Chapters 4.1 & 16.1 Lecture Notes PDF

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Chapter 4.1: Evolution ➢ Evolution: ○ A change in allele frequency in a population over time ➢ Natural Selection: ○ Adaptive mechanism by which evolution takes place and is often summarized as differential survival and reproduction. ➢ Five Basic Tenets of Natural Selection: ○ Overproduction : Each generation of an organism produces more offspring than nature can support. ○ Variation: With each new generation, individuals have slight differences in characteristics, which means they have slightly different abilities. ○ Competition: Overproduction of offspring results in competition for limited resources, such as water, food, and shelter. ○ Selective advantage : Variation results in some individuals who have an advantage over others, depending on the circumstances. Variations in strength, acquiring energy, stress resistance, and so on allows a subset of individuals to out-compete others for the limited resources. Those with the advantage continue living. ○ Reproduction: Those who survive the competition are able to reproduce and pass on to the next generation the genetic information that enabled them to out-compete others. The next generation exhibits additional variation based on the successful trait that they inherited from their parents. ➢ Biologists have defined four distinct mechanisms that cause evolution other than natural selection: ○ Mutation: ■ A change in DNA sequence; can happen with erroneous replication of DNA by DNA polymerase ○ Gene Flow: ■ The movement and incorporation of alleles from one population to another; changes allele frequency when an individual from one population transmits a new allele to one or more individuals in another population ○ Genetic Drift: ■ The loss of alleles by random causes and not natural selection; different from natural selection because the loss of an allele is due to random events, such as a large explosion that kills everything within a given radius

Biology Learning Objectives: ● Evaluate the processes by which variation is generated in organisms and how this affects information at the population level and natural selection. ● Differentiate between independent assortment and crossing over. Context: Variation among individuals is a key concept to understanding evolutionary change. Major themes: Life continues to evolve within a changing environment, and evolution acts on variation, which is produced by several mechanisms. Organisms can be linked by lines of descent from common ancestry. Bottom line: Variation in populations is caused by several mechanisms. _________________________________________________________________________________________ __________________________________________________________________________________________ Chapter 16.1: What Causes Individual Variation? ➢ Population ○ A group of individuals of the same species living in the same place at the same time ➢ Phenotype ○ The way an organism appears or behaves due to its genetic makeup or environmental influences. ➢ Genotype ○ Genetic composition that determines an organism’s appearance or behavior. ➢ Variation ○ The extent to which phenotypes differ from individual to individual Heritable variation, mutations and independent assortment ➢ Sir Francis Galton ○ Examined the relationship between the average height of a couple and the height of their adult offspring in one of the first scientific studies of variation of characteristics ○ Used statistics and mathematics and the slope of a best-fit line to quantify the influence of parents’ heights on the height of their offspring ➢ Individuals within populations that vary in characteristics also have varying degrees of success ○ Darwin defined natural selection as “…preservation of favourable individual differences and variations, and the destruction of those which are injurious…” ○ Darwin used variation as a central concept in his Theory of Evolution by Means of Natural Selection, but how variation among individuals in a population was generated or maintained was not known in Darwin’s time. ■ There are several different mechanisms that produce variation among individuals

