2.7 | Demographic inference using fastsimcoal2 and δaδi
We used the fastsimcoal2 (Excoffier, Dupanloup, Huerta-Sánchez, Sousa, & Foll, 2013) approach to deduce the recent demographic history ofParascaris spp. populations. We chose only SNPs located in intergenic regions to avoid the influence of SNPs under selection(Zhou et al., 2018). We used δaδi (Gutenkunst, Hernandez, Williamson, & Bustamante, 2009) to investigate alternative demographic scenarios for the species complex. In the absence of historical evidence, we hypothesized that there may or may not be any form of gene flow between roundworm populations. In order to get the best model, we first simulated a total of ten δaδi 3D models, including one simple model, three simultaneous splitting models, one ancient migration model, one simultaneous splitting variations model, one admixed (“Hybrid”) origin model and three divergences with gene flow variations models. When fitting demographic models, we perform multiple runs (100 rounds) and ensure that final optimizations are converging on a similar log-likelihood score. To estimate demographic parameters, the derivative-based BFGS algorithm was used to optimize the composite log-likelihood. All models and scripts are available athttps://github.com/dportik/dadi_pipeline.