2.9 | Null modelling between communities
The same principles which underlie the use of phylogenetic null modelling within a given community, can be used to infer possible mechanisms for the variation observed between communities. For between community comparisons, nearest taxon distances are instead calculated between an ASV in one microbiome and its closest relative in a second microbiome (β mean nearest taxon distance [βMNTD]) (Stegen et al., 2012). As above, we standardized βMNTDs by the mean and standard deviation of a null distribution created via 999 randomly assembled community pairs (βMNTDses). Positive βMNTDses indicate that two communities are more phylogenetically disparate than would be expected given random sampling of a given pool of gamma diversity. Conversely, negative βMNTDses indicate that two communities are more phylogenetically similar than would be expected. Assuming taxa niche-spaces and phylogenies are correlated, then positive and negative βMNTDses values can indicate that the differences or similarities observed between two communities might be the result of differential or similar selective pressures, respectively (Stegen et al., 2012). |βMNTDses| values of < 2 are conventionally considered to indicate that inter-community differences might be the result of dispersal patterns or ecological drift, as phylogenetic patterns observed between communities do not differ greatly from those of randomly assembled community pairs. We analyzed βMNTDses using a PERMANOVA parameterized identically to the β-diversity analyses described above. Additionally, we ran a mantel test to test for a correlation between spatial separation and βMNTDses values, and a univariate PERMANOVA to test for an effect of social band. For all nearest taxon analyses, we used a phylogenetic tree made ultrametric (λ = 1) using the chronos() function from the R package ‘ape’.
Finally, we also used a phylogeny-independent extension of this null modeling framework by calculating Raup-CrickBray(RCbray) values (Chase et al., 2011; Stegen et al., 2013). Rather than consider greater- or less- than-expected phylogenetic similarities between communities, RCbray values indicate whether taxa co-occur at similar abundances more or less often than expected independent of their phylogenetic relatedness (Lowe & McPeek, 2014; Stegen et al., 2013). Among communities which do not show strong phylogenetic deviations from null expectations, RCbrayestimates < -0.95 indicate that taxa co-occur at similar abundances between communities more frequently than would be expected by chance alone, one indication of homogenizing dispersal. RCbray estimates > 0.95 indicate that taxa co-occur between communities less often than would be expected given random expectations, indicating dispersal limitation. Finally, |RCbray| < 0.95 indicate that rates of taxa co-occurrence do not differ from null expectations, suggesting possible ecological drift. Null distributions used to make comparisons were created via 9999 community pairs created through randomization. Like βMNTDses, RCbrayvalues were analyzed via PERMANOVA and a partial Mantel test was used to test for a correlation between RCbray values and longitudinal separation, after controlling for βMNTDsesvalues.