i

Concepts of Homology and Analogy applied to nucleotide character states

    The branching diagram shows the correct phylogenetic relationships among taxa A, B, C, & D. The plesiomorphic (ancestral) character state is a, and the apomorphic (derived) character state is g. The distribution of a & g at three different nucleotide positions illustrates the concepts of homology and analogy as applied to molecular data. The information content of each position differs.

  1 2 3
A g g g
B g a a
C a a g
D a a a

(Pos 1) Synapomorphy (shared derived character): the shared nucleotide state g in A & B correctly indicates they are each others closest relatives.

(Pos 2) Symplesiomorphy (shared ancestral character): the shared nucleotide state a in B, C, & D incorrectly suggests that B is closely related to C & D. However, the nucleotide state g in A is an autapomorphy (unique derived character), and cannot be used to infer relationship to B, C, or D.

(Pos 3) Convergence (analogy): the shared nucleotide state g in A & C incorrectly suggests that they are closely related. This is sometimes called parallel evolution, because the a g change is the same in both mutations. The term convergence is a bit misleading, as the ancestral and derived character states in A & C are not more similar afterward than before. However, because (AB) and (CD) are in fact separate clades, the g state makes them appear more closely related than they actually are.

AN IMPORTANT DISTINCTION between morphological & molecular character states is that all bases of the same type look exactly alike, whether they are analogous or homologous. Inspection of the character itself will not reveal anything. In contrast, analogy or homology of morphological structures such as wings can often be distinguished readily.