Synapomorphy and apomorphy

In phylogenetics, apomorphy and synapomorphy[2] refer to derived characters of a clade: characters or traits that are derived from ancestral characters over evolutionary history.[3] An apomorphy is a character that is different from the form found in an ancestor, i.e., an innovation, that sets the clade apart from other clades. A synapomorphy is a shared apomorphy that distinguishes a clade from other organisms.[1][4] In other words, it is an apomorphy shared by members of a monophyletic group, and thus assumed to be present in their most recent common ancestor.

Phylogenies showing the terminology used to describe different patterns of ancestral and derived character or trait states.[1]

Description

An apomorphy is a character that is different from the form found in an ancestor, i.e., an innovation, that sets the clade apart ("apo–") from other clades. A synapomorphy is a shared ("syn") apomorphy that distinguishes a clade from other organisms.[1][4] In other words, it is an apomorphy shared by members of a monophyletic group, and thus assumed to be present in their most recent common ancestor.

Example

In most groups of mammals, the vertebral column is highly conserved, with the same number of vertebrae found in the neck of a giraffe, for example, as in mammals with shorter necks. However, in the Afrotheria clade, which includes elephant shrews, golden moles and elephants, there is an increase in the number of thoracolumbar vertebrae. This is a synapomorphy of the clade: a shared feature considered to be derived from a common ancestor.[5]

Etymology

The word synapomorphy—coined by German entomologist Willi Hennig—is derived from the Greek words σύν, syn = shared; ἀπό, apo = away from; and μορφή, morphe = shape.

Phylogenetic similarities

These phylogenetic terms are used to describe different patterns of ancestral and derived character or trait states as stated in the above diagram in association with synapomorphies.[6][7]

  • Symplesiomorphy – an ancestral trait shared by two or more taxa.
    • Plesiomorphy – a symplesiomorphy discussed in reference to a more derived state.
    • Pseudoplesiomorphy – is a trait that cannot be identified as neither a plesiomorphy nor an apomorphy that is a reversal.[8]
  • Reversal – is a loss of derived trait present in ancestor and the reestablishment of a plesiomorphic trait.
  • Convergence – independent evolution of a similar trait in two or more taxa.
  • Apomorphy – a derived trait. Apomorphy shared by two or more taxa and inherited from a common ancestor is synapomorphy. Apomorphy unique to a given taxon is autapomorphy.[9][10][11][12]
    • Synapomorphy/Homology – a derived trait that is found in some or all terminal groups of a clade, and inherited from a common ancestor, for which it was an autapomorphy (i.e., not present in its immediate ancestor).
    • Underlying synapomorphy – a synapomorphy that has been lost again in many members of the clade. If lost in all but one, it can be hard to distinguish from an autapomorphy.
    • Autapomorphy – a distinctive derived trait that is unique to a given taxon or group.[13]
  • Homoplasy in biological systematics is when a trait has been gained or lost independently in separate lineages during evolution. This convergent evolution leads to species independently sharing a trait that is different from the trait inferred to have been present in their common ancestor.[14][15][16]
    • Parallel Homoplasy – derived trait present in two groups or species without a common ancestor due to convergent evolution.[17]
    • Reverse Homoplasy – trait present in an ancestor but not in direct descendants that reappears in later descendants.[18]
  • Hemiplasy is the case where a character that appears homoplastic given the species tree actually has a single origin on the associated gene tree.[19][20] Hemiplasy reflects gene tree-species tree discordance due to the multispecies coalescent.

Analysis

A new method of measuring phylogenetic characteristics is the use of Relative Apparent Synapomorphy Analysis (RASA). The objective of analysis is to determine if a given characteristic is common between taxa as a result of either shared ancestors or the process of convergence.[21] This method allows for several advantages such as computational efficiency and it also administers an unbiased and reliable measure of phylogenetic signal.[22]

The concept of synapomorphy is relative to a given clade in the tree of life. What counts as a synapomorphy for one clade may well be a primitive character or plesiomorphy at a less inclusive or nested clade. For example, the presence of mammary glands is a synapomorphy for mammals in relation to tetrapods but is a symplesiomorphy for mammals in relation to one another—rodents and primates, for example. So the concept can be understood as well in terms of "a character newer than" (autapomorphy) and "a character older than" (plesiomorphy) the apomorphy: mammary glands are evolutionarily newer than vertebral column, so mammary glands are an autapomorphy if vertebral column is an apomorphy, but if mammary glands are the apomorphy being considered then vertebral column is a plesiomorphy.

