The Origin of Gene Subfunctions and Genotypic Complexity by Modular Restructuring

The Origin of Gene Subfunctions and Genotypic Complexity by Modular

Restructuring

Allan Force, Bill Cresko, F Bryan Pickett, Chris Amemiya, and Mike Lynch

Evolutionary Time

Subdivision and specialization - a trend in evolution

Is the Increasing Phenotypic Specialization Reflected in

Underlying Genetic Circuitry?

What is the default contribution to specialization of body regions at the

genotypic level produced by mutation pressure and genetic drift?

Modular Restructuring

Evolution of differential connectivity of the genotypic-phenotypic map via subfunction formation and resolutionin developmental genetic networks by nearly neutral processes

.

Subfunction Formation

Modular Restructuring

Evolution of differential connectivity of the genotypic-phenotypic map via subfunction formation and resolutionin developmental genetic networks by nearly neutral processes

.

.The processes which lead to origin of new gene subfunctionseither by co-option or fission mechanisms

Subfunction Formation

Subfunction Resolution

Modular Restructuring

Evolution of differential connectivity of the genotypic-phenotypic map via subfunction formation and resolutionin developmental genetic networks by nearly neutral processes

The processes which lead to origin of new gene subfunctionseither by co-option or fission mechanisms

The processes which lead to the partitioning of existingsubfunctions between gene duplicates by DDC mechanisms

.

.

.

Subfunction 1

Subfunction 2

Multifunctional gene

Given that many genes are multifunctional, how do new subfunctions evolve?

Subfunction Co-option

Subfunction Fission

TFA

TFA

AA

TFA and TFB

TFA

TFB TFA

AA

TFA and TFB

TFA and TFC

TFA

A

TFB TFC

A

TFA and TFB

TFA and TFC

TFA

A

TFB

B

TFC

B A

TFA and TFB

TFA and TFC

TFA

A

TFB

B

TFC

CB CA

TFA

BC

TFB TFC

B C

TFB TFC

B C

B

C

Fission Phase 1: Accretion, Degeneration, and Replacement

Abc

ABc AbC

aBC

ABC

Tim

e?

abc

aBc Abc abC

ABc aBC AbC

ABC

State W(Abc)

State X(AbC) or (ABc)

State Y(ABC)

State Z(aBC)

PXW= (1/2a + 4Ne)-1 PYX= (1/a + 4Ne)

-1 PZY= (1/d + 4Ne)-1

PZY= (1/2a + 4Ne)-1PXY= (1/2d + 4Ne)

-1PWX= (1/d + 4Ne)-1

Effective Population Size (Ne)

101 102 103 104 105 106

Mean T

ime t

o S

ubfu

nction F

issio

n (

genera

tions)

104

105

106

107

108

a = 10-4

a = 10-6

a = 10-5

Time for subfunction fission phase 1 when the addition and deletion rates are equal

When the time to fission for phase 1 is very long in large effective population sizes does this mean the precursor allele

(ABC allele) is unavailable?

0

0.25

0.5

0.75

1

0 5 10 15 20

Abc

ABc+AbC

aBC

ABC

Equ

ilib

rium

Fre

quen

cies

Addition Deletion Rate ratio

Infinite population size equilibrium frequencies for the 3 site fission model

a/ d )

Effective Population Size

Equ

ilib

rium

Fre

quen

cy

101 103 105 107

0.1

0.15

0.2

0.25

0.3

The effect of population size on the equilibrium frequencies under the 3 site fission model

ABC

aBC

Abc

ABc or AbC

d= a

What about multiple TF binding Sites?

AABBCC

Sim3 10-4

Sim3 10-5

Sim6 10-4

Sim6 10-5

104

106

108

Gen

erat

ions

101 103 105

1010

Effects of additional TF binding sites on the time to fission phase 1 under the 6 site model

Effective Population Size

1) Increasing the number of TF binding sites in the 6-site model does not significantly change the behavior relative to the 3-site model, but does reduce the time for phase 1

2) Allowing for different rates of mutation of the A site relative to the B and C sites does not significantly change the behavior of 3 site model for reasonable mutation rates

More complex models have similar behavior to that of the basic 3-site model

Phase II Enhancer Subfunctionalization

0.001

0.1

1.0

101 103 105

Ratio1=.25

Ratio2=.75

Ratio1 est 1

Ratio1 est 2

Ratio2 est 1Ratio2 est 2

Pr(

Enh

a nce

r S

ubf u

n cti

ona l

iza t

i on )

Effective Population Size

The probability of enhancer subfunctionalization

Modular Restructuring

Subfunction fission leads to the emergence of new subfunctions from the splitting of old subfunctions and may proceed under the guidance of mutation pressure in small populations (N< .1).

More generally, small effective population size and mutation may be sufficient to drive the evolution of the complexity of genes, networks, and developmental pathways passively by modular restructuring.

Changes in the underlying genetic architecture may not be initially observed at the phenotypic level. However, the long-term cumulative effects of modular restructuring may lead to abrupt and rapid changes at the phenotypic level when organisms find themselves exposed to novel environments.

Summary:

Allan Force Tom MiyakeTom PowersWendy LippmanAlicia Hill -ForceAndrew StuartDebTinnemoreJosh DankeMichael SchoenbornGarnet NavarroAyumi AokiMary West

Chris Amemiya

AMEMIYA LABORATORY

Funding sources: NSF, DOE, NHGRI, NCRR