Appendix A. A table presenting results of a sensitivity analysis for torus translation tests completed on soil chemical and physical properties and topography on a 100-ha Eleme ya Ngombe plot in Dzanga-Sangha Dense Forest Reserve, Central African Republic.

A table presenting results of a sensitivity analysis for torus translation tests completed on soil chemical and physical properties and topography on a 100-ha Eleme ya Ngombe plot in Dzanga-Sangha Dense Forest Reserve, Central African Republic

Data used in Lai et al. (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology.

<div><b>Data from: </b>Lai, H.R., J.S. Hall, S.A. Batterman, B.L. Turner & M. van Breugel (2018). Nitrogen fixer abundance has no effect on biomass recovery during tropical secondary forest succession. Journal of Ecology</div><div><br></div><div><b>Methods and materials;</b></div><div>See 'Methods & Materials' section in Lai et al. 2018 for details </div><div><br></div><div><div><b>Summary</b>:</div><div>1) Nitrogen-fixing trees (N2 fixers) provide new nitrogen critical for rapid biomass accumulation of tropical forests during early secondary succession, but it remains unclear how the abundance of N2 fixers in the forest community affects the growth of non-fixers or the primary productivity of the whole forest. </div><div>2) On the one hand, N2 fixers may enhance forest productivity by providing a facilitative effect through the provision of plant-available nitrogen to non-fixing trees. On the other hand, N2 fixers may suppress the growth of non-fixers by growing faster and competing more vigorously for light and other resources. A third alternative is that the growth of N2 fixers themselves accumulate biomass rapidly, while having a neutral effect on non-fixers, leading to an overall increase in forest biomass.</div><div>3) We examine these alternative hypotheses using five-year tree census data from 88 plots in 44 seasonal tropical moist secondary forests (3–32 years old) across a human-modified landscape in central Panama. We examined whether N2 fixers accumulated biomass more rapidly than non-fixers, and how relative biomass of N2 fixers as a functional group and as individual species influenced the growth of non-fixer and whole stand primary productivity.</div><div>4) Surprisingly, we found no evidence for either a net competitive or a facilitative effect of N2 fixers as a functional group or individual species on the biomass recovery in these young forests. N2 fixers did not grow faster than non-fixers. Individual mortality rates were lower among N2 fixers, but biomass losses due to mortality were similar between the two groups. Overall, we found no relationship between the relative abundance of N2 fixers and stand primary productivity during succession. </div><div>5) Synthesis: N2-fixing trees may be critical for reducing nitrogen limitation and accelerating biomass growth during tropical secondary forest succession, thereby impacting the global carbon cycle. However, our findings indicate that, in early successional seasonal tropical moist forests, N2 fixers provide neither a net competitive nor a facilitative effect on non-fixing trees or the whole forest stand, likely because tropical N2 fixers utilize facultative fixation and hence abundance poorly approximates the ecosystem function of fixation. Our results indicate that models should not simply scale symbiotic fixation and its effects from N2-fixing tree abundance.</div></div><div><br></div

Succession of Ephemeral Secondary Forests and Their Limited Role for the Conservation of Floristic Diversity in a Human-Modified Tropical Landscape

<div><p>Both local- and landscape-scale processes drive succession of secondary forests in human-modified tropical landscapes. Nonetheless, until recently successional changes in composition and diversity have been predominantly studied at the patch level. Here, we used a unique dataset with 45 randomly selected sites across a mixed-use tropical landscape in central Panama to study forest succession simultaneously on local and landscape scales and across both life stages (seedling, sapling, juvenile and adult trees) and life forms (shrubs, trees, lianas, and palms). To understand the potential of these secondary forests to conserve tree species diversity, we also evaluated the diversity of species that can persist as viable metapopulations in a dynamic patchwork of short-lived successional forests, using different assumptions about the average relative size at reproductive maturity. We found a deterministic shift in the diversity and composition of the local plant communities as well as the metacommunity, driven by variation in the rate at which species recruited into and disappeared from the secondary forests across the landscape. Our results indicate that dispersal limitation and the successional niche operate simultaneously and shape successional dynamics of the metacommunity of these early secondary forests. A high diversity of plant species across the metacommunity of early secondary forests shows a potential for restoration of diverse forests through natural succession, when trees and fragments of older forests are maintained in the agricultural matrix and land is abandoned or set aside for a long period of time. On the other hand, during the first 32 years the number of species with mature-sized individuals was a relatively small and strongly biased sub-sample of the total species pool. This implies that ephemeral secondary forests have a limited role in the long-term conservation of tree species diversity in human-modified tropical landscapes.</p></div

