External Review on CCS, University of Tsukuba @ Oct. 30, 2007

Can we include EF2 in multigene
phylogenetic analyses?

Yuji Inagaki

Translation elongation factor 2 (EF2)• Catalyzes translocation of aa-tRNA from A
site to P site in ribosomes– Highly conserved• EF2 is a major “maker”– Monophyly of red algae and green plants(Moreira, Le Guyader & Philippe 2000)– Stiller, Riley & Hall. (2001) suggested that redand green genes were recombined• Here we tested– Multi-gene data w/ and w/o EF2– “Recombination” hypothesis by Stiller et al.

Model & genes• ML method under the unlinked WAG + Γmodel– Among-site rate variation– Variation of evolutionary patterns across genes• 24 nuclear-encoded protein genes– EF-1α, EF2, IleRS, ValRS, RPS14, RPS15a, RPL5,RPL8, RPL10a, RPB1, cytosolic-Hsp70, ER-Hsp70,
mitochondrial-Hsp70, cytosolic-Hsp90, Cpn60, CCTα,CCTδ, CCTγ, CCTζ, Actin, α-Tubulin (Tba), β-Tubulin(Tbb), vATPA, vATPB• >10,000 aa positions

Eukaryotic groups considered• Assumed the monophyly of the 7 groups– Opisthokonts– Amoebozoa– Green plants– Red algae– Euglenozoa + Heterolobosea– Alveolates + stramenopiles– Diplomonads + parabasalids• Exhaustively searched for the ML tree from945 test trees• Bootstrap analysis

Exhaustive search for the ML tree

• Calculated the lnL of 945 trees for each gene
– Parameters optimized for each geneT3··· TN

Data 1lnL

lnL

lnL ···lnL

Data 2lnL

lnL

lnL ···

lnL···

lnLlnL

Data 3lnLlnLlnL ···

lnL···

lnLlnL···lnL

lnL···

lnL···

lnL·········

T945···

T2······ T944···

T1

Data 10lnLlnL

lnL ···

lnL·····················

Data 23lnLlnL

lnL ···

lnL···

lnLlnL

Data 24lnLlnL

lnL ···

lnL···lnL

lnLTotallnL1 lnL2 lnL3 ···lnLN ··· lnL944 lnL945

MPI-Puzzle – For exhaustive tree search• Calculated lnL by a modified Tree-Puzzle
Sequential

T2lnLT2T3lnLT3···

TNlnLTN

T945

lnLT945lnLT2T3

lnLT3TN+1

lnLTN+1

Data

TN+2

lnLTN+2TN+3lnLTN+3TN+1

lnLTN+1TN+2lnLTN+2TN+3

lnLTN+3······
lnLT944

T2···

···
T944

lnLT1···

lnLT1T1···

T1···

DataParallel······24-gene phylogeny• Are strong supportstrue?
– EF2 prefers R+G

Opisthokonta

49• Are the signals
uniform?
87– Single-gene JK– More systematic97
way to compare98
signal in each gene
– By using P values ofSH tests

Amoebozoa
Diplomonads/
Parabasalids
Stramenopiles/
Alveolates
Euglenozoa/
Heterolobosea
Green plants
Red algaeP value heat map• “Gene-specific signal” was represented by
P values of SH tests– P values are color-coded– EF2: 109 trees passed– All trees w/ “R+G” passed
Trees (945)
1.0

Not many “red bands”

EF20

23-gene analyses – w/o EF2• R+G recovered

Opisthokonta– BP decreased– Other genes alsoprefer R+G46

Amoebozoa

49

Diplomonads/
Parabasalids
Stramenopiles/
AlveolatesEuglenozoa/Heterolobosea• EF2 signal– Is not incongruent
with those of othergenes• OK to use EF2758790976998• How about the GR?

Green plants
Red algae

EF2: gene recombination between Red & Green?

• Stiller, Riley & Hall. JME 2001 52:527-39– Red & Green EF2 were recombined– EF2 phylogeny: Artifact from the GR signal• Test the “GR” hypothesis– R+G tree: the ML tree
– RxG tree: the best tree with no R+G clade• Calculated site-lnLs over the two trees– Sites that prefer the R+G tree over the other– Do the R+G sites pack in a short region?

EF2: gene recombination between Red & Green?
2R+G<RxG
601

501

401

301

201

-1

101

0
1Δsite-lnL

1-2-3-4

R+G>RxG-5Site number• R+G signal locates the non-pink area
• The ML tree of the green area: no R+G clade– A R+G tree: The 2nd best (ΔlnL = 0.2; P = 0.828)• No strong reason to invoke the GR proposed