Biology 331 Genetics

Population Genetics (Microevolution)

Introduction to Evolution:

Population Genetics (Microevolution): Evolution occurring at and below the species level

Macroevolution:Evolution occurring at and above the species level

Outgrowth of agricultural revolution in the 20's-40's

Modern importance of population genetics:

Agriculture

Other genetic engineering

Forensics

Medicine

Conservation

"Pure" Science speciation, systematics, evolution of behaviors etc.

Variation

Qualitative

Quantitative

Evolution:

What is it? Means Change

Biological/Organic Evolution Change in an organism over time

Change in allele frequency over time

Not = Natural Selection

Natural Selection: How does it work? More offspring are produced than can survive (Species could reproduce at an exponential rate) Most populations have a stable size Therefore: There is a struggle for existence

Members of a population vary in their characteristics(short, tall, fast, slow)

Much of this variation is heritable Therefore: Struggle for existence is not random. It depends on individual characteristics

(which are heritable)

Natural Selection ContinuedThose which are best adapted to the environment survive and reproduce (Differential Reproduction) Over time this process brings about changes in populations with favorable changes accumulating. Examples:

Cheetah's Speed, Cow's Milk etc.

Fitness: The ability of an organism to leave offspring in a given environment

Genetics: Darwin lacked a method. Mechanism provided by the monk Gregor Mendel. 1932-1953 modern synthesis

Pepper Moth

Items of note: Selection on individuals, but individuals do not evolve, populations do Natural selection acts on phenotypes but evolution is change in gene frequency Natural selection does not "think ahead". Selects organisms adapted to past environments. But, some traits may be favorable in new environments

human bipedalism

Natural Selection acts only on existing traits, variation is crucial Natural selection results in organisms better adapted for an environment...NOT optimally designed

human bipedalism

Natural selection normally acts on individuals not groups/species.

Hardy-Weinberg:

An introduction

Hardy-Weinberg Theorem:

Allele frequencies stay constant if there is no selection and it's other assumptions are met

Thus if we have 25% green eye genes, 25% blue eye genes, and 50% brown eye genes it will stay that way.

Heterozygosity will also stay the same

Two allele equation:

p2 + 2pq + q2 = 1 p= frequency of allele A

q = Frequency of allele a

p + q = 1.

So p2 = AA, q2 = aa, and pq = Aa

Sophisticated Punnet square:

Genotype frequency

Assumptions:

Random mating

Very large Population size

Diploid

Sexual

Non-overlapping generations

No migration

No mutation

No selection.

So what good is it?

Provides an evolutionary baseline

Calculate deviations from the H.W. Ideal

Hardy-Weinberg and Selection:

Problem #1 Assume a population has two co-dominant alleles for a gene (B, B')

Assume there are 1000 individuals, 250BB, 500BB', and 250B'B'

So: Freq. B = 500+500/2000 = .5; B'= 500+500/1000 = .5

Assuming H.W. BB = p2 = .25; BB'= 2pq = .5; B'B'= q2 = .25 (No Change)

Add Selection:

Fitness = Survival (for this example) BB = 1; BB'= 0.9, B'B'= 0.8 BB = 250; BB'= 0.9(500) = 450; B'B'= 0.8(250) =200 Frequency BB = 250/900 = .278; BB'= 450/900 = 0.5; B'B'= 200/900 = .222 Frequency B = .278+1/2(.5) = .528, B' = .472 Deviation From H.W.!

Types of selection

Frequency dependant selection

Fitness of an allele depends upon its frequency

Mutation and Hardy Weinberg:

Assume p has a frequency of 1 What is the frequency of q ?

Now allow a mutation to occur from p to q

Instant evolution!

But is this a "strong" evolutionary effect? Highest rate of mutation recorded is 0.0007/mutant cells/cell division

Result....no real effect over one generation

Over time?

Mutation alone is typically a weak evolutionary force

Mutation over time

So why does in matter?

Raw material for evolution

Creates new genes

Mutation selection balance

Migration:

Transfer of alleles from one gene pool to another

One island model:

Assume you have genotypes A1A1, A1A2, A2A2

frequencies p2, 2pq, and q2

A1 is fixed on the continent; A2 is fixed on the island

N on the island is much smaller than on the continent

Migration (m) from the continent to the island is more important than vice versa (Why?)

m=20% of the island population/generation A1A1 = 0.2 after migration (was 0)

A2A2 = 0.8 after migration (was 1.0)

Not H.W. equilibrium Both allele frequencies and genotype frequencies changed

Islands

Long term effect??

