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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Claims 7
Claim · model-written summary
DArT recovered 1349 markers in A. viride.
- Taxon
- Asplenium viride
Asplenium viridee0 - Outcome
- markers of largely low copy-number locie0
- Value
- 1349 markerse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”
Claim · model-written summary
DArT recovered 1349 markers in G. elegans.
- Taxon
- Garovaglia elegans
Garovaglia eleganse0 - Outcome
- markers of largely low copy-number locie0
- Value
- 1349 markerse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”
Claim · model-written summary
Sequencing 148 DArT markers identified 30 putative loci.
- Taxon
- plantsViridiplantaee0
- Outcome
- putative locie0
- Value
- 30 putative locie0
Verbatim
e0“Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants.”
Claim · model-written summary
Four identified loci are routinely sequenced for plant evolutionary studies.
- Taxon
- plantsViridiplantaee0
- Outcome
- routinely sequenced for evolutionary studies in plantse0
- Value
- foure0
Verbatim
e0“Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants.”
Claim · model-written summary
DArT genotypes showed phylogeographic and substrate specificity patterns in A. viride.
- Taxon
- A. virideAsplenium viridee0
- Outcome
- phylogeographic and substrate specificity patternse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride”
Claim · model-written summary
DArT genotypes showed no phylogeographic pattern in Australian G. elegans.
- Taxon
- G. elegansGarovaglia eleganse0
- Outcome
- lack of phylogeographic patterne0
- Setting
- Australiane0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a lack of phylogeographic pattern in Australian G. elegans”
Claim · model-written summary
DArT revealed additive variation in hybrid or mixed samples.
- Taxon
- Asplenium virideAsplenium viridet0
- Outcome
- additive variation in hybrid or mixed samplese0
Not reportedValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“and additive variation in hybrid or mixed samples.”
t0“the diploid fern Asplenium viride and the haploid moss Garovaglia elegans”