BIO120 Fall 2024 Lecture 5 PDF

Beyond BIO: Upcoming Events What is Beyond BIO? A series of optional events offered to BIO120 students throughout the course. They are meant to be fun and informative for any students who are interested. For more information and the complete schedule for this term, see Quercus under Modu...

Beyond BIO: Upcoming Events What is Beyond BIO? A series of optional events offered to BIO120 students throughout the course. They are meant to be fun and informative for any students who are interested. For more information and the complete schedule for this term, see Quercus under Modules  Beyond BIO. Upcoming Events: Birds & Wildlife of Toronto Thursday September 19th from 11:10 am – 12:00 pm Room 432 on fourth floor of Ramsay Wright (25 Harbord) Learn about local wildlife, where to see wildlife in Toronto, and how to get out into nature and identify what you see. Free snacks provided! Research Tips and Library Resources Thursday September 26th from 11:10 am – 12:00 pm On Zoom (link on Quercus) 1 Learn about different study and research resources on campus with on‐campus librarians! 1 © BIO120 Fall 2024  Genetic Variation: Models & Measurement Sonora semiannulata; Cox & Chippindale 2014 1) What forces act on genetic variation? 2) How can we measure genetic variation? 3) How much genetic variation exists in natural populations? Relevant reading in Charlesworth & Charlesworth – Chapter 5 This lecture will be recorded and posted on Quercus. 2 © BIO120 Fall 2024 Introduction Foundations of Population Genetics 1920s‐1950s: Mathematical evolutionary theory for population genetic change – Initiated by Fisher, Haldane & Wright – Provided the foundations for “Neo‐Darwinism” and the “New Synthesis” R.A. Fisher J.B.S. Haldane Continuous variation and Darwinian natural selection are 1890 ‐1960 1882 ‐1964 entirely consistent with Mendel’s Laws Demonstrated the evolutionary significance of genetic variation – Led to several key questions and development of the fields of ecological & evolutionary genetics S. Wright 1889 ‐1988 3 © BIO120 Fall 2024 Introduction Key Questions in Ecological & Evolutionary Genetics What forces can influence patterns of genetic diversity in natural populations? How can we measure the amount of genetic variation in populations? How much and what types of genetic variation occur in populations? 4 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? I) Mutation Ultimate source of genetic variation Caused by errors during replication (not directed) Increases genetic variation in populations Generation 1 Population of 3 diploid individuals Generation 2 5 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? II) Recombination Creates new combinations of mutations Increases genetic variation in populations Generation 1 Generation 2 6 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? III) Genetic drift Random sampling affects every generation Genetic Drift: Change in the frequency of an More important for populations that are smaller existing gene variant (allele) Acts to decrease genetic variation in populations due to random chance. 7 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? IV) Natural selection: a) Negative (purifying) selection Mutations that reduce fitness are removed by natural selection Decreases genetic variation in populations 8 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? IV) Natural selection: b) Positive (directional) selection (adaptation) Mutations that increase fitness will eventually become fixed in a population Decreases genetic variation in populations Fixation: Occurs when a polymorphic locus becomes monomorphic due to the loss of all but one allele. (note: can occur due to natural selection or genetic drift) 9 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? IV) Natural selection: c) Selection favoring diversity Natural selection can act to maintain diversity over the long term (e.g., heterozygote advantage) Increases (or retains) genetic variation in populations 10 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? V) Migration (gene flow): Gene Flow: Migration influences the structuring of diversity over Movement of genetic material a large spatial scale from one population to Decreases differences between populations another. Increases genetic diversity in populations Population 1 Population 2 Population 1 Population 2 11 © BIO120 Fall 2024 What Forces Influence Patterns of Genetic Diversity and Evolution? Different Processes Can Increase or Decrease Genetic Diversity Within Populations Many controversies in evolutionary biology concern the relative importance of these forces in evolution Factor influencing genetic diversity Tends to I. Mutation I. Increase diversity II. Recombination II. Increase diversity III. Genetic drift III. Decrease diversity IV. Natural selection IV. Increase or decrease diversity V. Migration V. Increase diversity 12 © BIO120 Fall 2024 How Can We Measure Genetic Variation? Metrics of Genetic Variation Heterozygosity (H) Fraction of individuals that are heterozygous, averaged across gene loci Recall from Mendelian genetics: – Heterozygote individuals have both alleles Polymorphism (P) Proportion of gene loci that have 2 or more alleles in the population A locus can be polymorphic without being heterozygous 13 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) What Maintains Genetic Variation? 