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Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms.

James KE, Schneider H, Ansell SW, Evers M, Robba L, Uszynski G, Pedersen N, Newton AE, Russell SJ, Vogel JC, Kilian A - PLoS ONE (2008)

Bottom Line: Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns.Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, The Natural History Museum, London, United Kingdom. k.james@nhm.ac.uk

ABSTRACT

Background: High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms.

Methodology/principal findings: This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.

Conclusions/significance: These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.

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Two dimensional PCO scatter plot of the Asplenium viride DArT marker data set (triangles) plus a single specimen of A. adulterinum (star) and A. trichomanes (hexagon).Color of symbol corresponds to the substrate on which the sample was growing: limestone = white, serpentine = black and magnesit = gray. Numbers correspond to the sample number (Table 1).
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pone-0001682-g001: Two dimensional PCO scatter plot of the Asplenium viride DArT marker data set (triangles) plus a single specimen of A. adulterinum (star) and A. trichomanes (hexagon).Color of symbol corresponds to the substrate on which the sample was growing: limestone = white, serpentine = black and magnesit = gray. Numbers correspond to the sample number (Table 1).

Mentions: PCO and PCoA analyses of the Asplenium and Garovaglia DArT data sets derived from the standard DArT procedure (not subtracted) recovered a cumulative explanatory percentage for axes 1 and 2 of 72.7% for Asplenium and 73.5% for Garovaglia, the latter increasing to 100% in the exclusively Papua New Guinean sample subset, but not in the exclusively Australian subset. These DArT data enabled reconstruction of intraspecific structure in A. viride revealing phylogeographic and substrate specificity patterns (Figures 1 & 2). These patterns were not detectable in our analyses of cpDNA or nrDNA sequences, due to insufficient polymorphisms to generate a fully resolved phylogeny (data not shown). The rps4-trnS IGS contained just two polymorphic positions, while the trnL-F region had one unambiguous polymorphic nucleotide position. In both cpDNA regions, one polymorphic site separates samples Avi169 and Avi272 from the remaining samples of A. viride. Variation in the nuclear pgiC data set was similarly low, with seven unambiguous polymorphic sites each of which was specific to only one specimen (e.g. Avi69, Avi245, Avi284a).


Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms.

James KE, Schneider H, Ansell SW, Evers M, Robba L, Uszynski G, Pedersen N, Newton AE, Russell SJ, Vogel JC, Kilian A - PLoS ONE (2008)

Two dimensional PCO scatter plot of the Asplenium viride DArT marker data set (triangles) plus a single specimen of A. adulterinum (star) and A. trichomanes (hexagon).Color of symbol corresponds to the substrate on which the sample was growing: limestone = white, serpentine = black and magnesit = gray. Numbers correspond to the sample number (Table 1).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2244804&req=5

pone-0001682-g001: Two dimensional PCO scatter plot of the Asplenium viride DArT marker data set (triangles) plus a single specimen of A. adulterinum (star) and A. trichomanes (hexagon).Color of symbol corresponds to the substrate on which the sample was growing: limestone = white, serpentine = black and magnesit = gray. Numbers correspond to the sample number (Table 1).
Mentions: PCO and PCoA analyses of the Asplenium and Garovaglia DArT data sets derived from the standard DArT procedure (not subtracted) recovered a cumulative explanatory percentage for axes 1 and 2 of 72.7% for Asplenium and 73.5% for Garovaglia, the latter increasing to 100% in the exclusively Papua New Guinean sample subset, but not in the exclusively Australian subset. These DArT data enabled reconstruction of intraspecific structure in A. viride revealing phylogeographic and substrate specificity patterns (Figures 1 & 2). These patterns were not detectable in our analyses of cpDNA or nrDNA sequences, due to insufficient polymorphisms to generate a fully resolved phylogeny (data not shown). The rps4-trnS IGS contained just two polymorphic positions, while the trnL-F region had one unambiguous polymorphic nucleotide position. In both cpDNA regions, one polymorphic site separates samples Avi169 and Avi272 from the remaining samples of A. viride. Variation in the nuclear pgiC data set was similarly low, with seven unambiguous polymorphic sites each of which was specific to only one specimen (e.g. Avi69, Avi245, Avi284a).

Bottom Line: Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns.Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, The Natural History Museum, London, United Kingdom. k.james@nhm.ac.uk

ABSTRACT

Background: High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms.

Methodology/principal findings: This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.

Conclusions/significance: These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.

Show MeSH