Computational protocol: Pollen and seed flow patterns of Carapa guianensis Aublet. (Meliaceae) in two types of Amazonian forest

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[…] The average number of alleles per locus (A), allelic richness (RS) (), gene diversity (He) and fixation index (F) were estimated for juveniles and adults of both plots. The statistical significance of F values was tested using 500 permutations of alleles among individuals and the Bonferroni correction. These analysis were done using FSTAT software ver. (). Allelic information for the loci is available in . A small proportion of null alleles (∼ 9%) were estimated only for one locus. Combined exclusionary power for parent pair, genetic identity parameters and parentage inferences were determined with CERVUS ver. 3.0 (). We attempted to determine the possible pollen donor and seed tree of juveniles from the two forest plots by simple exclusion based on multilocus genotypes for all adults in each plot. This technique uses mismatching between parents and offspring genotypes to reject particular parent-offspring hypotheses and has been successfully used in other studies (; ; ; ). We considered as candidate parents only adult trees sampled in the same plot as the juveniles. We did not test for parentage between plots since the plots were separated by continuous forest with C. guianensis individuals between plots (see ). Whereas not testing for parents between plots may underestimate seed and pollen flow, testing between plots without accounting for individuals in between the two plots would likely overestimate dispersal distances. In parentage assignment, a minimum number of five typed loci was considered and the genotyping error was set at zero, following ; no mismatching between juveniles and candidate parents was allowed.In view of our assumption of limited seed dispersal distance for this species, when a juvenile had a parent pair within the plot then the closest parent was considered the seed tree. Although our strategy of considering the closest parent as the seed tree may underestimate seed dispersal distances, this assumption, which was introduced by , has been used for monoecious and hermaphroditic species in conjunction with prior knowledge of seed and pollen dispersal vectors (; ; ; ). This strategy provides conservative estimates of seed dispersal distances (; ; ). Distances between the two parents of a given juvenile were used to calculate the pollen dispersal curve and the distance between the juvenile and the seed tree was used to obtain a seed dispersal curve. Differences between pollen and seed flow distances, as well as differences in the pollen flow distances and seed flow distances between forest types, were tested with the Mann-Whitney test using SPSS ver. 15.0 (SPSS, Chicago, IL, USA) since the data had a normal distribution but the variances were not homogeneous. The cryptic gene flow, which is the probability that foreign seeds (from outside the plot) have a multilocus genotype that matches local parents (in the plot), was estimated as described by using the equation 1−Pexnp, where Pex is the combined exclusionary power for the parental pair (in this study) and np is the number of putative pollen donors in the plot.Finally, we compared the distribution of pollen flow distances with the distribution of distances between each seed tree and all the potential parents in each plot to determine whether gene flow distances were a function of the average distance between pollen donors and seed trees. We tested for significance with the Kolmogorov-Smirnov test in SPSS ver. 15.0. [...] We characterized the spatial genetic structure (SGS) in each forest type and within size classes (juveniles and adults) using spatial autocorrelation procedures and calculated the mean kinship coefficients (Fij) from for ten distance classes of constant intervals. For each distance interval, 95% confidence intervals (CIs) for the null hypothesis of no genetic structure (Fij = 0) were obtained using the permutation of individuals among distance classes (; ).Average pairwise Fij estimates were plotted against the logarithm of the pairwise spatial distances to test the overall pattern of SGS in adults and juveniles of each forest type. Under isolation by distance in a two dimensional space, kinship is expected to decrease approximately linearly with the logarithm of the spatial distance (). The regression slope (bF) was used to quantify the extent of spatial genetic structure based on the Sp statistic described in . The Sp statistic was obtained by the ratio – bF/(1 – F(1)), where F(1) is the average Fij between adjacent individuals, i.e., the first distance interval included trees < 25 m apart. The significance of bF was tested by 10,000 permutations of individuals among spatial positions. All computations were done using the SPAGeDi 1.2 program (). […]

Pipeline specifications

Software tools Cervus, SPSS, SPAGeDi
Applications Miscellaneous, Phylogenetics
Diseases Blood Platelet Disorders