Statistical phylogenetic analysis for codivergence
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Statistical phylogenetic analysis for codivergence
2010 PRE-SUMMIT KENTUCKY BIOINFORMATICS SESSION, UT-ORNL-KBRIN Bioinformatics
March 19, 2010
Ruriko Yoshida
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Epichloë/Neotyphodium in a grass plant
• Symbioses are:– Systemic– Constitutive– Often heritable
• Symbiotic continuum:– Mutualistic– Pleiotropic– Antagonistic
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Life cycles of Epichloë and Neotyphodium spp.
asexual cycle & vertical
transmission
sexual cycle & horizontal transmission
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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
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Endophytes protect against insects, nematodes, etc.
E–
E+
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nutritionshelter
dispersal
anti-insectanti-vertebrateanti-nematodedrought toleranceetc.
Mutualisticexchanges between grasses and
endophytes
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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 ?
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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 ?
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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.
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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.
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Epichloë gene trees
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Lineage sorting effects and the species cloud
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Host and epichloë phylogeniesHost cpDNA Fungus tubB + tefA
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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
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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))
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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))
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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)
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Apply MRCALink to Pooideae-epichloae
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Full
p = 0.123
Bivariate plots: Full and trimmed
p < 0.001
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Codivergence of epichloae and Pooideae.• Suggests ancestral symbiosis 30–40
Mya.
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Working on identifying likely host jumps
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cysD and lolC relationships
• Why?– Paralogs with many
losses?– Long-branch
attraction?– Horizontal transfer?
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lolC vs. tub2 phylogeny
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• 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)