FIG. 1.

A figurative demonstration of the effect of allele choice or sampling on the inference of the species tree from a single nuclear gene. (A) The full gene tree will contain two alleles (or gene copies) from each individual chosen to represent a species (or higher taxon). For heterozygous individuals, the two different alleles may coalesce at a point in the past (dots on nodes) that is deeper than the speciation events that gave rise to them. (B) Four possible different trees (out of many), resulting from choosing a single allele from each heterozygous individual depicted in (A). The overall figure is meant to convey the possible variation in the information content of a concatenated matrix when multiple loci are used that contain heterozygous individuals.