Processes of Evolution

15 Processes of Evolution

Chapter 15 Processes of Evolution Key Concepts 15.1 Evolution Is Both Factual and the Basis of Broader Theory 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution 15.3 Evolution Can Be Measured by Changes in Allele Frequencies 15.4 Selection Can Be Stabilizing, Directional, or Disruptive

Chapter 15 Mechanisms of Evolution Key Concepts 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features 15.7 Evolutionary Theory Has Practical Applications

Chapter 15 Opening Question How do biologists use evolutionary theory to develop better flu vaccines?

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory Evolution is the change in genetic composition of populations over time. Evolutionary change is observed in laboratory experiments, in natural populations, and in the fossil record. These underlying genetic changes drive the origin and extinction of species and fuel the diversification of life.

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory Evolutionary theory is the understanding and application of the processes of evolutionary change to biological problems. Applications: Study and treatment of diseases Development of crops and industrial processes Understanding the diversification of life It also allows us to make predictions about the biological world.

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory Theory in everyday speech, an untested hypothesis or a guess Evolutionary theory is not a single hypothesis It refers to our understanding of the processes that result in genetic changes in populations over time and to our use of that understanding to interpret changes we observe in natural populations.

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory Even before Darwin, biologists had suggested that species had changed over time, but no one had proposed a convincing mechanism for evolution.

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory Charles Darwin was interested in geology and natural history.

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory In 1831, Darwin began a 5-year voyage around the world on a Navy survey vessel, the HMS Beagle.

Figure 15.1 The Voyage of the Beagle

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory From the observations and insights made on the voyage and new ideas from geologists on the age of the Earth, Darwin developed an explanatory theory for evolutionary change: Species change over time Divergent species share a common ancestor (descent with modification) The mechanism that produces change is natural selection

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory In 1858, Darwin received a paper from Alfred Russel Wallace with an explanation of natural selection nearly identical to Darwin s. Both men are credited for the idea of natural selection. Darwin s book, The Origin of Species, was published in 1859.

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory By 1900, the fact of evolution was established, but the genetic basis of evolution was not yet understood. Then the work of Gregor Mendel was rediscovered, and during the 20 th century, work continued on the genetic basis of evolution. A modern synthesis of genetics and evolution took place 1936 1947.

Figure 15.2 Milestones in the Development of Evolutionary Theory

Concept 15.1 Evolution Is Both Factual and the Basis of Broader Theory The structure of DNA was established by 1953 by Watson and Crick. In the 1970s, technology developed for sequencing long stretches of DNA and amino acid sequences in proteins. Evolutionary biologists now study gene structure and evolutionary change using molecular techniques.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution In biology, evolution refers specifically to changes in the genetic makeup of populations over time. Population a group of individuals of a single species that live and interbreed in a particular geographic area at the same time. Individuals do not evolve; populations do.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution The origin of genetic variation is mutation. Mutation any change in nucleotide sequences. Mutations occur randomly with respect to an organism s needs; natural selection acts on this random variation and results in adaptation.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Mutations can be deleterious, beneficial, or have no effect (neutral). Mutation both creates and helps maintain genetic variation in populations. Mutation rates vary, but even low rates create considerable variation.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Because of mutation, different forms of a gene, or alleles, may exist at a locus. Gene pool sum of all copies of all alleles at all loci in a population Allele frequency proportion of each allele in the gene pool Genotype frequency proportion of each genotype among individuals in the population

Figure 15.3 A Gene Pool

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution An experiment demonstrates how mutations accumulate in populations: Lines of E. coli were grown in the laboratory for 20,000 generations, and genomes were sequenced every 5,000 generations. The lines accumulated about 45 changes to their genomes, and these changes appeared at a fairly constant rate.

Figure 15.4 Mutations Accumulate Continuously

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution The gene pools of nearly all populations contain variation for many traits. Selection that favors different traits can lead to many different lineages that descend from the same ancestor. Artificial selection on different traits in a single species of wild mustard produced many crop plants.

Figure 15.5 Many Vegetables from One Species

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Many of Darwin s observations of variation and selection came from domesticated plants and animals. Darwin bred pigeons and recognized similarities between selection by breeders and selection in nature. In both cases, selection simply increases the frequency of the favored trait from one generation to the next.

Figure 15.6 Artificial Selection

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Laboratory experiments also demonstrate genetic variation in populations. Selection for certain traits in the fruit fly Drosophila melanogaster resulted in new combinations of genes that were not present in the original population.

