Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete

Abstract

Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgression between several of the incipient species. Next generation sequencing data may help to overcome some of these problems. We evaluated methods for species delimitation based on genome-wide markers in a land snail radiation on Crete. Species delimitation in the Albinaria cretensis group was based exclusively on shell characters until now and resulted in classifications distinguishing 3–9 species. We generated sequences of 4270 loci for 140 specimens of the Albinaria cretensis group from 48 populations by double-digest restriction site-associated DNA sequencing. We evaluated three methods for species discovery. The multispecies coalescent approach implemented in the program Bayesian Phylogenetics and Phylogeography resulted in a drastic overestimating of the number of species, whereas Gaussian clustering resulted in an overlumping. Primary species hypotheses based on the maximum percentage of the genome of the individuals derived from ancestral populations as estimated with the program ADMIXTURE moderately overestimated the number of species, but this was the only approach that provided information about gene flow between groups. Two of the methods for species validation that we applied, BFD* and delimitR, resulted in an acceptance of almost all primary species hypotheses, even such based on arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast, secondary species hypotheses, resulting from an evaluation of primary species hypotheses based on ADMIXTURE with isolation by distance tests, approached the morphological classification, but also uncovered two cryptic species and indicated that some of the previously delimited units should be combined. Thus, we recommend this combination of approaches that provided more detailed insights in the distinctness of barriers between the taxa of a species complex and the spatial distribution of admixture between them than the other methods. The recognition and delimitation of undersampled species remained a major challenge.

Diversity of Siphonaria Sowerby I, 1823 (Gastropoda, Siphonariidae) in the Seychelles Bank and beyond

“…The PTP approach (Zhang et al, 2013) subdivided the Siphonaria data set also into a quite high number of primary species hypotheses (89). Overestimations of the number of species by these tree-based approaches have also been observed in several other empirical studies (Bamberger et al, 2022;Puillandre et al, 2021;Sauer & Hausdorf, 2012;Talavera et al, 2013). Thus, the over-splitting by these approaches can probably not be exclusively attributed to badly reconstructed trees in the case of our Siphonaria data set.…”

Hierarchical heuristic species delimitation under the multispecies coalescent model with migration

“…(2020) analyzed 99 population pairs in the genus Drosophila and found that bpp identified 80 pairs as distinct species, whereas reproductive isolation was identified in only 69 pairs. Similarly, Bamberger et al . (2022) examined 48 Albinaria cretensis land snail populations, and found that morphological classifications suggested 3–9 species while bpp suggested 45–48.…”

“…For example, Campillo et al (2020) analyzed 99 population pairs in the genus Drosophila and found that bpp identified 80 pairs as distinct species, whereas reproductive isolation was identified in only 69 pairs. Similarly, Bamberger et al (2022) examined 48 Albinaria cretensis land snail populations, and found that morphological classifications suggested 3-9 species while bpp suggested 45-48. Barley et al (2018) simulated multiple populations from a single species that exhibits population structure and isolation by distance, and found that bpp delimits geographically separated populations as distinct species.…”

Metazoa‐level USCOs as markers in species delimitation and classification

“…They have been applied to a wide range of systems, in particular as a validation method in integrative species delimitation analyses (e.g. Bacon et al, 2012;Bamberger et al, 2022;Carstens et al, 2013).…”