Table 1.
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 Gi |
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" >) |
Consider i as the number of the event (and the row number) in a fixed enumeration pattern; “Condition” defines the applicability of the event to current pair <e, d >; “Name” is the event type; “Description” is the event synopsis; “Cost” contains formulas to compute the costs of scenarios initiated from an event in a current row. A notation d ~ d' designates that “tubes d and d' differ and belong to the same time slice”. The constants c(dupl), c(loss), c(gain), c(gain_big), c(tr_without), c(tr_with), c(sleep) define the costs of individual events and constitute parameters of the algorithm.