title: Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Department of Botany, The Natural History Museum, London, United Kingdom. k.james@nhm.ac.uk
authors.forename: Karen E
authors.initials: KE
authors.lastname: James
authors.forename: Harald
authors.initials: H
authors.lastname: Schneider
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Ansell
authors.forename: Margaret
authors.initials: M
authors.lastname: Evers
authors.forename: Lavinia
authors.initials: L
authors.lastname: Robba
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Uszynski
authors.forename: Niklas
authors.initials: N
authors.lastname: Pedersen
authors.forename: Angela E
authors.initials: AE
authors.lastname: Newton
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Russell
authors.forename: Johannes C
authors.initials: JC
authors.lastname: Vogel
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
mesh_terms: D005075:Biological Evolution; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D012106:Research
chemical_list: D005819:Genetic Markers