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 pairwise 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.

农业转型是生物多样性面临的最重大威胁之一，其会引发栖息地退化与丧失，进而导致群落物种丰富度与组成结构发生改变。这类丰富度与组成结构的变化，继而可能引发物种共现（co-occurrence）关系的改变，但目前学界对该现象的认知仍较为有限。本研究采用一种全新的物种共现网络（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172000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。研究对比了完整景观与受改造景观环绕的样地中的群落集合，并验证了四项核心假说：农业转型会（H1）导致物种丰富度下降，（H2）改变群落集合结构，（H3）降低整体物种共现水平，以及（H4）使物种间的成对关联发生复杂重构。研究结果显示，与完整景观样地相比，受改造景观样地的群落组成存在显著差异，但物种丰富度并无明显变化。受改造景观的物种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（共现连接率（co-occurrence connectance）降低），高度关联的物种数量更少（共现度（co-occurrence degree）频率分布出现截尾），且共现网络的模块化（modularity）程度升高。至关重要的是，整体共现水平的下降实则由物种间成对共现关联的数量与分布的复杂变化所驱动——其中41%至44%的物种反而获得了与其他物种的新关联。物种共现关系的变化，既与物种占据率（occupancy）的变化无关，也不受其功能性状（functional trait）类群的影响，这为我们对物种受农业转型影响的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可能被掩盖的农业转型影响。