2.3 Measurement of species richness, species composition and
community stability
We calculated species number in a quadrat as species richness. To
distinguish differences in species composition among different fencing
duration or shrub cover treatments, non-metric multidimensional scaling
(NMDS) based on Bray-Curtis distance was run. We used the envfit
function from vegan to test the community composition difference between
treamtments of different fencing duration or shrub cover, with treatment
type as a categorical factor variable. Significance of these differences
was tested using Analysis of Similarity (Anosim) by calculating 999
random permutations. Theses anlyses were performed in the ‘vegan’
package in R (R Core Development Team).
M-Gordon stability index, a popular international method, is used for
determining community stability (Hou et al., 2019). It uses the number
and frequency of all species in a plant community to establish a
mathematical model, and calculates the reference point of the community.
Then, the stability of the plant community was calculated according to
the reciprocal of the distance between the reference point and the
stable point. More details for calculation methods of M-Gordon stability
index see Supplementary material. The closer the reference point to the
stable point, the higher the stability of plant community (Hou et al.,
2019).
2.4 Measurement of phylogenetic structure and trait
phylogenetic conservatism
Before quantifying
phylogenetic
structure and phylogenetic conservatism, we constructed a phylogenetic
tree for our study species. All the 19 species investigated in this
study were identified based on Angiosperm Phylogeny Group III system
(The Angiosperm Phylogeny Group, 2009) using the Plant List database
(http://www.theplantlist.org/). And then, the completed
phylogenetic tree with branch lengths (Figure. S1) was directly
assembled within the online tool Phylomatic (http://
phylodiversity.net/phylomatic/) based on the ultrametric phylogeny of
Zanne et al. (2014). Next, a phylogenetic tree was randomly solved by
‘multi2di’ function, and then we ultrametrized the tree using
‘compute.brlen’ function from ‘ape’ package in R (R Core Development
Team).
To characterize community phylogenetic diversity and structure, we
calculated Faith’s phylogenetic diversity (PD) (Faith 1992), mean
nearest taxon distance (MNTD) and mean pairwise distance (MPD) (Webb,
2000). PD is defined as the total branch length among all taxa in a
comnunity. MPD generally reflects phylogenetic structure across the
entire tree, whereas MNTD is sensitive to patterns among closely related
species towards the tips of the phylogeny (Blaimer et al., 2015). In
additon, we calucaluted the standardized effect sizes (SES, differences
of observed values versus null communities) of MPD and MNTD
(SESMPD and SESMNTD) by weighting
species abundance and their associated quantiles (p value) to
assess statistical significance.
To further strengthen the conclusion, we analyzed the SES with two null
models: 1) randomizing the community data matrix (‘independent swap’)
and 2) shuffling taxon labels randomly across the phylogeny (‘taxa
labels’), this algorithm randomizes the relatedness of species to one
another, but it maintains species occurrence frequency and abundance.
SESMPD and SESMNTD are equivalent to net
relatedness index (NRI) and nearest taxon index (NTI) multiplied by –
1. Phylogenetic clustering is indicated by negative SES values and low
quantiles (p <0.05), corresponding to -1.96, and
overdispersion by positive SES values and high quantiles
(p >0.95), corresponding to 1.96. Non-significant
positive or negative values indicate observed values close to the median
of the random dispersion.
To quantify trait phylogenetic conservatism, we employed a widely used
Blomberg’s K statistic with 999 iterations (Blomberg et al., 2003).
Blomberg’s K statistic is assessed by using the Brownian motion (BM) of
trait evolution, and is considered as one of the most powerful
approahces (Pavoine and Ricotta, 2013). K-value close to 1, greater than
1 and less than 1 indicate that the trait distribution perfectly matches
BM expectation of trait evolution on the phylogeny, is more conserved
and is less conserved than BM expecatation, respectively (Kraft et al.,
2007). K-values between 0.4 and 0.7 are hereby in the following
considered to represent intermediate, whereas values below 0.4 express
low levels of conservatism. We assessed the statistical significance of
K by comparing observed variances of phylogenetic independent contrasts
to a null model generated by shuffling tips randomly across the
phylogeny. Analyses of phylogenetic structure and trait phylogenetic
conservatism were performed in the ‘picante’ package in R (R Core
Development Team).