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

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. K E Y W O R D Sgastropoda, mito-nuclear discordance, molecular species delimitation, RAD-seq

Random PCR‐based genotyping by sequencing technology GRAS‐Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes

“…In this way, GRAS-Di has the advantages of simplicity in library construction and number of SNPs. The number of SNPs is an important factor for genetic analysis because analyses with a large number of SNPs often increase the power to detect population structure, which cannot be unveiled with a limited number of molecular markers (Attard et al, 2018;Weiss, Weigand, Weigand, & Leese, 2018). This is typically the case for marine organisms, where geographically distant populations are often connected via passive larval dispersal, making it difficult to detect genetic differentiation with few SNPs (Carreras et al, 2017;DiBattista et al, 2017;Vendrami et al, 2017).…”

Individual small in-stream barriers contribute little to strong local population genetic structure five strictly aquatic macroinvertebrate taxa

“…For G. fossarum , DNA from 315 specimens from a previous study (Weiss & Leese, 2016) was used. Four ddRAD libraries were generated for D. gonocephala (containing 83, 83, 87 and 89 samples), two for A. fluviatilis (62 and 61 samples) and four for G. fossarum (92, 66, 65 and 95 (3 repeated from library 1) samples) according to the protocol described in Vendrami et al (2017), with modifications described in Weiss et al (2018) and Weigand et al (2018). An overview of the protocol with species-specific details and the general workflow is given in Appendix S1 and sample preparation details are given in Table S1.…”

“…Further, the distances between sites were chosen within the dispersal ability of all species (∼200 m), so that without a barrier, gene flow should be high. All species, including the amphipod Gammarus fossarum clade 11 (after Weiss, Macher, Seefeldt, & Leese, 2014), the planarian Dugesia gonocephala and three snail species of the Ancylus fluviatilis species complex ( A. fluviatilis I, II, III; Weiss, Weigand, Weigand, & Leese, 2018), are strictly confined to the aquatic environment (i.e., all are hololimnic) and commonly occur in rhithral streams in Europe but differ in feeding type, reproductive strategy and dispersal mode (Baršiene, Tapia, & Barsyte, 1996; Brittain & Eikeland, 1988; Burch, 1962; de Vries, 1986; Eder et al, 1995; Elliott, 2003; MacNeil, Dick, & Elwood, 1997; Minshall & Winger, 1968; Moog, 1995; Nesemann & Reischütz, 1995; Patrick, Cooper, & Uzarski, 2014; Schmidt-Kloiber & Hering, 2015).…”

Analyzing drivers of speciation in the Southern Ocean using the sea spider species complex Colossendeis megalonyx as a test case

“…New genomic tools allow to test for evidence of neutral versus adaptive divergence. With the establishment of highthroughput sequencing technologies and bioinformatics programs, these tools become accessible even for non-model species (e.g., Faircloth et al 2012;Lemmon et al 2012;Hugall et al 2015;Mayer et al 2016;Weiss et al 2018;Breinholt et al 2018). Although full genome sequencing followed by annotation and detailed analysis is the ideal method to perform genomic analyses and test for selection (e.g., Ellegren 2014;Nater et al 2015), the high costs for high-quality genomes of multiple samples limit its application.…”