Species delimitation in the presence of strong incomplete lineage sorting and hybridization: lessons fromOphioderma(Ophiuroidea: Echinodermata)

Abstract

Accurate species delimitation is essential to properly assess biodiversity, but also for management and conservation purposes. Yet, it is not always trivial to accurately define species boundaries in closely related species, as strong incomplete lineage sorting might still be present. Additional difficulties may be caused by hybridization, now evidenced as a frequent phenomenon. Here, we propose a three-step framework for species delimitation and divergence history inference: i) unsupervised species discovery based on multilocus genotypes; ii) species validation using the multi-species coalescent; iii) divergence scenario testing (including gene flow) using Approximate Bayesian Computation (ABC) methods. To test this framework, we used the brittle star cryptic species complex Ophioderma longicauda that encompasses six mitochondrial lineages, including broadcast spawners and internal brooders. 30 sequence markers Our study shows that despite strong incomplete lineage sorting and complex speciation history, accurate species delimitation is possible using a three-step framework combining complementary methods.

Too strict or too loose? Integrative taxonomic assessment of Bombus lapidarius complex (Hymenoptera: Apidae)

“…genetic divergence with or without reciprocal monophyly) was regarded as a strong evidence of speciation between taxa (Lecocq, Dellicour, et al, ). Although a reciprocal monophyly between taxa in mitochondrial and nuclear phylogeny is a stronger evidence of potential speciation, it was not considered as minimal condition to detect speciation process because a recent speciation event can result in an incomplete lineage sorting (Weber, Stöhr, & Chenuil, ). Moreover, mitochondrial and nuclear differentiations between geographically overlapping taxa (when physical barrier cannot explain the genetic distinctness) were considered as a more conclusive evidence of speciation process than the same differentiated between allopatric taxa.…”

BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries

“…Operational errors include morphology‐based misidentifications, cross‐contamination of samples, mislabelling, accidental mistakes when recording data, among others (Packer et al., 2009; Pentinsaari et al, 2019; Rulik et al., 2017). Possible biological reasons for discordances include recently diverged species and incomplete lineage sorting, introgression, insufficient discrimination capacity of the barcode marker, phenotypic plasticity, among others (Costa & Antunes, 2012; Lin et al., 2018; Weber et al., 2019; Weigand et al., 2011). Although some data quality assurance and quality control (QA/QC) criteria have been implemented upstream and along the DNA barcode production workflow (e.g., Hanner, 2005), no comprehensive tool for downstream quality control of the taxonomic accuracy in DNA barcode reference libraries is available to check QA/QC in a standardized way.…”

The African timber tree Entandrophragma congoense (Pierre ex De Wild.) A.Chev. is morphologically and genetically distinct from Entandrophragma angolense (Welw.) C.DC

“…Main factors as environment, phenology, growth stage can affect phenotypic variability among species (Poorter 1999;Tarasjev et al 2009). Using molecular methods can help but they have their own drawbacks, for example hybridization can blur the delineation of species boundaries (Duminil and Di Michele 2009;Ley and Hardy 2017;Weber et al 2017). Accordingly, applying an approach integrating morphological and genetic data is generally necessary to unravel species delimitation.…”