Table 1 Number of positively selected genes (PSGs), initially identified from the set of 119 PSGs (out of 2,310 genes tested) using BUSTED-E and analyzed using aBSREL, BUSTED-PH, and RELAX across the three ecological transitions
HABITAT TRANSITION | |||||
|---|---|---|---|---|---|
Marine-to-freshwater transition (coding euryhaline species based on the most probable tip state) | Marine-to-freshwater transition (excluding euryhaline species and reversals to the ancestral marine condition) | Shared genes between the two coding schemes for the marine-to-freshwater transitions | Stenohaline-to-euryhaline transitions | Benthic-to-pelagic planktivore transitions | |
aBSREL (stem lineages - during transitions to derived habitats) | |||||
aBSREL | 40 | 39 | 32 | 28 | 17 |
BUSTED-PH: ancestral vs derived habitats | |||||
BUSTED-PH ANCESTRAL HABITAT | 45 | 49 | 43 | 67 | 58 |
BUSTED-PH DERIVED HABITAT | 67 | 88 | 61 | 33 | 13 |
BUSTED-PH: derived habitats AU-NG vs derived habitats non-radiating clades elsewhere | |||||
BUSTED-PH AU-NG | 64 | 45 | 41 | 18 | 10 |
BUSTED-PH REMAINING TEST CLADES | 59 | 51 | 49 | 69 | 73 |
RELAX: ancestral vs. derived habitats | |||||
RELATIVE INTENSIFICATION OF SELECTION OF DERIVED COMPARED TO ANCESTRAL HABITATS | 8 | 7 | 3 | 4 | 2 |
RELATIVE RELAXATION OF SELECTION OF DERIVED COMPARED TO ANCESTRAL HABITATS | 11 | 9 | 4 | 5 | 5 |
RELAX: derived habitats AU-NG vs. derived habitats non-radiating clades elsewhere | |||||
RELAX GUIS AU-NG | 14 | 6 | 4 | 5 | 1 |
RELAX GUIS REMAINING TEST CLADES | 13 | 9 | 5 | 3 | 1 |
RELAX GURS AU-NG | 5 | 7 | 4 | 2 | 1 |
RELAX GURS REMAINING TEST CLADES | 3 | 2 | 1 | 2 | 1 |
Habitat Transitions Identified | |||||
BASED ON COMPLETE TREES | 10-12 | 10-12 | 10-12 | 9 − 11 | 5 − 6 |
BASED ON PRUNED TREES USED FOR HYPHY ANALYSES | 9 − 10 | 9 − 10 | 9 − 10 | 9 − 11 | 5 − 6 |
