Q1) Explain how background selection and genetic hitchhiking could explain the positive correlation between genetic diversity and recombination rate.

Size: px
Start display at page:

Download "Q1) Explain how background selection and genetic hitchhiking could explain the positive correlation between genetic diversity and recombination rate."

Transcription

1 OEB 242 Exam Practice Problems Answer Key Q1) Explain how background selection and genetic hitchhiking could explain the positive correlation between genetic diversity and recombination rate. First, recall that by genetic diversity (or polymorphism or heterozygosity ) we typically mean Π. Thus, it matters not only how many segregating sites we have, but also whether the alleles at those sites are more often at intermediate frequencies (which inflate the number of pairwise differences) or at rare/high frequencies (recall that if one allele is rare the other must be common, assuming a biallelic locus). Background selection means that deleterious mutations and nearby linked variants are removed from the population as they arise. A large rate of recombination will more easily allow neutral linked variants to detach themselves from deleterious variants and so persist in the population, whereas a small rate of recombination ensures that neutral variants are often removed along with the targets of background selection proper. More formally, Charlesworth showed that we can calculate the effective population size by scaling N by a factor of e (-µ/r), where µ and r are the mutation and recombination rate, respectively. Thus recombination rate is positively correlated with Ne, which in turn is positively correlated with per-site diversity (recall that the infinite sites model predicts that E(Π) = θ = 4N e µ). In other words, big r à big N e à big θ à big Π. Genetic hitchhiking means that beneficial mutations and nearby linked variants proliferate through a population together, causing a local reduction in diversity surrounding the adaptive allele. This process is counteracted by recombination, which breaks up haplotypes and restores diversity to the population. When the recombination rate is high, diversity is restored quickly, whereas when it is low haplotypes can persist for long stretches of time, preserving a low value of Π. Q2) What is the inbreeding coefficient of individual I in the pedigree below, assuming that the only nonzero values of F among the ancestors of I are F A = 1/16 and F D = 1/8. You should leave your answer in the form of an unreduced expression.

2 Calculate F by tracing all possible paths through common ancestors: KGCADJL KHDACGL KHEBFJL KHDJL KGL F I = 2 *(1/ 2) 7 (1+ F A )+ (1/ 2) 7 (1+ F B )+ (1/ 2) 5 (1+ F D )+ (1/ 2) 3 (1+ F G ) = 2 *(1/ 2) 7 ( )+ (1/ 2)7 + (1/ 2) 5 (1+ 1 )+ (1/ 2)3 8 = Q3) A population at steady state in the infinite-alleles neutral model has a homozygosity equal to 10%. What value of θ can you infer? With random mating, how many equally frequent alleles would be required to produce the same level of homozygosity? At steady-state, F = 1/(1+θ), so θ = (1 F)/F = 9. With n equally frequent alleles, each! has frequency p = 1/n, giving us homozygosity!""!"#$ p! =! =! (think of, for example,!!! a Punnett square with n possibilities: each square is equally probable with p=(1/2) 2, and there are n homozygotes). Hence, N = 10. Q3) An agronomist is studying grain yield in an outbred variety of maize. The variety has a mean yield of 200 bushels per acre. The table below shows estimates of the additive genetic variance V A, the dominance variance V D, the environmental variance V E, and the total phenotypic variance, each expressed either as its estimated value in [bu/acre] 2 or as its estimated value as a fraction of the total phenotypic variance V P. Variance component Estimated value Value as fraction of V P V A 300 [bu/acre] 2 V D 14.3% V E 300 [bu/acre] 2 V P 100.0% A. Complete the missing entries in the table. [You may round the value of each variance component to the nearest 100.] Let x = V P. Then the values given imply that x = x, hence x = 600/0.857 = 700 [bu/acre] 2. With this as the value of V P, the rest of the entries in the table are as follows. (The fact that the numbers in the percent column add to 99.9% not 100.0% is due to round-off error.) Variance component Estimated value Value as fraction of V P V A 300 [bu/acre] % V D 100 [bu/acre] % V E 300 [bu/acre] %

3 V P 700 [bu/acre] % B. What are the values of the narrow-sense heritability h 2 and of the broad-sense heritability H 2. [In estimating the broad-sense heritability, ignore any possible effects of interaction between different genes.] Recall that h 2 = V A /V P and that H 2 = V G /V P : h 2 = = and H = = C. As noted, the mean yield of the variety is 200 bu/acre. If the top yielding 20% of the plants are selected for breeding, and mated randomly among themselves, this is equivalent to a selection differential S of S = 37 bu/acre. What is the expected mean yield of the progeny of the selected parents? Use the breeder s equation, R =h 2 S, where h 2 =.428 and S=37, hence R = Because R = M M, where M = progeny mean and M = population mean, we can infer M = = bu/acre. Q4) Consider the two following phylogenetic topologies. If you were to calculate Tajima s D for each of them, what do you expect your results would be, and how would you interpret that? What if you were to use a McDonald-Kreitman test? When would it be appropriate to apply one or the other? The left tree has relatively deep /ancient coalescent times, whereas the tree on the right has relatively shallow /recent coalescent times. We would expect Tajima s D to be negative in the former case. Most mutations that we sprinkle onto this tree will happen on private branches, and so will be rare. Rare alleles contribute less to per-site heterozygosity than do intermediate frequency alleles (consider how many pairwise differences: AAAC vs AACC?), so we will deflate θ Π relative to θ S for an overall negative statistic. This might suggest directional selection or population growth, for example. (Negative selection against deleterious alleles will reduce frequencies, and positive selection can also lead to a surplus of rare alleles as mutations appear on the homogenous background produced by a selective sweep. To

