3  Phylogeny Fundamentals

This is part of the UHH MSc Biology Course EvoSys 2023 (2/11)

3.1 Character States

  • Apomorphy = a derived trait, shared by two or more taxa from a common ancestor is synapomorphy, unique to a given taxa is autapomorphy
  • Synapomorphy = character present in an ancestral species and shared exclusively by its evolutionary descendants
  • Autapomorphy = apomorphy unique to a given taxa or group, not parsimony informative
  • Symplesiomorphy / Plesiomorphy = ancestral state shared by all the membre of a clade, which can not distinguish the clade from other clades

… these are the state of a character, based on the objective observations and data.

Symplesiomorphy is synapomorphy at a less inclusive level, which is not useful for phylogenetic classification (Patterson, 1982; de Pinna, 1991; Schuh and Brower, 2009).

3.2 Convergent Evolution

Convergent evolution = independent evolution of similar features, creates analogous

  • Morphologcial convergence > e.g., similar body form of succulent plant (Euphorbia and Astrophytum)

  • Homology, Homoplasy: is a hypothesis, which describe how a character has evolved.

As aptly remarked by Müller (2003, p. 54:

[…] its [element] absence, may serve as a shared, derived (taxonomical) character – a synapomorphy. Moreover, a taxonomical character is not necessarily the same as a morphological character. All homologues are synapomorphics, but not vice-versa. Absence of an anatomical element, for instance, can be a taxonomical synapomorphy but not a homology, because homologues are positive anatomical parts. Hence synapomorphy and homology should not be considered as synonymous.

  • Orthology: originated from speciation

  • Paralogy: originated from gene duplication

  • Xenology: originated from horizontal gene transfer

3.3 Paraphyly vs. Polyphyly

However, paraphyletic and polyphyletic groups are not realistically acceptable (Hennig, 1965, 1966), even though these groups are defined by symplesiomorphies and homoplasies, respectively. Ironically, there exists a clear distinction between character evolution and group classification.

Symplesiomorphy entails paraphyly, so that some, not all, descendant species inherited a particular (plesiomorphic) condition from a common ancestor of them. Homoplasy entails polyphyly—i.e. independent origin (non-homology) of a similar condition in two or more groups—but it is synapomorphy at a more restricted phylogenetic level (compare Hall, 2007; Scotland, 2011; Nixon and Carpenter, 2012).