Methods
Study site: The study was conducted in a 30-km 2 tropical humid forest in central Western Ghats, a biodiversity hotspot in southern India, Kadumane village (12°53'03.4"N, 75°41'25.3"E, 900 to 1100 m.a.s.l., Fig. S1). The site receives ca. 4100 mm of rainfall annually with a dry season of about 6 months from November to April with monthly precipitation less than 100 mm. This human-modified landscape consists of forest fragments, grassland, tea plantations, roads, and small human settlements. The forest fragments offer a gradient in abiotic conditions from forest edge to interiors. To capture the variability in canopy openness, soil moisture, and nutrients across the landscape, we established 250 2-m X 2-m plots (demarcated into four 1-m X 1-m sub plots) across 30 transects laid from the edge of roads or tea plantations into the forest interior (Fig. S1).
Seedling census: In November 2021, we tagged, identified and recorded tree seedlings of height 5-50 cm within each plot. We censused seedlings twice a year, pre-monsoon (March – April) and post-monsoon (November – December), totalling seven censuses until November 2024. During each census, all the new seedling recruits were also tagged and monitored, totalling 9613 seedlings of 80 tree species across 3.5 years.
Abiotic variables : In each plot, we assessed canopy openness as a proxy for understorey light availability using 180-degree hemispherical photographs. In March 2023, canopy images were taken at 50 cm above the ground in the center of each plot (details in Methods S1). We analysed the percent of open canopy from these images using Gap Light Analyzer version 2.0 (Frazer et al., 1999). Gravimetric soil moisture was assessed monthly for each plot every year during the dry season (January to April, details in Methods S2). While CDD varies with wet season moisture (Lebrija-Trejos et al., 2023), this will play out primarily for the seed-to-seedling transition and early seedling recruitment in this system (Krishnadas et al., 2018; Krishnadas & Comita, 2018), whereas we wanted to examine CDD in older seedlings. Moreover, CDD has been observed during the dry season here (Krishnadas et al., 2020; Krishnadas & Comita, 2018) and evidence from seasonal forests suggests that CDD effects on seedlings in tropical wet forests can be strong in the dry season (Lin et al., 2012). For soil nutrients, soil from the top 10 cm of each 1 m 2 plot was collected during October 2022 to quantify the concentration of Nitrate (NO 3 -, mg Kg -1 ), Ammonium (NH 4 +, mg Kg -1 ) and plant-available phosphorus (P, mg Kg -1 ) (Details in Methods S3). Nutrient analysis was outsourced to the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India, and performed accoring to standard lab protocols.
Trait measurements: We measured specific leaf area (SLA, mm 2 mg -1 ), leaf dry matter content (LDMC, mg g -1 ) and specific root length (SRL, mm g -1 ) as the key traits relevant to classifying species along a spectrum of fast-growing, resource-acquisitive to slow growing, resource-conservative strategies (Laliberté, 2017; Reich, 2014), which is in turn associated with a growth-defence trade-off (Coley et al., 1985). Higher SLA, higher SRL and lower LDMC values reflect a resource-acquisitive strategy and low defenses. SLA and LDMC were measured for 28 most common species (making up more than 95% of seedling abundance, Table S1), and SRL was measured for 21 common species (making up 90% of seedling abundance Table S1) following Pérez-Harguindeguy et al. (2013). Refer to supplementary Methods S4 for more details of measurements.
Statistical analys is
Seedling survival models: Quantifying CDD in a robust and reliable manner has been the subject of much recent debate (Chesson, 2000a; Detto et al., 2019), and we followed the recent best practices to estimate CDD (Hülsmann et al., 2024). Specifically, to account for nonlinearity and saturation in the effects of neighbours on seedling survival we used Generalized Additive Mixed Models (GAMM) with thin plate splines (more details below). Furthermore, conspecifics must have a stronger effect on the plant performance as compared to heterospecifics for stabilising effects to shape the community (Chesson, 2000a). To estimate the difference between the effect of conspecific and heterospecific density dependence (HDD), we included the density of conspecific seedlings as well as total seedlings in our models (Chesson, 2000a; Hülsmann et al., 2024; LaManna et al., 2024). Including the total density gives us the conspecific effects adjusted for the heterospecific density effects (Hülsmann et al., 2024), and can be interpreted as stabilizing CDD.
