DOI: 10.5061/dryad.0zpc8674f
title: Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species

description: Most Central African rainforest canopies consist of light-demanding tree
 species that hold high commercial value but also suffer locally from
 regeneration deficits, raising concerns about the sustainability of
 logging. Regeneration is influenced by factors such as past perturbations
 (including human activity), mating systems, and seed/pollen dispersal
 processes that impact demographic, spatial, and genetic structures within
 populations. To gain a better understanding of these interactions, we
 studied the spatial distribution and trunk diameter structure
 of Cylicodiscus gabunensis (Fabaceae) - a
 wind-dispersed, insect-pollinated, timber species - in three plots ranging
 from 400 to 839 ha situated in various environmental contexts
 (e.g. forest types and elephant densities) across Central Africa. We also
 genotyped adults and juveniles using microsatellite markers to analyze the
 spatial genetic structure of each population and infer the selfing rate,
 seed and pollen dispersal capacities and selection gradients using
 the ‘neighborhood model’. The selfing rate was low (3 –
 4 %), and seed dispersal distances
 (ds = 184 m) were much shorter than pollen
 dispersal distances (dp &gt; 2 km). The
 three populations displayed contrasted spatial, demographic and genetic
 structures. One population showed no spatial aggregation or genetic
 structure, and a multimodal diameter structure indicating pulses of
 regeneration events. Two populations showed strong spatial aggregation and
 genetic structures. One exhibited a unimodal diameter structure indicating
 one ancient pulse of regeneration, while the other displayed a
 'reverse J-shaped' diameter structure, typical of ongoing
 regeneration. In the latter, reproductive success appeared leptokurtic,
 three mother trees accounting for over 90 % of the regeneration
 and no tree below the minimum cutting diameter implemented by logging
 companies had offspring. The idiosyncratic nature of population
 characteristics observed in C. gabunensis suggests that, for
 sustainable management, a nuanced approach is needed. This involves
 protecting productive seed trees in areas where natural regeneration is
 occurring and actively supporting regeneration in areas exhibiting
 deficits, especially in contexts with low elephant densities.
description: In a 400 ha
 forest plot in Cameroon (site A), all <em>C. gabunensis</em>
 trees with a diameter at breast height (dbh) ≥ 10 cm were systematically
 inventoried and georeferenced with a GPS. To
 ensure exhaustive sampling, six individuals, spaced regularly between
 them, position themselves between two lines 100 meters apart, moving
 abreast and systematically sample the individuals found.  Individuals with
 a dbh &lt;10 cm were also inventoried when encountered although we do
 not expect to have reached an exhaustive inventory for them. The dbh of
 each sampled tree was measured and the dominance status of each
 tree, indicating
 whether the position of the tree crown is below, within, or above relative
 to the surrounding canopy layer (dominant, co-dominant or dominated)
 was also recorded. For each individual we collected a sample of a few
 cm<sup>2</sup> of cambium or a leaf that was immediately dried
 with silica-gel to preserve DNA. We
 used the ‘neighborhood model’ (parentage model) to estimate seed and
 pollen dispersal kernels, selfing rate and effects of phenotypic
 characters on reproductive success. The model is implemented in the
 software NMπ (Chybicki, 2018) that requires genotype data on progeny and
 their putative parents, their spatial coordinates, and optionally tree
 quantitative phenotypic characters to estimate their effects on male and
 female reproductive success. Saplings and juveniles (dbh &lt; 20
 cm) were assigned as dispersed progeny, considering that potential
 parental trees have a dbh of at least 20 cm. Such data
 provides insights into female reproductive success and seed
 dispersal.  Pollen and seed
 dispersal were measured by: the selfing rate <em>s</em>, the
 proportion of pollen and seed immigration <em>mp</em> and
 <em>ms</em> (indicating that the father or both parents were
 located outside the sampled plot, or were missed during sampling) as well
 as four parameters of the exponential-power-von Misses distribution for
 modelling forward dispersal kernel (i.e., distribution of seed or pollen
 rains around parents). These kernel parameters are: the mean pollen and
 seed dispersal distance <em>dp</em> and
 <em>ds</em>, the shape parameter of the dispersal distribution
 <em>bp</em> and <em>bs</em> (i.e.,
 <em>b</em> = 2 for a Gaussian distribution,
 <em>b</em> = 1 for an exponential distribution,
 <em>b</em> &lt; 1 for a fat‐tailed distribution), the
 intensity of directionality (anisotropy) in dispersal
 <em>kp</em> and <em>ks</em> (with
 <em>k</em> = 0 under isotropic dispersal), and the azimuth of
 the prevailing dispersal direction <em>ap</em> and
 <em>as</em> (when <em>kp</em> &gt; 0 or
 <em>ks</em> &gt; 0). The effect of
 phenotypic characters on female and male reproductive success (selection
 gradients) was assessed through NMπ. This analysis involved centered and