4 see why this topology is consistent with population growth, recall the relationship between population size and coalescent times predicted by the Kingman coalescent). We would expect Tajima s D to be positive in the latter case. Most mutations that we sprinkle onto this tree will be shared, and so will be common. By the above reasoning, this will inflate θ Π relative to θ S for an overall positive statistic. This might suggest balancing selection or admixture, for example. (Balancing selection will preserve polymorphisms at intermediate frequencies against the effects of drift, and admixture will have an overall averaging effect on allele frequencies between the two populations.) Tajima s D is often applied broadly, as it assumes only the infinite sites model, and people are generally willing to make this assumption across a broad range of time scales. However, arguably this model begins to lose validity when our tree spans long evolutionary times (e.g. spanning speciation events), at which point multiple substitutions at a site become feasible hence, not every mutation happens at a new site. The McDonald-Kreitman test, on the other hand, assumes that we can partition our data into polymorphism and divergence, where the former refers to variation within a population of some species and the former generally refers to variation between two species. Thus, we would generally only want to use this test if the root of the trees pictured above represents a speciation event. Moreover, we could only use this test if we are examining coding regions, because we need to be able to compare synonymous and non-synonymous changes, whereas Tajima s D can be applied to any genomic region. If we applied the MKT to a topology like the one on the left, we would expect to find that polymorphism exceeds divergence (again, mutations sprinkled on the tree will create differences among individuals on the left branch). This could be indicative of purifying selection between the species (keeps divergence low) or balancing selection within the population (keeps polymorphism high). If we applied the MKT to a topology like the one on the right, we would expect to find that divergence exceeds polymorphism. This could be indicative of positive selection between the species (accelerates the accumulation of differences between them). Q5) A geneticist is studying the hierarchical population structure of a species of ground squirrel in an area where there is a confluence of two wide streams to form a river. To determine whether the watercourses are significant barriers to gene flow, the researcher estimates allele frequencies of a biallelic gene from large samples of individuals from three subpopulations in each region. A diagram of the area and the allele frequencies in the subpopulations are shown below.

5 A. Estimate H S, H R, and H T for the subpopulations, regional populations, and total area. Recall that when we look at the different levels of structure (subpops, regions, total) we are changing the granularity at which we define our allele frequencies, which we then use to calculate heterozygosity according to Hardy-Weinberg. In each the case of subpops or regions, we then take an average. (In the case of the total population, doing so would be trivial.) 9 2(0.1* i)(1 0.1* i) i=1 H S = 9 = (0.4)(.6)+ 2(0.5)(0.5)+ 2(0.6)(0.4) H R = = H T = 2(0.5)(0.5) = 0.5 B. Estimate F SR, F RT, and F ST for these populations. Recall that F XY = [H Y H X ]/H Y. In other words, F XY is the reduction in heterozygosity relative to Y, due to structure at the X level. F SR = F RT = F ST = C. Based on these estimates, do the watercourses appear to be a significant impediment to gene flow? (Please answer with either "Yes" or "No.") No, because F RT is smaller than F SR. Thus, the reduction in heterozygosity due to population structure at the level of regions is not as great as the reduction in heterozygosity due to structure at the level of subpops within those regions. In other words, most of the population structure appears at the subpop level, rather than the regional (watercourse-defined) level.

6 Q6) The equation d(t) = (1 e 40αt ) gives the Jukes-Cantor-corrected proportion of amino acid differences between two aligned protein sequences from different species that diverged from a common ancestral species that existed t years ago. The rate of amino acid replacement in each lineage is given by 20 α. Orthologous protein molecules were compared in two pairs of species. One species pair had diverged twice as long ago as the other species pair. In the more divergent species, the observed percentage of amino acid differences in the protein was 91.1%, whereas in the more recently diverged species pair the observed percentage of amino acid differences in the protein was 52.3%. A. Are these data consistent with a molecular clock? Letting t = τ equal the time of divergence of the less divergent species pair, the question states that the time of divergence of the more divergent species pair is t = 2τ. The equation for d(t) implies that ln[1 20d(t)/19] = 40αt. Hence 40ατ = ln[1 (20)(0.523)/19] = or 20ατ = in the less divergent species pair. In the more divergent species pair, 40α(2τ) = ln[1 (20)(0.911)/19] = or 20ατ = The rates of amino acid replacement (20α) are therefore 0.04/τ and 0.08/τ in the two comparisons, which is not consistent with a molecular clock. B. From these data, can one estimate the absolute rate of amino acid replacement in each lineage? No, the percent differences depend on the product ατ, and since neither is known, neither can be specified. A faster rate would result in the same percent differences in a shorter time, and a slower rate would result in the same percent differences in a longer time. C. From these data, can one estimate the relative rate of amino acid replacement in each lineage? Yes, from these data we can say that the rate of amino acid replacement (20α) in the more divergent species pair, relative to that in the less divergent species pair, is greater by a factor of (0.08/τ)/(0.04/τ) = 2. Q7) You are examining a species of flower that is normally blue. Occasionally plants with red flowers are observed in wild populations. You determine that flower color is controlled at a single locus, with the red allele completely recessive to the blue allele. You conduct a survey in a field and find 3000 blue flowers and 500 red flowers. You then look at the mean number of seed pods produced by the flowers, and find that the blue plants on average produce 20 pods whereas the red flowers on average produce 15. Assuming that the alleles are currently in HWE, but that selection is operating, predict the genotype frequencies after another generation. Assume that seed pod count is a perfect proxy for fitness (e.g. all seeds produced successfully take root, etc.) If the blue

