Geographic variation, null hypotheses, and subspecies limits in the California Gnatcatcher: A response to McCormack and Maley

We interpreted the results of nuclear DNA sequencing to be inconsistent with the recognition of California Gnatcatcher (Polioptila californica) subspecies. McCormack and Maley (2015) suggested that our data did support 2 taxa, one of which was P. c. californica, listed as Threatened under the Endangered Species Act (ESA). We summarize here how 2 sets of researchers with access to the same data reached different conclusions by including different analyses. We included the southern subspecies' boundary from the taxonomy of Atwood (1991), the taxonomic basis for the ESA listing, which resulted in an Analysis of Molecular Variance that provided no support for subspecies. In contrast, using a novel taxonomic hypothesis without precedent in the literature, McCormack and Maley (2015) found statistically significant F-ST values for 2 loci, which they suggested supports P. c. californica. We propose that our mitochondrial and nuclear data had sufficient power to capture geographical structure at either the phylogenetic (monophyly) or traditional 75% rule'' level. McCormack and Maley (2015) suggested that finding an absence of population structure was a negative result,'' whereas we consider it to be the null hypothesis for a species with gene flow and no geographical barriers. We interpret the unstructured mtDNA and nuclear DNA trees, the STRUCTURE analysis supporting one group, the identification of just 26% (and not 75%) of individuals of P. c. californica with the most diagnostic nuclear locus, the overall G(ST) that suggests that over 98% of the variation is explained by nontaxonomic sources, and the lack of evidence of ecological differentiation to indicate that P. c. californica is not a valid subspecies. McCormack and Maley (2015) suggest that statistically significant differences at 2 loci that explained <6% of the genetic variation, and previous morphological data, support recognition of P. c. californica. If ornithology continues to recognize subspecies, these different standards should be reconciled.