Diversity metrics
While species richness (SR) offered a simple measure of taxonomic
diversity at each site, phylogenetic diversity was calculated as Faith’s
phylogenetic diversity (PD) index, or the sum of all branch lengths of
the phylogeny connecting all species at a site (Faith 1992), using the
function ‘pd’ in R package picante (Kembel et al. 2010). The
branch lengths are taken to represent evolutionary time, with higher PD
indicating group of species that are more evolutionarily apart in time
(Tucker et al. 2019). Absolute functional diversity was estimated as
functional richness, FRic (Villéger et al. 2008), which represents the
multidimensional volume of functional space occupied by the species
within a community (Villéger et al. 2008). We estimated FRic by
computing the pairwise distance between all birds (branch lengths of the
functional dendrogram for species within a community) at every site
which had more than two species. The dimensions of the functional
distance matrix were condensed using PCoA to estimate the convex hull
volume of functional spaces for species within a community in R using
the package ‘FD’ (Laliberté et al. 2014).
Dispersion metrics for continuous traits were measured by quantifying
the community-weighted mean (CWM) of traits showing phylogenetic signal
using the ’dbFD’ function in the ’FD’ R package (Laliberté et al.
2014).The rationale behind this was that environmental filtering would
lead to a decrease in trait range or variance in communities(e.g. Graham
et al. 2012; Zhang et al. 2020).CWM statistics were calculated by taking
averages of trait values of species that were present in each site
(communities), weighted by species abundance.
Mean pairwise phylogenetic
distance (MPD)and mean pairwise functional distance (MFD) at each site
(Webb et al. 2002) were derived from the average functional or
phylogenetic distance between each pair of species that co-existed at
each site calculated as
\begin{equation}
MPD(or\ MFD)=\frac{\sum_{i}^{n}{\sum_{j}^{n}\delta_{i,j}}}{n}\left(i\neq j\right)\nonumber \\
\end{equation}where n is species richness in each band, \(\delta_{i,j}\) is the
pair-wise functional or phylogenetic distance (Euclidean distance)
between species i and species j .
For a phylogenetic or functional tree ‘T’ with a set of species
‘n’ represented by a subset of branching nodes, the MPD of‘n’ is equal to the average of the distances of all possible
simple paths in ‘T’ that connect pairs of nodes in ‘n’(Tsirogiannis and Sandel 2014). We compared these indices to 1000
randomized communities to test whether the functional and phylogenetic
community structures differed from random expectations. For this we used
the function ‘ses. mpd’ in package picante (Kembel et al.
2010) to generate random communities by shuffling the tips of the
branches of the phylogenetic and functional trees used to calculate
distance matrices for the entire community of river birds keeping the
species richness constant. This procedure assumes that all species could
colonize habitats across the whole gradient but are excluded due to
local biotic and abiotic factors. We calculated the standardized effect
size (SES) of MPD and MFD for each site comparing the observed values
versus the expected values from the null communities (Kembel et al.
2010). The SES aids in inferring community assembly processes like
environmental filtering and competition. When traits and lineages are
conserved (i.e. with phylogenetic signals) with SES values <0,
it indicates that communities are phylogenetically and functionally
clustered and are shaped by environmental filtering. Community
overdispersion with SES > 0 for MPD and MFD values are
taken to indicate competitive exclusion (Webb et al. 2002).