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

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.

对分布于澳大利亚西南部干旱梯度带的268株萨卢伯桉（Eucalyptus salubris）开展全基因组多样性阵列测序（DArTseq）扫描，结果揭示了其隐秘种群结构，该结构暗示了此前未被认知的生态型分化与基因流障碍。本研究从9个种群中各采集30份野生个体开展全基因组扫描，并针对每个种群的10个个体测定了其生长习性与功能性状。DArTseq共获得16122个高质量分子标记，其中56.3%的标记可定位至大桉（Eucalyptus grandis）的染色体上。9个种群的遗传亲缘关系与地理距离仅呈弱相关；相反，这些种群可划分为两个截然不同的分子谱系，二者在地理重叠区域仍保持了遗传分化特征。共有24个异常位点标记表明这两个推定谱系受到了趋异选择并产生了遗传分化。两个谱系的种群在叶片厚度、比叶面积（specific leaf area, SLA）以及单位质量叶氮含量（leaf nitrogen per unit mass, Nmass）这三个性状上存在表型分化。分布更靠北的谱系（叶片更薄）栖息于辐射更强、更炎热干旱的生境；而分布更靠南的谱系的种群则栖息于磷含量相对较低的土壤中，对应的植株叶片更厚、比叶面积更低且单位质量叶氮含量更少，这与低养分条件下的通用响应模式相符。尽管历史隔离与遗传漂变可能促成了本次观测到的隐秘种群结构，但现有证据表明存在生态型适应，这或许为基因流构成了外源障碍。本研究彰显了新型分子技术在解析野生种群遗传架构方面的强大潜力，可为野生种群的遗传结构研究提供全新视角。