chapter 3: evolutionary genetics of natural populations · how can migration effect genetic...

Chapter 3: Evolutionary genetics of natural populations

What is Evolution?

– Change in the frequency of an allele within a population

– Evolution acts on DIVERSITY to cause adaptive change

• Ex. Light vs. Dark wings in the pepper moth

– High levels of diversity are GOOD for conservation biology!!!

Imagine you are an inventor and you can pick a toolkit, which will you choose?

Having many diverse tools available to use allows you to create novel things!

• Genetic diversity gives evolution more to select on and novel changes can result!

Genetic Diversity is Evolution’s Toolkit

What is the goal of conservation genetics..

• Preserve genetic diversity within species

• Keep species dynamic entities, capable of evolving

• Here we address the questions how is genetic

diversity produced, and how quickly is it regenerated if it is lost?

What can cause a change in genetic diversity?

• Mutation • Migration • Selection • Chance events • Fragmentation

A sudden genetic change in an allele or chromosome The source of all genetic diversity

Mutation can refer to…

– The process by which novel genetic variants arise – The phenotypic products of the genetic changes

Mutation

Central Dogma of Biology

DNA

RNA

AUGGUUUAA

ATGGTTTAA

(MET)(VAL)(STOP)

Proteins

Tissue, body, etc

Transcription

Translation

There are several types of mutations

• Point mutations – Substitution – Insertions – Deletions

• Inversions

Point Mutations: Substitution

Synonymous substitution

Nonsynonymous substitution

GUU CUU Leu

GUU GUC Val

Synonymous: having the same meaning as another word or phrase in the same language.

Point mutation - Insertions

(ATG)(CGT)(GAG)(TCG)(AGA) (MET)(ARG)(GLU)(SER)(ARG)

(ATG)(CGT)(AGA)(GTC)(GAG)A (MET)(ARG)(ARG)(VAL)(GLU)(...)

Insertion

Original Sequence

Mutated Sequence

Amino Acid Product

New Amino Acid Product

Point mutation - Deletions (ATG)(CGT)(TTG)(AAG)(AGA) (MET)(ARG)(LEU)(LYS)(ARG)

(ATG)(CGT)-(TGA)(AGA)(GA (MET)(ARG)(STOP)

Deletion

Original Sequence

Mutated Sequence

Amino Acid Product

New Amino Acid Product

Frameshifts

The fat cat sat The fat cat sat Hef atc ats at

Other types of mutations

Inversion

• Is the mutation rate is equal across the genome?

• Is the frequency of SNPs the same in all regions of the genome?

What mutations will be under the strongest selection pressures?

What will the most common mutations be?

What will the most rare mutations be?

How will mutations affect genes ?

Coding region vs promoter vs introns

Mutation Selection Balance

• Only 1-2% of all mutations that occur in coding DNA will be advantageous

• Deleterious alleles are selected against • The balance between the formation of

deleterious alleles and their removal via selection is called

Neutral Mutations

• Do not effect the protein end product – no strong selection pressure

• They are used as genetic markers

• Helpful used to compare individuals

Mutation load

• Low frequencies of deleterious alleles are found in all naturally out breeding populations

• Inbreeding increases the probability of these

alleles being expressed in homozygous genotypes

Can Mutations help restore genetic diversity?

• To restore genetic diversity via mutation you need hundreds to millions of generations Mutations can’t restore genetic diversity fast enough from a conservation perspective. What are other options???

What can change allele frequency? • Migration • Why can migration can rapidly restore genetic

diversity to a population

Migration • Partially isolated populations diverge over

time as a result of chance and selection • Prior to Mongol invasions the B blood allele

was absent from Europe.

Cline: gradual change in allele frequency across a geographical area

How can migration effect genetic diversity? The genetic impact of migration depends on the proportion of alleles contributed by immigrants and on the difference in frequency between the native population and the immigrants

q = m(qm − qo ) m – migration rate qm - allele frequency in immigrants qo- allele frequency in original population

Migration can be an effective way to restore genetic

diversity

BUT

Is migration always beneficial for conservation?

Introgression Many endangered species can be threatened by gene flow from related,

but not endangered, species

What is the overall accumulation of alleles from dogs in the Web Valley wolf population?

ql - qo M = qm - qo

0.78 – 1.0 M = = 0.22 0 – 1.0

The Web Valley population derives about 22% of its genetic composition from domestic dogs at this locus

THIS IS FOR A SINGLE LOCI – CONSERVATION GENETICS IS INTERESTED IN A GENOME WIDE

SCALE

What can change allele frequency?

• Natural Selection Organisms are better adapted to their environment

• Physical and biotic

environments of virtually all species are continually changing

• Species must ADAPT to these changes

What are environmental and anthropogenic changes that cause selection?

