Comparison of the Efficiency of Single-Locus Species Delimitation Methods: A Case Study of a Single Lake Fish Population in Comparison against the Barcodes from International Databases

To date, a rather large set of both mathematical theories for species delimitation, based on single-locus genetic data, and their implementations as software products, has been accumulated. Comparison of the efficiencies of different delineation methods in the task of accumulating and analyzing data with reference to different taxa in different regions, is vital. The aim of this study was to compare the efficiency of fifteen single-locus species delimitation methods using the example of a fish species found in a single lake in European Russia (Lake Plescheyevo) with reference to other sequences of revealed taxa deposited in international databases. We analyzed 186 original COI sequences belonging to 24 haplotypes, and 101 other sequences previously deposited in GenBank and BOLD. Comparison of all 15 alternative taxonomies demonstrated that all methods adequately separate only the genera, while the number of delimited mOTUs differed from 16 (locMin) to 43 (HwM/CoMa). We can assume that the effectiveness of each method is correlated with the number of matches based on Ctax and MatchRatio criteria. The most comparable results were provided by bGMYC, mPTP, STACEY, KoT and ASAP and the most synchronous results were obtained from bGMYC, mPTP, STACEY and ASAP. We believe that these results are maximally realistic in the number of revealed mOTUs. A high genetic diversity, resulting in the existence of several mOTUs and phylogenetic lineages within many species, demonstrates the usefulness of the “polymorphic species” concept, which does not underestimate species richness and does not prevent the rational use and protection of biodiversity.