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

Martina Weiss,Florian Leese,Hannah Weigand,Alexander M Weigand

doi:10.1002/ece3.3706

Abstract

DNA barcoding utilizes short standardized DNA sequences to identify species and is increasingly used in biodiversity assessments. The technique has unveiled an unforeseeably high number of morphologically cryptic species. However, if speciation has occurred relatively recently and rapidly, the use of single gene markers, and especially the exclusive use of mitochondrial markers, will presumably fail in delimitating species. Therefore, the true number of biological species might be even higher. One mechanism that can result in rapid speciation is hybridization of different species in combination with polyploidization, that is, allopolyploid speciation. In this study, we analyzed the population genetic structure of the polyploid freshwater snail Ancylus fluviatilis, for which allopolyploidization was postulated as a speciation mechanism. DNA barcoding has already revealed four cryptic species within A. fluviatilis (i.e., A. fluviatilis s. str., Ancylus sp. A–C), but early allozyme data even hint at the presence of additional cryptic lineages in Central Europe. We combined COI sequencing with high‐resolution genome‐wide SNP data (ddRAD data) to analyze the genetic structure of A. fluviatilis populations in a Central German low mountain range (Sauerland). The ddRAD data results indicate the presence of three cryptic species within A. fluviatilis s. str. occurring in sympatry and even syntopy, whereas mitochondrial sequence data only support the existence of one species, with shared haplotypes between species. Our study hence points to the limitations of DNA barcoding when dealing with organismal groups where speciation is assumed to have occurred rapidly, for example, through the process of allopolyploidization. We therefore emphasize that single marker DNA barcoding can underestimate the true species diversity and argue in strong favor of using genome‐wide data for species delimitation in such groups.

Highlights

Biodiversity assessments and ecological status monitoring typically depend on reliable species identification
Using genome-wide single-nucleotide polymorphism (SNPs) data, we revealed an unexpectedly high differentiation within the freshwater snail A. fluviatilis sensu stricto, which is one species of a cryptic species complex delimited by molecular taxonomy (Albrecht et al, 2006; Pfenninger et al, 2003)
The strong differentiation of three clusters was already visible in the principle component analysis (PCA)

Summary

| INTRODUCTION

Biodiversity assessments and ecological status monitoring typically depend on reliable species identification. Multilocus sequencing data as, for example, obtained by ddRAD sequencing can provide unprecedented and accurate insights into species delimitation and the process of speciation (e.g., Altermann et al, 2014; Card et al, 2016; Knowles & Carstens, 2007; Weisrock et al, 2010; Yang & Rannala, 2010) These methods can be highly useful when dealing with taxa, where taxonomy is complicated like in the form group Ancylus fluviatilis We further discuss potential evolutionary scenarios and general implications for species assignments using mitochondrial gene markers in cases of rapid or ongoing speciation

| MATERIALS AND METHODS

| DISCUSSION

Findings

CONFLICT OF INTEREST