Cladogram comprehension

Cladograms are diagrams that depict evolutionary relationships within groups of taxa. These illustrations are accurate predictive device in modern genetics. They are usually depicted in either tree or ladder form. Synapomorphies then create evidence for historical relationships and their associated hierarchical structure. Evolutionarily, a synapomorphy is the marker for the most recent common ancestor of the monophyletic group consisting of a set of taxa in a cladogram.[23]

References
  1. Roderick D.M. Page; Edward C. Holmes (14 July 2009). Molecular Evolution: A Phylogenetic Approach. John Wiley & Sons. ISBN 978-1-4443-1336-9.
  2. Currie PJ, Padia K (1997). Encyclopedia of Dinosaurs. Elsevier. p. 543. ISBN 978-0-08-049474-6.
  3. Concise Encyclopedia Biology. Tubingen, DEU: Walter de Gruyter. 1996. p. 366.
  4. Barton N, Briggs D, Eisen J, Goldstein D, Patel N (2007). "Phylogenetic Reconstruction". Evolution. Cold Spring Harbor Laboratory Press.
  5. Sánchez‐Villagra, Marcelo R.; Narita, Yuichi; Kuratani, Shigeru (2007-03-01). "Thoracolumbar vertebral number: The first skeletal synapomorphy for afrotherian mammals". Systematics and Biodiversity. 5 (1): 1–7. doi:10.1017/s1477200006002258. ISSN 1477-2000. S2CID 85675984.
  6. Roderick D.M. Page; Edward C. Holmes (14 July 2009). Molecular Evolution: A Phylogenetic Approach. John Wiley & Sons. ISBN 978-1-4443-1336-9.
  7. Calow PP (2009). Encyclopedia of Ecology and Environmental Management. John Wiley & Sons. ISBN 978-1-4443-1324-6. OCLC 1039167559.
  8. Williams D, Schmitt M, Wheeler Q (July 2016). The Future of Phylogenetic Systematics: The Legacy of Willi Hennig. Cambridge University Press. ISBN 978-1-107-11764-8.
  9. Simpson MG (9 August 2011). Plant Systematics. Elsevier. Amsterdam: Elsevier. ISBN 9780080514048.
  10. Russell PJ, Hertz PE, McMillan B (2013). Biology: The Dynamic Science. Cengage Learning. ISBN 978-1-285-41534-5.
  11. Lipscomb D (1998). "Basics of Cladistic Analysis" (PDF). Washington D.C.: George Washington University.
  12. Choudhuri S (2014-05-09). Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools (1st ed.). Academic Press. p. 51. ISBN 978-0-12-410471-6. OCLC 950546876.
  13. Appel, Ron D.; Feytmans, Ernest. Bioinformatics: a Swiss Perspective."Chapter 3: Introduction of Phylogenetics and its Molecular Aspects." World Scientific Publishing Company, 1st edition. 2009.
  14. Gauger A (April 17, 2012). "Similarity Happens! The Problem of Homoplasy". Evolution Today & Science News.
  15. Sanderson MJ, Hufford L (21 October 1996). Homoplasy: The Recurrence of Similarity in Evolution. Elsevier. ISBN 978-0-08-053411-4. OCLC 173520205.
  16. Brandley MC, Warren DL, Leaché AD, McGuire JA (April 2009). "Homoplasy and clade support". Systematic Biology. 58 (2): 184–98. doi:10.1093/sysbio/syp019. PMID 20525577.
  17. Archie JW (September 1989). "Homoplasy Excess Ratios: New Indices for Measuring Levels of Homoplasy in Phylogenetic Systematics and a Critique of the Consistency Index". Systematic Biology. 38 (1): 253–269. doi:10.2307/2992286. JSTOR 2992286.
  18. Wake DB, Wake MH, Specht CD (February 2011). "Homoplasy: from detecting pattern to determining process and mechanism of evolution". Science. 331 (6020): 1032–5. doi:10.1126/science.1188545. PMID 21350170. S2CID 26845473. Lay summary – Science Daily.
  19. Avise JC, Robinson TJ (June 2008). "Hemiplasy: a new term in the lexicon of phylogenetics". Systematic Biology. 57 (3): 503–7. doi:10.1080/10635150802164587. PMID 18570042.
  20. Copetti D, Búrquez A, Bustamante E, Charboneau JL, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ (November 2017). "Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti". Proceedings of the National Academy of Sciences of the United States of America. 114 (45): 12003–12008. doi:10.1073/pnas.1706367114. PMC 5692538. PMID 29078296.
  21. Lyons-Weiler J, Hoelzer GA, Tausch RJ (July 1996). "Relative apparent synapomorphy analysis (RASA). I: The statistical measurement of phylogenetic signal". Molecular Biology and Evolution. 13 (6): 749–57. doi:10.1093/oxfordjournals.molbev.a025635. PMID 8754211.
  22. Simmons MP, Randle CP, Freudenstein JV, Wenzel JW (January 2002). "Limitations of relative apparent synapomorphy analysis (RASA) for measuring phylogenetic signal". Molecular Biology and Evolution. 19 (1): 14–23. doi:10.1093/oxfordjournals.molbev.a003978. PMID 11752186.
  23. Novick LR, Catley KM. Understanding phylogenies in biology: the influence of a Gestalt perceptual principle. J Exp Psychol Appl. 2007;13:197–223.
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