Fig. 3: Evolutionary time ariid lineages have spent in each habitat or state, and the number of positively selected genes (PSGs) for each, based on the ten analyzed trees.

Time spent in each habitat is differentiated in two ways: (i) complete tree (CT; black stroke; 119 species), and (ii) sampling restricted to taxa with whole-genome sequences used for HyPhy analyses (HT; gray stroke; 66 species). a Ariid lineages spent ~78% of their evolutionary history in the ocean (red) and 22% in rivers (blue) (61% vs. 39%, respectively, considering trees with whole-genome species only). In both scenarios, freshwater lineages exhibit a higher number of genes under positive selection, both in total count and specifically for body size and elongation, compared to marine lineages, aligning with the greater morphological disparity observed in younger freshwater lineages, with a mean disparity of 234.85, compared to 103.1 in their more ancient marine counterparts (refer to Supplementary Information, Fig. S19 for similar analyses of marine-to-freshwater transitions coded after excluding euryhaline species). b Euryhaline species (magenta) and (c) pelagic planktivores (pink), representing derived (test) states or habitats, have considerably fewer PSGs compared to their ancestral (reference) counterparts (stenohaline, purple; benthic, amaranth). While this coincides with the proportional evolutionary time spent in each habitat (15–20% euryhaline, 5–17% pelagic versus 80–86% stenohaline, 83–95% benthic), these two transitions also involve fewer lineages in the derived state compared to marine-to-freshwater transitions. Therefore, the relative proportions of PSGs are not necessarily comparable across the three different transitions. Boxplots depict the median (center line), interquartile range (box), and range (whiskers). Source data are provided as a Source Data file.