup 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.

<span class="mw-page-title-main">Apomorphy and synapomorphy</span> Two concepts on heritable traits

In phylogenetics, an apomorphy is a novel character or character state that has evolved from its ancestral form. A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor. In cladistics, synapomorphy implies homology.

In phylogenetics and computational phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy. In other words, under this criterion, the shortest possible tree that explains the data is considered best. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.

<span class="mw-page-title-main">Substitution model</span> Description of the process by which states in sequences change into each other and back

In biology, a substitution model, also called models of DNA sequence evolution, are Markov models that describe changes over evolutionary time. These models describe evolutionary changes in macromolecules represented as sequence of symbols. Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. Thus, substitution models are central to maximum likelihood estimation of phylogeny as well as Bayesian inference in phylogeny. Estimates of evolutionary distances are typically calculated using substitution models. Substitution models are also central to phylogenetic invariants because they are necessary to predict site pattern frequencies given a tree topology. Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree.

In phylogenetics, long branch attraction (LBA) is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related. LBA arises when the amount of molecular or morphological change accumulated within a lineage is sufficient to cause that lineage to appear similar to another long-branched lineage, solely because they have both undergone a large amount of change, rather than because they are related by descent. Such bias is more common when the overall divergence of some taxa results in long branches within a phylogeny. Long branches are often attracted to the base of a phylogenetic tree, because the lineage included to represent an outgroup is often also long-branched. The frequency of true LBA is unclear and often debated, and some authors view it as untestable and therefore irrelevant to empirical phylogenetic inference. Although often viewed as a failing of parsimony-based methodology, LBA could in principle result from a variety of scenarios and be inferred under multiple analytical paradigms.

<span class="mw-page-title-main">Ferae</span> A clade of mammals consisting of Carnivores and Pholidotes

Ferae is a mirorder of placental mammals from grandorder Ferungulata, that groups together clades Pan-Carnivora, which includes modern carnivorans, and Pholidotamorpha, which includes pangolins.

Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood, parsimony, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space.

<span class="mw-page-title-main">Autapomorphy</span> Distinctive feature, known as a derived trait, that is unique to a given taxon

In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon. It can therefore be considered an apomorphy in relation to a single taxon. The word autapomorphy, introduced in 1950 by German entomologist Willi Hennig, is derived from the Greek words αὐτός, autos "self"; ἀπό, apo "away from"; and μορφή, morphḗ = "shape".

Ancestral reconstruction is the extrapolation back in time from measured characteristics of individuals, populations, or specie to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence, the amino acid sequence of a protein, the composition of a genome, a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species. This is desirable because it allows us to examine parts of phylogenetic trees corresponding to the distant past, clarifying the evolutionary history of the species in the tree. Since modern genetic sequences are essentially a variation of ancient ones, access to ancient sequences may identify other variations and organisms which could have arisen from those sequences. In addition to genetic sequences, one might attempt to track the changing of one character trait to another, such as fins turning to legs.

Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model. Bayesian inference was introduced into molecular phylogenetics in the 1990s by three independent groups: Bruce Rannala and Ziheng Yang in Berkeley, Bob Mau in Madison, and Shuying Li in University of Iowa, the last two being PhD students at the time. The approach has become very popular since the release of the MrBayes software in 2001, and is now one of the most popular methods in molecular phylogenetics.

Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species. However, the fact that closely related lineages share many traits and trait combinations as a result of the process of descent with modification means that lineages are not independent. This realization inspired the development of explicitly phylogenetic comparative methods. Initially, these methods were primarily developed to control for phylogenetic history when testing for adaptation; however, in recent years the use of the term has broadened to include any use of phylogenies in statistical tests. Although most studies that employ PCMs focus on extant organisms, many methods can also be applied to extinct taxa and can incorporate information from the fossil record.

<span class="mw-page-title-main">Character evolution</span>

Character evolution is the process by which a character or trait evolves along the branches of an evolutionary tree. Character evolution usually refers to single changes within a lineage that make this lineage unique from others. These changes are called character state changes and they are often used in the study of evolution to provide a record of common ancestry. Character state changes can be phenotypic changes, nucleotide substitutions, or amino acid substitutions. These small changes in a species can be identifying features of when exactly a new lineage diverged from an old one.

<span class="mw-page-title-main">Phylogenetic signal</span>

Phylogenetic signal is an evolutionary and ecological term, that describes the tendency or the pattern of related biological species to resemble each other more than any other species that is randomly picked from the same phylogenetic tree.

