Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses

Abstract

DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic distance threshold that distinguishes between-species divergence from within-species diversity. Recently developed species delimitation methods based on the multispecies coalescent (MSC) model offer an alternative approach to individual assignment using either single-locus or multiloci sequence data. Here, we use simulations to demonstrate three features of an MSC method implemented in the program bpp. First, we show that with one locus, MSC can accurately assign individuals to species without the need for arbitrarily determined distance thresholds (as required for barcoding methods). We provide an example in which no single threshold or barcoding gap exists that can be used to assign all specimens without incurring high error rates. Second, we show that bpp can identify cryptic species that may be misidentified as a single species within the library, potentially improving the accuracy of barcoding libraries. Third, we show that taxon rarity does not present any particular problems for species assignments using bpp and that accurate assignments can be achieved even when only one or a few loci are available. Thus, concerns that have been raised that MSC methods may have problems analysing rare taxa (singletons) are unfounded. Currently, barcoding methods enjoy a huge computational advantage over MSC methods and may be the only approach feasible for massively large data sets, but MSC methods may offer a more stringent test for species that are tentatively assigned by barcoding.

Veronica officinalis Product Authentication Using DNA Metabarcoding and HPLC-MS Reveals Widespread Adulteration with Veronica chamaedrys

“…Setting the clustering threshold to 100% yielded 1572 MOTUs, 99% yielded 824 MOTUs, and 97% yielded only 287 MOTUs. The low number of MOTUs obtained using the 97% clustering threshold is likely the result of multiple species being grouped together into the same MOTU as 3% divergence far exceeds interspecific variation in many genera (Yang and Rannala, 2017). Setting the clustering threshold to 100%, on the other hand, likely resulted in more than one MOTU being formed for a single taxonomic species as a result of infraspecific variation and/or sequencing errors between reads.…”

Unraveling the diversification and systematic puzzle of the highly polymorphicPsammobates tentorius(Bell, 1828) complex (Reptilia: Testudinidae) through phylogenetic analyses and species delimitation approaches

“…The MSC model‐based species delimitation approach seems useful for delineating putative species, as it outperforms the simple distance threshold‐based DNA barcoding methods (Yang & Rannala, ). However, a simulation‐based study found that the MSC species delimitation approach identifies genetic structure rather than species, resulting in an inflated estimation of the number of species (Sukumaran & Knowles, ).…”

“…The MSC model-based species delimitation approach seems useful for delineating putative species, as it outperforms the simple distance threshold-based DNA barcoding methods (Yang & Rannala, 2017).…”

Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon

“…We retained all singleton cytb haplotypes for these analyses (i.e. haplotypes that were represented by one sample), as BPP has been shown to be robust to the inclusion of species represented by a single individual [65]. Following standard approaches [16, 66] we conducted four BPP analyses using different combinations of diffuse population size (θ) and divergence time (τ) priors to evaluate the sensitivity of analyses to variation in these parameters.…”