Pests, parasites, and diseases

Temperature

Rainfall / Drought

Competitors Habitat loss

Pollution

Example of Adaptation

Introduced into Australia in 1859 for sport hunting Rapidly increased in numbers and became serious pests. Had a negative effect on the local species Myxoma virus introduced in 1950 and caused 99% mortality

Strong directional selection resulted in rapid increases in genetic resistance of rabbits to the myx The myxoma virus also evolved lower virulence, as this increased the probability of being transm

Pg 39 in your textbook

With every infection the mortality decreases. The mortality to this virus strain dropped from around 90% to 25% in 1958.

Some other examples of adaptations

• Genetic – change in allele frequency

• Physiological – modifications in haemoglobin levels to cope with

altitude

• Behaviors – avoidance behaviors

Illustrating Natural Selection: California Condor

Natural Selection in Action

• Recessive lethal: an allele that does not effect the fitness of a heterozygote but all homozygotes die

• California condors homozygous for the dwdw gene die shortly after hatching

Genotypes: ++ : normal homozygote dominant +dw : normal heterozygote dwdw : dwarf lethal homozygous recessive

How rapidly does the frequency of the recessive lethal dwdw allele decline due to selection in

the endangered California condor?

If the dwdw allele has a frequency of 0.17 at fertilization and all homozygotes die. What will be the expected frequency of the dwdw allele in adults as a result of natural selection?

0.17 = 0.145 (1+0.17)

The frequency of the dwdw allele will drop from 17% to 14.5% in one generation

q q1 = 1+q

q = frequency of the lethal allele

Conservation biology is not only concerned with selection against deleterious mutations, but also

selection on favorable mutations

The Pepper Moth and the

Industrial Revolution

How quickly can allele frequency change?

• The melanic form was first recorded in 1848 • By 1900 99% of all moths living in polluted areas were

melanic

• The rate of change for a particular allele will depend on the selection strength (s) and the allele frequencies (p and q)

• What do you predict to happen if pollution controls were put in place and trees became lighter in color again?

Cook, 2003

Why did these changes occur

• Very strong predation pressure

Selection on quantitative characters

• So far we have discussed selection on a single loci

• But conservation genetics is primarily concerned with reproductive fitness a quantitative trait influenced by many loci

• We can determine the evolutionary potential of a population by…

heritability

Heritability

• Heritability (h2) is a measure of how well a quantitative trait is transmitted from one generation to the next.

• Most easily measured by comparing the trait among relatives

Human Height

• Quantitative trait • 60 % - 80 % heritability – genetics • This means that 40 % - 20 % of the variation is due

to the environment • nutrition

:: Comparing Heritability ::

The slope is a direct measure of the heritability (h2 ) of a trait

Both parents and the environment play a role in the phenotype of the offspring

There is no relationship between parent and offspring values. The slope of the relationship is 0.

• Complete heritability: Fingerprint ridge count in humans

• Incomplete heritability: Shell width in Partula snails

• Zero heritability: Conception rate in cattle

Why is heritability important? • Selection Response: predict how particular populations will

respond to selection for particular characters.

Vg h2 = Vp

Heritability

Vg = variation due to genetic diversity Vp = total phenotypic variation

Vp = Vg + Ve

Total Variation Among Individuals

Vp = total variation in population Vg = variation due to genetic differences Ve = variation due to the environment

What contributes to genetic variation? Vg = Va + Vd + Vi

Vg = Variation due to genetic diversity Va = Variation due to the average effect of alleles. Determines immediate evolutionary potential Vd = Variation due to dominance Reflects the susceptibility to inbreeding depression Vi = Variation due to interactions among loci Determines the impact of outcrossing

Genotype × environment interaction

• Populations adapt to particular environmental conditions • Survive and reproduce better in their native conditions than in other environments.

Genotype × environment interaction

Genotype × environment interactions & Management of endangered species

High performance in captivity does not guarantee success in the wild

Mixing of genetic material from different populations may generate underperforming genotypes Knowledge of genotype × environment interaction can strongly influence the choice of populations for reintroduction Ex. Disease resistance

What happens if the selection is to strong and the organisms cannot adapt?!

Adaption is not a cure all!

It is limited by genetics and by time

• Mass extinction: a widespread and rapid decrease in the amount of life on

• Changes are occurring to fast for the species to adapt • Humans have also been responsible for…

– translocations of species – extinction of food species – introduction of novel chemicals to

the environment – habitat fragmentation

The sixth extinction


• Chance effects: – natural disasters


What can change allele frequency? • Fragmentation • Limits gene flow • Random differences among subpopulations

Take Home Points

• Genetic diversity is GOOD! • Diversity is key for maintaining a healthy

population

Take Home Points • Factors that can effect evolution, aka the frequency

of alleles in a population are..


chapter 3: evolutionary genetics of natural populations · how can migration effect genetic...

Documents