Evolution Lecture 16

Clean up bits from Chapter 9 and Chapter 10

Check on-line syllabus for updated lecture topics and assignments

Please complete mid-course evaluation on Moodle

Topics for today

1. Coalescence
2. Neutral theory of molecular evolution
3. Gene flow

EvoBeaker: Sickle cell alleles Exercise 5

Fig. 10.3

Genetic drift causes coalescence

• Imagine a haploid population (bacteria)
• Two different alleles at time zero
• Lineages differ in the number of decendants
• Over time, lineages tend to go extinct
• Now look backward in time as we do when we build phylogenies
• All gene copies are descended from a single ancestral copy
• Mitochondrial Eve is the single ancestral female

Fig. 10.1

Time to coalencence differs according to population size

Expected relationship?

Fig. 10.15

How much evolution is random?

• Phenotypic traits
• Highly debated
• DNA sequence
• Major force

• Major transition in thought since the 1960’s

Basic ideas underlying the neutral theory of molecular evolution

Effects of mutation

• Minority are advantageous and are fixed by natural selection

• Many are disadvantageous and eliminated by natural selection

• Majority are effectively neutral with respect to fitness

Causes of variation

• Most genetic variation at the sequence level is neutral

• Most phenotypic variation (morphology, physiology, behavior) is due to natural selection

Basic principals

Overall mutation rate: uT per gamete per generation

Fraction that are neutral: fo

Neutral mutation rate: uo = fouT

uo differs among genes

What is the most important factor that determines the neutral mutation rate, uo?

Function determines uo for any given gene

• If changes in many positions of the amino acid sequence alter protein function (active site, folding properties)
• Then strong selection produces functional constraint
• Variation not tolerated
• uo will be low
• If changes in many positions of the amino acid sequence do not alter function
• Selection is weak or nonexistant (third codon)
• Variation is tolerated
• uo will be higher

b polypeptide chain of hemoglobin

All sites except those numbered are variable

uo depends upon functional constraint

What kinds of genes or gene regions should show the least constraint?

Fig. 10.12

Synonymous substitutions more common

14 nuclear genes

Rates differ among lineages

Synonymous rate low in primates

Fig. 10.13

Evolution of neutral variation

• Most new alleles are lost to drift
• Some fraction drift to fixation
• Over long time, successive new mutations drift to fixation
• Time to fixation depends upon Ne
• Number of new mutations = 2Neuo
• Probability that a new mutation will be fixed = p
• Frequency of a brand new mutation p = 1/2Ne
• Number of neutral mutations that arise in any generation and will someday become fixed?
• = 2Neuo * 1/2Ne
• = uo

Evolution of neutral variation

• Number of neutral mutations that arise in any generation and will someday become fixed

= 2Neuo * 1/2Ne

= uo

The rate of fixation for any given gene is theoretically constant and equals the neutral mutation rate

• Population size falls out of the equation
• Relationship between population size and fixation?
• Bigger populations are slower to achieve fixation
• Relationship between population size and number of mutations?
• More individuals produce more mutations
• These effects cancel each other out
• Theoretical underpinnings of the molecular clock

How to estimate the rate of neutral evolution?

• Two species diverged t generations ago

• Each species had uo substitutions per generation
• Then the number of base pair differences between them, D, should be D = 2uot
• If you know the time since divergence
• Experimentally
• Fossil record
• Then can rearrange and solve for neutral mutation rate
• uo = D/2t

Important qualification

• Quality of the information degrades over time because of multiple hits at the same site

Fig. 10.10

Neutral theory of evolution describes constant approach to fixation

• What evolutionary processes counter the effects of drift?

· Mutation

· Certain kinds of natural selection (more on this topic in future lectures)

· Gene flow

Summary from simulations

· Populations diverge from each other due to genetic drift (and selection but that wasn’t modeled).

· Genetic drift has a strong effect in small populations

· Migration counters the effects of genetic drift and causes:

· fixation of alleles

· loss of genetic diversity

· Migration is especially important for maintaining genetic variation in small populations

· Populations that are already diverged are homogonized by migration

Migration reduces divergence

• Counters negative effects of drift
• Counters the positive effects of selection

Fig. 9.28

How do we know the extent of gene flow?

• Track movement of individuals

• Many species are philopatric (return to natal site)

Measure gene flow with genetic markers

• Corn plants with dominant marker planted at various distances from plants with a recessive marker

• Germinate offspring to determine how far pollen traveled

Infer gene flow from natural patterns of diversity

• Pocket gopher burrows and rarely emerges

• Highly variable in coloration

• Differ in chromosome arrangements

How much genetic divergence among populations?

• Vq = variance in frequency among populations

• q mean frequency of one allele

Infer gene flow from natural patterns of diversity

• Alternative expression

• N = population size

• m = migration rate per generation

• Nm = number of migrants per generation

• Rearrange to solve for Nm

Topics for today

1. Coalescence
2. Neutral theory of molecular evolution
3. Gene flow

EvoBeaker: Sickle cell alleles Exercise 5 – modeling the relationship between genetic drift and population size