Deciphering the origin of mito‐nuclear discordance in two sibling caddisfly species

Abstract

An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species. Application of genome sequencing, ddRAD and DNA barcoding revealed ongoing hybridization, as well as historical hybridization in Pleistocene refugia, leading us to identify introgression as the ultimate cause of the observed discordance pattern. Our novel genomic data, the discovery of a European-wide hybrid zone and the availability of established techniques for laboratory breeding make this species pair an ideal model system for studying species boundaries with ongoing gene flow.

Genome‐wide single‐nucleotide polymorphism data reveal cryptic species within cryptic freshwater snail species—The case of the Ancylus fluviatilis species complex

“…The strong differentiation of three clusters was already visible in the PCA. Comparably high proportions of variance between groups had been found in other taxa for inter‐ and not intraspecific comparisons (e.g., Christe et al., ; Stemshorn, Reed, Nolte, & Tautz, ; Weigand et al., ). The strong clustering was further confirmed with the sNMF approach (Frichot et al., ), where individual ancestry coefficients are calculated comparable to methods such as STRUCTURE (Pritchard, Stephens, & Donnelly, ).…”

“…This seems intuitive, given the complex set of, for example, diagnostic behavioral, ecological, genetic, and/or phenotypic differences we can observe among sister lineages, and which may arise at different times in the speciation process and are thus no necessities for defining the species category (de Queiroz, ). As speciation is not always correlated with morphological differentiation (Daïnou et al., ), morphological species identification can be impeded by low phenotypic differentiation or even so‐called morphological stasis, high intraspecific phenotypic variability with only the phenotypically “extreme” forms being recognizable or an inadequate set of potentially diagnostic characteristics (Bickford et al., ; Fontaneto, Giordani, Melone, & Serra, ; Weigand et al., , ). To deal with this problem, molecular markers are increasingly integrated in the process of species identification, an approach termed “DNA barcoding”.…”

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

“…Furthermore, combinations of multiple markers increase delimitation success for closely related species compared to single marker work (Dupuis, Roe, & Sperling, ). Nevertheless, as multiple markers derived from mitochondrial reads represent a single linkage group or could represent mitonuclear discordance as a result of introgression (Weigand et al., ), the use of independent nuclear markers should also be considered to resolve the presence of cryptic species (Campos‐Soto, Torres‐Pérez, & Solari, ; Miyamoto, Allard, Adkins, Janecek, & Rodney, ).…”

Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming

“…The database comprised in silico translated gene‐prediction sequences of genomic data of four Trichoptera species: Stenopsyche tienmushanensis (Luo, Tang, Frandsen, Stewart, & Zhou, ), Glossosoma conformis (Weigand et al, ), Sericostoma personatum (Weigand et al, ) and Limnephilus lunatus (Poelchau et al, ). Predicted protein sequence data were downloaded from respective repositories and fasta files concatenated using command‐line tool cat (Unix).…”

“…The database comprised in silico translated gene-prediction sequences of genomic data of four Trichoptera species: Stenopsyche tienmushanensis (Luo, Tang, Frandsen, Stewart, & Zhou, 2018), Glossosoma conformis (Weigand et al, 2018), Sericostoma personatum (Weigand et al, 2017) and Limnephilus lunatus (Poelchau et al, 2015).…”