The general effect of migration is homogenization This effect is proportional to m, and the difference between Pc and PI

Migration selection balance

Migration as mutation

Gene flow and natural selection

Genetic Drift:

Random variation in allele frequencies due to sampling error

Yields evolution but not necessarily adaptation

Drift more important in small populations

Coin flipping/beanbag examples

Drift

Absorbing States:

The random fixation of alleles

The frequencies of alleles vary through time

Eventually alleles go to either fixation or loss

Assumes no Migration, mutation, selection etc.

Probability of loss or fixation proportional to initial frequency

"C" allele example

Loss and Fixation

Drift

What determines probability of loss?

Probability of loss or fixation proportional to initial frequency

So why does population size matter?

"C" allele example

Speed

Bottle Necks:

"Random" reduction in population size (Disasters)

Only a fraction of the alleles in the initial population survive

• "Instant" Evolution (sampling error) • Small population size after the bottleneck enhances drift • Repeated bottlenecks have huge effect!

European Jews, Lynx, Whales S. African Cheetahs and Northern Elephant seals almost

"Clones"

Bottlenecks

Bottlenecks

• "Instant" Evolution (sampling error) • Small population size after the bottleneck enhances

drift • Repeated bottlenecks have huge effect!

European Jews, Lynx, Whales S. African Cheetahs and Northern Elephant seals almost

"Clones"

Founder Effect:

• Genetic drift in a new colony

• May be only one gravid female

• Sampling error can result in "instant" evolution

• Very much like a bottleneck

• Extreme sampling error possible

Founder Effect

Picture Wing Drosophila

Examples

• Tristan da Cunha (Classic Example) Founded by a small number of colonists (15) Retinitis Pigmentosa (one founder was a carrier)

• Amish in PA Founded by 200 people 1-2 founders have Ellis-van Creveld syndrom Frequency 0.07 in Amish, 0.001 in the population as

a whole

Village of Salinas:In the remote mountains of the Dominican Republic:

• One village founder Altagracia Carrasco

• Several children with at least 4 women

• Large contribution to a small population

• Mutant for 5-alpha reductase-2 gene

• Low catalytic activity

• He was a heterozygote

• Enzyme responsible for conversion of testosterone to DHT

• Required for full masculinization of external genitalia

• Results in XY “females”

What happens at puberty?

• Guevedoces (penis at twelve)

Effective Population Size:• Theoretical "ideal" population having the same

magnitude of drift as the "Real"(tm) population • Census size:

All the individuals in a population Assume No selection, No migration, No mutation, Non

overlapping generations, Diploid, Sexual

• No population obeys the rules so we need a "fudge factor"

• Effective population size almost always smaller than the census size

Example:

• Assume 500 individuals

• 250 breeding age

• Only 5 "dominant" males breed

• EPS = 130

Drift and selection:

• Can allow selection to act

• "C" allele again!

Nonrandom Mating:

ANY deviation from totally random mating

Inbreeding:

• Mating between genetic relatives

• Need to calculate the probability that an allele is Identical By Decent (ibd)

• f = probability 2 gametes are ibd beyond random mating expectaions

• Does not require inbreeding in a social sense

F values

Effect of selfing with time:

• Increase in number of homozygotes Why?

• Selfing homozygotes yield homozygotes

• Selfing heterozygotes yield 50% heterozygotes and 25% of each homozygote

Increase in homozygosity

Inbreeding continued

• Does not affect gene frequencies

• Does affect genotype frequencies Excess homozygotes

• Potential affect on evolutionary process?

Effects of inbreeding:

• Loss of heterozygosity What effect might this have?

• Inbreeding depression Due in part to deleterious recessives Effect of inbreeding depression varies among

lineages Resistance to inbreeding depression Inbreeding more likely to be detected in stressed

organisms Inbreeding affects often show up later in life

• Maternal effects

Effect of low values of "f"

• f = 0.0005 (cousin mating)

• % of affected individuals from first cousin mating

• 18-24% albinism

• 27-53% tay-sachs

• 20-26% xeroderma pigmentosa

Positive Assortative mating:

• Like breeds with like

• Acts like inbreeding but only for selected alleles Increases homozygosity

• Can increase variance in a trait Short w/ short, tall w/ tall More variation for selection to act on

• Alternative to inbreeding to fix "type"

Negative assortative mating:

• Avoidance of like types

• To an extent this is the opposite of inbreeding

• Does not affect all genes equally

• Excess heterozygotes

Avoidance of inbreeding:

• Behavior Dispersal (how far is far enough?) Not coming into season before dispersal

• Social Mores

• Mate Choice: Self incompatibility MHC rejection

• Why do we want variation at MHC?

Spontaneous abortion/mate choice