Two recent steps towards a statistically objective phylogenetic species concept have used bifurcating trees in a maximum likelihood or Bayesian framework. Matz & Nielsen (2005)
and Nielsen & Matz (2006)
developed a likelihood ratio test for inclusion of a test sequence in a single species sample. Pons et al. (2006)
identified the boundary between two species as a shift from short branches within taxa (caused by coalescence processes in populations) to long branches between taxa (caused by speciation and extinction events), analogous to the difference between within- and among-species lineage sorting evident in statistical parsimony networks.
Recent analyses of specific taxa (cited above) show that the 95% parsimony connection limit can provide an additional and simple quantitative standard for phylogenetic species (Monaghan et al. 2006
). Our review and reanalyses suggest that this standard has a low rate of false-positive errors across a broad range of taxa, speciation problems and genetic markers, and that it may be generally useful for assigning unknown specimens to known, well-sampled taxa (DNA barcoding as defined by Vogler & Monaghan 2007
). This approach might be particularly useful for barcoding studies in which morphological or ecological species markers are labile (such as caterpillar host plant use by INGCUP and FABOV forms of A. fulgerator
; Hebert et al. 2004
). The parsimony connection limit appears to have a higher true-positive rate for successful identification of known species boundaries, and by extension for discovering new cryptic species from sequence data (DNA taxonomy; Vogler & Monaghan 2007
), when applied to non-recombining loci with rapid lineage sorting (mtDNA; Moore 1995
). In contrast, frequent recombination between nuclear alleles (and the associated intraspecific homoplasy) may limit the rate at which ancestral polymorphisms shared between recently diverged species are lost from one (or both) of them by lineage sorting and thus reduce the rate at which haplotype differences between sister species approach the parsimony connection limit. Within these constraints, our observations and those of other recent studies suggest that the 95% parsimony connection limit might provide a useful general tool in species assignment (conventional DNA barcoding), species discovery (more controversial DNA taxonomy) and other applications in evolutionary ecology and conservation.