Table 1 Types of evolutionary events and their costs

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" >)