2.8 | Null modelling within communities
Like macro-ecological communities, the bacterial microbiome can be
shaped by deterministic processes (e.g. selection), stochastic processes
(e.g. ecological drift), and dispersal (Adair & Douglas, 2017). If a
given community is strongly shaped by selection acting on microbial
traits, and microbial traits are phylogenetically conserved, then the
phylogenetic structure of this community is expected to deviate from
communities assembled through random chance (Webb et al., 2002).
Conversely, if a community is strongly influence by ecological drift,
then phylogenetic structure of this community is not expected to deviate
strongly from null expectations.
To evaluate evidence for the strength of stochastic and deterministic
processes in the Sable Island horse microbiome, we first calculated mean
nearest taxon distances (MNTDs) using the R package picante (Kembel et
al., 2010). MNTD is a measure of the average phylogenetic distance
separating every taxon (in this instance ASV) in a community to its
nearest neighbour and emphasizes diversity at the tips of a phylogenetic
tree. For each horse microbiome, a MNTD null distribution was generated
via 9999 randomly assembled communities of ASV richness equal to that of
the observed community. Randomized communities were generated by
re-shuffling taxa labels and relative abundances across a fixed
phylogenetic tree comprising the gamma diversity observed across the
entire sample-set. MNTDs were effect size-standardized
(MNTDses) relative to the mean and standard deviation of
the null distribution for a given community (Stegen, Lin, Konopka, &
Fredrickson, 2012). A MNTDses value smaller than -2 or
greater than 2 indicate that a community is more phylogenetically
clustered or over-dispersed than expected by chance, respectively. While
these thresholds have historically been used to make inferences about
the relative strength of competition versus environmental filtering
(Cavender-Bares, Kozak, Fine, & Kembel, 2009), thought experiments and
mixed results from the literature demonstrate such cut-offs are overly
simplistic and can lead to a misattribution of pattern to ecological
process (Mayfield & Levine, 2010). We instead considered only the
magnitude of phylogenetic departure from stochastic expectations
(|MNTDses|) in a mixed model
inference.