Data from: Species co-occurrence networks show reptile community reorganization under agricultural transformation

Agricultural transformation represents one of the greatest threats to biodiversity, causing degradation and loss of habitat, leading to changes in the richness and composition of communities. These changes in richness and composition may, in turn, lead to altered species co-occurrence, but our knowledge of this remains limited. We used a novel co-occurrence network approach to examine the impact of agricultural transformation on reptile community structure within two large (>172 000 km2; 224 sites) agricultural regions in southeastern Australia. We contrasted assemblages from sites surrounded by intact and modified landscapes and tested four key hypotheses that agricultural transformation leads to (H1) declines in species richness, (H2) altered assemblages, (H3) declines in overall co-occurrence, and (H4) complex restructuring of individual species associations. We found that modified landscapes differed in composition but not richness compared with intact sites. Modified landscapes were also characterized by differences in co-occurrence network structure; with species sharing fewer sites with each other (reduced co-occurrence connectance), fewer highly-connected species (truncation of the frequency distribution of co-occurrence degree) and increased modularity of co-occurrence networks. Critically, overall loss of co-occurrence was underpinned by complex changes to the number and distribution of pair-wise co-occurrence links, with 41-44% of species also gaining associations with other species. Change in co-occurrence was not correlated with changes in occupancy, nor by functional trait membership, allowing a novel classification of species susceptibility to agricultural transformation. Our study reveals the value of using co-occurrence analysis to uncover impacts of agricultural transformation that may be masked in conventional studies of species richness and community composition.

农业转型是对生物多样性的最主要威胁之一，会造成栖息地退化与丧失，进而引发群落物种丰富度和群落组成的改变。这类丰富度与组成的变化，又可能进一步改变物种共现（species co-occurrence）模式，但目前学界对此的认知仍较为有限。本研究采用一种新颖的共现网络（co-occurrence network）分析方法，针对澳大利亚东南部两个大型农业区域（面积均超过17.2万平方千米，共包含224个调查样地），探究农业转型对爬行动物群落结构的影响。本研究对比了受原生景观与受改造景观环绕的样地中的物种组合，并检验了四项核心假说：农业转型会（H1）导致物种丰富度下降，（H2）改变群落组成，（H3）降低整体共现水平，以及（H4）引发单个物种种间关联的复杂重构。研究结果显示，与原生景观样地相比，受改造景观的群落组成存在显著差异，但物种丰富度并无明显变化。受改造景观的共现网络结构同样存在显著差异：物种间共享的样地数量更少（共现连接度降低），高度连接的物种数量更少（共现度频率分布出现截尾），且共现网络的模块化程度升高。尤为关键的是，整体共现水平的下降，源于物种种间共现关联的数量与分布发生了复杂变化：41%至44%的物种反而获得了与其他物种的新关联。共现模式的变化与物种占用率的变化、以及功能类群归属均无关联，这为我们对农业转型下的物种敏感性进行全新分类提供了可能。本研究证实，采用共现分析方法，可以揭示那些在传统物种丰富度与群落组成研究中被掩盖的农业转型生态影响。