Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis.

Serap Gonen,Stephen C Bishop,Ross D Houston

doi:10.1186/s13104-015-1261-2

Abstract

BackgroundRestriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. RAD-Seq has been extensively utilised, both at the population level and across species, for example in the construction of phylogenetic trees. However, the consistency of RAD-Seq data generated in different laboratories, and the potential use of cross-species orthologous RAD loci in the estimation of genetic relationships, have not been widely investigated. This study describes the use of SbfI RAD-Seq data for the estimation of evolutionary relationships amongst ten teleost fish species, using previously established phylogeny as a benchmark.ResultsThe number of orthologous SbfI RAD loci identified decreased with increasing evolutionary distance between the species, with several thousand loci conserved across five salmonid species (divergence ~50 MY), and several hundred conserved across the more distantly related teleost species (divergence ~100–360 MY). The majority (>70%) of loci identified between the more distantly related species were genic in origin, suggesting that the bias of SbfI towards genic regions is useful for identifying distant orthologs. Interspecific single nucleotide variants at each orthologous RAD locus were identified. Evolutionary relationships estimated using concatenated sequences of interspecific variants were congruent with previously published phylogenies, even for distantly (divergence up to ~360 MY) related species.ConclusionOverall, this study has demonstrated that orthologous SbfI RAD loci can be identified across closely and distantly related species. This has positive implications for the repeatability of SbfI RAD-Seq and its potential to address research questions beyond the scope of the original studies. Furthermore, the concordance in tree topologies and relationships estimated in this study with published teleost phylogenies suggests that similar meta-datasets could be utilised in the prediction of evolutionary relationships across populations and species with readily available RAD-Seq datasets, but for which relationships remain uncharacterised.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1261-2) contains supplementary material, which is available to authorized users.

Highlights

Restriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets
Datasets generated by RAD-Seq using the SbfI restriction enzyme were obtained from previously published studies for ten teleost fish species
In this study, RAD-Seq datasets derived from different laboratories were utilised in the estimation of evolutionary relationships between ten teleost fish species

Summary

Introduction

Restriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. Genome-wide multi-locus data, such as those generated by RAD-Seq, are advantageous for the estimation of evolutionary relationships. This is because unlike estimates obtained by comparing a single orthologous locus across multiple species, methods to address the problem of incomplete lineage sorting using multi-locus datasets are available [4, 10,11,12,13,14]. A particular advantage of RAD-Seq is that the inference of cross-population and cross-species orthologous loci is potentially simplified by the use of the same rarecutting restriction enzyme (such as SbfI) for the digestion of genomic DNA across all included individuals. Genetic relationships estimated using RAD data have been congruent with those seen in previously published literature (e.g. see Eaton et al [4], Wang et al [16]), suggesting that RAD data could prove useful in non-model taxa for which the evolutionary relationships are unknown

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