Abstract
In the context 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 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 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, and (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 data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.
Highlights
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
GMYC and PTP require as input a phylogeny of taxa estimated from DNA sequences: GMYC uses the topology of a tree to identify the maximum likelihood solution separating the branches between species modelled by a Yule process and the branches within species modelled by neutral coalescent (Fujisawa & Barraclough, 2013); PTP finds the transition point between intra- and inter-specific processes assuming a two parameter model that accounts for speciation and for the coalescent process based on the Poisson distribution of branch lengths (Zhang et al, 2013; Kapli et al, 2017)
The aim of the study is to analyse the influence of data-related factors on the efficiency of six molecular species delimitation methods
Summary
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. 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. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. 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. In the context of the rapid impoverishment of global biodiversity (Hallmann et al, 2017; Sánchez‐Bayo & Wyckhuys, 2019; Van Klink et al, 2020), it is easy to understand the reason of the success of molecular taxonomy that, exploiting molecular information, has the potential to accelerate the identification of organisms and the discovery process of new taxa
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