Genome-wide scans reveal cryptic population structure in a dry-adapted eucalypt
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Genome-wide DArTseq scans of 268 individuals of Eucalyptus salubris, distributed along an aridity gradient in southwestern Australia, revealed cryptic population structure that appears to signal hitherto unappreciated ecotypic differentiation and barriers to gene flow. Genome-wide scans were undertaken on 30 wild-sampled individuals from each of nine populations; 10 individuals per population were measured for habit and functional traits. DArTseq generated 16,122 high-quality markers, of which 56.3 % located to E. grandis chromosomes. Genetic affinities of the nine populations were only weakly correlated with geographic distances. Rather, populations appeared to form two distinct molecular lineages that maintained their distinctiveness in an area of geographic overlap. Twenty-four outlier markers signalled divergent selection and differentiation of the two putative lineages. Populations from the two lineages were phenotypically differentiated in leaf thickness, specific leaf area (SLA) and leaf nitrogen per unit mass (Nmass). The more northerly lineage (with thinner leaves) occurred in hotter, drier conditions with higher radiation. Populations of the more southerly lineage occurred on soils that were relatively low in phosphorus; the trees had thicker leaves, lower SLA and lower leaf Nmass, consistent with general responses to low nutrient levels. While historic isolation and drift may have contributed to the cryptic population structure observed, there is evidence of ecotypic adaptation, which may provide an exogenous barrier to gene flow. This study highlights the power of new molecular technologies to provide novel insights into the genetic architecture of wild populations.
KeywordsEcotypic variation Soil phosphorus Eucalyptus Outlier analysis DArTseq Population genetics
This work was funded by a grant from the Australian National Climate Change Adaptation Research Facility (TB11 03) with additional support through the Great Western Woodlands Supersite of Australia’s Terrestrial Ecosystem Research Network and ARC Discovery Grant DP130104220. We thank: Craig Macfarlane, Nat Raisbeck-Brown, Georg Wiehl, Didier Alanoix (CSIRO Land and Water Flagship) and Anne Rick for assistance with field work; Bronwyn MacDonald, Rachel Binks and Donna Bradbury (Department of Parks and Wildlife, Western Australia), Carl Gosper (CSIRO Land and Water Flagship and Department of Parks and Wildlife, Western Australia), Paul Tilyard and Chris Burridge (University of Tasmania) for technical assistance; the project’s end-user advisory group, David Freudenberger, Gary Howling, Neil Riches and Richard Mazanec; the Western Australian Herbarium for accession of samples and assistance with and access to FloraBase data; and the Tasmanian Partnership for Advanced Computing (TPAC).
Data archiving statement
Data relating to this study is available from Dryad: doi: 10.5061/dryad.h06r3. These include Climate data, soil data, isotope data (relating to physiology), morphometric data and dominant (presence/absence) DArTseq data (including DNA sequences of each DArTseq marker).
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