Effects of phylogenetic distance, niche overlap and habitat alteration on spatial co-occurrence patterns in Neotropical bats and birds

Ecological interactions influence which species can coexist locally, but assessing the effects of interactions on species distributions at landscape to regional scales has proven challenging. Here, we present a new statistical method to address this question at the assemblage level. Our method, which we call mixed-effects co-occurrence modelling, entails fitting pairwise species co-occurrence data to generalized linear mixed models using Fisher's non-central hypergeometric distribution. We use this method to examine the effects of phylogenetic relatedness, dietary-niche overlap (a proxy for potential food competition) and human-induced habitat alteration on pairwise co-occurrence patterns for bat and bird assemblages that span most of the Neotropics. For both assemblages, average pairwise co-occurrence increased with phylogenetic relatedness, indicating that phylogenetic niche conservatism contributes to environmental filtering at broad spatial scales. After controlling for phylogeny, variance in co-occurrence tended to be highest for species pairs in the same dietary guilds, suggesting varied responses to food competition. Effects of habitat alteration were relatively weak and inconsistent, though our analysis precluded identifying effects that were phylogenetically structured. Overall, our findings indicate that phylogenetic relationships among species pairs are instrumental in determining patterns of species co-occurrence and thereby influence how biological interactions play out at broad spatial scales.