Testing Classical Species Properties with Contemporary Data: How “Bad Species” in the Brassy Ringlets (Erebia tyndaruscomplex, Lepidoptera) Turned Good

Abstract

All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods (1) rely on simplified demographic models that may fail to capture some attributes of biological species, (2) do not make explicit use of the geographic information contained in the data, and (3) are often computationally intensive. In this article, we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We (1) obtained restriction-site associated DNA (RAD) sequencing data from a carefully designed sample, (2) applied two genotype clustering algorithms to identify genetic clusters, and (3) performed within-clusters and between-clusters analyses of isolation by distance as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes factor delimitation coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analyzed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.

Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko

“…The use of genetic data to study variation among populations and delimit species has provided unprecedented insight into the patterns and processes of speciation (Casillas and Barbadilla, 2017, Domingos et al, 2017, Gratton et al, 2015, Harvey et al, 2017, Lemmon et al, 2012, McKay et al, 2013, Nazareno et al, 2017a, Nazareno et al, 2017b, Weir et al, 2015. Genetic data have been particularly useful in the investigation of poorly-studied taxa from Neotropical regions, such as Amazonia (Angulo andIcochea, 2010, Antonelli et al, 2011).…”

Deciphering range dynamics: effects of niche stability areas and post‐glacial colonization on alpine species distribution

“…Here, we adopted a conservative approach, considering the tyndarus complex composed by only two taxa: the Ponto‐Mediterranean ( Erebia PM) clade and the Euro‐Siberian ( Erebia ES) clade ( sensu Albre et al ., ). A recent re‐analysis of E. tyndarus complex, limited to the ES ‘terminal’ clade ( E. tyndarus , E. cassioides , E. nivalis and E. calcaria ) based on nucleotide sequence variation at genome‐wide markers and morphometry, confirmed the ‘traditional’ four‐species taxonomy (Gratton et al ., ). However, all these taxa show a strictly parapatric distribution with overlaps confined to narrow contact zones, indicating that some degree of competitive exclusion is likely and, hence, also some niche similarity.…”

“…Within the Erebia tyndarus complex, very different numbers of species were recognized by different authors (Descimon & Mallet, 2009). Here, we adopted a conservative approach, considering the tyndarus complex composed by only two taxa: the Ponto-Mediterranean (Ere- sioides, E. nivalis and E. calcaria) based on nucleotide sequence variation at genome-wide markers and morphometry, confirmed the 'traditional' four-species taxonomy (Gratton et al, 2016). However, all these taxa show a strictly parapatric distribution with overlaps confined to narrow contact zones, indicating that some degree of competitive exclusion is likely and, hence, also some niche similarity.…”

Speciation in a biodiversity hotspot: phylogenetic relationships, species delimitation, and divergence times of the Patagonian ground frogs ofEupsophus roseusgroup (Alsodidae)

“…Although the importance of species concepts debate [7,8], and that the species as taxonomic hierarchy is also considered a fundamental topic in biology [9], it is broadly accepted that species are best conceptualized as dynamic entities, connected by “grey zones” where their delimitation will remain inherently ambiguous [4,10]. Under this perspective, species delimitation, i.e.…”