Figure 15.7 Artificial Selection Reveals Genetic Variation

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Natural selection: Far more individuals are born than survive to reproduce. Offspring tend to resemble their parents but are not identical to their parents or to one another. Differences among individuals affect their chances of survival and reproduction, which will increase the frequency of favorable traits in the next generation.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Adaptation a favored trait that evolves through natural selection Adaptation also describes the process that produces the trait. Individuals with deleterious mutations are less likely to survive, reproduce, and pass their alleles on to the next generation.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Migration of individuals or movement of gametes (e.g., pollen) between populations results in gene flow, which can change allele frequencies.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Genetic drift random changes in allele frequencies from one generation to the next In small populations, it can change allele frequencies. Harmful alleles may increase in frequency, or rare advantageous alleles may be lost. Even in large populations, genetic drift can influence frequencies of neutral alleles.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Population bottleneck an environmental event results in survival of only a few individuals This can result in genetic drift and changing allele frequencies. Populations that go through bottlenecks loose much of their genetic variation. This is a problem for small populations of endangered species.

Figure 15.8 A Population Bottleneck

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Founder effect genetic drift changes allele frequencies when a few individuals colonize a new area It is equivalent to a large population reduced by a bottleneck.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Nonrandom mating: Self-fertilization is common in plants. When individuals prefer others of the same genotype, homozygous genotypes will increase in frequency, and heterozygous genotypes will decrease.

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Sexual selection occurs when individuals of one sex mate preferentially with particular individuals of the opposite sex rather than at random. Some seemingly nonadaptive traits may make an individual more attractive to the opposite sex. There may be a trade-off between attracting mates (more likely to reproduce) and attracting predators (less likely to survive).

Figure 15.9 What Is the Advantage?

Concept 15.2 Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom Mating Result in Evolution Studies of African long-tailed widowbirds showed that females preferred males with longer tails. Males with artificially elongated tails attracted four times more females than males with artificially shortened tails. Thus males with long tails pass on their genes to more offspring, which leads to the evolution of this unusual trait.

Figure 15.10 Sexual Selection in Action (Part 1)

Figure 15.10 Sexual Selection in Action (Part 2)

Concept 15.3 Evolution Can Be Measured by Changes in Allele Frequencies Evolution can be measured by changes in allele frequencies. Allele frequency: p = number of copies of allele in population total number of copies of all alleles in population

Concept 15.3 Evolution Can Be Measured by Changes in Allele Frequencies For two alleles at a locus, A and a, three genotypes are possible: AA, Aa, and aa. p = frequency of A; q = frequency of a p = 2 N + AA 2N N Aa q = 2 N + aa 2N N Aa

Figure 15.11 Calculating Allele and Genotype Frequencies

Concept 15.3 Evolution Can Be Measured by Changes in Allele Frequencies For each population, p + q = 1, and q = 1 p. Monomorphic: only one allele at a locus, frequency = 1; the allele is fixed Polymorphic: more than one allele at a locus Genetic structure frequency of different alleles and genotypes in a population

Concept 15.3 Evolution Can Be Measured by Changes in Allele Frequencies Hardy Weinberg equilibrium a model in which allele frequencies do not change across generations; genotype frequencies can be predicted from allele frequencies For a population to be at Hardy Weinberg equilibrium, there must be random mating and infinite population size, but no mutation, no gene flow, and no selection of genotypes.

Concept 15.3 Evolution Can Be Measured by Changes in Allele Frequencies At Hardy Weinberg equilibrium, allele frequencies do not change. Genotype frequencies after one generation of random mating: Genotype: AA Aa aa Frequency: p 2 2pq q 2

Figure 15.12 One Generation of Random Mating Restores Hardy Weinberg Equilibrium (Part 1)

Figure 15.12 One Generation of Random Mating Restores Hardy Weinberg Equilibrium (Part 2)

Concept 15.3 Evolution Can Be Measured by Changes in Allele Frequencies Probability of two A-gametes coming together: p p = p 2 = (0.55) 2 = 0.3025 Probability of two a-gametes coming together: q q = q 2 = (0.45) 2 = 0.2025 Overall probability of obtaining a heterozygote: 2pq = 0.495

Concept 15.3 Evolution Can Be Measured by Changes in Allele Frequencies Populations in nature never meet the conditions of Hardy Weinberg equilibrium all biological populations evolve. The model is useful for predicting approximate genotype frequencies of a population. Specific patterns of deviation from Hardy Weinberg equilibrium help identify processes of evolutionary change.

Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Qualitative traits influenced by alleles at one locus; often discrete qualities (black versus white) Quantitative traits influenced by alleles at more than one locus; likely to show continuous variation (body size of individuals)

Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection favors average individuals. Directional selection favors individuals that vary in one direction from the mean. Disruptive selection favors individuals that vary in both directions from the mean.

