Insect and tree diversity estimation
For beetles diversity, both canopy and understory FITs within each plot
were combined as the smallest sampling unit for diversity estimation,
and trees diversity were recorded for each plot. The analyses of
α-diversity were the number of species recorded in each sampling unit
(Appendix 1 and Appendix 2). Because observed species richness values in
field studies are typically an underestimate of the actual number of
species occurring at a plot (Colwell and Coddington 1994), sampling
completeness and estimated species richness were also calculated using
the Chao1 (Chao 1984), Shannon
and Simpson diversity estimator based on
sample units.
The β-diversity was calculated using the package ‘vegetarian’ (Charney
& Record, 2012) in R. The Horn similarity index was used as recommended
by Jost (2007) as the only overlap measure that is not
disproportionately biased toward rare or common species. This index is
considered a true overlap measure that quantifies the overlap of
effective species between sampling units (Tuomisto, 2010). The Horn
similarity index is defined as:
1Dβ =
(ln2-H βShan)/ln2
where H βShan is the Shannon entropy based on Hill
numbers and β-diversity is thus independent of α-diversity (Jost, 2007).
We visualized β-diversity as
1-1Dβ (i.e., compositional
dissimilarity), such that values of 1 indicate complete species turnover
between sampling units.
A second similarity matrix was created treating transects as the unit of
sampling using the function ‘sim.table’ in the R package ‘vegetarian’.
Additionally, geographic distance matrices were constructed at the plot
and transect levels using the function ‘earth.dist’ in the R package
‘fossil’ (Vavrek, 2011). Given that we were computing and comparing
turnover between identical sampling units in all cases, it is not
necessary to consider the species accumulation curve to check whether
sampling is adequate (Kemp & Ellis, 2017).
For the plant phylogenetic α and β diversity, the family and genus names
of all the enumerated species (215 species in total) in the APG III
system were obtained with the R package ‘plantlist’ (Zhang, 2018). Then,
their phylogenetic relationships were examined using the online
phylomatic tool (Webb & Donoghue, 2005)
(www.phylodiversity.net/phylomatic/) based on the Angiosperm consensus
tree from Davies et al. (2004). Further, similarity matrices were
constructed for plant phylogenetic β-diversity (PhyloSor Index, Bryantet al ., 2008) with the function ‘phylosor’ in ‘picante’ in R
(Kembel et al. , 2010). PhyloSor is a modified Sørensen similarity
index which quantifies phylogenetic similarity of communities as the
proportion of shared phylogenetic branch-lengths between two samples.
And the phylogenetic α diversity were calculated with ‘pd’ in ‘picante’
in R (Kembel et al. , 2010). ‘pd’ is the sum of the total
phylogenetic branch length for the sample.