Genome-wide scans reveal cryptic population structure in a dry-adapted eucalypt

Genome-wide DArTseq scans of268 individuals of Eucalyptus salubris, distributed along an aridity gradient in southwestern Australia, revealed cryptic population structure that appears to signal hitherto unappreciated ecotypic differ- entiation 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 chro- mosomes. Genetic affinities of the nine populations were only weakly correlated with geographic distances. Rather, popula- tions appeared to form two distinct molecular lineages that maintained their distinctiveness in an area of geographic over- lap. 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 radia- tion. 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 popu- lation structure observed, there is evidence of ecotypic adap- tation, which may provide an exogenous barrier to gene flow. This study highlights the power of new molecular technolo- gies to provide novel insights into the genetic architecture of wild populations.