7 allele mutates to a red allele at the rate of 10-5 /gen, what will the equilibrium frequency of the red allele be at mutation-selection balance? We first need to calculate the relative fitness of each genotype. We can let B represent the dominant (blue) allele and b represent the recessive allele. In this case, our relative fitnesses are as follows: w BB = 1; w Bb = 1; w bb = 15/20 =.75 We can next calculate mean fitness by assuming HWE. The frequency of the bb genotype is 500/3500, suggesting that q =.378 and p =.622. Our mean fitness is p 2 (w BB ) + 2pq(w Bb ) + q 2 (w bb ) = (.387)(1) + (.4702)(1) + (.1429)(.75) =.964 We can now divide each term in the above sum by wbar to get the predictions for genotype frequencies: w BB =.401; w Bb =.488; w bb =.111 To find the equilibrium frequency, we can use the formula q =!!, which holds when the harmful allele is a complete recessive (h=0). We now need to find s. Since w bb = 1-s =.75, we can infer that s =.25. Our equilibrium frequency =!"!!.!" =.006.

Solutions to Even-Numbered Exercises to accompany An Introduction to Population Genetics: Theory and Applications Rasmus Nielsen Montgomery Slatkin

Solutions to Even-Numbered Exercises to accompany An Introduction to Population Genetics: Theory and Applications Rasmus Nielsen Montgomery Slatkin Solutions to Even-Numbered Exercises to accompany An Introduction to Population Genetics: Theory and Applications Rasmus Nielsen Montgomery Slatkin CHAPTER 1 1.2 The expected homozygosity, given allele

More information

Population Genetics I. Bio

Population Genetics I. Bio Population Genetics I. Bio5488-2018 Don Conrad dconrad@genetics.wustl.edu Why study population genetics? Functional Inference Demographic inference: History of mankind is written in our DNA. We can learn

More information

Processes of Evolution

Processes of Evolution 15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection

More information

Classical Selection, Balancing Selection, and Neutral Mutations

Classical Selection, Balancing Selection, and Neutral Mutations Classical Selection, Balancing Selection, and Neutral Mutations Classical Selection Perspective of the Fate of Mutations All mutations are EITHER beneficial or deleterious o Beneficial mutations are selected

More information

Neutral Theory of Molecular Evolution

Neutral Theory of Molecular Evolution Neutral Theory of Molecular Evolution Kimura Nature (968) 7:64-66 King and Jukes Science (969) 64:788-798 (Non-Darwinian Evolution) Neutral Theory of Molecular Evolution Describes the source of variation

More information

19. Genetic Drift. The biological context. There are four basic consequences of genetic drift:

19. Genetic Drift. The biological context. There are four basic consequences of genetic drift: 9. Genetic Drift Genetic drift is the alteration of gene frequencies due to sampling variation from one generation to the next. It operates to some degree in all finite populations, but can be significant

More information

NOTES CH 17 Evolution of. Populations

NOTES CH 17 Evolution of. Populations NOTES CH 17 Evolution of Vocabulary Fitness Genetic Drift Punctuated Equilibrium Gene flow Adaptive radiation Divergent evolution Convergent evolution Gradualism Populations 17.1 Genes & Variation Darwin

More information

Chapter 6 Linkage Disequilibrium & Gene Mapping (Recombination)

Chapter 6 Linkage Disequilibrium & Gene Mapping (Recombination) 12/5/14 Chapter 6 Linkage Disequilibrium & Gene Mapping (Recombination) Linkage Disequilibrium Genealogical Interpretation of LD Association Mapping 1 Linkage and Recombination v linkage equilibrium ²

More information

Major questions of evolutionary genetics. Experimental tools of evolutionary genetics. Theoretical population genetics.

Major questions of evolutionary genetics. Experimental tools of evolutionary genetics. Theoretical population genetics. Evolutionary Genetics (for Encyclopedia of Biodiversity) Sergey Gavrilets Departments of Ecology and Evolutionary Biology and Mathematics, University of Tennessee, Knoxville, TN 37996-6 USA Evolutionary

More information

I. Short Answer Questions DO ALL QUESTIONS

I. Short Answer Questions DO ALL QUESTIONS EVOLUTION 313 FINAL EXAM Part 1 Saturday, 7 May 2005 page 1 I. Short Answer Questions DO ALL QUESTIONS SAQ #1. Please state and BRIEFLY explain the major objectives of this course in evolution. Recall

More information

Recombina*on and Linkage Disequilibrium (LD)

Recombina*on and Linkage Disequilibrium (LD) Recombina*on and Linkage Disequilibrium (LD) A B a b r = recombina*on frac*on probability of an odd Number of crossovers occur Between our markers 0

More information

LECTURE # How does one test whether a population is in the HW equilibrium? (i) try the following example: Genotype Observed AA 50 Aa 0 aa 50

LECTURE # How does one test whether a population is in the HW equilibrium? (i) try the following example: Genotype Observed AA 50 Aa 0 aa 50 LECTURE #10 A. The Hardy-Weinberg Equilibrium 1. From the definitions of p and q, and of p 2, 2pq, and q 2, an equilibrium is indicated (p + q) 2 = p 2 + 2pq + q 2 : if p and q remain constant, and if

More information

7. Tests for selection

7. Tests for selection Sequence analysis and genomics 7. Tests for selection Dr. Katja Nowick Group leader TFome and Transcriptome Evolution Bioinformatics group Paul-Flechsig-Institute for Brain Research www. nowicklab.info

More information

Understanding relationship between homologous sequences

Understanding relationship between homologous sequences Molecular Evolution Molecular Evolution How and when were genes and proteins created? How old is a gene? How can we calculate the age of a gene? How did the gene evolve to the present form? What selective

More information

Breeding Values and Inbreeding. Breeding Values and Inbreeding

Breeding Values and Inbreeding. Breeding Values and Inbreeding Breeding Values and Inbreeding Genotypic Values For the bi-allelic single locus case, we previously defined the mean genotypic (or equivalently the mean phenotypic values) to be a if genotype is A 2 A

More information

List the five conditions that can disturb genetic equilibrium in a population.(10)

List the five conditions that can disturb genetic equilibrium in a population.(10) List the five conditions that can disturb genetic equilibrium in a population.(10) The five conditions are non-random mating, small population size, immigration or emigration, mutations, and natural selection.

