Matthew B. Hamilton - Population Genetics

4 Chapter 5Figure 5.1 A hypothetical distribution of the effects of mutations on phenot...Figure 5.2 The results of the classic Drosophila melanogaster mutation‐accum...Figure 5.3 Because the majority of mutations are deleterious, the drift barr...Figure 5.4 The probability that a novel mutation is lost from a population d...Figure 5.5 The frequencies over time of new mutations that each have an init...Figure 5.6 A hypothetical example of mutation surfing. A 3 × 9 grid of cells...Figure 5.7 R. A. Fisher's geometric model of mutations fixed by natural sele...Figure 5.8 The probability that a mutation is fixed by natural selection dep...Figure 5.9 Simulation results show the action of Muller's Ratchet in increas...Figure 5.10 Patterns of mutational change in DNA sequences under the infinit...Figure 5.11 Hypothetical DNA sequences at one locus for four individuals and...Figure 5.12 Expected change in allele frequency due to irreversible or one‐w...Figure 5.13 Expected change in allele frequency due to reversible or two‐way...Figure 5.14 Expected homozygosity ( F or autozygosity, solid line) and hetero...Figure 5.15 Haploid reproduction in the context of coalescent and mutation e...Figure 5.16 A genealogy constructed under the simultaneous processes of coal...Figure 5.17 A genealogy constructed under the simultaneous processes of coal...Figure 5.18 A genealogy constructed under the simultaneous processes of coal...

5 Chapter 6Figure 6.1 Population growth in two genotypes with clonal reproduction that ...Figure 6.2 Allele frequencies at the protease locus over time in the HIV pop...Figure 6.3 A diagram of the life cycle of organisms showing some points wher...Figure 6.4 The change in genotype and allele frequencies caused by viability...Figure 6.5 The change in the genotype and allele frequency of a completely d...Figure 6.6 Allele frequencies over time for three types of gene action with ...Figure 6.7 The change in the genotype and allele frequency when there is und...Figure 6.8 The change in the genotype and allele frequency when there is ove...Figure 6.9 The strength of natural selection influences the rate of change i...Figure 6.10 Mean fitness in a population ( ) and change in allele frequency ...Figure 6.11 Mean fitness in a population ( ) and change in allele frequency ...Figure 6.12 Sir Ronald A. Fisher (1890–1963), photographed in 1943, was a pi...Figure 6.13 A graphical illustration of R.A. Fisher's fundamental theorem of...

6 Chapter 7Figure 7.1 A fitness surface made by including mean fitness on a de Finetti ...Figure 7.2 Fitness surfaces for the A, S, and C alleles at the human hemoglo...Figure 7.3 A fitness surface for two loci that each have two alleles where g...Figure 7.4 A fitness surface for two loci that each have two alleles where g...Figure 7.5 The relative fitness of each genotype ( w xx) and the change in all...Figure 7.6 The results of density‐dependent natural selection on the numbers...Figure 7.7 The expected distribution of allele frequencies for a very large ...Figure 7.8 Frequency of the Bar allele in 108 replicate Drosophila melanogas ...Figure 7.9 Distributions of for 1000 independent biallelic loci under the ...Figure 7.10 The absolute value of the change in allele frequency due to muta...Figure 7.11 Haploid reproduction with the possibility of coalescence and nat...Figure 7.12 The ancestral selection graph used to include natural selection ...Figure 7.13 A genealogy where balancing natural selection is modeled by type...Figure 7.14 Sewall Wright's original adaptive landscape diagram. The high fi...Figure 7.15 Wright's schematic representation of the simultaneous action of ...Figure 7.16 Wright's representation of the action of drift‐mutation balance ...Figure 7.17 An ancestral selection graph where the MRCA has the haplotype st...

7 Chapter 8Figure 8.1 Motoo Kimura (left) and James Crow (right) in 1986 on the occasio...Figure 8.2 The fate of selectively neutral mutations in a population. New mu...Figure 8.3 The dwell time for new mutations is different if fixation and los...Figure 8.4 The process of divergence for two DNA sequences that descended as...Figure 8.5 The probability of eventual fixation for a new mutation under the...Figure 8.6 The caricatures of the mutation fitness spectrum drawn to illustr...Figure 8.7 The impact of natural selection on new mutations as well as on as...Figure 8.8 Consequences of natural selection on polymorphism at nucleotide s...Figure 8.9 Plots of nucleotide diversity within Drosophila melanogaster popu...Figure 8.10 An electrophorogram resulting from electrophoresis of single bas...Figure 8.11 Substitutions that occur repeatedly at the same nucleotide site ...Figure 8.12 The three types of events that a single nucleotide site may expe...Figure 8.13 The probability that a nucleotide site retains its original base...Figure 8.14 The hierarchy of nucleotide substitution models that can be used...Figure 8.15 A hypothetical sample of four DNA sequences that are each 10 nuc...Figure 8.16 Rates of nucleotide change in the NS gene that codes for “nonstr...Figure 8.17 Rates of protein evolution as amino acid changes per 100 residue...Figure 8.18 A schematic phylogenetic tree that can be used with to date dive...Figure 8.19 Substitution patterns under a Poisson process. The top panel sho...Figure 8.20 Two representations of rate at which substitution events (circle...Figure 8.21 AN illustration of the history of two DNA sequences that might b...Figure 8.22 Patterns of nucleotide changes that are possible when comparing ...Figure 8.23 Three types of variation in substitution rate, each associated w...Figure 8.24 Estimates of the scaled mutation rate θ are estimated differentl...Figure 8.25 Differences in the shape of genealogies are the basis of Tajima'...Figure 8.26 The basis of the mismatch distribution. Panel A shows a neutral ...Figure 8.27 Diploid (A) and haploid (B) reproduction in the context of coale...Figure 8.28 An ancestral recombination graph with mutation for three loci in...

8 Chapter 9Figure 9.1 Examples of continuous quantitative trait distributions. The top ...Figure 9.2 The phenotypic distribution for a trait determined by two Mendeli...Figure 9.3 The effect of environmental variation on phenotypic variation. Th...Figure 9.4 Phenotypic distributions for a trait determined by two loci in po...Figure 9.5 Phenotypic distributions for a trait determined by two loci with ...Figure 9.6 Examples of phenotypic variation due to genetic ( V G), environment...Figure 9.7 The longest stem and number of stems phenotypes for seven Achille ...Figure 9.8 Broad‐sense and narrow‐sense heritabilities for five blood pressu...Figure 9.9 General types of natural selection on quantitative traits. Direct...Figure 9.10 A hypothetical example of directional selection and response to ...Figure 9.11 Parent–offspring regressions used to estimate heritability ( h 2) ...Figure 9.12 Simulations of directional selection on a quantitative trait wit...Figure 9.13 Phenotypic means for oil and protein content for high and low se...Figure 9.14 Long‐term selection for muscle mass in mice (measured as protein...Figure 9.15 The F2 or recombinant inbred line design for QTL mapping assumin...Figure 9.16 Interval mapping utilizes two maker loci (A and B) that sit on e...Figure 9.17 The difference in phenotypic mean values for each of 17 genetic ...Figure 9.18 The genotypes and distribution of phenotypic values for a trait ...