Use of RAD sequencing for delimiting species

Abstract

RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as 470% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity.

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

“…'s (2014) cetacean study are more promising in the applicability of RADseq to studies of divergent species, while Pante et al. (2015) findings of lower than 30% shared loci in octocoral species that diverged only 1–2 mya offer a cautionary note. Ultimately, pilot testing of RADseq protocols across multiple study species is necessary to evaluate their potential for generation of large‐scale SNP datasets for interspecific analyses.…”

“…These studies, using both simulated and empirical data, have quantified the number of retained homologous loci among species with varying divergence dates. Simulations suggest that hundreds of orthologous, phylogenetically informative loci can be identified in species with divergence times of up to 60 million years (Cariou, Duret, & Charlat, 2016a,2016b; Rubin, Ree, & Moreau, 2012), but empirical studies have successfully applied RADseq to phylogenetic studies of species only from more recent radiations (<100,000 years; Keller et al., 2013; Wagner et al., 2013) and find that the number of shared SNPs drops, sometimes quickly, as divergence dates increase (Lexer et al., 2013; Pante et al., 2015). Among our two studied seal species, harbor and gray, that diverged approximately 5 mya (Arnason et al., 2006), we found over 100,000 homologous RAD loci.…”

“…Among our two studied seal species, harbor and gray, that diverged approximately 5 mya (Arnason et al., 2006), we found over 100,000 homologous RAD loci. This level of observed overlap is comparable and intermediate to that which has been previously described for other interspecific comparisons (Lexer et al., 2013; Pante et al., 2015; Viricel, Pante, Dabin, & Simon‐Bouet, 2014). For example, in one other RADseq study of two marine mammals, Viricel et al.…”

“…The variation in how quickly the number of homologous RAD loci declines with increasing divergence between species could be due to differences in sequencing protocols or analytical pipelines (though Pante et al. (2015) reports little change in the number of homologous loci across multiple pipelines), but more likely reflects true differences in rates of molecular evolution across lineages. Our pinniped study and Viricel et al.…”

Unexpected mosaic distribution of two hybridizing sibling lineages in the teleplanically dispersing snail Stramonita haemastoma suggests unusual postglacial redistribution or cryptic invasion

“…There is little need to discuss at length the discovery of cryptic lineages with molecular markers as this observation is pervasive in the sea (Appeltans et al., 2012; Knowlton, 1993; Pante, Abdelkrim, et al., 2015; Pante, Puillandre, et al., 2015). However, the geographic distribution of molecularly identified cryptic lineages is usually compatible with vicariant divergence between well recognized biogeographic regions, especially when the divergence is recent and hybridization happens in the contact zone.…”