More information

Gene Genealogies Coalescence Theory. Annabelle Haudry Glasgow, July 2009

Gene Genealogies Coalescence Theory. Annabelle Haudry Glasgow, July 2009 Gene Genealogies Coalescence Theory Annabelle Haudry Glasgow, July 2009 What could tell a gene genealogy? How much diversity in the population? Has the demographic size of the population changed? How?

More information

CHAPTER 23 THE EVOLUTIONS OF POPULATIONS. Section C: Genetic Variation, the Substrate for Natural Selection

CHAPTER 23 THE EVOLUTIONS OF POPULATIONS. Section C: Genetic Variation, the Substrate for Natural Selection CHAPTER 23 THE EVOLUTIONS OF POPULATIONS Section C: Genetic Variation, the Substrate for Natural Selection 1. Genetic variation occurs within and between populations 2. Mutation and sexual recombination

More information

Big Idea #1: The process of evolution drives the diversity and unity of life

Big Idea #1: The process of evolution drives the diversity and unity of life BIG IDEA! Big Idea #1: The process of evolution drives the diversity and unity of life Key Terms for this section: emigration phenotype adaptation evolution phylogenetic tree adaptive radiation fertility

More information

It all depends on barriers that prevent members of two species from producing viable, fertile hybrids.

It all depends on barriers that prevent members of two species from producing viable, fertile hybrids. Name: Date: Theory of Evolution Evolution: Change in a over a period of time Explains the great of organisms Major points of Origin of Species Descent with Modification o All organisms are related through

More information

Notes on Population Genetics

Notes on Population Genetics Notes on Population Genetics Graham Coop 1 1 Department of Evolution and Ecology & Center for Population Biology, University of California, Davis. To whom correspondence should be addressed: gmcoop@ucdavis.edu

More information

Population Structure

Population Structure Ch 4: Population Subdivision Population Structure v most natural populations exist across a landscape (or seascape) that is more or less divided into areas of suitable habitat v to the extent that populations

More information

The neutral theory of molecular evolution

The neutral theory of molecular evolution The neutral theory of molecular evolution Introduction I didn t make a big deal of it in what we just went over, but in deriving the Jukes-Cantor equation I used the phrase substitution rate instead of

More information

Lecture 1 Hardy-Weinberg equilibrium and key forces affecting gene frequency

Lecture 1 Hardy-Weinberg equilibrium and key forces affecting gene frequency Lecture 1 Hardy-Weinberg equilibrium and key forces affecting gene frequency Bruce Walsh lecture notes Introduction to Quantitative Genetics SISG, Seattle 16 18 July 2018 1 Outline Genetics of complex

More information

Inbreeding depression due to stabilizing selection on a quantitative character. Emmanuelle Porcher & Russell Lande

Inbreeding depression due to stabilizing selection on a quantitative character. Emmanuelle Porcher & Russell Lande Inbreeding depression due to stabilizing selection on a quantitative character Emmanuelle Porcher & Russell Lande Inbreeding depression Reduction in fitness of inbred vs. outbred individuals Outcrossed

More information

Quantitative Genetics I: Traits controlled my many loci. Quantitative Genetics: Traits controlled my many loci

Quantitative Genetics I: Traits controlled my many loci. Quantitative Genetics: Traits controlled my many loci Quantitative Genetics: Traits controlled my many loci So far in our discussions, we have focused on understanding how selection works on a small number of loci (1 or 2). However in many cases, evolutionary

More information

The Wright-Fisher Model and Genetic Drift

The Wright-Fisher Model and Genetic Drift The Wright-Fisher Model and Genetic Drift January 22, 2015 1 1 Hardy-Weinberg Equilibrium Our goal is to understand the dynamics of allele and genotype frequencies in an infinite, randomlymating population

More information

Evolution. Before You Read. Read to Learn

Evolution. Before You Read. Read to Learn Evolution 15 section 3 Shaping Evolutionary Theory Biology/Life Sciences 7.e Students know the conditions for Hardy-Weinberg equilibrium in a population and why these conditions are not likely to appear

More information

AEC 550 Conservation Genetics Lecture #2 Probability, Random mating, HW Expectations, & Genetic Diversity,

AEC 550 Conservation Genetics Lecture #2 Probability, Random mating, HW Expectations, & Genetic Diversity, AEC 550 Conservation Genetics Lecture #2 Probability, Random mating, HW Expectations, & Genetic Diversity, Today: Review Probability in Populatin Genetics Review basic statistics Population Definition

More information

Laboratory III Quantitative Genetics

Laboratory III Quantitative Genetics Laboratory III Quantitative Genetics Genetics Biology 303 Spring 2007 Dr. Wadsworth Introduction Mendel's experimental approach depended on the fact that he chose phenotypes that varied in simple and discrete

More information

Since we re not going to have review this week either

Since we re not going to have review this week either Since we re not going to have review this week either I am posting these slides to help with reviewing the material that we didn t cover during discussion sessions these past two weeks. Of course, take

