Molecular Evolution -...
Transcript of Molecular Evolution -...
Molecular Evolution
GE3M17
Mario A. Fares
Nothing in biology makes sense except in the light of evolution
Dobzhansky, 1973
Sung to the tune of "The Ba/le Hymn of the Republic" My bones proclaim a story of incompetent design. My back s?ll hurts, my sinus clogs, my teeth just won’t align. If I had drawn the blueprint, I would cer-‐tain-‐ly resign. Incompetent Design! Evo-‐Evo-‐Evo-‐lu?on! Design is but a mere illusion. Darwin sparked our revolu?on. Science SHALL prevail!
Don Wise
Incompetent Design!
Course aims
• Look at evidence for evolution • Discuss how to measure evolution • Describe evolutionary processes
Fossil record
Transi?ons
Ex?nc?ons
Sinosauropteryx
Dromaeosaurid dinosaur
Nothing in biology makes sense except in the light of evolution
Dobzhansky, 1973
molecular molecular
actgaatg |||||||| tgacttac
The molecule : DNA
MALVK
gene
genome
protein
Population …. Speciation
Molecules versus Morphology • Strictly heritable • Unambiguous
description • Model of evolution • More amenable to
mathematical analysis • Easier homology
assessment • Distant comparisons • Abundant
• Environmental factors • Classification
differences • Unclear models
DNA: Material and Markers
• DNA is both the raw material and the marker of evolution – Genes determine inherited differences, which
is what evolution acts on – Genes change and can be used to measure
evolution
Jean Bap?ste de Lamarck
Besoin -‐ the need or desire for change in phenotype
Change in phenotype
Change in genotype
Inherited Change in phenotype of offspring
August Weismann
Genotype unaffected by changes in phenotype
Offspring has changed genotype
Change in phenotype of offspring
Spontaneous and random changes in
genes during reproduc6on
Weismann dis6nguished soma6c and germline muta6on
Descent with modification
• Charles Darwin • For evolution to happen, must have
heredity and variation
Natural Selec?on: Survival of the Fi/est
“In the struggle for survival, the fi/est win out at the expense of their rivals because they succeed in adap?ng themselves best to their environment”
Variation by DNA mutation • Nucleotide substitution
– Replication error – Chemical reaction
• Insertions or deletions (indels) – single base indels – Unequal crossing over
• Consequences of point muta?ons within genes Figure 15-2
• Point muta?ons can alter mRNA splicing
Measuring evolution ...
• DNA sequences change very slowly • Cannot directly observe evolution • Compare two or more homologous sequences • Homologous = descended from a common
ancestor (= related)
• Analysis requires statistical models – See later
“Evolu6on has been observed. It’s just it has not been observed while it’s happening”
Natural Selec?on: adap?ve Evolu?on and Fitness Traps
Fitness
Fitness traps preclude innova?on leaps
FITNESS
(a)
(b)
• Stable systems navigate landscapes of low complexity with smooth and densely populated adap?ve picks and lowly populated deleterious valleys
• Non-‐robust systems present more complex landscapes with very dense deleterious valleys in genotypes
Observing Evolu?on of Novel Func?ons while it’s Happening
Two stages for observing evolu?on: 1) Describe what we observe 2) Iden?fy the mechanism underlying that we observe
Gener. 440
Gener. 660
Gener. 1100
Gener. 1,540
Gener. 1,980 Gener. 2,200
Evolutionary models
• Neo-Darwinian (Pan-selectionist) – positive selection only
• Mutationist – mutation and random drift
• Neutralist – mutation, random drift, and negative selection
Positive selection
• A new allele (mutant) confers some increase in the fitness of the organism
• Selection acts to favour this allele
• Also called adaptive evolution
NOTE: Fitness = ability to survive and reproduce
Advantageous allele
Herbicide resistance gene in nightshade plant
Negative selection
• A new allele (mutant) confers some decrease in the fitness of the organism
• Selection acts to remove this allele
• Also called purifying selection
Deleterious allele Human breast cancer gene, BRCA2
Normal (wild type) allele
Mutant allele (Montreal 440 Family)
4 base pair deletion Causes frameshift
Stop codon
5% of breast cancer cases are familial Mutations in BRCA2 account for 20% of familial cases
Neutral mutations
• Neither advantageous nor disadvantageous
• Invisible to selection (no selection) • Frequency subject to ‘drift’ in the
population • Random drift – random changes in small
populations
Frequency of ABO Blood Group B-allele
0.4 2
13
3
9
19
18
24
20
13
12
14
14
8 7
Neo-Darwinian Model
• Mutation is recognised as the origin of variation
• Gene substitution (new allele replacing old) occurs by positive selection only
• Polymorphism (multiple alleles co-existing) caused by balancing selection
Large variation unexplained by Natural selection
• Zuckerkandel & Pauling – 1960s
• Electrophoretic gel separation of proteins
• Proteins travel at different speeds according biochemical properties or molecular weight
• 15-50% of genes have 2 or more electrophoretic alleles
• Consequences of point muta?ons on gene products
Unexplained variation
• Too much polymorphism to be explained by mutation and positive selection alone (NeoDarwinian model)
• Why so much?
Neutral Theory
• Neutral Theory of Molecular Evolution – Motoo Kimura, 1968
• Most polymorphism is selectively neutral • Majority of evolutionary changes caused
by random genetic drift of selectively neutral (or almost neutral) alleles
• Still allows for some selection
Motoo Kimura (1924-‐94)
Genetic Drift
Random Genetic Drift Selection A
llele
freq
uenc
y
0
100
advantageous
disadvantageous
Genetic Drift • Each new allele (mutant) has a
chance of being fixed (= present in all individuals) in the population
• Probability is proportional to frequency
• Selection (positive or negative) also affects rate and likelihood
• Neutral alleles have no selection
• May ‘drift’ to fixation or extinction
• Under genetic drift the probability of fixation is simply equal to freq.
Rate of Neutral Evolution
µ = neutral muta6on rate per allele
Neutral muta6on
New allele Frequency of 1/2N
Popula?on of N diploid individuals Containing 2N alleles (2 per individual)
Probability of being fixed
2Nµ = number of new muta?ons in a popula?on of N
Muta?on Rate
Rate of neutral evolu?on = rate of muta?on X probability of muta?on being fixed
= 2Nµ X 1/2N
= µ
Under the neutral theory, the rate of subs:tu:on = rate of muta:on
Molecular clock
But …
• Molecular clock does not always hold
• Still is a useful concept
• … more details later …