Skip to main content
. 2012 Dec 22;7:48. doi: 10.1186/1745-6150-7-48

Table 1.

Types of evolutionary events and their costs

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, dd*
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
dd0: 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
dd0: 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
dd0, 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 d1d*, 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*, d2d*
nout_r
same as #8
c=c(e,d2)
10
d=d0, tube d bifurcates into d1=d*, d2d*
out_l
gene e is absent in the root R
c=c(e,d1)
11
d=d0, tube d bifurcates into d1d*, d2=d*
out_r
same as #10
c=c(e,d2)
12
edge e bifurcates into e1 and e2, dd* 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, dd*, dd0
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
ee0, dd*, dd0, 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
dd*, dd0
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
ee0, 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, dd*, dd0
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
ee0, edge e bifurcates into e1 and e2, dd*
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
dd*, dd0
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
ee0, 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, dd*, dd0
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, ee0, 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, dd*, dd0
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 ee0, 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.