RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

Abstract

Species delimitations is problematic in many cases due to the difficulty of evaluating predictions from species hypotheses. In many cases delimitations rely on subjective interpretations of morphological and/or DNA data. Species with inadequate genetic resources needed to answer questions regarding evolutionary relatedness and genetic uniqueness are particularly problematic. In this study, we demonstrate the utility of restriction site associated DNA sequencing (RAD-seq) to objectively resolve unambiguous phylogenetic relationships in a recalcitrant group of deep-sea corals with divergences >80 million years. We infer robust species boundaries in the genus Paragorgia by testing alternative delimitation hypotheses using a Bayes Factors delimitation method. We present substantial evidence rejecting the current morphological species delimitation model for the genus and infer the presence of cryptic species associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences cannot be assessed in terms of absolute time, but are contingent on taxon-specific factors. We show that classical taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypotheses. Our results lead the way for addressing further questions in marine biogeography, community ecology, population dynamics, conservation, and evolution.

RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs

“…To analyze many small sequence fragments, covering the whole genome for many samples at low costs is a great advantage compared to traditional techniques. Our study confirms the utility of RAD sequencing data in resolving difficult phylogenetic problems where standard "fast-evolving" markers have failed, joining several other examples (e.g., Jones et al, 2013;Wagner et al, 2013;Eaton & Ree, 2013;Wang et al, 2013;Escudero et al, 2014;Hipp et al, 2014;Ebel et al, 2015;Herrera & Shank, 2016;Mort et al, 2015;Vargas et al, 2017). We proved that RAD sequencing is a suitable tool to work on the species level as well as within and between subgenera in the genus Salix.…”

“…This method combines enzymatic fragmentation of genomic DNA with high-throughput sequencing methods. Established mainly for population genetics (Baird et al, 2008;Baxter et al, 2011), it is nowadays used for species delimitation in closely related groups (e.g., Herrera & Shank, 2016;Pante et al, 2015;Wang et al, 2013) as well as genus-wide analyses (e.g., Eaton & Ree, 2013;Vargas, Ortiz, & Simpson, 2017). Also deep-scale phylogenies are possible using RAD sequencing data (Eaton, Springs, Park, & Donoghue, 2017).…”

“…Many recent studies have used RAD sequencing data to resolve phylogenetic relationships in groups where Sanger sequence-based data have failed due to insufficient variation (e.g., Eaton & Ree, 2013;Herrera & Shank, 2016;Jones, Fan, Franchini, Schartl, & Meyer, 2013;Wagner et al, 2013). Therefore, RAD sequencing seems a promising tool to resolve relationships within complicated genera like willows (Salix).…”

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

“…Cruaud et al, 2014;Herrera and Shank, 2015;Leaché et al, 2015). Yet some studies have shown that gathering a suitable set of phylogenetically informative markers from RAD-seq data relies on the ability to discover enough orthologous loci among the species under study, which largely depends on divergence times between lineages and filtering and assembly parameters applied for orthology inference (Jones et al, 2013;Leaché et al, 2015;Rubin et al, 2012;Wagner et al, 2013).…”

Large-Scale Genotyping-by-Sequencing Indicates High Levels of Gene Flow in the Deep-Sea Octocoral Swiftia simplex (Nutting 1909) on the West Coast of the United States

“…RAD-tag sequencing has been effectively used in studies of phylogeography and population genomics [29, 30] to show low but significant variation amongst groups indistinguishable with other marker types [31–33], reveal local selection [34], and detect cryptic species [7, 8]. The goals of this study were twofold: to develop novel molecular resources for the study of the ecology of Swiftia simplex through RAD-tag sequencing, and to apply the SNPs developed in this process to define the population structure and connectivity of this species across a portion of the United States West Coast.…”