Figure 15.13 Natural Selection Can Operate in Several Ways

Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Stabilizing selection reduces variation in populations but does not change the mean. Example: Stabilizing selection operates on human birth weight. It is often called purifying selection, meaning selection against any deleterious mutations to the usual gene sequence.

Figure 15.14 Human Birth Weight Is Influenced by Stabilizing Selection

Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive In directional selection, individuals at one extreme of a character distribution contribute more offspring to the next generation. For a single gene locus, directional selection may favor a particular variant positive selection for that variant. If directional selection operates over many generations, an evolutionary trend is seen. Example: Texas Longhorn cattle.

Figure 15.15 Long Horns Are the Result of Directional Selection

Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive In disruptive selection, individuals at opposite extremes of a character distribution contribute more offspring to the next generation. Results in increased variation in the population Can result in a bimodal distribution of traits Example: bill sizes in the black-bellied seedcracker (Pyrenestes ostrinus)

Figure 15.16 Disruptive Selection Results in a Bimodal Character Distribution

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Types of mutations: Nucleotide substitution change in one nucleotide in a DNA sequence (a point mutation) Synonymous substitution (silent) does not change the encoded amino acid (most amino acids are specified by more than one codon) Nonsynonymous substitution (missense) usually deleterious but can be selectively neutral or advantageous

Figure 15.17 When One Nucleotide Changes

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Substitution rates are highest at positions that do not change the amino acid being expressed (synonymous substitutions). Substitution rate is even higher in pseudogenes, copies of genes that are no longer functional.

Figure 15.18 Rates of Substitution Differ

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Types of mutations: Insertions, deletions, and rearrangements of DNA sequences: Can have a larger effect than point mutations Can change the reading frame of proteincoding sequences

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Neutral theory at the molecular level, the majority of variants in most populations are selectively neutral. Because they confer neither advantages nor disadvantages, neutral variants must accumulate through genetic drift rather than positive selection.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Rate of fixation of neutral mutations by genetic drift is independent of population size. m 1 = 2 Nµ 2N N = population size µ = neutral mutation rate

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution The rate of evolution of particular genes and proteins is often relatively constant over time and can be used as a molecular clock to calculate evolutionary divergence times between species.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Relative rates of synonymous and nonsynonymous substitutions: The rates should be similar if an amino acid can be one of many alternatives without changing the protein s function amino acid replacement is neutral with respect to fitness of the organism. If an amino acid position is under positive selection, the rate of nonsynonymous substitutions should exceed the rate of synonymous substitutions.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution If an amino acid position is under purifying selection, the rate of synonymous substitutions is expected to be much higher than nonsynonymous substitutions.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Particular codons in a gene sequence can be under different modes of selection. Evolution of lysozyme: Lysozyme digests bacterial cell walls. It is found in almost all animals as a defense mechanism. Some mammals have foregut fermentation, which has evolved twice in ruminants and langurs. Lysozyme in these lineages has been modified to rupture only some bacteria in the foregut to release nutrients.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Lysozyme-coding sequences were compared in foregut fermenters and their nonfermenting relatives, and rates of substitutions were determined. For many amino acid positions, the rate of synonymous substitution in the lysozyme gene was much higher than nonsynonymous, indicating that many of the amino acids are evolving under purifying selection.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution But at other positions, the rates were similar. Amino acid replacements happened at a much higher rate in the langur lineage. Lysozyme went through a period of rapid change in adapting to the stomachs of langurs. Lysozymes of langurs and cattle share five convergent amino acid replacements, which make the protein more resistant to degradation by the stomach enzyme pepsin.

Figure 15.19 Convergent Molecular Evolution of Lysozyme

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution The hoatzin is the only foregut-fermenting bird. It has independently evolved modifications to lysozyme similar to those found in cattle and langurs.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Heterozygosity can be advantageous as environmental conditions change; because of the advantage, polymorphic loci are maintained. Colias butterflies live in an environment with temperature extremes. The population is polymorphic for an enzyme that influences flight at different temperatures. Heterozygotes are favored because they can fly over a larger temperature range.

Figure 15.20 A Heterozygote Mating Advantage (Part 1)

Figure 15.20 A Heterozygote Mating Advantage (Part 2)

Figure 15.20 A Heterozygote Mating Advantage (Part 3)

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Genome size varies greatly. There is some correlation between genome size and organismal complexity, but not always. If only the protein and RNA coding portions of genomes are considered, there is much less variation in size.

Figure 15.21 Evolution of Gene Number

Figure 15.22 A Large Proportion of DNA Is Noncoding

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution Some of the noncoding DNA can alter the expression of surrounding genes. Some noncoding DNA consists of pseudogenes, which are nonfunctional but occasionally develop novel functions. Other noncoding sequences help maintain chromosome structure, and some consist of parasitic transposable elements.

