Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family

Abstract

In the contest of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than empirical datasets, derived from a set of 7,237 COI sequences attributed to leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: i) the number of haplotypes per species (as a proxy for genetic diversity); ii) the geographic distance among conspecific collection localities (as a proxy of sampling width); iii) the difficulty related to morphological identification of species; iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the dataset was GMYC, showing lower efficiency in datasets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input datasets for species delimitation analyses to obtain a more reliable representation of biological diversity.

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

“…Also, the congruence between the different delimitation methods, although using the same data, was moderate. This is in line with graphical summaries of many DNA taxonomy studies that have shown rather inconsistent results among different species delimitation approaches using the same marker (see above; Bergsten et al, 2012; Magoga et al, 2021). However, some studies, particularly those with limited geographical (i.e., regional) scope in the northern hemisphere, showed almost perfect matches of MOTUs with morphospecies among nearly 90% of the studied species (Hendrich et al, 2015; Pentinsaari et al, 2014; Rulik et al, 2017).…”

Hidden island endemic species and their implications for cryptic speciation within soil arthropods

“…While bPTP infers 8, 6 and 5 species, respectively, ASAP delimits 5 species within Gf5, and single species within each Gf7 and Gf8. This is in agreement with previous works reporting a tendency of tree based methods to over split species within geographically structured lineages and/or lineages that are over sampled (Magoga et al, 2021; Mason et al, 2020). We evaluated morphological traits for the taxonomy of Geomitopsis in the Canary Islands at the level of the eight principle lineages within the obtained Bayesian tree (See Figure 2).…”

New insights into the genetic diversity of the Balkan bush-crickets of the Poecilimon ornatus group (Orthoptera: Tettigoniidae)

“…On the other hand, GMYC analysis reveals 26 hypothetical species among the group. The discrepancy in the results of species delimitation may indicate a greater conservatism of ASAP, ABGD, and bPTP over GMYC, which shows lower efficiency in data sets at the genus than at higher levels (Magoga et al 2021). Though spe-cies delimitation has been defined as a method that sometimes causes confusion about almost every aspect of the definition of the 'species' level (Stanton et al 2019), the problem with delineating species' boundaries at the tree top must be related to the low-level independent genetic differentiation of the third clade in our tree.…”