The phylogenetic analysis of allozyme data: invalidity of coding alleles by presence/absence and recommended procedures
1993
Murphy, R.W.
Recently, the dominant way of analyzing allozyme data for phylogenetic estimation has been to code the presence or absence of alleles as characters, despite the invalidity of this method having been demonstrated over 10 years ago. Adding to the previous arguments, four problems are discussed: (1) independent losses of relatively primitive alleles are considered as synapomorphies; (2) loci having a greater number of alleles are given a correspondingly higher weight in the tree reconstruction; (3) unnecessary character conflicts arise when no alleles are shared between the ingroup and outgroup; and (4) polymorphism in the outgroup may result in erroneous hypotheses. This coding method can result in the resolution of a less parsimonious solution than could be obtained by using the locus as the character. The "mutation model" of allozyme coding, which equates apomorphies with mutation events, is described and used in a four stage method for character-state evaluations, termed the "quadraphenic evaluation procedure". In order of preference these stages are: (1) taxonomic outgroup analysis; (2) functional outgroup analysis; (3) use of loss data, including shifts in gene frequency; and (4) nonadditive (unordered) evaluations. Conclusions drawn from the last two levels should not be used in taxonomy.
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