Population Genetics. Matthew B. Hamilton

Haploid (top, A) and diploid (bottom, B) reproduction in the con...Figure 3.25 The distribution of the probabilities of coalescence over time p...Figure 3.26 Six independent realizations of the coalescent tree for six line...Figure 3.27 A schematic coalescent tree for six lineages shows one realizati...Figure 3.28 The distribution of times to a MRCA (or genealogy heights) for 1...Figure 3.29 The effects of a population bottleneck on gene genealogies. Duri...Figure 3.30 The effects of exponential population growth or shrinkage on coa...Figure 3.31 Additional models of finite sampling approximate different life ...

      3 Chapter 4Figure 4.1 An example of population structure and allele frequency divergenc...Figure 4.2 The plant Linanthus parryae or “desert snow” is found in the Moja...Figure 4.3 Isolation by distance causes spatial structuring of allele and ge...Figure 4.4 Moran's I for simulated populations like those in Figure 4.3. To ...Figure 4.5 Models of population structure make different assumptions about t...Figure 4.6 Allele frequency in the island population for a diallelic locus u...Figure 4.7 Allele frequency in the two‐island model of gene flow for a diall...Figure 4.8 Dispersal kernel probability distributions that show how dispersa...Figure 4.9 An individual Corythophora alta tree found at the Biological Dyna...Figure 4.10 Illustration of the hierarchical nature of heterozygosity in a s...Figure 4.11 Allele frequencies at a diallelic locus for populations that con...Figure 4.12 Genetic differentiation in a finite island model simulation that...Figure 4.13 A graphical demonstration of the Wahlund effect for a diallelic ...Figure 4.14 A hypothetical example of how the Wahlund effect relates variati...Figure 4.15 Expected levels of fixation among subpopulations depend on the p...Figure 4.16 Allele frequencies, hierarchal heterozygosities, and fixation in...Figure 4.17 The distribution of F_ST values for 1000 replicate neutral loci i...Figure 4.18 Subpopulations in a stepping‐stone model exhibit an increase in ...Figure 4.19 Landscapes (represented by the topographical map in the lower pl...Figure 4.20 An example circuit with resistors representing the genetic conne...Figure 4.21 Clustering of individuals into four populations based on Bayesia...Figure 4.22 Principle components analysis of genotype data exhibits populati...Figure 4.23 A hypothetical genealogy for two demes. Initially, there are thr...Figure 4.24 Genealogies for six lineages initially divided evenly between tw...Figure 4.25 Sample configurations for two lineages and two demes (A) and thr...Figure 4.26 The possible events that can occur when two lineages are in the ...

      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