Changes in diversity with successional stand development on local and landscape scale.

<p>Indices of species diversity were calculated for four different groups of woody plants, and for individual sites (white dots and regression lines) and the metacommunity (diamonds and triangles). A-D) ⁰<i>D</i>  =  species density. E-H) ¹<i>D</i>  =  the exponential of Shannon entropy. I-L), ²<i>D</i>  =  the inverse Simpson concentration. For all three diversity measures, units are in number of species. Metacommunity diversity was calculated for the pooled data of randomized samples of 12 SFD sites. Colors indicate SBA classes as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082433#pone-0082433-g001" target="_blank">figure 1</a> and error bars give the 95% confidence limits. The lines connecting the symbols are for illustrative purposes only. Sample area per plot and per SBA class is indicated above the graphs. Equation type and regression statistics are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082433#pone-0082433-t002" target="_blank">Table 2</a>.</p

Compositional change with successional stand development.

<p>Variation in species composition was assessed for four different groups of woody plants by calculating the relative positions of sites along the axes of a non-metric multidimensional scaling (NMDS) ordination, based on the Jaccard abundance-based dissimilarity index. See methods for definition of plant groups and sample areas. Equation type and regression statistics are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082433#pone-0082433-t002" target="_blank">Table 2</a>.</p

Regression models and coefficients of determination for the relationships between indices of community structure (response variables) and age since abandonment, stand basal area (SBA), or light (predictor variables).

<p>⁽²⁾ calculated with presence/absence data; M  =  Model. P  =  power model; L  =  Linear model; E  =  Exponential model. <i>ns</i>  =  non-significant relationship (p>0.05), in all other cases significance is p ≤ 0.01.⁽¹⁾ Calculated with abundance weighted data; </p

Diversity in relationship with relative size and forest age.

<p>A) Number of tree and shrub species per age class (lianas and palms not included!), when all individuals are taken into account (blue dots), when only individuals above the relative size threshold (RST) of 10% (green dots) or of 30% (darker orange dots) are counted and when only species are counted with individuals ≥ RST_30% in more than one plot (lighter orange dots). Per age class, species were counted for the pooled data of 15 SFD plots (3 ha). Dotted lines are for illustrative purposes. B-C) Number of species per maximum-size class (blue) and the subsamples of species with individuals above relative size thresholds of 10% (green) and 30% (orange). D-E) Number of stems per maximum size class. Graphs show data for the 2–7 y age class (B, D) and the 18–32 y age class (C, E).</p

Increasing dissimilarity between seedling and the initial assemblages of trees.

<p>Mean of pair-wise dissimilarities between the seedling assemblages of SBA classes 1, 2 and 3 with the assemblages of plants ≥ 1 cm DBH of SBA class 1, using the Chao Jaccard Abundance Estimator. Error bars indicate ± 95% confidence limits. Calculations included only species that can potentially grow to a diameter of at least 5 cm.</p

Changes in encounter rate at 10 sites across Grauer’s gorilla range.

<p>Changes in encounter rate at 10 sites across Grauer’s gorilla range.</p

Model results comparing deviance values and percentage of deviance explained.

<p>Model results comparing deviance values and percentage of deviance explained.</p