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Chapter 14Molecular Evolution and

Population Genetics

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Molecular Evolution

• The discovery that DNA is the genetic material made it possible to compare corresponding genes even in distantly related species

• DNA and protein sequences contain information about evolutionary relationships among species

• Comparative studies of macromolecules, the study of how and why their sequences change through time constitutes molecular evolution

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• Accumulation of sequence differences through time is the basis of molecular systematics, which analyzes them in order to infer evolutionary relationships

• A gene tree is a diagram of the inferred ancestral history of a group of sequences

• A gene tree is only an estimate of the true pattern of evolutionary relations

Molecular Evolution

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Molecular Evolution

• Neighbor joining = one of the ways to estimate a gene tree

• Bootstrapping = a common technique for assessing the reliability of a node in a gene tree

• Taxon = the source of each sequence

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Figure 14.1: Analysis of beta globin sequences

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• A gene tree does not necessarily coincide with a species tree:The sorting of

polymorphic alleles in the different lineages

Recombination within gene make it possible for different parts of the same gene to have different evolutionary histories

Molecular Evolution

Figure 14.2: A gene tree vs species tree

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• Rate of sequence evolution = the fraction of sites that undergo a change in some designated time interval = number of replacements per site per billion years

• Rates of evolution can differ dramatically from one protein to another

• Some proteins in some taxa show a rough constancy in their rate of amino acid replacement over long periods of evolutionary time.

• The apparently constant rate of change has been called a molecular clock.

Molecular Evolution

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• There are different kinds of nucleotide sites and nucleotide substitutions depending on their position and function in the genome

• Synonymous substitution = no change in amino acid sequence = primarily at the third codon position

• Nonsynonymous substitution = amino acid replacement

• Rates of evolution of nucleotide sites differ according to their function

Molecular Evolution

9Figure 14.3: Rates of nucleotide substitution in mammalian genes

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• New genes usually evolve through duplication and divergence

• Ortologous genes = duplicated as an accompaniment to speciation, retain the same function

• Paralogous genes = duplicated in the genome of the same species, acquire new or more specialized function

• Pseudogenes = duplicated genes that have lost their function

Molecular Evolution

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• Population genetics = application of genetic principles to entire populations of organisms

• Population = group of organisms of the same species living in the same geographical area

• Subpopulation = any of the breeding groups within a population among which migration is restricted

• Local population = subpopulation within which most individuals find their mates

Population Genetics

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Population Genetics

• Gene pool: the complete set of genetic information in all individuals within a population

• Genotype frequency: proportion of individuals in a population with a specific genotype

• Genotype frequencies may differ from one population to another

• Allele frequency: proportion of any specific allele in a population

• Allele frequencies are estimated from genotype frequencies

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Population Genetics

• The allele frequencies among gametes equal those among reproducing adults.

Figure 14.8: Calculation of the allele frequencies in gametes

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Mating Systems

• Random mating means that mating pairs are formed independently of genotype

• Random mating of individuals is equivalent of the random union of gametes

• Assortative mating: nonrandom selection of mating partners; it is positive when like phenotypes mate more frequently than would be expected by chance and is negative when reverse occurs

• Inbreeding = mating between relatives

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Hardy–Weinberg Principle

• When gametes containing either of two alleles, A or a, unite at random to form the next generation, the genotype frequencies among the zygotes are given by the ratio

p2 : 2pq : q2

this constitutes the Hardy–Weinberg (HW) Principle

p = frequency of a dominant allele A

q = frequency of a recessive allele a

p + q =1

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Figure 14.10: Hardy–Weinberg principle

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Hardy–Weinberg Principle

• One important implication of the HW Principle is that allelic frequencies will remain constant over time if the following conditions are met:

• The population is sufficiently large• Mating is random• Allelic frequencies are the same in males and

females• Selection does not occur, i.e., all genotypes have

equal in viability and fertility• Mutation and migration are absent

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Hardy–Weinberg Principle• Another important implication is that for a rare allele,

there are many more heterozygotes than there are homozygotes for the rare allele

Figure 14.12: Allele frequency graphs

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Hardy–Weinberg Principle:Multiple alleles

• HW frequencies can be extended to multiple alleles:

• Frequency of any homozygous genotype equals square of allele frequency = pi

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• Frequency of any heterozygous genotype equals 2 product of allele frequencies = 2pipj

20Figure 14.13: Results of random mating with three alleles

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Hardy–Weinberg Principle: X-linked genes

• X-linked genes are a special case because males have only one X-chromosome

• Genotype frequencies among females: HH = p2 ; Hh = 2pq; hh = q2

• Genotype frequencies among males are the same as allele frequencies:

H = p, h = q

Figure 14.15: The results of random mating for an X-linked gene

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• An important implication: if h is a rare recessive allele, then there will be many more males exhibiting the trait than females because the frequency of affected females (q2) will be much smaller than the frequency of affected males (q)

Hardy–Weinberg Principle:X-linked genes

Figure 14.16: The ratio of affected males to affected females increases as the allele frequency decreases

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DNA Typing

• The use of polymorphisms in DNA to link suspects with samples of human material is called DNA typing

