Fundamentals of Evolutionary Biology

UNIT 3: INTRODUCTION TO EVOLUTION Definition: Evolution is the cumulative change in the heritable characteristics of a population over time. The word “cumulative” means all the increasing changes occurring. * The word “heritable” (inheritable) means that the changes must be passed on genetically from one generation to the next, which implies that evolution, requires many generations to be seen. * The word “population” means the changes do not affect just one individual within the population but act on the entire population. * The word “time” means the gradual development of things. It is the changes that occur in living organisms, over many generations. * Evolution has led to biodiversity within populations HOW DID EVOLUTIONARY THOUGHT EVOLVE? * Early biological thought did not include the concept of evolution * Prior to the 18th century, the church heavily influenced science. * The acceptable theory was that all organisms were created simultaneously by God (CREATIONISM) and that each distinct life form remained fixed and unchanging from the moment of its creation * This view reigned unchallenged for nearly 2000 yrs. * By the 18th century, however several lines of new emerging evidence began to erode the dominance of this static view of creation * As early European naturalists explored the newly discovered lands of Africa, Asia, and America they found that the number of species or different types of organisms was much greater than anyone had suspected. * They also observed that some species closely resembled one another yet differed in some characteristics. * These observations led some naturalists to consider that perhaps species could change after all. Some of the similar species might have developed from a COMMON ANCESTOR. COMMON ANCESTORY Definition: * an organism, which is the shared ancestor of two (or more) different descendant groups of organisms. Image result for common ancestry * A group of organisms have common descent if they have a common ancestor. * According to modern biology, all living organisms on Earth are descended from a common ancestor or ancestral gene pool. THEORIES OF EVOLUTION * Evolution is something that happens to living organisms. It is the alteration of life throughout history. * Important scientists that helped to explain evolution are: JEAN BAPTISTE de LAMARCK (French Naturalist) 1st evolutionary theory to propose species evolve over time (early 1800’s) Believed organisms changed for THREE REASONS: 1. Universal Force willing organisms to change: * Organisms had an “imaginary” force or “desire” to change themselves for the better. Organisms had the ability to produce new parts to satisfy their needs and become better adjusted to their environment. * ie. birds can fly because they wanted to 2. Use and disuse of body parts: * Use and disuse of certain body parts could be passed onto offspring. Organs that were regularly used became stronger and more developed to perform their function, and organs not used withered away. * ie. Giraffes necks became longer because they used them extensively for feeding 3. Acquired Characteristics: * Species modification is the result of acquired characteristics, which are passed from generation to generation, and eventually these changes make permanent changes to a species. * Ie. One giraffe acquires a larger, longer neck and will produce longer, larger necked babies Even though Lamarck’s theories were incorrect, they did attempt to explain adaptations. He showed that evolution is adaptive, and that evolution of life is the result of adaptations. He helped set the stage for Charles Darwin. CHARLES LYELL: (1820) a geologist who studied the changing Earth Image result for charles lyell * Wrote the book “Principles of Geology” * influenced Darwin’s thinking because he believed the earth was an ancient arena in which rock formations slowly appeared, changed, and disappeared. * demonstrated that Earth’s surface changed over time by wind, water, ice, volcanoes, etc… * He recognized that competition between species leads to a “struggle for existence” and even discussed the extinction of species caused by humans. THOMAS MALTHUS: (1798’s) Image result for THOMAS MALTHUS * an economist who influenced Darwin’s thinking with his Malthusian Doctrine: every human population must eventually outgrow its food supply; stated that more babies would be produced than people dying off. This would lead to over population, which would be rectified by disease, famine, or war. * he realized his theory applied to all living things CHARLES DARWIN and EVOLUTION BY NATURAL SELECTION Darwin’s Research was based on: At the age of 22, Darwin makes a 5-year scientific exploration on board the H.M.S. Beagle ship to chart stretches of the South American coast. Image result for charles darwin 1. Observations of South American plants, animals and fossils 2. Galapagos Islands, a chain of volcanic islands located about 900 km off the Pacific coast of South America studying diversity of species of animals such as blue-footed boobies, giant tortoises, marine iguanas and many species of finches. 