 standardized dbh values and, for site A, centered and standardized
 dominance status (high values for trees dominating the surrounding
 canopy). Kendall's rank correlation coefficient
 (<em>τ</em><em><sub>b</sub></em>) was used to examine the relationship between DBH and tree dominance status. Once all parameters were estimated, NMπ provided the most likely mother and father of each seed and seedling with an associated probability, accounting simultaneously for the spatial, genotypic and phenotypic character data. Considering the progeny (seedlings and juveniles) for which a father/mother was inferred with a probability of P ≥ 0.8, the dbh structure was compared between all trees, inferred mothers and inferred fathers.  The fine-scale spatial genetic structure (FSGS) in site A was characterized by the decay of the kinship coefficient, <em>Fij</em>, between trees (dbh ≥20 cm) with spatial distance (kinship–distance curve) following the procedure described by Vekemans & Hardy (2004), using SPAGeDi ver. 1.5d (Hardy & Vekemans, 2002). For each pair of individuals i and j from the same population, <em>F<sub>ij</sub></em><sub> </sub>was estimated using J. Nason's estimator (Loiselle et al., 1995) and the set of <em>F<sub>ij</sub></em><sub> </sub>values were regressed on the spatial distance <em>ln(d<sub>ij</sub>)</em> between individuals providing the regression slope <em>b<sub>Ld</sub></em>. The later can inform about the strength of FSGS through the statistic Sp, which synthesizes the decay of kinship coefficient between individuals with distance (Vekemans & Hardy, 2004). To visualize FSGS, <em>F<sub>ij</sub></em> values were also averaged for a set of nonoverlapping distance intervals (delimited by 50, 100, 200, 300, 500, 700, 1000, and 1500 m) to obtain the <em>F(r)</em> curve. Standard errors were provided by jackknifing loci (i.e. deleting information from one locus at a time). To test for FSGS, spatial positions of trees were permuted 999 times to draw 95% confidence intervals of the <em>F(r)</em> curves under the null hypothesis (random spatial distribution of genotypes).
description: # Dataset for investigating the spatial, demographic, and genetic
 structures of *Cylicodiscus gabunensis* Harms, a light-demanding African
 timber species
 [https://doi.org/10.5061/dryad.0zpc8674f](https://doi.org/10.5061/dryad.0zpc8674f) The dataset comprises files with information on *Cylicodiscus gabunensis* individuals sampled in two 400 ha forest plots (site A and B) and a 839 ha one (site C). It also includes NMpi and SPAGeDi input data files for the three plots (only site A and C for NMpi). This dataset is valuable for examining both diameter distribution and spatial patterns, spatial genetic structure, mating system, gene flow and determinants of reproductives success. ## Description of the data and file structure There are three types of data files provided. The first type consists of lists of Cylicodiscus gabunensis individuals that were sampled. The first row in these datasets serves as the header. These datasets contain individual names in the first column, longitude (x coordinates) and latitude (y coordinates) in the second and third columns, diameter at breast height in the fourth column, and canopy dominance status (Dawkins' crown illumination index) in the fifth column (only for site A). These datasets have versatile applications, enabling the creation of size-class maps for individuals categorized as saplings (dbh &lt; 10 cm), juveniles (dbh from 10 cm to &lt; 20 cm), and trees with dbh from 20 cm up to &lt; 200 cm, grouped in 10 cm intervals. They can also be used to generate histograms showing frequency distribution per dbh class and calculate stand density. Additionally, they facilitate the characterization of the spatial distribution of trees (dbh ≥ 20 cm) using the 'spatstat' R package (Baddeley et al., 2015) through the pair correlation function g (PCF), which is a distance-dependent correlation function related to the derivative of the widely used K-function (Ripley, 1976). The second type of files are the NMpi input data files. The header of each file follows this structure: np no nl nf, where np is the number of parents, no is the number of progeny, nl is the number of loci (limited to nuclear genetic markers), and nf is the number of phenotypic characters. Subsequent lines contain individual data, with each parent or progeny line starting with 0 (indicating generation), followed by ID, X and Y coordinates, cytotype, genotype, phenotypic characters, and the femaleness index. The third type of files are the SPAGeDi input data files. These datasets follow a specific format: The first line contains six format numbers for individuals, categories, spatial coordinates, loci, allele coding digits, and ploidy level. The second line defines distance intervals, while the third line lists column labels. Starting from the fourth line, individual data is presented, including names, categories, coordinates (either coordinates or latitude and longitude), and genotypes at each locus. Each dataset concludes with the word "END." Additionally, there may be optional lines for dominant markers or polyploid data following this structured format, ensuring data organization for analysis.