Population genomic of Dinizia jueirana-facao (Fabaceae). Raw sequences for Dinizia jueirana-facao (Fabaceae)

By performing sensitivity analyses, we empirically investigated how decisions about the percentage of missing data (MD) and the minor allele frequency (MAF) set in bioinformatic processing of genomic data affect direct (i.e., parentage analysis) and indirect (i.e., fine-scale spatial genetic structure - SGS) gene flow estimates. We focus specification on these manifestations in small plant populations, and specifically, in the rare tropical plant species Dinizia jueirana-facao, where assumptions implicit to analytical procedures for accurate estimates of gene flow may not hold. Avoiding biases in dispersal estimates are essential given this species is facing extinction risks due to habitat loss, and so we also investigate the effects of forest fragmentation on the accuracy of dispersal estimates under different filtering criteria by testing for recent decrease in the scale of gene flow. Our sensitivity analyses demonstrate that gene flow estimates are robust to different setting of MAF (0.05 to 0.35) and MD (0 to 20%). Comparing the direct and indirect estimates of dispersal, we find that contemporary estimates of gene dispersal distance (σrt = 41.8 m) was ~ fourfold smaller than the historical estimates, supporting the hypothesis of a temporal shift in the scale of gene flow in D. jueirana-facao, which is consistent with predictions based on recent, dramatic forest fragmentation process. While we identified settings for filtering genomic data to avoid biases in gene flow estimates, we stress that there is no ‘rule of thumb’ for bioinformatic filtering or that relying on default program settings is advisable. Instead, we suggest that the approach implemented here be applied independently in each separate empirical study to confirm appropriate settings to obtain unbiased population genetics estimates.