From: Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios
i | Condition | Name | Description | Cost |
---|---|---|---|---|
0 | cohered leaf edge e and leaf tube d | fin | evolution of gene e ends in species d | c=0 |
1 | non-cohered leaf edge e and leaf tube d, d≠d* | tr_fin | gene e evolves into a non-cohered species and transfers without retention to a cohered species | c=с(tr_without) |
2 | same as #1 but d=d* | ga_fin | gene e emerges in a cohered terminal species | c=с(gain) |
3 | tube d has the single child d1 | pass | gene e transfers to the next time slice, tube d1 | c=c(e,d1) |
4 | edge e bifurcates into e1 and e2, tube d bifurcates into d1 and d2 | fork_lr | d≠d0: gene e evolves with speciation into two descendants: e1 transfers to d1, e2 – to d2; d=d0: one of the two descendants of gene e is absent in the root R | c=c(e1,d1)+c(e2,d2) |
5 | same as #4 | fork_rl | d≠d0: gene e evolves with speciation into two descendants: e1 transfers to d2, e2 – to d1; d=d0: same as #4 | c=c(e2,d1)+c(e1,d2) |
6 | d≠d0, tube d bifurcates into d1 and d2 | pass_l | gene e transfers with speciation to d1 and is lost in d2 | c=c(e,d1)+c(loss) |
7 | same as #6 | pass_r | gene e transfers with speciation to d2 and is lost in d1 | c=c(e,d2)+c(loss) |
8 | d=d0, tube d bifurcates into d1≠d*, d2=d* | nout_l | gene e is present in the root R | c=c(e,d1) |
9 | d=d0, tube d bifurcates into d1=d*, d2≠d* | nout_r | same as #8 | c=c(e,d2) |
10 | d=d0, tube d bifurcates into d1=d*, d2≠d* | out_l | gene e is absent in the root R | c=c(e,d1) |
11 | d=d0, tube d bifurcates into d1≠d*, d2=d* | out_r | same as #10 | c=c(e,d2) |
12 | edge e bifurcates into e1 and e2, d≠d* and genes e1 and e2 do not undergo the events out_l or out_r | dupl | gene e in d duplicated | c=c(e1,d)+c(e2,d)+c(dupl) |
13 | same as #12 but d=d0 and at least one of the genes e1 or e2 undergoes the events out_l or out_r | dup0 | one of the descendants of e is absent in the root R | c=c(e1,d)+c(e2,d) |
14 | edge e bifurcates into e1 and e2, d=d* | outd | gene e is duplicated in the outgroup | c=c(e1,d)+c(e2,d) |
15 | edge e bifurcates into e1 and e2, d≠d*, d≠d0 | tr1 | one copy e1 of e from d transfers to d' ~ d, d' ≠ d*, another copy e2 of e retains in d | с=c(e1,d')+c(e2,d)+c(tr_with) (minimization over d', if uncertainty select one closest to d) |
16 | same as #15 | tr2 | one copy e2 of e from d transfers to d' ~ d, d' ≠ d*, another copy e1 of e retains in d | с=c(e2,d')+c(e1,d)+c(tr_with) (minimization over d', if uncertainty select one closest to d) |
17 | edge e bifurcates into e1 and e2, d=d* | ga1 | gene e1 emerges in the species d' ~ d | с=c(e1,d')+c(e2,d)+c(gain) (minimization over d') |
18 | same as #17 | ga2 | gene e2 emerges in the species d' ~ d | с=c(e2,d')+c(e1,d)+c(gain) (minimization over d') |
19 | e≠e0, d≠d*, d≠d0, d is not terminal | sl | gene e stops functioning | c=c(e,d*)+c(sleep) |
20 | e=e0, d=d* | ga_big | gene e0 emerges in d' ~ d as a common ancestor of all G i | с=c(e0,d')+c(gain_big) (minimization over d') |
21 | d≠d*, d≠d0 | tr_pass | gene e transfers without retention to d' ~ d, d' ≠ d*, that produces the single descendant d'1, and then transfers to d'1 | c=c(e,d'1)+c(tr_without) (minimization over d', if uncertainty select one closest to d) |
