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.