Chapter 3: Evolutionary genetics of natural populations

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1 Chapter 3: Evolutionary genetics of natural populations

2 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!!!

3 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!

4 Genetic Diversity is Evolution s Toolkit Genetic diversity gives evolution more to select on and novel changes can result!

5 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?

6 What can cause a change in genetic diversity? Mutation Migration Selection Chance events Fragmentation

7 Mutation 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

8 Central Dogma of Biology DNA Transcription ATGGTTTAA RNA Translation AUGGUUUAA Proteins (MET)(VAL)(STOP) Tissue, body, etc

9 There are several types of mutations Point mutations Substitution Insertions Deletions Inversions

10 Point Mutations: Substitution Synonymous substitution GUU GUC Val Nonsynonymous substitution GUU CUU Leu Synonymous: having the same meaning as another word or phrase in the same language.

11 Point mutation - Insertions Original Sequence Amino Acid Product (ATG)(CGT)(GAG)(TCG)(AGA) (MET)(ARG)(GLU)(SER)(ARG) Mutated Sequence (ATG)(CGT)(AGA)(GTC)(GAG)A Insertion New Amino Acid Product (MET)(ARG)(ARG)(VAL)(GLU)(...)

12 Point mutation - Deletions Original Sequence Amino Acid Product (ATG)(CGT)(TTG)(AAG)(AGA) (MET)(ARG)(LEU)(LYS)(ARG) Mutated Sequence (ATG)(CGT)-(TGA)(AGA)(GA Deletion New Amino Acid Product (MET)(ARG)(STOP)

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

14 Other types of mutations Inversion

15 Is the mutation rate is equal across the genome? Is the frequency of SNPs the same in all regions of the genome?

16 What mutations will be under the strongest selection pressures? What will the most common mutations be? What will the most rare mutations be?

17 How will mutations affect genes? Coding region vs promoter vs introns

18 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 Mutation Selection Balance

19 Neutral Mutations Do not effect the protein end product no strong selection pressure They are used as genetic markers Helpful used to compare individuals

20 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

21 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???

22 What can cause a change in genetic diversity? Mutation Migration Selection Chance events Fragmentation

23 What can change allele frequency? Migration Why can migration can rapidly restore genetic diversity to a population

24 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

25 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(q m q o ) m migration rate q m - allele frequency in immigrants q o- allele frequency in original population

26 Migration can be an effective way to restore genetic diversity BUT Is migration always beneficial for conservation?

27 Introgression Many endangered species can be threatened by gene flow from related, but not endangered, species

28 What is the overall accumulation of alleles from dogs in the Web Valley wolf population? M = q l - q o q m - q o M = = 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

29 What can cause a change in genetic diversity? Mutation Migration Selection Chance events Fragmentation

30 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

31 What are environmental and anthropogenic changes that cause selection? Pests, parasites, and diseases Pollution Rainfall / Drought Temperature Competitors Habitat loss

32 Example of Adaptation

33 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

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37 With every infection the mortality decreases. The mortality to this virus strain dropped from around 90% to 25% in Pg 39 in your textbook

38 Some other examples of adaptations Genetic change in allele frequency Physiological modifications in haemoglobin levels to cope with altitude Behaviors avoidance behaviors

39 Illustrating Natural Selection: California Condor

40 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

41 How rapidly does the frequency of the recessive lethal dwdw allele decline due to selection in the endangered California condor? q q 1 = 1+q q = frequency of the lethal allele 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 (1+0.17) = The frequency of the dwdw allele will drop from 17% to 14.5% in one generation

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

43 The Pepper Moth and the Industrial Revolution

44 How quickly can allele frequency change? The melanic form was first recorded in 1848 By % 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)

45 What do you predict to happen if pollution controls were put in place and trees became lighter in color again? Cook, 2003

46 Why did these changes occur Very strong predation pressure

47 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

48 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

49 Human Height Quantitative trait 60 % - 80 % heritability genetics This means that 40 % - 20 % of the variation is due to the environment nutrition

50 :: 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.

51 Complete heritability: Fingerprint ridge count in humans Incomplete heritability: Shell width in Partula snails Zero heritability: Conception rate in cattle

52 Why is heritability important? Selection Response: predict how particular populations will respond to selection for particular characters. Heritability Total Variation Among Individuals h 2 = V g V p = V g + V e V p V g = variation due to genetic diversity V p = total phenotypic variation V p = total variation in population V g = variation due to genetic differences V e = variation due to the environment

53 What contributes to genetic variation? V g = V a + V d + V i V g = Variation due to genetic diversity V a = Variation due to the average effect of alleles. Determines immediate evolutionary potential V d = Variation due to dominance Reflects the susceptibility to inbreeding depression V i = Variation due to interactions among loci Determines the impact of outcrossing

54 Genotype environment interaction Populations adapt to particular environmental conditions Survive and reproduce better in their native conditions than in other environments.

55 Genotype environment interaction

56 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

57 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

58 The sixth extinction 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

59 What can cause a change in genetic diversity? Mutation Migration Selection Chance events Fragmentation

60 What can change allele frequency? What can change allele frequency? Chance effects: natural disasters

61 What can cause a change in genetic diversity? Mutation Migration Selection Chance events Fragmentation

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

63 Take Home Points Genetic diversity is GOOD! Diversity is key for maintaining a healthy population

64 Take Home Points Factors that can effect evolution, aka the frequency of alleles in a population are.. Mutation Migration Selection Chance events Fragmentation