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

Gonen S, Bishop SC, Houston RD - BMC Res Notes (2015)

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK. Serap.gonen@roslin.ed.ac.uk.

ABSTRACT

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.

No MeSH data available.


Expected evolutionary relationships as defined by Near et al. [49] and Shedko et al. [48]. Species images were taken from http://en.wikipedia.org/ or are published for open access use. Divergence times and branch lengths not drawn to scale. Divergence estimates for the non-salmonid teleost fish species were obtained from Near et al. [49], and divergence estimates for the salmonid species were obtained from Shedko et al. [48].
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Fig1: Expected evolutionary relationships as defined by Near et al. [49] and Shedko et al. [48]. Species images were taken from http://en.wikipedia.org/ or are published for open access use. Divergence times and branch lengths not drawn to scale. Divergence estimates for the non-salmonid teleost fish species were obtained from Near et al. [49], and divergence estimates for the salmonid species were obtained from Shedko et al. [48].

Mentions: To our knowledge, the most comprehensive study of teleost phylogeny is that described in Near et al. [49] (232 fish species; nine coding sequences and fossil calibration times). Based on this phylogeny and the salmonid species relationships described in Shedko et al. [48], the expected relationships between the ten teleost species in the current study are given in Figure 1.Figure 1


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

Gonen S, Bishop SC, Houston RD - BMC Res Notes (2015)

Expected evolutionary relationships as defined by Near et al. [49] and Shedko et al. [48]. Species images were taken from http://en.wikipedia.org/ or are published for open access use. Divergence times and branch lengths not drawn to scale. Divergence estimates for the non-salmonid teleost fish species were obtained from Near et al. [49], and divergence estimates for the salmonid species were obtained from Shedko et al. [48].
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4495686&req=5

Fig1: Expected evolutionary relationships as defined by Near et al. [49] and Shedko et al. [48]. Species images were taken from http://en.wikipedia.org/ or are published for open access use. Divergence times and branch lengths not drawn to scale. Divergence estimates for the non-salmonid teleost fish species were obtained from Near et al. [49], and divergence estimates for the salmonid species were obtained from Shedko et al. [48].
Mentions: To our knowledge, the most comprehensive study of teleost phylogeny is that described in Near et al. [49] (232 fish species; nine coding sequences and fossil calibration times). Based on this phylogeny and the salmonid species relationships described in Shedko et al. [48], the expected relationships between the ten teleost species in the current study are given in Figure 1.Figure 1

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK. Serap.gonen@roslin.ed.ac.uk.

ABSTRACT

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.

No MeSH data available.