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.

受特殊地质历史影响，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，使得该区域在相对狭小的空间尺度内形成了高度异质性的生境。柿属（Diospyros，柿科Ebenaceae）的20余个特有物种类群，在经历单次长距离扩散事件后，于该群岛快速发生了新近辐射演化。该辐射类群中的多数柿属物种在形态与生态特征上已形成显著分化，但DNA序列变异水平却较低。为探究驱动该类群多样化的潜在过程，本研究采用了限制性位点关联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（single nucleotide polymorphism, SNP）基本验证了现有物种界定方案，并构建了支持度良好的系统发育树。分析结果显示该类群存在局部基因渐渗现象，但长距离基因交流的潜力较为有限。系统发育关系表明，种群与物种间存在早期的区域聚类特征，提示针对大生境（即气候条件）的异域物种形成可能参与了该类群的初始分化过程。后续发生的更为快速的辐射演化，则涉及微生境（即土壤偏好）维度的分化。该类群中的若干姊妹物种在土壤生境偏好上呈现出平行分化的格局。针对这种重复出现的表型分化所对应的基因组区域进行筛查，发现了一批可能参与离子结合与细胞转运过程的基因位点。这些位点在适应重金属与矿物质含量存在差异的土壤类型时具有重要的适应意义。仅有两个此类位点发生了相同的核苷酸变异，说明基因渐渗在其演化历程中仅发挥了有限作用。本研究结果表明，异域多样化与（邻域）生态分化共同塑造了新喀里多尼亚群岛柿属辐射演化过程中的多轮物种形成事件。