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Pete Lockhart Massey University Allan Wilson Centre, New Zealand. Can we reconstruct the evolutionary history of ancient divergences from analyses of protein sequences?.

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pete lockhart massey university allan wilson centre new zealand
Pete Lockhart

Massey University

Allan Wilson Centre, New Zealand

slide2
Can we reconstruct the evolutionary history of ancient divergences from analyses of protein sequences?
slide3
If the substitution model is misspecified it can:(1) reduce reconstruction accuracy(and not favour a particular topology)
slide4
Felsenstein (1978)

B

A

C

D

D

C

A

B

out

Hendy&Penny(1989)

if the substitution model is misspecified it can
If the substitution model is misspecified it can:

(2) induce topological distortion

slide8
chlL

bchL

chlL

?

bchX

nifH

slide9
Asymmetrical rate variation (XTSRV)

rRNA, EF-1,  -tubulin, RPBI, actin

e.g. Embly and Hirt (1998) Current Opinion in Genetics and Development 8, 624-629; Philippe et al. (2000) Proc R Soc Lond B 267, 1213-1221; Inagaki et al. (2004) MBE 1340-1349; Guo and Stiller (2005) MBE 22, 2166-2178

slide10
Eukaryotic RNA Polymerase II Evolution

core functions co-evolution opportunistic interactions

Guo and Stiller (2005) MBE 22, 2166-2178

slide11
“in different lineages, co-evolution of proteins canalizes the evolution of a protein in different directions”

Lopez et al. 2002 MBE 19, 1-7

..”some of the EF-1 auxillary functions may have been lost/weakened during the reductive evolution of microsporidia”

Inagaki et al 2004 MBE 21, 1340-1349

rates across sites uzzell and corbin 1971
Rates Across Sites (Uzzell and Corbin 1971)

fast etc

slow

slow

=20

=5

=1

=0.1

Yang (1994)

=0.5

an alternative model fitch and markowitch 1970
N3

An alternative model

Fitch and Markowitch (1970)

plant

animal

N4

~ only 10% sites variable at any given time

covarion
S01

0

1

S10

covarion

Tuffley and Steel (1998)

Huelsenbeck (2002)

S01

slow

0

1

S10

S01

off

on

fast

0

1

S10

S01

faster

1

0

S10

off

on

covarion1
covarion

R1

S11

R2

R2

S11

S11

S11

S11

R3

S11

R4

Galtier (2001)

slide17
“the number of variable positions can be different between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”

Lopez, Casane & Philippe (2002) Mol Biol Evol 19: 1-7

slide18
increased ratein B&C

A B C D

increased pvar in B&C

A B C D

A B C D

A

B

C

D

Sys Biol (2005) 54, 948-951

mixtures can also be used to simulate changing pvar
B

B

D

A

on

on

A

D

C

long branch attraction

induced topological distortion

C

mixtures can also be used to simulate changing pvar

D

B

A

C

simulation 0 0 3 invariable sites switch on in b c ts98
Simulation: 0-0.3 invariable sites switch on in B+C (TS98)
  • assume ancestral pvar = 0.2
  • x = point where we increase pvar in B+C
  • simulate with seqgen-cov.exe http://www.liv.ac.uk/~matts/covarion.html
  • reconstruct with PAUP* (assuming simple model), report support for each of 3 unrooted trees
  • AB|CD, AD|BC, AC|BD

D

C

B

A

0.3

0.3

0.4

0.4

0.1

0.1

0.02

0.02

summary
Summary
  • Lineage specific differences in structural and functional constraint will affect which sites vary and how many of them vary
  • Lineage specific changes in proportions of variable sites motivated the concept of heterotachy
  • Simulations suggest that a relatively small increase in the proportion of variable sites in non adjacent lineages is a problem for reconstruction accuracy
slide27
Ellen Nisbet
  • Chris Howe
  • Bill Martin
  • Nicole Gruenheit
  • Mike Steel
  • PLG organisers
  • Microsoft
heterotachy
slow

fast

Heterotachy

fast

slow

Lopez et al. 2002 MBE 19, 1-7

slide29
Philippe et al.

BMC Evolutionary Biology

2005, 5:50

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