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Concepts of Homology and Analogy applied to nucleotide character states

    Assume that the tree structure shows the correct relationships among taxa A, B, C, & D. The distribution of character states 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. 
             [Note as well that the nucleotide state g in A is an autapomorphy (unique derived character)].

(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.

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. In contrast, analogy or homology of morphologically structures such as wings can often be readily distinguished.