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Here’s something new.  I had planned to read many, many papers early in PhD, but so far have only managed to read many.  This ‘what I read today’ section will hopefully keep me to this.  Here, I will show what I read today, give a short summary and some of my thoughts.  This likely to be a more technically worded section, so feel free to simply pass them by.

Day One: 17 Jan 2012

NIXON, K. C. and CARPENTER, J. M. 2011. On homology. Cladistics, 27, 10 pp., doi: 10.1111/j.1096-0031.2011.00371.x.

  • Homoplasy is non-homology.
  • Homology is the sharing of characters derived from the same phylogenetic origin.
  • Homoplasy can be treated as error in the phylogenetic hypothesis of homology — i.e. enforcing a separate origin for e.g. bird and insect wings (function in flight) or bird and platypus bills (morphology) — thus separating homoplasy and analogy in a phylogenetic framework.
  • This applies equally to morphological (characters and states) and genomic (position and base) data.
  • Parsimony acts to reduced error (homoplasy) in optimisation.
  • Homology between single-character states is not tested by cladistic analysis.

This is an informative paper but sometimes ends up being complicatedly worded — and has some awfully long sentences.  Aside from this the logic is fairly easy to follow.  The two main sections of the paper concern the link between homology and plesiomorphy and homoplasy as error.

Of particular interest to me was the ‘homoplasy as error’ section.  They argue that homoplasy is the erroneous treatment of analogous characters as homologous.  One of the examples used is the wings of insects and birds: although both have the same function (flight) they have very different origins (non-homology).  Having a single character (‘has wings’) would entail coding both in the positive (1) state.  That possession of wings is coded in a single character is — at least implicitly — a phylogenetic hypothesis of their homology.  Multiple codings — such as ‘has insect-type wings’ and ‘has bird-type wings’ in its simplest form — transforms this into a hypothesis of analogy.

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