Following the generation of phylogenetic trees, families were resolved to one-to-one or one-to-two human-to-fugu gene relationships based on visual inspection of the consensus trees.
For analysis of genetic distances within and among species, we first defined genetically distinct clusters within each species based on visual inspection of the NJ tree, using a combination of genetic distances and bootstrap support.
Based on visual inspection of the entire clustering tree related to BY/RM differences, we extracted 23 gene clusters showing specific patterns of divergence between the two strains (Fig. 3a).
Five simultaneous Markov chains were run for 1,000,000 generations with trees sampled every 10 generations, with 50,000 initial trees discarded as burn-in, based on visual inspection.
Four simultaneous Markov chains were run for 1,200,000 (Tub1) or 2,000,000 (Tub2) generations; trees were sampled every 100 generations, with 300,000 (Tub1) or 500,000 (Tub2) initial trees discarded as burn-in, based on visual inspection.
Twenty fruits per tree were harvested at commercial maturity based on visual colour change and manual evaluation of firmness and the date was recorded.
Based on visual field observation and previous vegetation studies (Belayneh et al. 2011), three dominant tree species, representing one leguminous (Acacia robusta Burch) and two non-leguminous tree species (Ziziphus spina-Christi and Balanites aegyptiaca L ., found in isolation, were selected for this study.
The first 20%% of sampled trees from all runs were discarded as burn-in based on visual inspection in Tracer version 1.4 [ 54].
The tree is not an immutable biological category but rather a human concept based on visual criteria.
One-way non-parametric analyses (Kruskal-Wallis tests) were used to compare patterns of seedfall among the four tree groups because neither log nor arcsine-square transformations met ANOVA assumptions based on visual inspection of the residuals against predicted variables.
