DOI: 10.5061/dryad.x3ffbg7j2
title: Data from: Tree recruitment failure in old-growth forest patches across human-modified rainforests

description: 1. Land-use change threatens biodiversity in tropical landscapes, but its
 impact on forest regeneration remains poorly known. In fact, the
 landscape-scale patterns driving the diversity of regenerating plants
 within forest fragments have been rarely explored, and we are uncertain
 whether such drivers vary across regions with different land-use change
 patterns.  2. We assessed the effect of landscape composition
 (forest cover and matrix openness) and configuration (forest patch
 density) on species diversity of sapling assemblages (trees ≥30 cm height
 and &lt;1 cm diameter) in old-growth forest fragments from three
 Mexican rainforest regions with different disturbance levels (n = 20
 landscapes per region). We separately assessed old-growth forest
 specialists (OGS) and forest generalist (FG) species to test the
 hypothesis that: (i) OGS species shows recruitment limitation (‘loser
 species’), and can therefore be negatively impacted by landscape changes,
 especially by forest loss and matrix openness in more deforested regions;
 and (ii) FG species can regenerate and even proliferate in more disturbed
 landscapes (‘winner’ species).  3. We recorded ~24,000 plants
 from 415 species. Landscape composition showed stronger effects than
 landscape configuration. The diversity of OGS species generally decreased
 in more deforested landscapes dominated by open matrices, and FG species
 followed the opposite response, especially in regions with
 high-to-intermediate degree of disturbance. Overall, forest fragmentation
 (patch density) showed weak or no effects on species diversity, especially
 after controlling for forest cover effects (i.e., fragmentation per se).
 In contrast to the fragmentation threshold hypothesis, the effect of
 fragmentation was independent of the regional context. Moreover, OGS
 species were affected by landscape attributes operating at larger scales
 than FG species.  4. Synthesis. Our findings support our
 hypotheses, and indicate that forest loss and matrix openness, not
 fragmentation per se, can cause the recruitment failure of tree
 assemblages in highly deforested rainforests. This can be related to
 source and dispersal limitation in more deforested landscapes with
 treeless matrices. Therefore, to promote the regenerative potential
 (resilience) of forest patches in human-modified tropical landscapes,
 conservation programs should focus on preventing forest loss (even the
 smallest forest patches) and improving matrix quality with treed elements,
 particularly in highly deforested tropical regions.
description: We worked in three rainforest regions from southeastern Mexico
 with different patterns and history of land-use change: (1) Marqués de
 Comillas region (in Selva Lacandona rainforest, Chiapas) and labeled
 as low-deforestation region (LDR) in the database; (2) Los Tuxtlas
 rainforest (Veracruz), labeled as intermediate-deforestation region (IDR);
 and (3) Northern Chiapas, labeled as high-deforestation region (HDR). In
 each region, we systematically selected 20 old-growth forest patches (that
 is, 60 old-growth forest patches in total). At each forest patch, we
 established 25 circular plots (1.60-m radius, 8 m<sup>2</sup>
 each; total sampling area per site = 200 m<sup>2</sup>) at the
 center of each forest patch, in a grid of 5 x 5 plots with 30 m separation
 between plots. In each plot, all tree saplings (excluding palms and
 lianas) with ≥ 30 cm height and &lt; 1 cm of diameter at breast height
 (DBH) were counted and identified. We classified sapling species into
 three groups (but we worked with only two): old-growth forest specialists
 ('OG' in the database) and forest generalists ('Gen'
 in the database). Basically, old-growth forest specialists (or late
 successional species) are species that mainly inhabits old-growth forests
 and forest generalists are species that can be found both in old-growth
 forests and at intermediate successional stages due to their greater
 adaptability to both environments.  We estimated
 species diversity (i.e., total number of species and number of common
 species) of OGS and FG saplings for each study site in each region. We
 summed the data of the 25 plots from each forest patch to avoid
 pseudoreplication. Then, we measured species diversity with Hill
 numbers using the <i>entropart</i> package. These diversity
 indexes measure the effective number of species in a community, which
 facilitates the comparison of diversities between different ecological
 communities. Specifically, we calculated Hill numbers of order 0
 (<sup>0</sup><i>D</i> = species richness),
 1 (<sup>1</sup><i>D</i> =
 exponential of Shannon index) and 2
 (<sup>2</sup><i>D</i> = inverse of Simpson
 index). As sample coverage varied among forest sites, ranging from 0.81 to
 0.98, we estimated species diversity with both observed data and expected
 one with Chao-Shen extrapolation (CS in the database).
 Regarding the landscape variables, we estimated four metrics of
 landscape structure in 13 different spatial extents: i.e., concentric
 landscapes or buffers of 100- to 1300-m radius (at 100-m intervals) from
 the geographic center of each focal forest site. We used this multi-scale
 approach because we did not know the scale of effect, that is, the spatial
 scale that yields the strongest responses for each landscape predictor. We
 selected four landscape metrics that can have strong influence on sapling
 diversity: two landscape composition variables (i.e., FC = forest cover,
 MO = matrix openness), and two landscape configuration variables (i.e., PD
 = patch density, ED = forest edge density). We estimated forest cover as
 the percentage of landscape area covered by old-growth forest. We
 calculated matrix openness as the percentage of the anthropogenic matrix
 covered by open areas (i.e., human settlements, pastures, annual crops,
 and water bodies). Patch density is the number of old-growth forest
 patches within the landscape divided by landscape area
 (<i>n</i>/ha). Finally, edge density is the perimeter length
 of all old-growth forest patches within the landscape divided by landscape
 area (m/ha).