Data from: Processes driving the adaptive radiation of a tropical tree (Diospyros, Ebenaceae) in New Caledonia, a biodiversity hotspot

Due to its special geological history, the New Caledonian Archipelago is a mosaic of soil types, and in combination with climatic conditions this results in a heterogeneous environment across relatively small distances. A group of over 20 endemic species of Diospyros (Ebenaceae) has rapidly and recently radiated on the archipelago after a single long-distance dispersal event. Most of the Diospyros species in the radiating group are morphologically and ecologically well differentiated, but they exhibit low levels of DNA variability. To investigate the processes that shaped the diversification of this group we employed restriction site associated DNA sequencing (RADseq). Over 8,400 filtered SNPs generally confirm species delimitations and produce a well-supported phylogenetic tree. Our analyses document local introgression, but only a limited potential for gene flow over longer distances. The phylogenetic relationships point to an early regional clustering among populations and species, indicating that allopatric speciation with respect to macrohabitat (i.e., climatic conditions) may have had a role in the initial differentiation within the group. A later, more rapid radiation involved divergence with respect to microhabitat (i.e., soil preference). Several sister species in the group show a parallel divergence in edaphic preference. Searches for genomic regions that are systematically differentiated in this replicated phenotypic divergence pointed to loci potentially involved in ion binding and cellular transport. These loci appear meaningful in the context of adaptations to soil types that differ in heavy-metal and mineral content. Identical nucleotide changes affected only two of these loci, indicating that introgression may have played a limited role in their evolution. Our results suggest that both allopatric diversification and (parapatric) ecological divergence shaped successive rounds of speciation in the Diospyros radiation on New Caledonia.

由于特殊的地质历史背景，新喀里多尼亚群岛（New Caledonian Archipelago）的土壤类型呈现镶嵌分布格局，结合当地气候条件，使得该区域在极小空间尺度内便形成了异质化生境。一类包含20余种柿属（Diospyros，柿科Ebenaceae）特有物种的类群，在经历单次长距离扩散事件后，于该群岛上发生了快速且近期的辐射演化。该辐射类群中的多数柿属物种在形态学与生态学上均已形成显著分化，但它们的DNA序列变异水平却极低。

为探究塑造该类群物种多样化的潜在过程，本研究采用了限制性位点相关DNA测序（restriction site associated DNA sequencing, RADseq）技术。经筛选得到的8400余个单核苷酸多态性位点（SNPs）总体上验证了物种划分方案，并构建出支持度较高的系统发育树。分析结果显示存在局部基因渐渗（introgression）现象，但该类群在长距离范围内的基因交流潜力却十分有限。

系统发育关系揭示了种群与物种间早期的区域聚类模式，表明基于大生境（即气候条件）的异地物种形成（allopatric speciation）可能在该类群的初始分化中发挥了作用。后续发生的更为快速的辐射演化，则涉及基于小生境（microhabitat）的适应性分化，具体体现为土壤偏好的差异。该类群中的多个姊妹物种（sister species）均表现出土壤偏好方面的平行分化现象。

针对这一重复出现的表型分化现象，我们对系统性分化的基因组区域进行了筛查，发现了若干可能与离子结合及细胞转运相关的基因位点。这些位点在适应重金属与矿物质含量各异的土壤环境过程中具有明确的生物学意义。仅其中两个位点存在一致的核苷酸变异，这表明基因渐渗在其演化过程中仅起到了有限的作用。

本研究结果表明，异地多样化与（邻域）生态分化共同塑造了新喀里多尼亚群岛上柿属辐射演化的多轮物种形成事件。