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

BMC Research Notes

Ross D Houston¹  Stephen C Bishop¹  Serap Gonen¹ 

[1]The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, Scotland, UK

关键词: Orthology;    Comparative mapping;    Teleost phylogeny;    RAD-sequencing;   

Others  :  1231575
DOI  :  10.1186/s13104-015-1261-2

 received in 2015-03-06, accepted in 2015-06-25,  发布年份 2015

【 摘 要 】

Background

Restriction 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.

Results

The 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.

Conclusion

Overall, 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.

【 授权许可】

   
2015 Gonen et al.

【 图 表 】

Figure1.

Figure2.

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