22 | e≠e0, d=d* | ga_pass | gene e emerges in d' ~ d that produces the single descendant d'1, and then transfers to d'1 | c=c(e,d'1)+c(gain) (minimization over d') |
23 | edge e bifurcates into e1 and e2, d≠d*, d≠d0 | tr_lr | gene e transfers without retention to d' ~ d, d' ≠ d*, that bifurcates into d'1 and d'2, then e1 transfers to d'1, and e2 – to d'2 | с=c(e1,d'1)+c(e2,d'2)+ c(tr_without) (minimization over d', if uncertainty select one closest to d) |
24 | same as #23 | tr_rl | gene e transfers without retention to d' ~ d, d' ≠ d*, that bifurcates into d'1 and d'2, then e1 transfers to d'2, and e2 – to d'1 | с=c(e1,d'2)+c(e2,d'1)+ c(tr_without) (minimization over d', if uncertainty select one closest to d) |
25 | e≠e0, edge e bifurcates into e1 and e2, d≠d* | ga_lr | gene e emerges in species d' ~ d that bifurcates into d'1 and d'2, then e1 transfers to d'1, and e2 – to d'2 | с=c(e1,d'1)+c(e2,d'2)+c(gain) (minimization over d') |
26 | same as #25 | ga_rl | gene e emerges in species d' ~ d that bifurcates into d'1 and d'2, then e1 transfers to d'2, and e2 – to d'1 | с=c(e1,d'2)+c(e2,d'1)+c(gain) (minimization over d') |
27 | d≠d*, d≠d0 | tr_l | gene e transfers without retention to species d' ~ d, d' ≠ d* that bifurcates into d'1 and d'2, and then transfers to d'1 and is lost in d'2 | с=c(e,d'1)+c(tr_without)+ c(loss) (minimization over d', if uncertainty select one closest to d) |
28 | same as #27 | tr_r | gene e transfers without retention to species d' ~ d, d' ≠ d* that bifurcates into d'1 and d'2, and then transfers to d'2 and is lost in d'1 | с=c(e,d'2)+c(tr_without)+ c(loss) (minimization over d', if uncertainty select one closest to d) |
29 | e≠e0, d=d* | ga_l | gene e emerges in species d' ~ d that bifurcates into d'1 and d'2, and then transfers to d'1 and is lost in d'2 | с1=c(e,d'1)+c(gain)+c(loss) (minimization over d') |
30 | same as #29 | ga_r | gene e emerges in species d' ~ d that bifurcates into d'1 and d'2, and then transfers to d'2 and is lost in d'1 | с1=c(e,d'2)+c(gain)+c(loss) (minimization over d') |
31 | edge e bifurcates into e1 and e2, d≠d*, d≠d0 | tr_dupl | gene e transfers without retention to species d' ~ d, d' ≠ d*, and then duplicates | c=c(e1,d')+c(e2,d')+ c(tr_without)+c(dupl) (minimization over d', if uncertainty select one closest to d) |
32 | edge e bifurcates into e1 and e2, e≠e0, d=d* | ga_dupl | gene e emerges in species d' ~ d, and then duplicates | c=c(e1,d')+c(e2,d')+c(gain)+ c(dupl) (minimization over d') |
33 | edge e bifurcates into e1 and e2, d≠d*, d≠d0 | tr_double | gene e transfers without retention to species d' ~ d, d'≠d*, then its copy e2 transfers to d” ~ d, d” ≠ d”, d” ≠ d*, and copy e1 – to d'; or vice versa replacing d' with d" and e1 with e2 | c=c(e1,d')+c(e2,d")+ c(tr_without)+c(tr_with) (minimization over pair < d', d" >, if uncertainty select a pair closest to d as per the sum of distances) |
34 | e≠e0, edge e bifurcates into e1 and e2, d=d* | ga_double | gene e emerges in species d' ~ d, then its copy e2 transfers to d" ~ d, d" ≠ d', and copy e1 retains in d'; or vice versa replacing d' with d" and e1 with e2 | c=c(e1,d')+c(e2,d")+c(gain)+ c(tr_with) (minimization over pair < d’, d" >) |