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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: 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.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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Related in: MedlinePlus

Two-dimensional PCO scatter plot of the Garovaglia elegans DArT marker data set superimposed with the phylogenetic tree obtained based on cpDNA.Garovaglia powelli is included to root the phylogenetic tree. Triangles correspond to single species samples, whereas the star corresponds to a mixed sample that includes individuals of G. elegans and G. powellii.
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pone-0001682-g004: Two-dimensional PCO scatter plot of the Garovaglia elegans DArT marker data set superimposed with the phylogenetic tree obtained based on cpDNA.Garovaglia powelli is included to root the phylogenetic tree. Triangles correspond to single species samples, whereas the star corresponds to a mixed sample that includes individuals of G. elegans and G. powellii.

Mentions: DNA sequence data from chloroplast (Asplenium trnL-F, rps4-trnS; Garovaglia trnG) and nuclear (Asplenium pgiC) loci largely corroborated the results of the above analyses of Asplenium and Garovaglia DArT data (Figures 2 & 4 and unpublished data). The analysis of Garovaglia chloroplast DNA sequence data resulted in a phylogram with a clear separation of Papua New Guinean and Australian specimens (Figure 4). The same clusters were recovered using Garovaglia DArT markers. Neither cpDNA nor the highly variable DArT markers recovered any phylogeographic patterns within Australia. In a hierarchical PCO analysis procedure (step by step exclusion of more distantly related samples), no increase in the cumulative percentage explained by axes 1 and 2 was observed.


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 Garovaglia elegans DArT marker data set superimposed with the phylogenetic tree obtained based on cpDNA.Garovaglia powelli is included to root the phylogenetic tree. Triangles correspond to single species samples, whereas the star corresponds to a mixed sample that includes individuals of G. elegans and G. powellii.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001682-g004: Two-dimensional PCO scatter plot of the Garovaglia elegans DArT marker data set superimposed with the phylogenetic tree obtained based on cpDNA.Garovaglia powelli is included to root the phylogenetic tree. Triangles correspond to single species samples, whereas the star corresponds to a mixed sample that includes individuals of G. elegans and G. powellii.
Mentions: DNA sequence data from chloroplast (Asplenium trnL-F, rps4-trnS; Garovaglia trnG) and nuclear (Asplenium pgiC) loci largely corroborated the results of the above analyses of Asplenium and Garovaglia DArT data (Figures 2 & 4 and unpublished data). The analysis of Garovaglia chloroplast DNA sequence data resulted in a phylogram with a clear separation of Papua New Guinean and Australian specimens (Figure 4). The same clusters were recovered using Garovaglia DArT markers. Neither cpDNA nor the highly variable DArT markers recovered any phylogeographic patterns within Australia. In a hierarchical PCO analysis procedure (step by step exclusion of more distantly related samples), no increase in the cumulative percentage explained by axes 1 and 2 was observed.

Bottom Line: 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.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
Related in: MedlinePlus