Table 2.
List of the most significant gene families identified as unlikely under the BD model
|
Family name name |
Family sizes in Newick notation |
Predicted branch |
Likelihood ratio |
|---|---|---|---|
| Stress response | (15 (33 (24 (30 31)))) | 1 | 6e6 |
| Amino acid biosynthesis | (3 (8 (6 (6 5)))) | 1 | 36 |
| PGM/PMM | (1 (3 (3 (2 1)))) | 1 | 9 |
| Ribosomal L1 | (1 (4 (1 (1 1)))) | 2 | 3e3 |
| Chaperone | (1 (4 (2 (2 1)))) | 2 | 47 |
| α/β hydrolase | (2 (2 (6 (2 2)))) | 3 | 2e4 |
| Dihydrouridine synthase | (1 (1 (6 (1 1)))) | 3 | 6e5 |
| Trichothecene pump | (5 (5 (7 (10 6)))) | 4 | 6e3 |
| RNA polymerase Rpb1 | (4 (3 (5 (7 4)))) | 4 | 1e3 |
| Transposon | (2 (8 (15 (34 83)))) | 5 | 4e54 |
| Helicase | (1 (3 (3 (2 34)))) | 5 | 1e39 |
| Thiol oxidase | (1 (1 (4 (2 3)))) | 6 | 1e3 |
| Leucine rich repeat | (4 (3 (1 (2 1)))) | 6 | 38 |
| Flocculation | (10 (6 (8 (11 14)))) | 7 | 85 |
| Transposon | (17 (14 (15 (1 5)))) | 7 | 6e10 |
| Myosin
|
(5 (9 (9 (5 5))))
|
7
|
76
|
-
The first column gives the gene family name; the second column describes the gene family size among the five Saccharomyces species in Newick notation. The third column gives the branch that is predicted to be responsible for the overall low p-value of the family using the likelihood ratio test, and the fourth column gives the corresponding likelihood ratio. Newick numbers in bold indicate the branch identified.
