An exploration of the impact of phylogenetic tree structure on NTI and βNTI estimates of community assembly

Abstract The nearest taxon index (NTI) and beta nearest taxon index (βNTI) are popular analytical tools for assessing the community assembly processes in a variety of ecosystems. However, the fundamental dependence of these models on the underlying phylogenetic tree is often overlooked and can potentially lead to erroneous conclusions. In this paper, we investigated how outlier sequences in the phylogenetic tree and reduction of the metacommunity richness affect estimates of the assembly processes. We estimated assembly in two datasets investigating fish-microbiota interactions. We found that outlier sequences can drastically change the interpretation of assembly processes. NTI consistently increased after outlier sequences were removed, which changed the ecological interpretation for 82.8% of the communities in one of the datasets. Similarly, βNTI was strongly affected by outliers in the phylogenetic tree, changing the ecological interpretation for 44.7% (Dataset 1) and 6.3% (Dataset 2) of the community comparisons. Lower metacommunity richness generally resulted in decreased NTI and increased βNTI, but the effect sizes were small and generally did not result in a change in ecological interpretation. This exploratory work highlights the need to assess the phylogenetic tree for spurious outlier sequences prior to null model analysis.