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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


Can we reconstruct the evolutionary history of ancient divergences from analyses of protein sequences?


If the substitution model is misspecified divergences from analyses of protein sequences? it can:(1) reduce reconstruction accuracy(and not favour a particular topology)


Felsenstein (1978) divergences from analyses of protein sequences?

B

A

C

D

D

C

A

B

out

Hendy&Penny(1989)


PNAS (1996) 93, pp. 1930-1934 divergences from analyses of protein sequences?


If the substitution model is misspecified it can
If the substitution model is misspecified divergences from analyses of protein sequences? it can:

(2) induce topological distortion


Biosynthesis of chlorophyll and bacteriochlorophyll
Biosynthesis of chlorophyll and bacteriochlorophyll divergences from analyses of protein sequences?

PNAS (1996) 93, pp. 1930-1934


chl divergences from analyses of protein sequences? L

bchL

chlL

?

bchX

nifH


Asymmetrical rate variation (XTSRV) divergences from analyses of protein sequences?

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


Eukaryotic RNA Polymerase II Evolution divergences from analyses of protein sequences?

core functions co-evolution opportunistic interactions

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


“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


Spatial heterogeneity
spatial heterogeneity the evolution of a protein in different directions”


Rates across sites uzzell and corbin 1971
Rates Across Sites the evolution of a protein in different directions”(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 the evolution of a protein in different directions”

An alternative model

Fitch and Markowitch (1970)

plant

animal

N4

~ only 10% sites variable at any given time


Covarion

S the evolution of a protein in different directions”01

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 the evolution of a protein in different directions”

R1

S11

R2

R2

S11

S11

S11

S11

R3

S11

R4

Galtier (2001)


“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


increased rate between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”in 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 between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”

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) between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”

  • 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 between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”

  • 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


  • Ellen Nisbet between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”

  • Chris Howe

  • Bill Martin

  • Nicole Gruenheit

  • Mike Steel

  • PLG organisers

  • Microsoft


Heterotachy

slow between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”

fast

Heterotachy

fast

slow

Lopez et al. 2002 MBE 19, 1-7


Philippe et al. between lineages (Germot and Philippe 1999), suggesting that a constant c is a limitation of the covarion model…”

BMC Evolutionary Biology

2005, 5:50


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