Graphing
We plotted the species network through the R package igraphv1.2.6 (Csardi & Nepusz 2006), chord diagrams through circlizev0.4.13 (Gu et al. 2014), dendrograms and phylogenetic trees through ggplot2 v3.3.5 (Wickham 2016) and ggtree v3.2.1 (Yu et al. 2017, 2018), and heatmaps in ComplexHeatmapv2.10.0 (Gu et al. 2016).
Results