Hypothesis testing
To test whether community size scales identically with elevation on the
two islands, as predicted if communities are locally saturated, we first
regressed local community size (total number of individuals derived from
mark-resight models) against elevation. Similarly, to assess whether
greater regional diversity enhanced community-level species diversity
across the same environmental gradient, we regressed
resight-model-derived plot-level species richness against elevation. In
both cases we used posterior means from the resight model to represent
the best-estimate of true values.
We evaluated trajectories of abundance and species richness along
elevation using linear mixed-effects models (LMMs). Our full model
predicted the response as a function of linear and quadratic elevation
terms, with full interactions with island identity. Models included a
random intercept of landscape to acknowledge that multiple plots
occurred in the same geographic area. We iteratively dropped terms from
these models, comparing the full model with the nested model, until a
likelihood-ratio test (evaluated against a chi-square distribution)
indicated that all remaining terms were significant (alpha = 0.05). We
square-root transformed resight-model-derived abundance and species
richness estimates to meet model assumptions of residual normality and
homoscedasticity (log transformation—more typical of richness and
abundance data—failed residual normality and homoscedasticity tests).
Next, to test whether greater macroevolutionary diversity facilitates
the evolution of environmental specialists, thereby permitting greater
partitioning of communities across space, we calculated
abundance-weighted pairwise Bray dissimilarities between sites within
each island using the betapart package (Baselga & Orme 2012). We
further examined abundance-weighted phylogenetic and morphological
dissimilarity to assess whether differences in turnover had deeper
evolutionary underpinnings, or resulted in ecomorphologically different
community structures, respectively. To do so we used the time-calibrated
phylogeny and measurements of ecologically-relevant morphological traits
for Greater Antillean anoles presented in Mahler et al. (2013).
We calculated phylogenetic dissimilarity of plots using
abundance-weighted unifrac from the weighted_unifrac function
within the abdiv package (Bittinger 2020). For morphological
dissimilarity we calculated abundance-weighted mean pairwise distances
between the species of all community pairs on each island in a
morphospace of ecologically-relevant traits (the four-dimensional
PC-space of Mahler et al. (2013), which represents 93% of total
morphological variation across Greater Antillean Anolis lizards).
In all cases we assessed the rate at which pairwise community
dissimilarities changed as a function of pairwise elevation differences
between sites on the same island. We used linear regression models
including both linear and quadratic effects of elevation as well as an
effect of island identity, and an island-by-elevation interaction.
Given that sub-regional faunas formed to differing degrees on the two
islands, we evaluated whether similar environments led to whole-fauna
morphological convergence at both island and sub-region levels, gauged
using community mean morphology. We applied a cut-off of 700m to split
lowland and highland elevational zones into subregions. This elevation
corresponded to the location of maximum turnover between highland and
lowland species (but results are not sensitive to exact cutoff value).
We assessed the abundance-weighted mean morphology along the four
ecomorphological PC axes described above. To test whether morphology
between faunas (or subfaunas) was more similar than expected by chance,
we shuffled species morphologies 10,000 times, and examined where the
observed Euclidean distance between fauna-mean morphologies fell
relative to the permuted null distribution (we obtained two-tailed
p-values by multiplying one-tailed p-values by two).
Finally, given the distinctiveness of the high-elevation fauna, we
examined whether these species drove patterns of diversity within local
communities across the elevational gradient. To do so we eliminated from
the community dataset all highland species (species whose abundances are
maximized above 700m, none of which occur at sea level). We then
reassessed how both abundance and species richness of lowland species
changed across the elevational gradient of each island using the same
LMMs and model selection process described above.