More information

Bustamante et al., Supplementary Nature Manuscript # 1 out of 9 Information #

Bustamante et al., Supplementary Nature Manuscript # 1 out of 9 Information # Bustamante et al., Supplementary Nature Manuscript # 1 out of 9 Details of PRF Methodology In the Poisson Random Field PRF) model, it is assumed that non-synonymous mutations at a given gene are either

More information

Mechanisms of Evolution Microevolution. Key Concepts. Population Genetics

Mechanisms of Evolution Microevolution. Key Concepts. Population Genetics Mechanisms of Evolution Microevolution Population Genetics Key Concepts 23.1: Population genetics provides a foundation for studying evolution 23.2: Mutation and sexual recombination produce the variation

More information

Effective population size and patterns of molecular evolution and variation

Effective population size and patterns of molecular evolution and variation FunDamental concepts in genetics Effective population size and patterns of molecular evolution and variation Brian Charlesworth Abstract The effective size of a population,, determines the rate of change

More information

Evolution. Species Changing over time

Evolution. Species Changing over time Evolution Species Changing over time Charles Darwin Evolution by Means of Natural Selection Reasons for Change Mutation A mutation could cause parents with genes for bright green coloration to have offspring

More information

Problems for 3505 (2011)

Problems for 3505 (2011) Problems for 505 (2011) 1. In the simplex of genotype distributions x + y + z = 1, for two alleles, the Hardy- Weinberg distributions x = p 2, y = 2pq, z = q 2 (p + q = 1) are characterized by y 2 = 4xz.

More information

D. Incorrect! That is what a phylogenetic tree intends to depict.

D. Incorrect! That is what a phylogenetic tree intends to depict. Genetics - Problem Drill 24: Evolutionary Genetics No. 1 of 10 1. A phylogenetic tree gives all of the following information except for. (A) DNA sequence homology among species. (B) Protein sequence similarity

More information

Chapter 16. Table of Contents. Section 1 Genetic Equilibrium. Section 2 Disruption of Genetic Equilibrium. Section 3 Formation of Species

Chapter 16. Table of Contents. Section 1 Genetic Equilibrium. Section 2 Disruption of Genetic Equilibrium. Section 3 Formation of Species Population Genetics and Speciation Table of Contents Section 1 Genetic Equilibrium Section 2 Disruption of Genetic Equilibrium Section 3 Formation of Species Section 1 Genetic Equilibrium Objectives Identify

More information

Febuary 1 st, 2010 Bioe 109 Winter 2010 Lecture 11 Molecular evolution. Classical vs. balanced views of genome structure

Febuary 1 st, 2010 Bioe 109 Winter 2010 Lecture 11 Molecular evolution. Classical vs. balanced views of genome structure Febuary 1 st, 2010 Bioe 109 Winter 2010 Lecture 11 Molecular evolution Classical vs. balanced views of genome structure - the proposal of the neutral theory by Kimura in 1968 led to the so-called neutralist-selectionist

More information

Gene Pool Genetic Drift Geographic Isolation Fitness Hardy-Weinberg Equilibrium Natural Selection

Gene Pool Genetic Drift Geographic Isolation Fitness Hardy-Weinberg Equilibrium Natural Selection CONCEPT 1 EVOLUTION 1. Natural Selection a. Major mechanism of change over time Darwin s theory of evolution b. There is variation among phenotypes genetic mutations play a role in increasing variation

More information

There are 3 parts to this exam. Use your time efficiently and be sure to put your name on the top of each page.

There are 3 parts to this exam. Use your time efficiently and be sure to put your name on the top of each page. EVOLUTIONARY BIOLOGY EXAM #1 Fall 2017 There are 3 parts to this exam. Use your time efficiently and be sure to put your name on the top of each page. Part I. True (T) or False (F) (2 points each). Circle

More information

Homework Assignment, Evolutionary Systems Biology, Spring Homework Part I: Phylogenetics:

Homework Assignment, Evolutionary Systems Biology, Spring Homework Part I: Phylogenetics: Homework Assignment, Evolutionary Systems Biology, Spring 2009. Homework Part I: Phylogenetics: Introduction. The objective of this assignment is to understand the basics of phylogenetic relationships

More information

Selection and Population Genetics

Selection and Population Genetics Selection and Population Genetics Evolution by natural selection can occur when three conditions are satisfied: Variation within populations - individuals have different traits (phenotypes). height and

More information

Introduction to population genetics & evolution

Introduction to population genetics & evolution Introduction to population genetics & evolution Course Organization Exam dates: Feb 19 March 1st Has everybody registered? Did you get the email with the exam schedule Summer seminar: Hot topics in Bioinformatics

More information

Lecture 22: Signatures of Selection and Introduction to Linkage Disequilibrium. November 12, 2012

Lecture 22: Signatures of Selection and Introduction to Linkage Disequilibrium. November 12, 2012 Lecture 22: Signatures of Selection and Introduction to Linkage Disequilibrium November 12, 2012 Last Time Sequence data and quantification of variation Infinite sites model Nucleotide diversity (π) Sequence-based

More information

(Write your name on every page. One point will be deducted for every page without your name!)

(Write your name on every page. One point will be deducted for every page without your name!) POPULATION GENETICS AND MICROEVOLUTIONARY THEORY FINAL EXAMINATION (Write your name on every page. One point will be deducted for every page without your name!) 1. Briefly define (5 points each): a) Average

More information

How robust are the predictions of the W-F Model?