➢ Every characteristic (phenotype) has some component of heritability; that is, there are one or more genes that control the phenotype for each individual ○ Eye color is an inherited trait influenced by more than one gene ○ Height is thought to be controlled by multiple genes, but there is also an environmental component of height, including factors such as nutrition and stress level during development ○ Malnutrition or exposure to toxins may negatively affect growth, whereas exposure to hormones may enhance growth ➢ Galton discovered that the heights of parents correlate with their offspring, but not perfectly. ○ Galton found that if the average height of parents was low, a high percentage of offspring were taller than their parents’ average height, (as indicated by the points above the dashed line for averages below 67 inches) ■ Likewise, tall parents tended to have more offspring below their average height ○ These two trends yielded a best-fit line that had a slope of 0.65, much less than 1.0 ○ In addition, he found a high degree of variability around the average for any set of parents, as indicated by the scattering of points around the best-fit line ■ Less variation would lead to more or all points falling on the best-fit line ➢ A characteristic may be heritable to some extent and yet highly variable ○ Therefore, the genetic code is one source of variability ➢ Charles Darwin wrote in The Origin of Species  that if variations in phenotypes, however slight, are in any way advantageous to an individual, those variations tend to increase the ability of the individual to survive and reproduce. ○ If the phenotype is inherited by offspring, then genes playing a role in determining that phenotype will spread in the population. ➢ Much of the variation among individuals in a population is caused by genetic differences (variation in deoxyribonucleic acid (DNA) sequences) ○ A study of blood pressure in rats illustrates this source of variation ➢ As in humans, some rats have higher blood pressure than others. ➢ The scientists developed two colonies of rats by breeding rats that had low blood pressure with each other in one colony, and rats that had higher blood pressure with each other in the other colony. ○ After 85 generations of doing this, the blood pressures were very similar among individuals within each colony, but very different between individuals in different colonies

➢ The DNA of several genes was tested to determine whether the rats were homozygous or heterozygous for these genes. ➢ Bianchi and colleagues tested twenty rats from each colony ○ they found that all rats tested were homozygous for each gene within each strain, with one exception ■ The exception was a protein called adducin,  which is composed of two subunits (called α and β) whose genes are located on two different chromosomes ■ The different versions, or alleles, of each protein subunit differed by only one amino acid ■ They named the alleles of the proteins αY , αF , βR , and βQ , depending on the subunit and the amino acid that was present at the variable position. ➢ The high blood pressure rats were found to be homozygous for the αY and βR versions of the adducin genes ➢ The low blood pressure rats were homozygous for the αF adducin gene, and the colony had all three possible genotypes for the β subunit: homozygous βR , homozygous βQ , and heterozygous with both βRand βQ . ○ When Bianchi and his colleagues compared the blood pressures of these rats, they found that, although lower than the high blood pressure rats, there were differences among the three genotypes in the low blood pressure rats (Fig. Below)

➢ The scientists crossbred rats from the two colonies ○ Rats from the high blood pressure colony were homozygous for both adducin genes ○ They chose rats from the low blood pressure colony that were also homozygous for the βQ gene ■ The resulting offspring in the first generation were rats heterozygous for both genes; that is, they carried one copy of αY and βR from their high blood pressure parent and one copy of αF and βQ from their low blood pressure parent. ■ All the first generation rats were then crossbred to produce rats of every possible combination of the two versions of the two genes. ● Blood pressure of these rats was measured to determine the impact of having any combination of these genes

➢ After many generations of breeding individuals from one colony with other individuals from the same colony, most genes were found to be homozygous. ➢ This study illustrates several processes that increase variation among individuals. ➢ Bianchi and his colleagues concluded that a Point Mutation (change in a single nucleotide in a DNA sequence) was responsible for producing the two alleles of the α and β subunits of adducin ○ These mutations increased the variation among rats, despite the fact that the scientists separated them out by selecting for rats that had either high or low blood pressure in the two colonies ■ The variation increased because after the mutations there were two alleles of each gene, leading to two versions of each adducin subunit. ■ That variation produced several combinations of the adducin protein, as you will discover later. ➢ Generations of inbreeding produced individuals that were mostly homozygous, at least for all but one of the genes tested. ○ Because the scientists were selecting for individuals with a certain phenotype, individuals with other phenotypes were subsequently lost from the population because those rats were removed by the researchers. ○ Eventually most of those alleles that cause undesirable traits in a population were removed from the population. ○ In the case of the β adducin gene in the low blood pressure colony, the heterozygous condition produced rats that had the lowest systolic blood pressure. ○ Although this outcome may be surprising, it illustrates that individual variation sometimes produces a phenotype that is selected for.