Concept 15.5 Genomes Reveal Both Neutral and Selective Processes of Evolution The amount of nonconding DNA may be related to population size. Noncoding sequences that are only slightly deleterious are likely to be purged by selection most efficiently in species with large population sizes. In small populations genetic drift may overwhelm selection against these sequences.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features Sexual reproduction results in new gene combinations and produces genetic variety that increases evolutionary potential.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features In the short term, sexual reproduction has disadvantages: Recombination can break up adaptive combinations of genes Reduced rate at which females pass genes to offspring Dividing offspring into genders reduces the overall reproductive rate

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features Why did sexual reproduction evolve? Possible advantages: Facilitates repair of damaged DNA damage on one chromosome can be repaired by copying intact sequences on the other chromosome Elimination of deleterious mutations through recombination followed by selection

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features In asexually reproducing species, deleterious mutations can accumulate; only death of the lineage can eliminate them Muller called this the genetic ratchet mutations accumulate or ratchet up at each replication; known as Muller s ratchet.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features The variety of genetic combinations in each generation can be advantageous (e.g., as defense against pathogens and parasites) Sexual recombination does not directly influence the frequencies of alleles, it generates new combinations of alleles on which natural selection can act.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features Lateral gene transfer individual genes, organelles, or genome fragments move horizontally from one lineage to another Species may pick up DNA fragments directly from the environment. Genes may be transferred to a new host in a viral genome. Hybridization results in the transfer of many genes.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features Lateral gene transfer can be advantageous; it increases genetic variation. Most common in bacteria; genes that confer antibiotic resistance are often transferred among species Relatively uncommon in eukaryotes, but hybridization in plants leads to gene exchange The endosymbiosis events that gave rise to mitochondria and chloroplasts were lateral gene transfers.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features Gene duplication genomes can gain new functions Gene copies may have different fates: Both copies retain original function, which can increase the amount of gene product. Gene expression may diverge in different tissues or at different times in development.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features One copy may accumulate deleterious mutations and become a functionless pseudogene. One copy retains original function, the other changes and evolves a new function.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features Sometimes entire genomes may be duplicated, providing massive opportunities for new functions to evolve. In vertebrate evolution, genomes of the jawed vertebrates have four diploid sets of many genes. Two genome-wide duplication events occurred in the ancestor of these species. This allowed specialization of individual vertebrate genes.

Concept 15.6 Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features Successive rounds of duplication and sequence evolution may result in a gene family, a group of homologous genes with related functions. The globin gene family probably arose via gene duplications.

Figure 15.23 A Globin Family Gene Tree

Concept 15.7 Evolutionary Theory Has Practical Applications Molecular evolutionary principles can be used to understand protein structure and function. Puffer fish produce a toxin (TTX) that blocks Na + channels and prevents nerve and muscle function. But Na + channels in the puffer fish itself are not blocked by the toxin. Nucleotide substitutions in puffer fish genes result in changes in the channel proteins that prevent TTX from binding.

Concept 15.7 Evolutionary Theory Has Practical Applications Mutations in human Na + channel genes cause several neurological diseases. Study of these gene substitutions aids in understanding how Na + channels function. Biologists compare rates of synonymous and nonsynonymous substitutions across Na + channel genes in various animals that have evolved TTX resistance.

Concept 15.7 Evolutionary Theory Has Practical Applications Living organisms produce many compounds useful to humans. The search for such compounds is called bioprospecting. These molecules result from millions of years of evolution. But biologists can imagine molecules that have not yet evolved. In vitro evolution new molecules are produced in the laboratory to perform novel functions

Figure 15.24 In Vitro Evolution

Concept 15.7 Evolutionary Theory Has Practical Applications In agriculture, breeding programs have benefited from evolutionary principles, including incorporation of beneficial genes from wild species. An understanding of how pest species evolve resistance to pesticides has resulted in more effective pesticide application and rotation schemes.

Concept 15.7 Evolutionary Theory Has Practical Applications Molecular evolution is also used to study disease organisms. All new viral diseases have been identified by evolutionary comparison of their genomes with those of known viruses. Studies of the origins, timing of emergence, and global diversity of human pathogens (including HIV) depend on evolutionary principles and methods, as do efforts to develop effective vaccines.

Answer to Opening Question Changes in surface proteins make influenza virus strains undetectable to the host s immune system (positive selection for changes in surface proteins). By comparing ratios of synonymous to nonsynonymous substitutions, biologists can detect which mutations are under positive selection.

Answer to Opening Question They then assess which current flu strains show the greatest number of changes in these positively selected codons. These flu strains are most likely to survive and lead to flu epidemics of the future, so they are the best targets for new vaccines.

Figure 15.25 Evolutionary Analysis of Surface Proteins Leads to Improved Flu Vaccines