learning goal understand the evolution of complexity
TRANSCRIPT
Learning Goal
• Understand the evolution of complexity
Expected Learning Outcomes
1) Visualize fitness as a function of gene function for one and two genes with and without pleiotropy
2) Construct and explain a plausible model for the evolution of increased complexity
3) Describe and discuss the role of gene duplication and pleiotropy in the evolution of complexity
4) Infer the history of gene duplication and shifts in gene function using phylogenetic inference
History of Life
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Last universal common ancestor was a derived, complex organism
First common ancestor was a very simple organism
Complex Unicellular
Life
Complex Unicellular
Life
Complex Multicellular
Life
Complexity
Complexity evolves by the piece-meal addition and modification of existing parts and the sorting of variation by natural selection over long periods of time.
Origin of LifeQuickTime™ and a
TIFF (Uncompressed) decompressorare needed to see this picture.
Hypercycles
The First Gene?
epistasis
self-replicating ribozymes
consolidationpleiotropy
GeneProofreadingMetabolismSynthesis
The First Gene
gene
functions
pleiotropy
ProofreadingMetabolismSynthesis
Pleiotropy
gene
pleiotropy
ReplicationProofreadingMetabolismSynthesis
How many functions are possible?
What is the limit to the number of different functions that can be encoded by a gene?
functions
GraphDraw a frequency distribution showing what you might expect if you examined each gene and recorded the number of different functions each gene performed (i.e. pleiotropy)
pleiotropy
Pleiotropy(Number of different functions)
Num
ber
of g
enes
Choose Your GraphA) B)
C) D)
E) None of these are my graph
Observed Pleiotropy
From Wagner and Zhang Nature Genetics Reviews
Yeast: a highly derived eukaryote
Only 1 function
Seven different functions
A More Complex Critter
From Wagner and Zhang Nature Genetics Reviews
Graph It
Number of different functions
Eff
icie
ncy
of a
pa
rtic
ular
fun
ctio
n
How does pleiotropy influence the ability of the gene product to perform a specific function?
A B
C D
E) My graph not shown
Evolutionary Model
gene
pleiotropy
The Fitness ModelDraw a graph of function (x-axis) versus fitness (y-axis) that represents a model for antagonistic pleiotropy
W
Function
1 2
Function
RedundancyPartial sub-functionalization
Full sub-functionalization
What does your graph look like?
Fitne
ss
Function
Fitne
ss
FunctionFitne
ss
Function
Fitne
ss
Function
A
B
C D
1 2
Function
E) My graph is not shown
Given the model, what is the expected function in the population?
A)
B)
C) The function where the two lines crossD) The average of and .
FunctionF
itnes
s
1 2
1 2
Function
Fitn
ess
X
1 2
On a piece of paper, draw this graph and use it as a model to show the fitness cost of pleiotropy relative to a model in which there is not antagonistic pleiotropy
Function
Fitn
ess
Function
A
Fitn
ess
1 2B
C
D
Choose the value that best represents the fitness cost of antagonistic pleiotropy relative to a model without pleiotropy.
Fitness cost of pleiotropy
Function
a
b
Fitn
ess
1 2
SubfunctionalizationPleiotropy
Fitness
Function
a b
Fitness cost of pleiotropy
Optimum
Ancestral Condition
Gene Duplication
gene
pleiotropy
gene gene
Duplication
redundant pleiotropy
Subfunctionalization
Redundancy Partial sub-functionalization
Pleiotropy
Fitness
Function
a b
Mutation
Selection
Reduced pleiotropy
Function
Blue
RedF
itnes
s
New expected fitness
Function
Fitn
ess
New expected fitness
A B C D E
Choose the expected trait value (function) for the red gene after the blue gene undergoes subfunctionalization
A) AB) BC) CD) DE) E
Subfunctionalization
Redundancy Partial sub-functionalization
Full sub-functionalization
Pleiotropy No pleiotropy
Fitness
Function
a b
Mutation
Selection
Mutation
Selection
Reduced pleiotropy
Draw the Fitness Model for the Derived Condition
Full sub-functionalization
Pleiotropy No pleiotropy
Fitness
Gene Function
a b
?Ancestral Derived
Conceptual Model
Full sub-functionalization
Pleiotropy No pleiotropy
Fitness
Gene Function
a b
Fitnes
s
Gene Function
a Gene Function
Single peak
b
Conceptual Model
Full sub-functionalization
Pleiotropy No pleiotropy
Fitness
Gene Function
a b
Fitnes
s
Gene Function
aGene Function
b
Two-fold increase in complexity
One axis to two
Neofunctionalization
Redundancy Partial sub-functionalization
Neofunctionalization
Time
New function
Mutation
Selection
Mutation
Selection
What Does This Fitness Model Look Like?
New function
Fitnes
s
Gene Function
Gene Function
Visualization
New function
Fitnes
s
Gene Function
Gene Function
MultiplePeaks
How Would You Visualize the Model with a Third Independent Variable?
(i.e 3 genes)
Visualization With Three Genes
Gene 3
Gene 1
Gene 2Fitness High
Low
Thinking About Duplication and Functional Divergence in
the Context of Phylogeny
Functions
Gene
GeneexpressionGenes
One geneTwo functions
Two genesEach gene has two functions
Three genesEach gene has one function
Gene
Functions
Note on the tree where gene duplication, subfunctionalization and neofunctionalization happen using parsimony
D = DuplicationS = SubfunctionN = Neofunction
Gene
Note on the tree where gene duplication, subfunctionalization (subfunction) and neofunctionalization (neofunction) happen using
parsimony
A) 1 = duplication, 2 = subfunction, 3 = neofunction
B) 1 = neofunction, 2 = subfunction3 = duplication
C) 1 = subfunction, 2 = neofunction,3 = duplication
D) 1 = duplication,2 = neofunction3 = subfunction
3
2
1
Gene
Functions
Note on the tree where gene duplication, subfunctionalization and neofunctionalization happen using parsimony
D = DuplicationS = SubfunctionN = Neofunction
D
S
N
Gene
Functions
Infer the history of gene duplication, loss and functional modification
Note the ancestral states for each internal node
D = DuplicationS = SubfunctionN = NeofunctionL = Gene loss
Gene
Nodes
Regulatory Genes
History of Gene Duplication