Mechanisms of Evolution. Key Concepts Evolution Is Both Factual and the Basis of Broader Theory Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom

Mechanisms of Evolution


Key Concepts

• Evolution Is Both Factual and the Basis of Broader Theory

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

• Evolution Can Be Measured by Changes in Allele Frequencies

• Selection Can Be Stabilizing, Directional, or Disruptive


Key Concepts

• Genomes Reveal Both Neutral and Selective Processes of Evolution

• Recombination, Lateral Gene Transfer, and Gene Duplication Can Result in New Features

• Evolutionary Theory Has Practical Applications

Evolution Is Both Factual and the Basis of Broader Theory

Biological populations change over time, or evolve.

Evolutionary change is observed in laboratory experiments, in natural populations, and in the fossil record.


Evolutionary theory—understanding the mechanisms of evolutionary change.

It has many applications: study and treatment of diseases, development of crops and industrial processes, understanding the diversification of life, and how species interact.

It also allows us to make predictions about the biological world.


Theory—In everyday speech, an untested hypothesis or a guess.

Evolutionary theory is not a single hypothesis, but refers to our understanding of the mechanisms that result in genetic changes in populations over time and to our use of that understanding to interpret changes in and interactions among living organisms.


Even before Darwin, biologists had suggested that species had changed over time, but no one had proposed a convincing mechanism for evolution.


Charles Darwin was interested in geology and natural history.


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


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.

• The mechanism that produces change is natural selection.


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.


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 20th 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


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.

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

Biological evolution refers 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.


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.


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.


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


Many of Darwin’s observations came from artificial selection of domesticated plants and animals.

Selection on different characters in a single species of wild mustard produced many crop plants.

Figure 15.4 Many Vegetables from One Species


Darwin bred pigeons and recognized similarities between selection by breeders and selection in nature.

Figure 15.5 Artificial Selection


Laboratory experiments also show 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 15.6 Artificial Selection Reveals Genetic Variation


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 to survive and reproduce, which will increase frequency of favored traits in the next generation.


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 and reproduce and to pass their alleles on to the next generation.


Migration of individuals between populations results in gene flow, which can change allele frequencies.


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.


A population bottleneck—an environmental event results in survival of only a few individuals.

Genetic drift can change allele frequencies.

Populations that go through bottlenecks loose much of their genetic variation.

Figure 15.7 A Population Bottleneck


Founder effect—genetic drift changes allele frequencies when a few individuals colonize a new area.


Nonrandom mating:

Selfing, or self-fertilization is common in plants. Homozygous genotypes will increase in frequency and heterozygous genotypes will decrease.


Sexual selection—mates are chosen based on phenotype, e.g., bright-colored feathers of male birds.

There may be a trade-off between attracting mates (more likely to reproduce) and attracting predators (less likely to survive).


Or, phenotype may indicate a successful genotype, e.g., female frogs are attracted to males with low-frequency calls, which are larger and older (hence successful).

Studies of African long-tailed widowbirds showed that females preferred males with longer tails, which may indicate greater health and vigor.

Figure 15.8 What Is the Advantage?

Figure 15.9 Sexual Selection in Action (Part 1)

Figure 15.9 Sexual Selection in Action (Part 2)

Evolution Can Be Measured by Changes in Allele Frequencies

Evolution can be measured by change in allele frequencies.

Allele frequency =

population in alleles all of copies of number total

population in allele of copies of number


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

N

NNp AaAA

2

2

N

NNq Aaaa

2

2

Figure 15.10 Calculating Allele and Genotype Frequencies


For each population, p + q = 1, and q = 1 – p.

Genetic structure—frequency of alleles and genotypes of a population.


Hardy–Weinberg equilibrium—allele frequencies do not change across generations; genotype frequencies can be calculated from allele frequencies.

If a population is at Hardy-Weinberg equilibrium, there must be no mutation, no gene flow, no selection of genotypes, infinite population size, and random mating.


At Hardy-Weinberg equilibrium, allele frequencies don’t change.

Genotypes frequencies:

Genotype AA Aa aaFrequency p2 2pq q2

Figure 15.11 One Generation of Random Mating Restores Hardy–Weinberg Equilibrium (Part 1)

Figure 15.11 One Generation of Random Mating Restores Hardy–Weinberg Equilibrium (Part 2)


Probability of 2 A-gametes coming together:

Probability of 2 a-gametes coming together:

Overall probability of obtaining a heterozygote:

3025.0)55.0( 22 ppp

0.2025qqq 22 )45.0(

0.495pq 2


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 mechanisms of evolutionary change.

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).


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 15.12 Natural Selection Can Operate in Several Ways (Part 1)




Stabilizing selection reduces variation in populations, but does not change the mean.

It is often called purifying selection—selection against any deleterious mutations to the usual gene sequence.

Figure 15.13 Human Birth Weight Is Influenced by Stabilizing Selection


Directional selection—individuals at one extreme of a character distribution contribute more offspring to the next generation.

An evolutionary trend may result.

Example: Texas Longhorn cattle.

Figure 15.14 Long Horns Are the Result of Directional Selection


Disruptive selection—individuals at opposite extremes of a character distribution contribute more offspring to the next generation.

