The Irrelevance of Allele Tree Topologies for Species Delimitation, and a Non-Topological Alternative

Abstract

Below the level of what is commonly accepted as the in sexual organisms there may be no phylogeny, only reticulate relationships (tokogeny) among individuals. The con- ventional molecular systematics research program, which infers organismal relationships from the topologies of allele or haplotype trees, will be misled below this critical level, in part because allele trees are not expected to track tokogenetic relationships. Yet there appears to be little or no consensus about how to delimit taxa that are appropriate for phylogenetic analysis. Individual sexual organisms cannot be the terminal units of analyses that employ typical nuclear genes, for which heterozygosity is expected, because heterozygous individuals cannot be uniquely placed on allele trees. Methods using the topologies of multiple allele trees also are flawed, in part for the same reason but also because, for an unknown fraction of the nuclear genome, allele phylogenies are not expected to track organismal relationships. A non-topological approach, which does not assume species or populations, is proposed here. This method identifies allele pools at individual loci by the dis- tribution of alleles in overlapping sets of heterozygous individuals. Individuals possessing alleles at a given allele pool of a locus belong to the same group, called here a field for recombination. Allele pools at each locus are a representation of the overall gene pool, which in turn can be inferred from multilocus genotypes; individuals sharing a common gene pool belong to the same multilocus field for recombination (ml-FFR). Once such gene pools are defined, allele topologies at suitable loci can be used to infer phylogenies. DNA sequence data are increasingly acces-