How robust are the predictions of the W-F Model? How robust are the predictions of the W-F Model? As simplistic as the Wright-Fisher model may be, it accurately describes the behavior of many other models incorporating additional complexity. Many population

More information

1. What is genetics and who was Gregor Mendel? 2. How are traits passed from one generation to the next?

1. What is genetics and who was Gregor Mendel? 2. How are traits passed from one generation to the next? Chapter 11 Heredity The fruits, vegetables, and grains you eat are grown on farms all over the world. Tomato seeds produce tomatoes, which in turn produce more seeds to grow more tomatoes. Each new crop

More information

Introduction to Advanced Population Genetics

Introduction to Advanced Population Genetics Introduction to Advanced Population Genetics Learning Objectives Describe the basic model of human evolutionary history Describe the key evolutionary forces How demography can influence the site frequency

More information

- point mutations in most non-coding DNA sites likely are likely neutral in their phenotypic effects.

- point mutations in most non-coding DNA sites likely are likely neutral in their phenotypic effects. January 29 th, 2010 Bioe 109 Winter 2010 Lecture 10 Microevolution 3 - random genetic drift - one of the most important shifts in evolutionary thinking over the past 30 years has been an appreciation of

More information

Quantitative Trait Variation

Quantitative Trait Variation Quantitative Trait Variation 1 Variation in phenotype In addition to understanding genetic variation within at-risk systems, phenotype variation is also important. reproductive fitness traits related to

More information

Genetic Variation in Finite Populations

Genetic Variation in Finite Populations Genetic Variation in Finite Populations The amount of genetic variation found in a population is influenced by two opposing forces: mutation and genetic drift. 1 Mutation tends to increase variation. 2

More information

NOTES Ch 17: Genes and. Variation

NOTES Ch 17: Genes and. Variation NOTES Ch 17: Genes and Vocabulary Fitness Genetic Drift Punctuated Equilibrium Gene flow Adaptive radiation Divergent evolution Convergent evolution Gradualism Variation 17.1 Genes & Variation Darwin developed

More information

Population Genetics. with implications for Linkage Disequilibrium. Chiara Sabatti, Human Genetics 6357a Gonda

Population Genetics. with implications for Linkage Disequilibrium. Chiara Sabatti, Human Genetics 6357a Gonda 1 Population Genetics with implications for Linkage Disequilibrium Chiara Sabatti, Human Genetics 6357a Gonda csabatti@mednet.ucla.edu 2 Hardy-Weinberg Hypotheses: infinite populations; no inbreeding;

More information

Chapter 17: Population Genetics and Speciation

Chapter 17: Population Genetics and Speciation Chapter 17: Population Genetics and Speciation Section 1: Genetic Variation Population Genetics: Normal Distribution: a line graph showing the general trends in a set of data of which most values are near

More information

Microevolution 2 mutation & migration

Microevolution 2 mutation & migration Microevolution 2 mutation & migration Assumptions of Hardy-Weinberg equilibrium 1. Mating is random 2. Population size is infinite (i.e., no genetic drift) 3. No migration 4. No mutation 5. No selection

More information

Exam 1 PBG430/

Exam 1 PBG430/ 1 Exam 1 PBG430/530 2014 1. You read that the genome size of maize is 2,300 Mb and that in this species 2n = 20. This means that there are 2,300 Mb of DNA in a cell that is a. n (e.g. gamete) b. 2n (e.g.

More information

Solutions to Problem Set 4

Solutions to Problem Set 4 Question 1 Solutions to 7.014 Problem Set 4 Because you have not read much scientific literature, you decide to study the genetics of garden peas. You have two pure breeding pea strains. One that is tall

More information

Genetical theory of natural selection

Genetical theory of natural selection Reminders Genetical theory of natural selection Chapter 12 Natural selection evolution Natural selection evolution by natural selection Natural selection can have no effect unless phenotypes differ in

More information

GENETICS - CLUTCH CH.22 EVOLUTIONARY GENETICS.

GENETICS - CLUTCH CH.22 EVOLUTIONARY GENETICS. !! www.clutchprep.com CONCEPT: OVERVIEW OF EVOLUTION Evolution is a process through which variation in individuals makes it more likely for them to survive and reproduce There are principles to the theory

More information

Microevolution Changing Allele Frequencies

Microevolution Changing Allele Frequencies Microevolution Changing Allele Frequencies Evolution Evolution is defined as a change in the inherited characteristics of biological populations over successive generations. Microevolution involves the

More information

Lecture 13: Variation Among Populations and Gene Flow. Oct 2, 2006

Lecture 13: Variation Among Populations and Gene Flow. Oct 2, 2006 Lecture 13: Variation Among Populations and Gene Flow Oct 2, 2006 Questions about exam? Last Time Variation within populations: genetic identity and spatial autocorrelation Today Variation among populations:

More information

Evolution PCB4674 Midterm exam2 Mar

Evolution PCB4674 Midterm exam2 Mar Evolution PCB4674 Midterm exam2 Mar 22 2005 Name: ID: For each multiple choice question select the single est answer. Answer questions 1 to 20 on your scantron sheet. Answer the remaining questions in

More information

Population genetics snippets for genepop

Population genetics snippets for genepop Population genetics snippets for genepop Peter Beerli August 0, 205 Contents 0.Basics 0.2Exact test 2 0.Fixation indices 4 0.4Isolation by Distance 5 0.5Further Reading 8 0.6References 8 0.7Disclaimer

More information

Population Genetics & Evolution

Population Genetics & Evolution The Theory of Evolution Mechanisms of Evolution Notes Pt. 4 Population Genetics & Evolution IMPORTANT TO REMEMBER: Populations, not individuals, evolve. Population = a group of individuals of the same

More information

Evolution. Species Changing over time

Evolution. Species Changing over time Evolution Species Changing over time Objectives I can differentiate between natural selection and artificial selection and I can give examples of each. I can explain several reasons for genetic variation

More information

Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Results in Evolution

Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Results in Evolution Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Results in Evolution 15.2 Intro In biology, evolution refers specifically to changes in the genetic makeup of populations over time.

