Data from: Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia

Phylogeographic patterns of trees in topographically subdued, unglaciated landscapes are under-reported, and might reflect population persistence and the influences of environment and distance over historical (~2.6Mya-present) and contemporary (recent generations) time-scales. We examined this hypothesis using genetic analyses of four slowly evolving non-coding chloroplast sequences and 16 nuclear microsatellites in the tree Corymbia calophylla from south-western Australia that has been unglaciated since the Permian (.300-250Mya). We found strong population differentiation for chloroplast DNA and low differentiation for nuclear loci, consistent with higher gene flow by pollen than seed. We identified three divergent chloroplast lineages distributed in central, north and south geographic regions, and diversifying from the early (.3.028Mya), mid- (.0.793Mya) and late- (.0.426Mya) Pleistocene, respectively. Moderate-high nucleotide diversity with population-specific haplotypes supported long-term persistence but diversification of lineages provided evidence of unexpected episodic range expansion. We suggest this pattern reflects environmental influences of climatic oscillations during progressive drying of south-western Australia from the early Pleistocene. Significant tests for isolation by environment for nuclear loci also supported an influence of contemporary environmental (aridity) conditions on genetic structure, but isolation by distance (IBD) was greater. Significant chloroplast and nuclear IBD suggested distance was a major influence on gene flow at both time-scales.

地形平缓且未经历冰川作用的林地的系统发生生物地理学（phylogeographic）格局相关研究仍较为匮乏，此类格局或可反映种群存续状态，以及环境与地理距离在历史（约260万年前至今）和当代（近世代）时间尺度上的综合影响。本研究以澳大利亚西南部自二叠纪（约3亿至2.5亿年前）起便未受冰川作用影响的美叶伞房桉（Corymbia calophylla）为研究对象，通过对4个缓慢演化的非编码叶绿体序列以及16个核微卫星进行遗传分析，对上述假说展开验证。研究结果显示，叶绿体DNA呈现显著的种群分化，而核基因座的分化程度较低，这与花粉介导的基因流强于种子的结论相符。本研究共鉴定出3个分化显著的叶绿体谱系，分别分布于中部、北部和南部地理区域，其分化时间分别为更新世早期（约302.8万年前）、中期（约79.3万年前）和晚期（约42.6万年前）。具有种群特异性单倍型的中至高核苷酸多样性，佐证了该物种种群的长期存续；而谱系分化则揭示了此前未被预见的阶段性种群范围扩张事件。我们认为，此类格局反映了更新世早期以来澳大利亚西南部持续干旱化过程中，气候波动所带来的环境影响。核基因座的环境隔离（isolation by environment, IBE）检验结果显著，证实当代环境（干旱程度）条件对遗传结构存在影响，但地理距离隔离（isolation by distance, IBD）的影响更为显著。叶绿体与核基因组的地理距离隔离检验结果均显著，表明地理距离在两个时间尺度上均为基因流的主要影响因素。