junglesm. a. charleston jungles a new solution to the host/parasite phylogeny reconciliation problem...

Jungles M. A. Charleston

Jungles

A new solution to the host/parasite

phylogeny reconciliation problem

M. A. Charleston

University of Glasgow

[email protected]


Problem Definition

Given: Host phylogeny H; Associate phylogeny P; Known associations between them .

What were the past associations of taxa?


Host/Parasite Phylogeny Reconciliation

Associations

Host phylogeny Associate Phylogeny


Multiple Solutions


The Model

Parasites are independent new species after speciation.

There are four event types: cospeciation, duplication, lineage sorting, and host switching.


The Four Event Types

time


Cospeciation

Associate

Host

Lineage Sorting

Host switch

Duplication


Event Costs

Event Cost

Cospeciation

Duplication

Lineage Sorting

Host Switch

c ≤ 0

d > 0

s > 0

w > 0


Jungles

The Jungle is a digraph (directed graph). The vertices of the jungle are the extant &

hypothesized host/parasite associations. The arcs of the jungle correspond to arcs of

the associate tree. The inferred events are dependent only on

the arcs in the jungle.


The Two J-Vertex Types

Type 1 vertex

h

p

Type 2 vertex

h

p

time


Jungle Arc Types - 1

sorting events

cospeciation event (type 1 vertex)

(type 1 or 2 vertex)p

p'

time


Jungle Arc Types - 2

sorting events

duplication event (type 2 vertex)


p'

time


Jungle Arc Types - 3sorting events

host switching event (type 2 vertex)


p'

take-off

landing sitetermination

time

Jungles M. A. CharlestonJungles M. A. Charleston

Host Switching

Host switching induces a partial ordering on the host tree

time

landing site

take-off

termination

w

w'

x

x'

w’ precedes x


Switch Incompatibility - 1

Weak Incompatibility:

Temporal incongruence can be fixed by moving landing sites back in time.

s1s2

u

u'

w

x

v

v'

x'

w'

s1 u’ precedes v

s2 w’ precedes x



s1 s2

induced sorting event

s1s2

induced sorting events

The order in which we consider host switches affects the number of induced sorting events.



Strong Incompatibility:

Moving the landing sites back cannot solve the temporal incongruity.

s1 u’ precedes w

s2 v’ precedes x

s1s2

xx'

w

w'

v

v'

u

u'

- Impossible!


From Tanglegram...

1

2

3

4

5

6

7

a

b

c

d

e

f

g


... to Jungle

Lineage sorting

Duplication

Cospeciation

Host switch✝

(f:7)*

(g:6)

(g:5)

(e:7)*

(a:1)

(c:2)

(b:3)

(d:4)

(f:4)

(e:1)

(g:7)*

(e:5)

(g:7)

(f:6)

(f:2)

(f:5)

(e:3)

(e:6)

✝

✝✝

✝✝

✝ ✝

✝

✝

✝

✝✝

✝✝

✝

✝

✝

✝

✝

✝

✝✝✝

✝

✝✝✝

✝

s12

s 1

s 3 s 4

s 5s 6

s 7

s 8

s 9s 10

s 11

s 13 s 14

2s

1

2

3

4

5

6

7

a

b

c

d

e

f

g


(f:7)*

(g:6)

(g:5)

(e:7)*

(a:1)

(c:2)

(b:3)

(d:4)

(f:4)

(e:1)

(g:7)*

(e:5)

(g:7)

(f:6)

(f:2)

(f:5)

(e:3)

(e:6)

1 1

221

3

2 21

3

4 44

4

4

444

6

6 5

7

88

38

8

8

83

88

6

65

7

1

2 21

331

2 2

1

10

10

3

0 0

00

2

33

5 5

8 6

5 5

3

2

JungleTraversal

1

2

3

4

5

6

7

a

b

c

d

e

f

g


Optimal Solutions Embedded

1

2

3

4

5

6

7

a

c

b

d

e

f

g


1

2

3

4

5

6

7

a

c

b

d

e

f

g

All Solutions Embedded


Gophers and Lice: Tanglegram

a:T.wardi

b:T.minor

c:G.thomomyus

d:G.actuosi

e:G.ewingi

f:G.chapini

g:G.panamensis

h:G.setzeri

i:G.cherriei

j:G.costaricensis

k

l

m

n

o

p

q

r

s

louse tree1:T.talpoides

2:T.bottae

3:G.busarius

4:O.hispidus

5:O.cavator

6:O.underwoodi

7:O.cherriei

8:O.heterodus

9

1011

12

13

14

15

gopher tree


Gophers and Lice: Jungle

(m:12)*(p:11)*

(p:12)

(p:12)*

(m:6)

(g:5)

(h:6)

(m:5)

(i:7)(j:8)

(n:10)*

(p:5)

(f:4)

(q:11)

(q:5)

(q:13)*

(q:4)

(l:14)

(o:3)

(o:14)

(o:15)*

(o:15)

(o:9)

(o:9)*

(r:15)*

(r:3)

(r:14)

(r:14)*

(r:4)

(r:11)

(r:12)

(r:5)

(r:13)

(s:12)

(s:5)

(s:13)

(s:4)

(s:3)

(s:15)*

(s:15)

(k:9)*

(l:15)*

(d:2)

(e:3)

(l:2)

(l:9)

(l:3)

(c:1)

(o:1)(r:1)

(r:9)

(r:15)

(a:1)

(b:2)

(s:9)

(s:11)

Page's solutionRonquist's solutionBoth solutionsRequired


1:T.talpoides

2:T.bottae

3:G.busarius

4:O.hispidus

5:O.cavator

6:O.underwoodi

7:O.cherriei

8:O.heterodus

a:T.wardi

b:T.minor

c:G.thomomyus

d:G.actuosi

e:G.ewingi

f:G.chapini

g:G.panamensis

h:G.setzeri

i:G.cherriei

j:G.costaricensis

Page’s Solution

Cospeciation

Duplication

Lineage Sorting

Host Switch

6

1

2

2


Ronquist’s Solution

1:T.talpoides

2:T.bottae

3:G.busarius

4:O.hispidus

5:O.cavator

6:O.underwoodi

7:O.cherriei

8:O.heterodus

a:T.wardi

b:T.minor

c:G.thomomyus

d:G.actuosi

e:G.ewingi

f:G.chapini

g:G.panamensis

h:G.setzeri

i:G.cherriei

j:G.costaricensis

Cospeciation

Duplication

Lineage Sorting

Host Switch

5

2

2

2


Conclusions

Complete representation of solution space in one figure Fast solution through dynamic programming Guarantees global optimality Correct accounting for host switches General model, extendable to maximum likelihood

junglesm. a. charleston jungles a new solution to the host/parasite phylogeny reconciliation problem...

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