➢ Rats with high blood pressure have associated health problems, such as red blood cell and kidney dysfunctions. ○ This led the scientists to conclude that slightly harmful mutations had occurred over the generations of inbreeding. ■ The harmful mutations were able to remain in the population because the rats were bred in the laboratory. In nature, these harmful mutations are eliminated by natural selection. ■ Although the scientists identified the two adducin genes as playing a role in high blood pressure, there are other genes involved. ■ The two alleles of the two subunits of adducin interact when in different combinations to cause wide variation in high blood pressure, as indicated by the mean blood pressures of rats in the second generation of crossbreeding. ■ However, none of these rats has blood pressure as low or high as their grandparents, and that variation is caused by other genes also controlling blood pressure. ● After two generations of crossbreeding, the different alleles of these other genes, from the homozygous grandparents, had been reshuffled independently of the adducin genes, increasing the variation of responses. ➢ The observation of blood pressure variation and the wide range of combinations of the two versions of the two adducin genes leads to another conclusion about how variation increases and is maintained in individuals. ○ Independent assortment, when non-homologous chromosomes migrate without regard to each other during meiosis, leads to recombination. ○ Recombination leads to new combinations of genes in offspring that did not occur in the parents, by independent assortment and crossing over, which occurs when paired chromosomes exchange portions of their DNA during meiosis. ➢ Bianchi and his colleagues knew that the genes coding for the two subunits of adducin were located on different chromosomes; so they could predict that when two heterozygous individuals mated, offspring of those individuals would exhibit one of nine different combinations of the two genes

➢ The heterozygotes were obtained from mating of rats from each colony that were homozygous for different versions of the two genes. ○ A heterozygote possesses two alleles for a particular gene, resulting in variation within an individual. ○ If the genes were on the same chromosome, the variation of outcomes would be limited ○ This scenario assumes no crossing over. If there were crossing over, the extent of variation would also increase.

Variation Caused By The Environment ➢ Variation can also be caused by the environment ➢ If expression of various genes is affected by the environment, variation among individuals in a population may be affected. ➢ Environmental Gradient ○ The gradual change in an environmental factor from one place to another ➢ For instance, levels of metal contamination in the soil surrounding metal ore smelting operations decrease as distance from the smelter increases. ○ Very few plants live in soils near smelters that have been operating for many decades. ➢ Nicholas Caiazza and James Quinn studied two species of plants near a smelting operation in eastern Pennsylvania, slender sandwort (Arenaria patula) a nd Japanese honeysuckle ○ They collected plants from sample sites that varied in their distance from the smelter, along the pollution gradient. ○ They also documented the level of metal pollutants at each site where plants were collected

➢ Caiazza and Quinn counted stomata, the gas exchange pores on leaves, and hairs on the leaves that they collected from the various sites over a period of 2 years ○ They also took seeds from the plants and grew them under standard conditions in a nearby courtyard; (this procedure would help the researchers determine whether differences they might find near the smelter were due to the environmental gradient or genetic differences that had evolved among the various populations). ■ After a period of time, they collected leaves from these courtyard grown plants and performed the same analyses (16.7) ➢ In another study, Curtis Lively studied an acorn barnacle (Chthamalus anisopoma) ○ Variations in shell shapes along a rocky intertidal habitat off the Gulf of California (Figure 16.8A). ■ Barnacles are non-motile marine animals that cement themselves to rocks and other substrates in tidal zones, in order to keep from being washed away by the waves. ■ Lively knew that a certain type of snail, Acanthina angelica , specialized on feeding on barnacles.