Conspecific seedling density and the total seedling density for each focal seedling was calculated as the number of conspecific seedlings and the total number of seedlings present in the plot in the census preceding the one when seedling survival was recorded. We then filtered our data to include species that occurred in at least three plots and had at least three levels of conspecific densities recorded. Of 80 species of tree seedlings found across 250 plots (2 X 2m), 39 species qualified for inclusion in models (Table S1), giving us 9148 seedlings over seven censuses.
To test if the effects of neighbor density varied with light, soil moisture and nutrients, we modelled individual seedling survival as a function of canopy openness, minimum dry-season soil moisture, nitrate, ammonium, total available nitrogen (sum of nitrate and ammonium) or available phosphorus in interaction with conspecific density and total seedling density (Box 1 Equation 1). Although the wet season can be a time of strong CDD for seedlings due to an increase in pathogens, there may be little spatial variation as it is unlikely that soil moisture is limiting anywhere. Because our goal was to understand spatial variation in CDD across an abiotically heterogeneous landscape, we chose to assess CDD with the dry season soil moisture (November through April), when there is marked spatial variation in soil moisture acting as an abiotic filter (Wilson et al. in preparation). At the same time, seedlings experience CDD in the dry season here (Krishnadas & Comita, 2018) as well as in other tropical forests (Lin et al., 2012), which may vary spatially with soil moisture.
We set up GAMMs with Bernoulli distribution and complementary log-log (cloglog) link to allow for asymmetric fit since our data was skewed with nearly 70% survival (Hardin & Hilbe, 2007). Abiotic variables were correlated (Fig. S2), so we implemented separate models for each variable. Seedling survival is known to depend on seedling height (Johnson et al., 2017), hence log-transformed initial height of the seedling was included as a predictor. All models had random intercepts and slopes per species for the effects of abiotic variables, conspecific and total densities, and their interaction with the abiotic predictor. To account for temporal and spatial autocorrelation, we added the census date and plot identity as random intercepts, respectively. All the models were fitted using the restricted maximum likelihood estimation (REML) using gam() function from mgcv package (Wood, 2025). Model performance was assessed from simulated residuals using package DHARMa (Hartig et al., 2024).
Equation 1:
cloglog(Survival) ~ season + log(height) + Con + Tot + Env + Con : Env + Tot : Env + (1 + Con * Env + Tot * Env | Species) + (1 | census) + (1 | plot)
Equation 2:
cloglog(Survival) ~ season + log(height) + Con + Tot + Env + trait + Env : trait + Con : Env + Con : trait + Con : trait : Env + Tot : trait + Tot : Env + Tot : trait : Env + (1+ Con * Env + Tot * Env | Species) + (1 | census) + (1 | plot)
Box 1: Generalised additive mixed effect model (GAMM) equations in Wilkinson-Rogers notation. Final GAMM model structure after trouble-shooting for convergence errors described in Wilkinson-Rogers notation. Con is conspecific seedling density, Tot is total seedling density, Env is either canopy openness , scaled minimum soil moisture or soil nutrients (nitrate, ammonium, total nitrogen or available phosphorus) and trait is either SLA , LDMC or SRL.
Finally, we tested whether SLA, LDMC and SRL explained the variation in CDD and its change with light, soil moisture, and soil nutrients. The 28 species with SLA and LDMC included 8752 seedlings and 21 species with SRL included 8302 seedlings (Table S1). For this, we fitted fifteen separate models, to predict seedling survival for the combinations of each trait and abiotic variable in a three-way interaction with conspecific and total densities (Box 1 Equation 2). For example, to test the effects of neighbour density with SLA and light, we modelled survival as a function of conspecific density, SLA and canopy openness in a three-way interaction as well as total density, SLA and canopy openness in a three-way interaction. The random effects were fitted similar to Equation 1 (Box 1). SLA, LDMC and SRL were not correlated in our dataset (Fig. S3).