References

  1. Torres-Montúfar A, Borsch T, Ochoterena H (May 2018). "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 . PMID   28645204.
  2. Stearns SC, Hoekstra RF (2005). Evolution: an introduction (2nd ed.). Oxford: Oxford University Press. ISBN   9780199255634.
  3. 1 2 Hall AR, Colegrave N (March 2008). "Decay of unused characters by selection and drift". Journal of Evolutionary Biology. 21 (2): 610–7. doi: 10.1111/j.1420-9101.2007.01473.x . PMID   18081745. S2CID   11165522.
  4. 1 2 Reece JB, Urry LA, Cain ML, Wasserman SA, Minorsky PV, Jackson RB (2011). Campbell Biology (9th ed.). Pearson. ISBN   9780321739759.
  5. 1 2 3 Sanderson MJ, Hufford L (1996). Homoplasy: The Recurrence of Similarity in Evolution. San Diego, CA: Academic Press, Inc. ISBN   0-12-618030-X.
  6. Silberfeld T, Leigh JW, Verbruggen H, Cruaud C, de Reviers B, Rousseau F (August 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): 659–74. doi:10.1016/j.ympev.2010.04.020. PMID   20412862.
  7. de Queiroz A, Wimberger PH (February 1993). "The usefulness of behavior for phylogeny estimation: levels of homoplasy in behavioral and morphological characters". Evolution; International Journal of Organic Evolution. 47 (1): 46–60. doi:10.1111/j.1558-5646.1993.tb01198.x. PMID   28568085. S2CID   205778379.
  8. Lankester ER (1870). "On the use of the term homology in modern zoology, and the distinction between homogenetic and homoplastic agreements" (PDF). Annals and Magazine of Natural History. 6 (31): 34–43. doi:10.1080/00222937008696201.
  9. Bailly A (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette. ISBN   2010035283. OCLC   461974285.
  10. Bailly A. "Greek-french dictionary online". www.tabularium.be. Retrieved October 25, 2018.
  11. Holt JR, Judica CA (February 4, 2014). "Systematic Biology - Dictionary of Terms: Homoplasy". Archived from the original on July 1, 2017. Retrieved September 21, 2018.
  12. Archie JW (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.
  13. 1 2 Wake DB (September 1991). "Homoplasy: The Result of Natural Selection, or Evidence of Design Limitations?". The American Naturalist. 138 (3): 543–567. doi:10.1086/285234. S2CID   85043463.
  14. 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.
  15. 1 2 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.
  16. 1 2 3 Wake DB, Wake MH, Specht CD (February 2011). "Homoplasy: from detecting pattern to determining process and mechanism of evolution". Science. 331 (6020): 1032–5. Bibcode:2011Sci...331.1032W. doi:10.1126/science.1188545. PMID   21350170. S2CID   26845473.
  17. Fong DW, Kane TC, Culver DC (1995). "Vestigialization and loss of nonfunctional characters". Annual Review of Ecology and Systematics. 26: 249–68. doi:10.1146/annurev.es.26.110195.001341.
  18. 1 2 Jones R, Culver DC (May 1989). "Evidence for selection on sensory structures in a cave population of Gammarus minus (Amphipoda)". Evolution; International Journal of Organic Evolution. 43 (3): 688–693. doi: 10.1111/j.1558-5646.1989.tb04267.x . PMID   28568387. S2CID   32245717.
  19. Skinner A, Lee MS (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.
  20. Skinner A, Lee MS, Hutchinson MN (November 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.
  21. Wiley EO, Lieberman BS (2011). Phylogenetics: Theory and Practice of Phylogenetic Systematics. Hoboken, NJ: John Wiley & Sons, Inc. ISBN   9780470905968.
  22. Schuh RT, Brower AV (2009). Biological Systematics: Principles and Applications. Ithaca, NY: Cornell University Press. ISBN   9780801462436.
  23. Felsenstein J (2004). Inferring phylogenies. Sinauer. ISBN   978-0878931774.
  24. Verheye ML, Martin P, Backeljau T, D'Udekem D'Acoz C (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. S2CID   86052388.
  25. Wu ZY, Milne RI, Chen CJ, Liu J, Wang H, Li DZ (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. Bibcode:2015PLoSO..1041821W. doi: 10.1371/journal.pone.0141821 . PMC   4631448 . PMID   26529598.
  26. Mejías JA, Chambouleyron M, Kim SH, Infante MD, Kim SC, Léger JF (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. S2CID   49873212.
  27. He L, Schneider H, Hovenkamp P, Marquardt J, Wei R, Wei X, Zhang X, Xiang Q (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.
  28. Schär S, Talavera G, Espadaler X, Rana JD, Andersen Andersen A, Cover SP, Vila R (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. S2CID   51832848.
  29. Henriques R, von der Heyden S, Matthee CA (2016-03-28). "When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensis and M. paradoxus)". PeerJ. 4: e1827. doi: 10.7717/peerj.1827 . PMC   4824878 . PMID   27069785.
  30. Ortiz D, Francke OF, Bond JE (October 2018). "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. PMID   29778724. S2CID   29152043.
  31. Lee MS, Yates AM (June 2018). "Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record". Proceedings. Biological Sciences. 285 (1881): 20181071. doi:10.1098/rspb.2018.1071. PMC   6030529 . PMID   30051855.
  32. Levin SR, Scott TW, Cooper HS, West SA (2017). "Darwin's aliens". International Journal of Astrobiology. 18: 1–9. doi: 10.1017/S1473550417000362 .
  33. Gould SJ (2000). Wonderful Life: The Burgess Shale and the Nature of History. London: Vintage Books. ISBN   9780099273455.
  34. Powell R, Mariscal C (December 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.