3. Carried out work of Domestic Breeding with pigeons 4. Work of other Scientists: Population Studies: Malthusian Work Geologist Charles Lyell 5. Developed the theory of evolution by Natural Selection How Darwin accomplished his research: * Darwin explained his theory in the Origin of Species published in 1859. * Darwin delayed publication of his ideas for many years, fearing a hostile reaction. He might never have published them if another biologist, Alfred Wallace, had not written a letter to him in 1858 suggesting very similar ideas. * Darwin believed that the Earth’s many species are descendants of ancestral species that were different from those living today. This is due to the many accumulation of adaptations to various environments. * In Darwin’s book he said: In the process of NATURAL SELECTION, organisms best suited to their environment reproduce more successfully than other organisms. Therefore, over generations the proportion of organisms with favorable traits increases in a population. * Darwin proposed that environment may affect individual organisms in a population in different ways because individuals of a species are not identical. * Some organisms have traits that make them better able to cope and survive within their environment. Organisms that have a greater number of these favorable traits tend to leave more offspring than organisms that do not have favorable traits. Note: if the trait both increases the reproductive success of an organism and is inherited, then the trait will be passed on to many offspring. (A population of organisms adapt to their environment as their proportion of genes for favorable traits increases). Fitness of an Organism: * In an evolving population, a single organism’s genetic contribution to the next generation is termed FITNESS. * Definition: Fitness is a measure of how well suited an organism is to survive in its habitat and its ability to maximize the number of offspring surviving to reproductive age. * Therefore, an individual with high fitness is well adapted to its environment and reproduces more successfully than an individual with low fitness. * Natural selection acts on the phenotype, or the observable characteristics of an organism, but the genetic (heritable) basis of any phenotype, which gives a reproductive advantage, will become more common in a population. * Over time, this process can result in adaptations that specialize populations for particular ecological niches and may eventually result in the emergence of new species. * In other words, natural selection is an important process (though not the only process) by which evolution takes place within a population of organisms. NATURAL SELECTION Natural Selection: (Nature selects) * NATURAL SELECTION is a passive process; organisms do not purposefully acquire traits that they may need. * The environment “selects” those traits that will increase within a population. * The kinds of traits that are favorable depend on the demands of the environment. The environment acts as a sieve through which only certain variations can pass. * Natural selection is an ongoing process in nature, and is the single most significant factor that disrupts genetic equilibrium. * As a result of natural selection, some members of a population are most likely to contribute their genes to the next generation than are other members. * Natural selection is uneven reproduction. Individuals whose traits are best suited to the environment (better enable them to obtain food or escape predators or tolerant physical conditions) will survive and reproduce more successfully; passing these adaptive traits to their offspring. Example: Walking Stick insect blending in with its environment, sunflowers bending toward light, antibiotic resistant bacteria allow them to survive when exposed to certain chemical. An organism that may be able to run fast, or it may be strong or have coloring that act as camouflage from predators. These characteristics make the organism better suited to their environment and nature favors them. It is important to recognize three key points about evolution by natural selection: 1. Natural selection occurs through interactions between individual organisms and the environment, individuals do not evolve. Rather it is a population (group of organisms) that evolves over time as adaptive traits become more common in the group and other traits change or disappear. 2. Natural selection can amplify or diminish only heritable traits, NOT acquired traits. Unless the trait is coded for in the genes of an organism’s gametes, it cannot be passed onto offspring. 3. Evolution is not goal directed; it does not lead to perfectly adapted organisms. Natural selection is the result of environmental factors that vary from place to place and over time. A trait that is favorable in one situation may be useless in another circumstance. Natural selection is contingent on time and place. It favors those heritable traits in a varying population that fit the current, local environment. 6 MAIN IDEAS OF DARWIN’S THEORY 1. OVERPOPULATION * All species are capable of producing more offspring than the environment can support. Examples: Fish lays millions of eggs annually, but only a few survive and reproduce, thus preventing overpopulation. 