Conspecific density dependence estimates: CDD was interpreted with predicted survival probabilities at representative density values, using predict.gam() function from package mgcv (Wood, 2025). Survival probabilities were generated depending on the question (see details below), and assessed or compared based on 95% confidence intervals (CI). For our first question, we assessed the difference (i.e. effect size) in survival probability between seedlings without conspecific neighbors (zero) and (a) at mean conspecific density (referred to as mean CDD effect) and (b) at the 95 th percentile of conspecific density (referred to as high CDD effect). Mean and high CDD effects were calculated at low (5 th percentile) and high (95 th percentile) levels of each of the respective environmental conditions (i.e. canopy openness, soil moisture, nitrate, ammonium, total nitrogen and available phosphorus), with other model terms held at their median. Significance of CDD was assessed based on the overlap with zero of 95% CIs of the difference in survival probability, and this was compared between each low and high level of the abiotic variable to assess change in CDD. Negative and positive effect sizes denote significant negative and positive CDD, respectively. For the second part of question 1, we evaluated species-level CDD by predicting effects of conspecific density as detailed above at species-specific low (5 th percentile), mean, and high (95 th percentile) values of conspecific seedling density, at low (5 th percentile) and high (95 th percentile) levels of each of the respective environmental conditions. For question two, we estimated the contribution of traits in explaining CDD by calculating CDD effect size, as mentioned above, for low and high values of each trait (5 th and 95 th percentile respectively): SLA, LDMC and SRL, repeated at low (5 th percentile) and high (95 th percentile) levels of each of the respective environmental conditions.
All analysis was done in R version 4.5.1 (R Core Team, 2025), using tidyverse (Wickham et al., 2019) for data management and ggplot2 (Wickham, 2016), ggpubr (Kassambara, 2025), ggrepel (Slowikowski et al., 2024), gratia (Simpson, 2024) and cowplot (Wilke, 2025) for plotting.
Results
Context-dependent CDD: In lower light (5 th percentile canopy openness = 0.45%), community-average seedling survival decreased between zero and mean conspecific density, indicating negative CDD (Fig. S3a, Table S2), which persisted in more open canopies (95 th percentile canopy openness = 2.63%, S3a, Table S2). At high conspecific densities, we found positive CDD in lower light where seedling survival increased relative to no conspecific seedlings (S3a, Table S2) and no CDD under more open canopies (S3a, Table S2).
In wetter conditions (95 th percentile soil moisture = 35.78%), survival decreased between zero and mean conspecific density, indicating negative CDD (Fig. 1a, Table S3), but negative CDD disappeared at high conspecific density (Fig. 1a, Table S3). By comparison, in drier conditions (5 th percentile soil moisture = 3.76%), survival probability increased considerably at high density relative to no conspecifics, indicating positive CDD (Fig. 1a, Table S3), with no discernible CDD at mean conspecific density (Fig. 1a, Table S3). We also fitted models using average dry season soil moisture. However, these had higher AIC than models using minimum dry season soil moisture (Table S4).
In high nitrate soils (95 th percentile nitrate = 72.3 mg Kg -1 ), survival probability decreased between zero and mean as well as zero and high conspecific density, indicating negative CDD (Fig. 1b, Table S5). In lower nitrate soils by comparison (5 th percentile nitrate = 17.5 mg Kg -1 ), survival probability increased between zero to high conspecific density, indicating positive CDD (Fig. 1b, Table S5). In higher ammonium soils (95 th percentile ammonium = 17.95 mg Kg -1 ), seedling survival decreased between zero and mean conspecific density, indicating negative CDD (Fig. S4c, Table S6), which became positive between zero and high conspecific density (Fig. S4c, Table S6). In lower ammonium soils (5 th percentile ammonium = 10.35 mg Kg -1 ), we found negative CDD between zero and mean conspecific density (Fig. S4c, Table S6), but no discernible CDD between zero and high conspecific density. Patterns of CDD with total available nitrogen (sum of ammonium and nitrate) was similar as compared to nitrate (Fig. 1b, S4d, Table S5, S7). In higher phosphorus soils (95 th percentile phosphorus = 3.31 mg Kg -1 ), survival probability decreased between zero and mean as well as zero and high conspecific density, indicating negative CDD (Fig. S4b, Table S8). At lower phosphorus levels by comparison (5 th percentile phosphorus = 0.2 mg Kg -1 ), there was no discernible CDD (Fig. S4b, Table S8).
