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I present the largest survey of seed germination yet for Barro Colorado Island (BCI) and central Panama, based on 1,226 seed collections from 732 species, in 103 families, including trees, shrubs, lianas, vines, herbs, and epiphytes. Most collections were germinated in both sun and shade habitats in growing houses on BCI, simulating tree fall gap and shaded understory conditions. Many ad hoc treatments were also utilized. Data were collected during the field portion (1985–1989) of the BCI Seedling Flora Project. This publication marks the public release of the entire dataset, parts of which have previously been shared with BCI colleagues. I hope that this dataset will provide background information for those needing to produce seedlings from seed for experimental studies and that it will encourage others to incorporate seed germination as an additional plant trait into community analyses. 

Abstract In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4 Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM threefold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype-like gene expression.