2.5 Diversity and community structure metrics
In this study, we calculated the TD, FD and PD of small mammals.
Besides, we used landscape diversity indices (calculated by all species
recorded in each forest landscape using six surveys’ data) and site
diversity indices (calculated by six-surveys data recorded at one sample
site; to maintain the consistency of sampling efforts, we did not use
the survey data for the Meigu Dafengding Nature Reserve in June 2017) to
understand small mammal diversity at different scales (all of sample
sites were sampled three times). TD was calculated as the total number
of species in each forest type (species richness). We used the function
“specaccum” in the R package “vegan” to compare the rarefaction
curves of species richness. PD and FD were calculated as the average of
Faith’s index, where Faith’s index is the sum of branch lengths of the
phylogenetic or functional tree for all species within a given community
(Faith, 1992). We used the function “pd.query” in the R package
“PhyloMeasures” to calculate PD and FD (Tsirogiannis, 2016).
We used the function “ses.mpd” and the null model “taxa.labels” in
the R package “picante” to compute the standardized effect size of
mean phylogenetic distances (SES.MPD), which represented the
phylogenetic relatedness of small mammal assemblages (Webb et al.,
2002). A positive value of SES.MPD indicates that the small
mammal
community is more distantly related than expected (overdispersed)
because of interspecific competition, while a negative value of SES.MPD
indicates that the small mammal community is more closely related than
expected (clustered) because of environmental filtering (Webb et al.,
2002). SES.MPD is computed as
\begin{equation}
SES.MPD={(MPD}_{\text{obs}}-mean\text{MPD}_{\text{null}})/sd\text{MPD}_{\text{null}}\nonumber \\
\end{equation}where \(\text{MPD}_{\text{obs}}\) is the observed mean phylogenetic
distance (MPD) of small mammals in a community,\(\text{mean}\text{MPD}_{\text{null}}\) is the mean MPD of the null
models (with distance matrix labels shuffled 999 times), and\(\text{sd}\text{MPD}_{\text{null}}\) is the standard deviation of MPD
of the null models.
We calculated the standardized effect size of mean functional distances
based on the functional dendrogram, following methods similar to those
used for the standardized effect size of mean
phylogenetic
distances.