Data from: A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled eighteen lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within a small geographical area. The results showed highly diverse communities non-randomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity approach shared similar patterns and were primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies for microorganisms.

将系统发育（phylogenetic）数据与分布及生态记录相结合，以解析自然群落在演化视角下的组织规律，正日益成为学界的研究热点。在微生物研究领域，同样亟需突破存在争议的物种定义桎梏，借助遗传数据深入挖掘生态模式。本研究依托高海拔湖泊区域数据集的细菌16S rRNA基因（16S rRNA gene）信息，探究演化与系统发育和群落生态学之间的关联；研究未依赖特定的操作分类单元（operational taxonomic unit，OTU）定义，而是通过演化亲缘关系，刻画了群落的系统发育组成、空间分布、β多样性（β-diversity）及生物地理模式。高海拔湖泊区域通常由大量高度多样化的小型水体镶嵌构成，是空间邻近但环境异质性显著的生态系统的优质生物地理模型。研究团队在比利牛斯山脉选取了18个湖泊，采样标准以在较小地理范围内捕捉最大环境异质性为核心目标。研究结果显示，群落多样性极高且分布非随机，其β多样性模式主要受环境因素调控，而非空间距离影响。基于细菌分类组成与系统发育β多样性分析的群落相似性模式高度一致，且均主要受相似的环境驱动因子调控。研究发现湖泊面积与系统发育多样性呈正相关关系，其斜率特征与扩散能力极强的浮游生物相符。系统发育分析方法将共同祖先演化模式纳入细菌群落分析，可直接用于生物群系间及生物群系内的生物多样性比较，还能有效区分微生物生境，在微生物保护研究中具备良好的应用潜力。