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