Increases variation in the population; can result in a bimodal distribution of traits.

Figure 15.15 Disruptive Selection Results in a Bimodal Character Distribution

Genomes Reveal Both Neutraland Selective Processes of Evolution

Types of mutations:

• Nucleotide substitution—change in one nucleotide in a DNA sequence (a point mutation).

• Synonymous substitution—most don’t affect phenotype because most amino acids are specified by more than one codon.

• Nonsynonymous substitution—deleterious or selectively neutral.

Figure 15.16 When One Nucleotide Changes (Part 1)

Figure 15.16 When One Nucleotide Changes (Part 2)


Substitution rates are highest at positions that do not change the amino acid being expressed.

Substitution is even higher in pseudogenes, copies of genes that are no longer functional.

Figure 15.17 Rates of Substitution Differ


Types of mutations: Insertions, deletions, and rearrangements

Can have larger effect than point mutations.

Can change the reading frame of protein-coding sequences.


Neutral theory—at the molecular level, the majority of variants in most populations are selectively neutral.

Neutral variants must accumulate through genetic drift rather than positive selection.

Suggest a trait that might demonstrate neutral variance.

Why won’t neutral variants accumulate through natural selection?


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.


Fitness of genotypes:

Genotypes of higher fitness increase in frequency over time; those of lower fitness decrease over time.


Relative rates of substitution types differ as a function of selection:

• If similar, the corresponding amino acid is likely drifting neutrally among states.

• If nonsynonymous substitution exceeds synonymous, positive selection results in change in the corresponding amino acid.

• If synonymous substitution exceeds nonsynonymous, purifying selection resists change in the corresponding amino acid.


Evolution of lysozyme:

Lysozyme digests bacteria cell walls; found in almost all animals as a defense mechanism.

Some mammals are foregut fermenters, which has evolved twice—in ruminants and leaf-eating monkeys (langurs). Lysozyme in these lineages has been modified to rupture some bacteria in the foregut to release nutrients.


Lysozyme-coding sequences were compared in foregut fermenters and their non-fermenting relatives, and rates of substitutions were determined.

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.


Replacements in lysozyme happened at a much higher rate in 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 15.18 Convergent Molecular Evolution of Lysozyme (Part 1)

Figure 15.18 Convergent Molecular Evolution of Lysozyme (Part 2)


Lysozyme in the crop of the hoatzin, a foregut-fermenting bird, has similar adaptations as those of langurs and cattle.

Genomes Reveal Both Neutral and Selective Processes of Evolution

Heterozygotes can be advantageous as environmental conditions change, and 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 15.19 A Heterozygote Mating Advantage (Part 1)

Figure 15.19 A Heterozygote Mating Advantage (Part 2)


Genome size and organization also evolves.

Genome size varies greatly.

If only the protein and RNA coding portions of genomes are considered, there is much less variation in size.

Figure 15.20 Genome Size Varies Widely

Figure 15.21 A Large Proportion of DNA Is Noncoding


Much of the noncoding DNA does not appear to have a function.

Some noncoding DNA can alter the expression of surrounding genes.

Some noncoding DNA consists of pseudogenes.

Some consists of parasitic transposable elements.


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.

Recombination, Lateral Gene Transfer,and Gene Duplication Can Result in New Features

Sexual reproduction results in new combinations of genes and produces genetic variety that increases evolutionary potential.

But in the short term, it has disadvantages:

• Recombination can break up adaptive combinations of genes

• Reduces rate at which females pass genes to offspring

• Dividing offspring into genders reduces the overall reproductive rate


Why did sexual reproduction evolve? Possible advantages:

• It 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.


• 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; Muller’s ratchet.


• 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. Rather, it generates new combinations of alleles on which natural selection can act.


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.


Lateral gene transfer can be advantageous to a species that incorporates novel genes.

Genes that confer antibiotic resistance are often transferred among bacteria species.


Gene duplication—genomes can gain new functions.

Gene copies may have different fates:

1.Both copies retain original function (may increase amount of gene product).

2.Gene expression may diverge in different tissues or at different times in development.


3. One copy may accumulate deleterious mutations and become a functionless pseudogene.

4. One copy retains original function, the other changes and evolves a new function.


Sometimes entire genomes may be duplicated, providing massive opportunities for new functions to evolve.

In vertebrate evolution, genomes of the jawed vertebrates have 4 diploid sets of many genes.

Two genome-wide duplication events occurred in the ancestor of these species. This allowed specialization of individual vertebrate genes.


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 15.22 A Globin Family Gene Tree

Evolutionary Theory Has Practical Applications

Molecular evolutionary principles are used to understand protein structure and function.

Puffer fish have a toxin (TTX) that blocks sodium ion channels and prevents nerve and muscle function.

Genes for sodium channel proteins in puffer fish have substitutions that prevent TTX from binding.

Study of these gene substitutions aid in understanding how sodium channels function.


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.


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.


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.

Figure 15.24 Evolutionary Analysis of Surface Proteins Leads to Improved Flu Vaccines

Documents

Mechanisms of Evolution. Key Concepts Evolution Is Both Factual and the Basis of Broader Theory Mutation, Selection, Gene Flow, Genetic Drift, and Nonrandom