Allopatric speciation followed by the evolution of range overlap (sympatry) allows the build-up of regional diversity. However, local species richness requires that species co-occur locally (syntopy). Importantly, correct estimates of syntopy must be available to identify ecological traits facilitating it. We thus provide a method to correctly estimate local co-occurrence and demonstrate it on the evolution of secondary syntopy. First, we performed probabilistic co-occurrence analyses on simulated data across a sympatry gradient from 0 to 100%. Second, we extracted 116 species pairs younger than 10 My from a dated phylogeny of Meliphagoidea songbirds. We constructed a presence–absence matrix of 58 species across 470 sites based on 37 250 censuses in Australia and Tasmania from 1989 to 1995. We also constructed a spatial mask based on species ranges, identifying sites within versus outside the area of sympatry. We ran both unconstrained and range mask-constrained co-occurrence analyses. We compared the resulting syntopy and predicted it by species ecology. Simulations and exact analyses showed that co-occurrence analyses must be limited to sites in the area of sympatry between species. Without this spatial limit, syntopy was negatively biased, especially in common species. Accordingly, syntopy was negatively biased in Meliphagoidea when data from all sites were used, but this bias decreased with increasing sympatry, in agreement with numerical and exact analyses. When using correct estimates, syntopy increased with increasing divergence in the use of foraging stratum (ground, shrub, subcanopy and canopy) and with decreasing divergence in diet. In conclusion, we introduced a general method for calculating local species co-occurrence and confirmed its validity by simulations. We illustrated its use by analyzing the evolution of secondary syntopy in a phylogenetic framework. We found support for both niche divergence (foraging stratum) and niche conservatism (diet) in facilitating evolutionary transitions to secondary syntopy, allowing the build-up of local species richness.

中文翻译：

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资源利用差异促进鸣禽大陆辐射中次级同位素的进化（Meliphagoidea）：来自无偏见共现分析的见解

异域物种形成之后是范围重叠（同域）的演变，可以建立区域多样性。然而，当地物种丰富度要求物种在当地共同出现（共生）。重要的是，必须提供对同位素的正确估计，以确定促进它的生态特征。因此，我们提供了一种正确估计局部共现的方法，并在次级同位素的演变中证明了这一点。首先，我们对从 0 到 100% 的同域梯度上的模拟数据进行概率共现分析。其次，我们从 Meliphagoidea 鸣禽的过时系统发育中提取了 116 个小于 10 My 的物种对。我们基于 1989 年至 1995 年在澳大利亚和塔斯马尼亚进行的 37,250 次人口普查，构建了 470 个地点的 58 个物种的存在-不存在矩阵。我们还构建了一个基于物种范围的空间掩码，识别同域区域内外的地点。我们运行了无约束和范围掩码约束的共现分析。我们比较了由此产生的同位素，并通过物种生态学对其进行了预测。模拟和精确分析表明，共现分析必须仅限于物种间共生区域内的地点。没有这个空间限制，同位素是负偏的，特别是在普通物种中。因此，当使用来自所有站点的数据时，同位素在 Meliphagoidea 中存在负偏差，但这种偏差随着同源性的增加而减少，这与数值和精确分析一致。当使用正确的估计时，同位素随着觅食层（地面、灌木、亚冠层和​​冠层）以及饮食差异的减少。总之，我们介绍了一种计算本地物种共现的通用方法，并通过模拟验证了其有效性。我们通过分析系统发育框架中次级同位素的演变来说明它的用途。我们发现支持生态位分化（觅食层）和生态位保守主义（饮食）促进进化过渡到次级同位素，从而增加当地物种的丰富度。