More information

Evolu&on, Popula&on Gene&cs, and Natural Selec&on Computa.onal Genomics Seyoung Kim

Evolu&on, Popula&on Gene&cs, and Natural Selec&on Computa.onal Genomics Seyoung Kim Evolu&on, Popula&on Gene&cs, and Natural Selec&on 02-710 Computa.onal Genomics Seyoung Kim Phylogeny of Mammals Phylogene&cs vs. Popula&on Gene&cs Phylogene.cs Assumes a single correct species phylogeny

More information

The theory of evolution continues to be refined as scientists learn new information.

The theory of evolution continues to be refined as scientists learn new information. Section 3: The theory of evolution continues to be refined as scientists learn new information. K What I Know W What I Want to Find Out L What I Learned Essential Questions What are the conditions of the

More information

Evolution of Populations. Chapter 17

Evolution of Populations. Chapter 17 Evolution of Populations Chapter 17 17.1 Genes and Variation i. Introduction: Remember from previous units. Genes- Units of Heredity Variation- Genetic differences among individuals in a population. New

More information

STAT 536: Migration. Karin S. Dorman. October 3, Department of Statistics Iowa State University

STAT 536: Migration. Karin S. Dorman. October 3, Department of Statistics Iowa State University STAT 536: Migration Karin S. Dorman Department of Statistics Iowa State University October 3, 2006 Migration Introduction Migration is the movement of individuals between populations. Until now we have

More information

Model Building: Selected Case Studies

Model Building: Selected Case Studies Chapter 2 Model Building: Selected Case Studies The goal of Chapter 2 is to illustrate the basic process in a variety of selfcontained situations where the process of model building can be well illustrated

More information

Evolutionary Genetics Midterm 2008

Evolutionary Genetics Midterm 2008 Student # Signature The Rules: (1) Before you start, make sure you ve got all six pages of the exam, and write your name legibly on each page. P1: /10 P2: /10 P3: /12 P4: /18 P5: /23 P6: /12 TOT: /85 (2)

More information

UNIT V. Chapter 11 Evolution of Populations. Pre-AP Biology

UNIT V. Chapter 11 Evolution of Populations. Pre-AP Biology UNIT V Chapter 11 Evolution of Populations UNIT 4: EVOLUTION Chapter 11: The Evolution of Populations I. Genetic Variation Within Populations (11.1) A. Genetic variation in a population increases the chance

More information

Lecture 13: Population Structure. October 8, 2012

Lecture 13: Population Structure. October 8, 2012 Lecture 13: Population Structure October 8, 2012 Last Time Effective population size calculations Historical importance of drift: shifting balance or noise? Population structure Today Course feedback The

More information

F SR = (H R H S)/H R. Frequency of A Frequency of a Population Population

F SR = (H R H S)/H R. Frequency of A Frequency of a Population Population Hierarchical structure, F-statistics, Wahlund effect, Inbreeding, Inbreeding coefficient Genetic difference: the difference of allele frequencies among the subpopulations Hierarchical population structure

More information

Demography April 10, 2015

Demography April 10, 2015 Demography April 0, 205 Effective Population Size The Wright-Fisher model makes a number of strong assumptions which are clearly violated in many populations. For example, it is unlikely that any population

More information

- mutations can occur at different levels from single nucleotide positions in DNA to entire genomes.

- mutations can occur at different levels from single nucleotide positions in DNA to entire genomes. February 8, 2005 Bio 107/207 Winter 2005 Lecture 11 Mutation and transposable elements - the term mutation has an interesting history. - as far back as the 17th century, it was used to describe any drastic

More information

Theory a well supported testable explanation of phenomenon occurring in the natural world.

Theory a well supported testable explanation of phenomenon occurring in the natural world. Evolution Theory of Evolution Theory a well supported testable explanation of phenomenon occurring in the natural world. Evolution the process by which modern organisms changed over time from ancient common

More information

Gene Pool The combined genetic material for all the members of a population. (all the genes in a population)

Gene Pool The combined genetic material for all the members of a population. (all the genes in a population) POPULATION GENETICS NOTES Gene Pool The combined genetic material for all the members of a population. (all the genes in a population) Allele Frequency The number of times a specific allele occurs in a

More information

Reproduction and Evolution Practice Exam

Reproduction and Evolution Practice Exam Reproduction and Evolution Practice Exam Topics: Genetic concepts from the lecture notes including; o Mitosis and Meiosis, Homologous Chromosomes, Haploid vs Diploid cells Reproductive Strategies Heaviest

More information

Evidence of Evolution

Evidence of Evolution Evidence of Evolution Biogeography The Age of Earth and Fossils Ancient artiodactyl Modern whale Ancestors of Whales Ambulocetus could both swim in shallow water and walk on land. Rodhocetus probably spent

More information

Case Studies in Ecology and Evolution

Case Studies in Ecology and Evolution 3 Non-random mating, Inbreeding and Population Structure. Jewelweed, Impatiens capensis, is a common woodland flower in the Eastern US. You may have seen the swollen seed pods that explosively pop when

More information

1 Springer. Nan M. Laird Christoph Lange. The Fundamentals of Modern Statistical Genetics

1 Springer. Nan M. Laird Christoph Lange. The Fundamentals of Modern Statistical Genetics 1 Springer Nan M. Laird Christoph Lange The Fundamentals of Modern Statistical Genetics 1 Introduction to Statistical Genetics and Background in Molecular Genetics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

More information

A. Correct! Genetically a female is XX, and has 22 pairs of autosomes.

A. Correct! Genetically a female is XX, and has 22 pairs of autosomes. MCAT Biology - Problem Drill 08: Meiosis and Genetic Variability Question No. 1 of 10 1. A human female has pairs of autosomes and her sex chromosomes are. Question #01 (A) 22, XX. (B) 23, X. (C) 23, XX.

