Statistical phylogenetic analysis for codivergence

2010 PRE-SUMMIT KENTUCKY BIOINFORMATICS SESSION, UT-ORNL-KBRIN Bioinformatics

March 19, 2010

Ruriko Yoshida

Epichloë/Neotyphodium in a grass plant

• Symbioses are:– Systemic– Constitutive– Often heritable

• Symbiotic continuum:– Mutualistic– Pleiotropic– Antagonistic

Life cycles of Epichloë and Neotyphodium spp.

asexual cycle & vertical

transmission

sexual cycle & horizontal transmission

Vertical transmissibility

Lolium pratense shoot and meristem with Epichloë festucae (w/GFP)

Confocal micrograph by Dr. Koya Sugawara

Lolium perenne embryo with Epichloë festucae (w/GFP)

Christensen et al. 2008

Endophytes protect against insects, nematodes, etc.

E–

E+

nutritionshelter

dispersal

anti-insectanti-vertebrateanti-nematodedrought toleranceetc.

Mutualisticexchanges between grasses and

endophytes

Biological questions

• Can we elucidate patterns of host and symbiont/parasite codivergence?

• What happens (phylogenetically) during invasion of new niches?

• How do sex and asexsual affect evolution?• Do neofunctionalized genes have unusual

evolution ?

Biological questions

• Can we elucidate patterns of host and symbiont/parasite codivergence?

• What happens (phylogenetically) during invasion of new niches?

• How do sex and asexsual affect evolution?• Do neofunctionalized genes have unusual

evolution ?

Hypothesis:

• H0: Pooideae and epichloae have NOT codiverged

• H1:Pooideae and epichloae have codiverged.

Schardl CL, Craven KD, Speakman S, Stromberg A, Lindstrom A, Yoshida R. 2008. Systematic Biology 57: 483-498.

Hosts of Epichloë spp.

Hosts

Phleum pratense, Anthoxanthum odoratumBrachypodium spp.

Poa nemoralis, Poa trivialis, Dactylis glomerata, Puccinellia distans, Lolium perenne

AveneaeBrachypodieae

Poeae E. typhina (I)

Brachypodium sylvaticumBrachypodieae E. sylvatica (VII)Holcus lanatusPoeae E. clarkii (I)

Glyceria striataMeliceaeE. glyceriae (VIII)Festuca spp., Lolium spp., Koeleria sp. Poeae, AveneaeE. festucae (II)

Elymus spp.TriticeaeE. elymi (III)

Bromus spp.BromeaeE. bromicola (VI)

Brachyelytrum erectumBrachyelytreaeE. brachyelytri (IX)Holcus mollisAveneaeEpichloë sp.

Agrostis spp., Sphenopholis spp.AveneaeE. amarillans (IV)Host tribeEpichloë sp. (MP)

Roegneria kamojiTriticeaeEpichloë yangzii (VI)

Agrostis spp., Calamagrostis spp.AveneaeE. baconii (V)

Achnatherum sibiricum

StipeaeEpichloë sp.

Epichloë gene trees

Lineage sorting effects and the species cloud

Host and epichloë phylogeniesHost cpDNA Fungus tubB + tefA

Problem with pairwise distance approach

Distancesa b c d

a 0 2 6 6b 0 6 6c 0 3d 0a b

ef

g

c d

phylogenetic tree

t = 3

Pairwise distancesto compare divergence times

Host treeA B

E F

G

C D a be f

g

c dEndophyte tree (E,e)

(F,f)(G,g)

pw d

istan

ce (E

ndop

hyte

)

pw distance (Host)MRCA pair Pairs of H and E taxon pairs(E,e) ((A,B),(a,b))(F,f) ((C,D),(c,d))(G,g)((A,C),(a,c)), ((A,D),(a,d)), ((B,C),(b,c)), ((B,D),(b,d))

MRCALink: Sample each pair of nodes once if ‘valid,’ otherwise not.

Host treeA B

E F

G

C D a be f

g

c dEndophyte tree (E,e)

(F,f)(G,g)

Node

age

(End

ophy

te)

Node age (Host)MRCA pair Pairs of H and E taxon pairs(E,e) ((A,B),(a,b))(F,f) ((C,D),(c,d))(G,g)((A,C),(a,c)), ((A,D),(a,d)), ((B,C),(b,c)), ((B,D),(b,d))

MRCALink on incongruent trees

A BE F

G

C DHost tree

a be

fg

c dEndophyte tree

MRCA pair Pairs of H and E taxon pairs(E,e) ((A,B),(a,b))(G,f)

((C,D),(c,d))(G,g) ((A,D),(a,d)), ((B,D),(b,d))(F,g)

((A,C),(a,c)), ((B,C),(b,c))

Node

age

(End

o)

Node age (Host)

(E,e)(G,f)

(G,g)(F,g)

Apply MRCALink to Pooideae-epichloae

Full

p = 0.123

Bivariate plots: Full and trimmed

p < 0.001

Codivergence of epichloae and Pooideae.• Suggests ancestral symbiosis 30–40

Mya.

Working on identifying likely host jumps

cysD and lolC relationships

• Why?– Paralogs with many

losses?– Long-branch

attraction?– Horizontal transfer?

lolC vs. tub2 phylogeny

• NIGMS• NSF

Acknowledgments• Collaborators:

– Jerzy W. Jaromczyk (UK)- Chris Schardl (UK)- David Haws (UK)- David Weisrock (UK)- Eric O’Niell (UK)- Peter Huggins (Fall 2010,

UK)- Arny Stromberg (UK)