• Highly polymorphic sequences are used in DNA typing

• Polymorphic alleles may differ in frequency among subpopulations due to population substructure

• DNA exclusions are definitive

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Allelic Variation

• Allelic variation may result from differences in the number of units repeated in tandem: simple tandem repeat (STR)

• STRs can be used to map DNA since they generate fragments of different sizes that can be detected by various methods

• Most people are heterozygous for SSR alleles

25Figure 14.17: Allelic variation

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Inbreeding

• Inbreeding means mating between relatives

• Inbreeding results in an excess of homozygotes compared with random mating

• In most species, inbreeding is harmful due to rare recessive alleles that wouldn’t otherwise become homozygous

Figure 14.9: An inbreeding pedigree

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Figure 14.23: Graph on the effect of first-cousin mating on the frequency of offspring genotypes

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Inbreeding:Inbreeding Coefficient

• A convenient measure of effects of inbreeding is based on the reduction of heterozygosity HI and is called the inbreeding coefficient F

F = (2pq – HI )/2pq

• The overall genotype frequencies in the inbred population are

p2(1 – F) + pF 2pq(1 – F) q2(1 – F) + qF

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Figure 14.22: Frequency of heterozygous genotypes in an inbred population against allele frequency

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Evolution

• Evolution refers to changes in the gene pool of a population or in the allele frequencies present in a population

• Evolution is possible because genetic variation exists in populations

• Four processes account for most of the evolutionary changes

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Evolution

1. Mutation = the origin of new genetic capabilities in populations = the ultimate source of genetic variation

2. Migration = the movement of organisms among subpopulations

3. Natural selection = the process of evolutionary adaptation: genotypes best suited to survive and reproduce in a particular environment give rise to a disproportionate share of the offspring

4. Random genetic drift = the random, undirected changes in allele frequencies, especially in small populations

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Natural Selection

• The concept of natural selection was first proposed by Charles Darwin in 1859.

• Natural selection is the driving force of adaptive evolution and is a consequence of the hereditary differences among organisms and their ability to survive and reproduce in the prevailing environment.

• Adaptation = progressive genetic improvement in populations due to natural selection

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Natural Selection

• In its modern formulation, the concept of natural selection rests on three premises: More organisms are produced than can survive

and reproduce Organisms differ in their ability to survive and

reproduce, and some of these differences are due to genotype

The genotypes that promote survival are favored and contribute disproportionately to the offspring of the next generation

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Fitness

• Fitness is the relative ability of genotypes to survive and reproduce

• Relative fitness measures the comparative contribution of each parental genotype to the pool of offspring genotypes in each generation

• Selection coefficient refers to selective disadvantage of a disfavored genotype

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Selection in Diploids

• Frequency of favored dominant allele changes slowly if the allele is common

• Frequency of favored recessive allele changes slowly if the allele is rare

• Rare alleles are found most frequently in heterozygotes

• When favored, the allele is dominant, recessive allele in heterozygotes is not exposed to natural selection

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Selection in Diploids

• Selection for or against very rare recessive alleles is inefficient

• The largest reservoir of harmful recessive alleles is in the genomes of heterozygous carriers, who are phenotypically normal

37Figure 14.25: The selection coefficient against the least fit homozygous

genotype is 5 percent

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Selection in Diploids

• Selection can be balanced by new mutations

• New mutations often generate harmful alleles and prevent their elimination from the population by natural selection

• Eventually the population will attain a state of equilibrium in which the new mutations exactly balance the selective elimination

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Heterozygote Superiority

• Heterozygote superiority = fitness (measurement of viability and fertility) of heterozygote is greater than that of both homozygotes

• When there is heterozygote superiority, neither allele can be eliminated by selection

• In sickle cell anemia, the allele for mutant hemoglobin is maintained in high frequencies in regions of endemic malaria because heterozygotes are more resistant to this disease

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Random Genetic Drift

• Some changes in allele frequency are random due to genetic drift

• Random genetic drift comes about because populations are not infinitely large

• Only relatively few of the gametes participate in fertilization (sampling)

• With random genetic drift, the probability of fixation of an allele is equal to its frequency in the original population

41Figure 14.27: Random genetic drift

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Maternal Inheritance

• Maternal inheritance refers to the transmission of genes only through the female

• In higher animals, mitochondrial DNA (mtDNA) shows maternal inheritance

• Mitochondria are maternally inherited because the egg is the major contributor of cytoplasm to the zygote

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Maternal Inheritance

• Some rare genetic disorders are the result of mutations in mtDNA and are transmitted from mother to all offspring

• The severity of the disorder depends on the proportions of normal and mutant mitochondria among affected individuals

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Maternal Inheritance

• Recombination does not occur in mitochondrial DNA making it a good genetic marker for human ancestry

• Human mtDNA evolves at approximately a constant rate = 1 change per mt lineage every 3800 years

• Modern human populations originated in subsaharan Africa approximately 100,000 years ago.

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Figure 14.30: Phylogenetic tree of human mitochondrial DNA

Adapted from M. Ingman, et al., Nature 408 (2000): 708-713.