An efficient method to find potentially universal population genetic markers, applied to metazoans

Abstract

BackgroundDespite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families.ResultsIn order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals.ConclusionsOur new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.

Species are hypotheses: avoid connectivity assessments based on pillars of sand

“…These are the cox1 gene typically used for metazoans (Bucklin et al 2011), RbcL gene sequenced for macroalgae (Leliaert et al 2014), but also other mitochondrial and nuclear genes such as ribosomal genes or 'universal' introns (e.g. Jarman et al 2002;Chenuil et al 2010;G erard et al 2013). Using a set of unlinked genetic markers, it is possible both to refine the phylogenetic relationships and to test whether specimens from the same species are able to recombine and, conversely, whether specimens from different species cannot.…”

Molecular hyperdiversity and evolution in very large populations

“…As the sampling of new species grows with the increasing pace of molecular approaches in ecology (Box 2), it is essential that efforts akin to DNA barcoding mature to include multiple nuclear loci, as in multi-locus sequence typing (MLST) used commonly in bacteria (Maiden et al 1998; Perez-Losada et al 2006), so as to appropriately interrogate the evolutionary history of organisms (Chenuil et al 2010). With hyperdiverse lineages, standard thresholds of divergence – particularly for mitochondrial loci – are unlikely to be useful yardsticks of species membership (Vences et al 2005; Hajibabaei et al 2006).…”

Population genetic structure of blue-spotted maskray Neotrygon kuhlii and two other Indo-West Pacific stingray species (Myliobatiformes: Dasyatidae), inferred from size-polymorphic intron markers

“…The rationale for expecting cross-amplification with stingrays comes from the fact that exons of a number of EPIC genes are conserved across orders in Metazoans (e.g. Chenuil et al, 2010;Palumbi et al 1991). Three stingray species among the most common at fish landing sites in the Indo-Malay-Papua archipelago in the central Indo-West Pacific (White and Dharmadi, 2007) were chosen as test species: the sharpnose stingray, Himantura gerrardi (Gray, 1851), the blue-spotted maskray, Neotrygon kuhlii (Müller and Henle, 1841) and the ribbontail stingray, Taeniura lymna (Forsskål, 1775).…”