Species variation in CDD: Seedlings of seven out of thirty nine species were found in conspecific densities higher than community mean (of 26 seedlings, Table S1), and these species showed variation in CDD with varying abiotic conditions (Fig. 2, S5 - S16, Table S9-14). Canopy openness changed CDD for only one species; at high density, Reinwardtiodendron anamalaiense had negative CDD in lower light conditions (Fig. S6, Table S9). Soil moisture changed CDD for six species, consistently being more negative in wetter conditions (Fig. 2a-f, S7, S8, Table S10). Notably, Dimocarpus longan and Symplocos racemosa had positive CDD at high conspecific densities in drier conditions (Fig. 2e,f, S8, Table S10). In nitrate rich soils, seven species had negative CDD, surviving better at low conspecific density compared to mean or high conspecific density (Fig. 2g-l, S9, S10, Table S11). As in drier soil, D. longan, S. racemosa and Psychotria nigra had positive CDD in nitrate poor soils at high conspecific densities (Fig. 2j-l, S10, Table S11). Soil ammonium and available phosphorus changed CDD for fewer species (Fig. S11-S14, Table S12, S13) and total nitrogen changed CDD for species in a similar manner as with nitrate (Fig. S9, S10, S15, S16, Table S11, S14).
Traits mediate variation in CDD across gradients: Under more open canopy (Canopy openness = 2.63 %), species with low SLA (5 th percentile, 14.78 mm 2 mg -1 ) had negative CDD whereas species with high SLA (95 th percentile, 26.77 mm 2 mg -1 ) exhibited positive CDD (Fig. 3a; Table S15). Under more shaded conditions (Canopy openness = 0.45 %), there was no evidence for CDD for either low or high SLA species (Fig. 3b, Table S15). Low LDMC (5 th percentile, 175.95 mg g -1 ) and high SRL (95 th percentile, 1466.2 mm g -1 ) species similarly had positive CDD at high conspecific densities when in open canopy (Fig. S17a,b, S18a,b, Table S16, S17), but there were no other trait-mediated changes in CDD across light availability.
Under high soil moisture (Soil moisture = 35.79%), species with high SLA, low LDMC, and high SRL experienced negative CDD at mean conspecific density (Fig. 3c, S17c, S18c, Table S18, S19, S20), but this effect was not significant at higher conspecific densities (Fig. 3c, S17c, S18c, Table S18, S19, S20). In dry conditions (Soil moisture = 3.77%), species with high SLA, low LDMC, and high SRL had positive CDD at high conspecific density (Fig. 3d, S17d, S18d, Table S18, S19, S20). Low SLA, high LDMC (95 th percentile, 587.73 mg g -1 ), and low SRL (5 th percentile, 123.03 mm g -1 ) species had no discernible CDD in either wet or dry conditions (Fig. 3c,d, S17c,d, S18c,d, Table S18, S19, S20).
Where soil nitrate increased (Nitrate = 72.26 mg Kg -1 ), species with high SLA and low LDMC experienced positive CDD at higher conspecific densities (Fig 3e, S17e, Table S21, S22), while low SLA and high LDMC species experienced negative CDD (Fig 3e, S17e, Table S21, S22). In low nitrate soils (Nitrate = 17.48 mg Kg -1 ), species with high SLA experienced negative CDD (Fig. 3f, Table S21). Unexpectedly, low SLA and high LDMC species experienced positive CDD at higher conspecific densities in low nitrate conditions (Fig. Fig. 3f, S17f, Table S21, S22). CDD did not vary with SRL in either high or low nitrate conditions (Fig. S18e,f, Table S23). Trait-mediated CDD variation was explained better with soil nitrate as compared to ammonium and phosphorus (Fig. 3c,d, S17 - S19, Table S21 - S29), and patterns with total available nitrogen (sum of ammonium and nitrate) reflected patterns with nitrate (Fig. S17-19, Table S21 - S23, S30 - S32).
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