➢ This snail has a special spine on its shell that it uses to pry open barnacles from the top and gain access to the animal in its shell. ○ Lively knew from the observations of naturalists that few barnacles live near where a snail had a refuge, which it used for protection from desiccation. ○ At intermediate distances from snail refuges, barnacles with the “bent” shell type occur sparsely, but more frequently than barnacles with the “cone” shell type. ■ Far from snail refuges, cones occur at high density and more frequently than bent-shell barnacles. ➢ To determine whether the variation in shell type was due to an environmental factor that affected the development of barnacle shell shape, Lively needed to distinguish between correlation and causation; ○ the increased presence of bent-shell barnacles could be correlated with the presence of snails, or it could be caused by the presence of some other factor. ➢ Exclusion experiment ○ is where one or more species are excluded from experimental plots or habitats. ○ Set the experiment up with plots where the barnacles were allowed to develop with the snails present and with the snails excluded ○ Then set up other plots where he placed barnacles of each shell shape, some plots with the snail predator and others without, and tracked the survival of barnacles with each shell shape over time ➢ Both studies reveal variation caused by the environment. ➢ In the first example, both species of plants exhibit variation across the gradient. ○ The sandwort shows more consistent variation with distance from the smelter, and honeysuckle still has variation when plants from different sites are grown under controlled conditions. ■ However, the variation across years is evidence that some environmental factor affected the density of stomata and hairs. ○ Caiazza and Quinn speculated that heavy metals in the air affect plants. ■ Air pollution from the smelter affected the soil conditions, but air quality varies more from year to year than soil conditions, and this could have led to annual changes in variation among the sites. ○ There is also a genetic component, which is more evident with honeysuckle, but there is also an environmental component that increases variation among individuals. ■ The number of stomata tends to be lower and hairs are denser closer to the smelter, and that may be in response to polluted air. ■ The fewer stomata, the fewer pollutants will enter the plants when they open for gas exchange. ■ A high density of hairs on leaves may trap pollutants, acting as a filter. ● The drawback to these changes is that plants will not be able to obtain as much carbon dioxide as other plants with more stomata, but this may still be a phenotype that is advantageous and selected for in a polluted environment. ➢ The barnacle study demonstrated that a predator can cause developmental changes. ○ The bent variety is less common overall than the cone and never developed in the absence of the predator, but a significant number of them developed in the presence of the predator. ○ You observed that the cone phenotype was present in both the presence and absence of the snail.

○ Even in the presence of the predator, there was a large number of cone-shaped barnacles, indicating that these individuals either did not receive the “predator cue” during development or that they were genetically incapable of growing into the bent shape. ➢ As you discovered with plants, environmental factors can alter the physical appearance of animals but only within the scope of their genetic potential. ○ The bent shape may be rare in the absence of the predator because of a decrease in feeding efficiency, but the benefit of having this shell shape in the presence of the predator is that it increases the probability of survival. ➢ Careful experimentation with proper controls can determine the causes and extent of natural variation in populations and how this variation relates to information in populations. ○ Variation among individuals can lead to the evolution of populations, just as natural selection acts to alter the relative abundance of individuals with particular characteristics. ➢ Variation among individuals and information in populations increases through mutation, recombination, independent assortment, and environmental factors. ○ Those variations can have implications to survival and reproduction, as you saw with the barnacles, and may be acted upon by the mechanisms of evolution. Q&A Q: W  hat are ways in which recombination can occur, and how do they affect variation among individuals in populations? A: Independent assortment, when non-homologous chromosomes migrate without regard to each other during meiosis, leads to recombination. Recombination leads to new combinations of genes in offspring that did not occur in the parents, by independent assortment and crossing-over, which occurs when paired chromosomes exchange portions of their DNA during meiosis. Q: What is the importance of local habitat conditions and environmental gradients to the processes of adaptation? A: Populations may adapt to local habitat conditions and those adaptations may vary across environmental gradients.

Video Lecture Notes: Scientific Law vs. Theory ● ● ● ●

A scientific law predicts the results of certain initial conditions (predicts phenotypes, physics, etc.) A theory provides the most logical explanation as to why things happen as they do A law predicts what happens, while a theory purposes why A theory will never grow up into a law though the development of one often triggers progress on the other...