Data from: Tropical rainforest conversion and land-use intensification reduce understory plant phylogenetic diversity

1. Conversion of rainforest into agricultural land affects multiple facets of tropical plant diversity. While the effects of tropical land use change and intensification on species diversity are comparatively well studied, the effects on phylogenetic diversity and structure of plant communities are largely unknown. Furthermore, it is not clear how the loss of native species and addition of alien species collectively affect phylogenetic diversity and structure. 2. We investigated the phylogenetic diversity and structure of understorey plants; a diverse and ecologically important, yet poorly studied group. We studied four prominent land use systems (tropical lowland rainforest, jungle rubber agroforest, rubber plantations and oil palm plantations) in the lowlands of Sumatra (Indonesia), a region experiencing dramatic land use changes. 3. Across the four systems, we investigated differences in four metrics of phylogenetic community structure (phylogenetic diversity, mean pairwise distance, mean nearest taxon distance and their abundance-weighted variants). Our analyses were based on a comprehensive vegetation survey consisting of 32 plots, 1,197 species of vascular plants, and 146,599 plant individuals. 4. Our results showed that forest conversion into agricultural systems leads to a pronounced loss of phylogenetic diversity. Furthermore, the standard effect size of mean pairwise distance indicated a gradual change from clustered to overdispersed phylogenetic community structure with increasing land use intensity from forest over jungle rubber to the monoculture plantations. In most land use systems, the presence or absence of alien plant species did not affect phylogenetic structure. Only in oil palm plantations, removing alien species from the data led to a more overdispersed structure. In conclusion, conserving the phylogenetic diversity and structure requires efficient protection of the last remaining rainforests. 5. Synthesis and applications. Forest conversion into agricultural areas negatively affects phylogenetic understorey plant diversity and leads to a shift from clustered to overdispersed phylogenetic community structure. These trends are partly driven by alien species particularly in oil palm plantations. Protecting the remaining rainforests, and considering multi-species agroforestry systems in favour of intensive monoculture plantations are thus imperative to conserve phylogenetic plant diversity and community structure.

1. 热带雨林转为农业用地会对热带植物多样性的多个维度产生影响。尽管当前针对热带土地利用变化与集约化对物种多样性的影响已有较为充分的研究，但针对其对植物群落系统发育多样性（phylogenetic diversity）与系统发育群落结构（phylogenetic community structure）的影响，学界仍知之甚少。此外，本地物种丧失与外来物种新增二者共同如何作用于系统发育多样性与群落结构，目前尚无明确定论。
2. 本研究聚焦林下植物（understorey plants）这一类群多样、生态功能关键但研究相对匮乏的类群，展开系统发育多样性与群落结构相关调查。我们以正经历剧烈土地利用变革的印度尼西亚苏门答腊低地为研究区域，选取四类典型土地利用系统：热带低地雨林、丛林橡胶农林业系统、橡胶种植园与油棕种植园。
3. 针对上述四类土地利用系统，我们探究了四类系统发育群落结构指标的差异：系统发育多样性（phylogenetic diversity）、平均成对距离（mean pairwise distance）、平均最近分类单元距离（mean nearest taxon distance），以及上述指标的丰度加权变体（abundance-weighted variants）。本研究的分析基于覆盖32个样地的全面植被调查数据，涉及维管植物（vascular plants）1197种，总计146599株个体。
4. 研究结果显示，森林转为农业用地会导致系统发育多样性显著丧失。此外，平均成对距离的标准效应量（standard effect size）表明，随着土地利用强度从森林、丛林橡胶农林业系统逐步提升至单一种植园，植物群落的系统发育结构呈现出从聚集分布向过度分散分布的渐变过程。在多数土地利用系统中，外来植物物种的存在与否并未对系统发育群落结构产生显著影响；仅在油棕种植园中，移除数据中的外来物种后，群落系统发育结构会呈现出更强的过度分散特征。综上，若要保护植物系统发育多样性与群落结构，需对现存热带雨林实施高效保护。
5. 综合与应用。森林转为农业用地会对林下植物系统发育多样性产生负面影响，并导致群落系统发育结构从聚集分布向过度分散分布转变。这一变化趋势在油棕种植园中尤为显著，主要受外来物种驱动。因此，为保护植物系统发育多样性与群落结构，亟需保护现存热带雨林，并优先采用多物种农林业系统以替代集约化单一种植园。