1. Mutation‐selection balance Less fit types reintroduced by mutation Followed by selection acting to remove them 2. Selection maintaining variation Heterozygote advantage Frequency‐dependent selection Fitness varies in space or time Umbrella term “balancing selection” 14 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Two Schools of Thought Classical school Balance school T. H. Morgan H. J. Muller E.B. Ford T. Dobzhansky (1866‐1945) (1890‐1967) (1901‐1988) (1900‐1975) The two schools differed in their predictions on how much genetic variation occurs in natural populations 15 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Two Models of Population Genetic Variation Classical Balance Morgan, Muller Dobzhansky, Ford Low heterozygosity Heterozygote advantage Low polymorphism High heterozygosity Wild type is ‘normal’ genotype High polymorphism Selection typically negative Selection favours diversity 16 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Studying Genetic Diversity: Genetic “Markers” Pre‐1966 Morphological – e.g. snail colour polymorphism Cytological – e.g. chromosome inversions 17 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Model Systems In Ecological Genetics Cepaea Maniola nemoralis jurtina Linanthus Panaxia parryae dominula 18 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Early Quantitative Genetic Evidence for the Existence of Genetic Variation Rather than focus on Mendelian discrete traits, focus on continuous polygenic traits Selection experiments on different groups of organisms Involves controlled breeding of individuals with particular traits for many generations Artificial Selection 19 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Selection Response for Bristle Number in Fruit Flies ‐ Drosophila melanogaster Selection relaxed Mean number of bristles Generations Yoo 1980, Genet. Res. 20 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Selection Response in Maize Selection relaxed Percent oil High oil Selection resumed Selection relaxed Low oil Generation 21 Dudley & Lambert 1992, Maydica © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Evolutionary Responses of Continuous Traits Demonstrates existence of heritable variation in fitness‐related phenotypes Due to many underlying genes Are these responses due to: A) Many alleles previously at intermediate frequency that change in frequency? B) Many initially rare & deleterious alleles that increase in frequency? 22 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Summary: Artificial Selection Experiments on Quantitative Traits Selection responses demonstrate that abundant genetic variation exists for polygenic quantitative traits BUT often no information on P & H as key population genetic parameters Also: comparative studies difficult as traits studied often are group specific Still no solution to the question: What maintains genetic variation? 23 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Richard Lewontin and the Electrophoresis Revolution Allozyme* gel electrophoresis provided a way to ask: – “What proportion of genes are variable (P & H)?” – Answering it addresses a fundamental dispute between the classical and balance schools Initiated large scale surveys of electrophoretic variation in enzymes & proteins in diverse organisms * Allozymes = different allelic forms of the same protein R.C. Lewontin 24 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Protein Electrophoresis: Measuring Diversity at Genes that Encode Enzymes & Proteins Monomorphic gene FF FF FF FF FF FF FF FF Polymorphic gene FF FS SS MM FM MS FF FS 25 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Advantages of Studies of Enzyme Polymorphism Many loci can be examined Can be used in nearly any organism Loci co‐dominant, heterozygotes can be identified Variation examined close to DNA level Provides genetic marker loci for other studies 26 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) First Allozyme Studies: Genetic Variation is Very High! Genes studied P H Humans 71 0.28 0.07 Fruit Flies 24 0.53 0.15 Fish 21 0.31 0.08 Rodents 26 0.20 0.04 Plants 8 0.46 0.17 Aha! The balance school wins! Right? 27 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) First Allozyme Studies: Genetic Variation is Very High! 1. Mutation‐selection balance Less fit types maintained by repeated mutational input 2. Selection maintaining variation Heterozygote advantage Frequency‐dependent selection Fitness varies in space or time 3. Selectively neutral variation Different types do not differ in their fitness relative to one another New mutations neither eliminated nor retained by selection 28 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) The Neutral Theory: Most Molecular Variation May Be Selectively Neutral Negative selection rapidly eliminates detrimental mutations Positive selection rapidly fixes beneficial mutations The only mutations left to create genetic variation are selectively neutral How do we distinguish “mutation‐selection balance,” “balancing selection,” & “neutral” models? Motoo Kimura (1924‐1994) 29 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Studying Genetic Variation at the DNA Level 30 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Genetic Variation At the DNA Level Direct inference of genetic differences Genetic code for genes can distinguish changes that alter protein from those that don’t 31 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) DNA Sequence Variation Across Different Organisms 1/7 bases are polymorphic (bp) DNA sequence diversity 1/50 bp Alivia Dey 1/1200 bp Dey et al. 2013, PNAS 32 © BIO120 Fall 2024  How Much Genetic Variation Exists In Natural Populations? (And Why?) DNA Variation in Maize vs. Teosinte Corn has reduced genetic diversity compared to its wild ancestor teosinte A consequence of population bottleneck(s) during domestication (founder event) DNA diversity (maize) DNA diversity (teosinte) Wright et al. 2005, Science 33 © BIO120 Fall 2024  How Much Genetic Variation Exists In Natural Populations? (And Why?) DNA Variation in Maize vs. Teosinte Selection on some genes reduced diversity further than expected by genetic drift from the founder event DNA diversity (maize) DNA diversity (teosinte) Wright et al. 2005, Science 34 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Comparisons of Polymorphism in Arabidopsis lyrata Regions that were recently glaciated have lower DNA diversity Genetic drift following recolonization 0.025 DNA Diversity 0.020 0.015 0.010 0.005 0 Germany Sweden Canada Iceland Russia USA 35 © BIO120 Fall 2024 How Much Genetic Variation Exists In Natural Populations? (And Why?) Human Genetic Variation Humans show a loss of genetic variation with increasing distance from East Africa Reflects founder events as humans migrated from source population DeGiorgio et al. 2009 PNAS 36 © BIO120 Fall 2024 Recap Recall: schools of evolutionary thought – What do they predict? – Evidence for and against? Critical thinking: – Is the evidence strong or weak? – Does it actually test the predictions? Concepts: – Forces of evolution and what they do to genetic variation 37 © BIO120 Fall 2024 Next Lecture: Sex, Reproductive Systems, and Evolution 38 © BIO120 Fall 2024