2. COMPETITION * There is a struggle for existence in which some individuals survive and some die. 3. VARIATION * Living organisms vary. They may differ in the exact size, shape of a body part, in strength, running speed, resistance to diseases and so on. These differences are called variations. * If the variations are positive and increase the successfulness of the organism, the traits are passed onto the next generation. 4. SURVIVAL OF THE FITTEST (NATURAL SELECTION) * Those individuals in a species with traits that give them an advantage are better able to compete, survive, and reproduce. * All others will die off without leaving offspring. The phase “survival of the fittest” is used to summarize this idea. * Since nature selects the organisms to survive, the process is called NATURAL SELECTION. * The results of natural selection therefore accumulate. As one generation follows another, the characteristics of the species gradually change- the species evolves. 5. ADAPTATION * All living organisms are “adapted” in the sense that their appearance, behavior, structure, and mode of life made them well-suited to survive in a particular environment Examples: Snail shells with more stripes may improve camouflage and therefore reduce predation. 6. SPECIATION (ORIGIN OF NEW SPECIES) * Over numerous generations, new species arise by the accumulation of favorable, inherited variations. * If the range of inherited adaptations in one population of a species becomes so extreme that it prevents breeding with other populations of the same species, the “changed population” is effectively a “NEW SPECIES”. TYPES OF ADAPTATIONS 1. STRUCTURAL: changes to an organism’s anatomy or physical characteristics. (camouflage, fur, fat layers, mimicry) STRUCTURAL EXAMPLES: * Mammals have the same basic limb design. Humans however, have forelimbs that are well adapted for grasping and holding things and opposable thumbs. * Plants have become adapted to feeding on insects to increase protein. (Venus fly trap and pitcher plant). Leaves have become adapted in different ways to capture prey. * Monarch butterflies have a bitter taste and are avoided by birds. Viceroy butterflies look and act like Monarch butterflies, but are not bitter tasting, tricking birds into thinking they are Monarch butterflies to avoid been eaten. 2. PHYSIOLOGICAL: changes to the metabolic processes occurring within the body (chemical changes, temperature regulation, production of toxins sexual attractants, alarm signals). Production of enzymes that control body functions such as temperature, respiration, circulation, and muscle coordination can also help the organism adapt and survive. PHYSIOLOGICAL EXAMPLES: * Mutant strains of bacteria that are resistant to penicillin have evolved. Some strains of bacteria can produce an enzyme that inactivates penicillin, others have cell walls that block the penicillin molecule from entering. * Secretion of venom by snakes and the production of toxins by certain plants are also examples of physiological adaptations. 3. BEHAVIORAL: Are inherited behavioral patterns that allow an organism to survive in an environment, avoid danger or enable them to reproduce successfully. (hibernation, migration) BEHAVORIAL EXAMPLES: * Migration of Canada Goose. Hibernation of certain mammals. Storage of nuts by squirrels * Broken wing behavior of bird to draw enemy away from nest * Plant movement toward light called phototropism * Courtship behaviors to increase reproductive success. These allow species to recognize and attract members of the opposite sex of their own species. SCIENTISTS CAN OBSERVE NATURAL SELECTION IN ACTION CASE STUDY: Finches on Galapagos Islands Image result for finches natural selection The beak sizes of ground finch species were measured. Ground finch eats mostly small seeds. * In dry years, when all seeds were in short supply, birds must eat the larger seeds. * Birds with larger, stronger beaks have a feeding advantage and greater reproductive success. This lead to an increase in the average beak depth for the population. * In wet years, small seeds were abundant. * Birds with small beaks were more efficient in eating the small seeds, and now have greater reproductive success. This lead to a decrease in average beak depth. CASE STUDY: Peppered Moths in England pepfig1b.gif - 22175 Bytes * During 1800’s, there were two kinds of peppered moths in England: -a common light brown colored variety -a rare dark colored variety * The Peppered Moth spends much of its day resting on the bark of oak trees (light coloured bark). * Light brown variety had an advantage and could camouflage against the trees and avoid predatory birds. * This variety had greater reproductive success. This lead to an increase in numbers of the light coloured variety of Peppered Moths. * When the Industrial Revolution began in England, the air became full of smoke and soot from burning coal. This extreme pollution of the air settled on the tree trunks and stained the tree trunk bark dark brown. * By the end of the century, the dark coloured variety