More information

SEQUENCE DIVERGENCE,FUNCTIONAL CONSTRAINT, AND SELECTION IN PROTEIN EVOLUTION

SEQUENCE DIVERGENCE,FUNCTIONAL CONSTRAINT, AND SELECTION IN PROTEIN EVOLUTION Annu. Rev. Genomics Hum. Genet. 2003. 4:213 35 doi: 10.1146/annurev.genom.4.020303.162528 Copyright c 2003 by Annual Reviews. All rights reserved First published online as a Review in Advance on June 4,

More information

Bio 1B Lecture Outline (please print and bring along) Fall, 2007

Bio 1B Lecture Outline (please print and bring along) Fall, 2007 Bio 1B Lecture Outline (please print and bring along) Fall, 2007 B.D. Mishler, Dept. of Integrative Biology 2-6810, bmishler@berkeley.edu Evolution lecture #5 -- Molecular genetics and molecular evolution

More information

Lecture WS Evolutionary Genetics Part I 1

Lecture WS Evolutionary Genetics Part I 1 Quantitative genetics Quantitative genetics is the study of the inheritance of quantitative/continuous phenotypic traits, like human height and body size, grain colour in winter wheat or beak depth in

More information

Intraspecific gene genealogies: trees grafting into networks

Intraspecific gene genealogies: trees grafting into networks Intraspecific gene genealogies: trees grafting into networks by David Posada & Keith A. Crandall Kessy Abarenkov Tartu, 2004 Article describes: Population genetics principles Intraspecific genetic variation

More information

Chapter 5 Evolution of Biodiversity. Sunday, October 1, 17

Chapter 5 Evolution of Biodiversity. Sunday, October 1, 17 Chapter 5 Evolution of Biodiversity CHAPTER INTRO: The Dung of the Devil Read and Answer Questions Provided Module 14 The Biodiversity of Earth After reading this module you should be able to understand

More information

1 Errors in mitosis and meiosis can result in chromosomal abnormalities.

1 Errors in mitosis and meiosis can result in chromosomal abnormalities. Slide 1 / 21 1 Errors in mitosis and meiosis can result in chromosomal abnormalities. a. Identify and describe a common chromosomal mutation. Slide 2 / 21 Errors in mitosis and meiosis can result in chromosomal

More information

Mechanisms of Evolution

Mechanisms of Evolution Mechanisms of Evolution 36-149 The Tree of Life Christopher R. Genovese Department of Statistics 132H Baker Hall x8-7836 http://www.stat.cmu.edu/ ~ genovese/. Plan 1. Two More Generations 2. The Hardy-Weinberg

More information

8. Genetic Diversity

8. Genetic Diversity 8. Genetic Diversity Many ways to measure the diversity of a population: For any measure of diversity, we expect an estimate to be: when only one kind of object is present; low when >1 kind of objects

More information

Lecture 24: Multivariate Response: Changes in G. Bruce Walsh lecture notes Synbreed course version 10 July 2013

Lecture 24: Multivariate Response: Changes in G. Bruce Walsh lecture notes Synbreed course version 10 July 2013 Lecture 24: Multivariate Response: Changes in G Bruce Walsh lecture notes Synbreed course version 10 July 2013 1 Overview Changes in G from disequilibrium (generalized Bulmer Equation) Fragility of covariances

More information

STUDY GUIDE SECTION 16-1 Genetic Equilibrium

STUDY GUIDE SECTION 16-1 Genetic Equilibrium STUDY GUIDE SECTION 16-1 Genetic Equilibrium Name Period Date Multiple Choice-Write the correct letter in the blank. 1. The smallest unit in which evolution occurs is a. an individual organism. c. a species

More information

2. Map genetic distance between markers

2. Map genetic distance between markers Chapter 5. Linkage Analysis Linkage is an important tool for the mapping of genetic loci and a method for mapping disease loci. With the availability of numerous DNA markers throughout the human genome,

More information

EVOLUTION UNIT. 3. Unlike his predecessors, Darwin proposed a mechanism by which evolution could occur called.

EVOLUTION UNIT. 3. Unlike his predecessors, Darwin proposed a mechanism by which evolution could occur called. EVOLUTION UNIT Name Read Chapters 1.3, 20, 21, 22, 24.1 and 35.9 and complete the following. Chapter 1.3 Review from The Science of Biology 1. Discuss the influences, experiences and observations that

More information

Genetics and Natural Selection

Genetics and Natural Selection Genetics and Natural Selection Darwin did not have an understanding of the mechanisms of inheritance and thus did not understand how natural selection would alter the patterns of inheritance in a population.

More information

URN MODELS: the Ewens Sampling Lemma

URN MODELS: the Ewens Sampling Lemma Department of Computer Science Brown University, Providence sorin@cs.brown.edu October 3, 2014 1 2 3 4 Mutation Mutation: typical values for parameters Equilibrium Probability of fixation 5 6 Ewens Sampling

More information

122 9 NEUTRALITY TESTS

122 9 NEUTRALITY TESTS 122 9 NEUTRALITY TESTS 9 Neutrality Tests Up to now, we calculated different things from various models and compared our findings with data. But to be able to state, with some quantifiable certainty, that

More information