of Peppered Moth population in England had the advantage of camouflage, and was able to avoid the predatory birds. * This variety now had greater reproductive success. This lead to a decrease in the light brown colored moths. * Therefore, in each environment the moths that were better camouflaged (adapted) had the highest survival rate. * Scientist observed light and dark moths in both industrial and rural areas to determine if natural selection had caused the dark variety of moths to become more numerous. * Rural areas: Birds ate more dark colored moths on light tree trunks * Industrial areas: Birds ate more light brown colored moths on dark tree trunks ________________ CASE STUDY: Antibiotic Resistance in Bacteria * A well-known example of natural selection in action is the development of antibiotic resistance in microorganisms. Since the discovery of penicillin in 1928 by Alexander Fleming, antibiotics have been used to fight bacterial diseases. * Natural populations of bacteria contain, among their vast numbers of individual members, considerable variation in their genetic material, primarily as the result of mutations. * When exposed to antibiotics, most bacteria die quickly, but some may have mutations that make them slightly less susceptible. If the exposure to antibiotics is short, these individuals will survive the treatment. This selective elimination of maladapted individuals from a population is natural selection. * These surviving bacteria will then reproduce again, producing the next generation. Due to the elimination of the maladapted individuals in the past generation, this population contains more bacteria that have some resistance against the antibiotic. * At the same time, new mutations occur, contributing new genetic variation to the existing genetic variation. Spontaneous mutations are very rare, and advantageous mutations are even rarer. However, populations of bacteria are large enough that a few individuals will have beneficial mutations. If a new mutation reduces their susceptibility to an antibiotic, these individuals are more likely to survive when next confronted with that antibiotic. * Given enough time, and repeated exposure to the antibiotic, a population of antibiotic-resistant bacteria will emerge. This new changed population of antibiotic-resistant bacteria is optimally adapted to the context it evolved in. * At the same time, it is not necessarily optimally adapted any more to the old antibiotic free environment. The end result of natural selection is two populations that are both optimally adapted to their specific environment, while both perform substandard in the other environment. * The widespread use and misuse of antibiotics has resulted in increased microbial resistance to antibiotics in clinical use, to the point that the methicillin-resistant Staphylococcus aureus (MRSA) has been described as a "superbug" because of the threat it poses to health and its relative invulnerability to existing drugs. Response strategies typically include the use of different, stronger antibiotics; however, new strains of MRSA have recently emerged that are resistant even to these drugs. Resistance to antibiotics is increased though the survival of individuals which are immune to the effects of the antibiotic, who’s offspring then inherit the resistance, creating a new population of resistant bacteria. ________________ TYPES OF NATURAL SELECTION STABILIZING SELECTION: http://img.sparknotes.com/figures/A/a3aa6bb95c7d70781cc0089d17f9160f/stable.gif * Encourages the formation of average traits * Individuals with the average form of a trait have the highest fitness. The average represents the optimum for most traits. * Example: larger than average lizards might be easily seen, captured and eaten by predators or smaller than average lizards are not able to run as fast as average and might not be able to escape predators. DIRECTIONAL SELECTION: http://img.sparknotes.com/figures/A/a3aa6bb95c7d70781cc0089d17f9160f/direct.gif * Encourages the formation of one extreme trait, such as a very long tongue in anteaters * Individuals that display a more extreme form of a trait have greater fitness than individuals with an average form of the trait. * Example: Anteaters with longer than average tongues would have an advantage obtaining termites in very deep nests. DISRUPTIVE SELECTION: http://img.sparknotes.com/figures/A/a3aa6bb95c7d70781cc0089d17f9160f/disrupt.gif * Selects for both extreme traits rather than average traits * Individuals with either extreme variation of a trait have a greater fitness than individuals with the average form of that trait. * Example: Studying shell color on marine animals called limpets shows that the white and dark variation have an advantage camouflaging themselves against rocks and barnacles compared to the average intermediate colored limpets in both the white and dark backgrounds. Practice Questions Set #1 - THEORIES OF EVOLUTION QUESTIONS EVIDENCE OF EVOLUTION 1. FOSSIL RECORD and BIOGEOGRAPHY The best clues scientists have about what life was like thousands or millions of years ago comes from fossils. Fossils: Are the petrified remains or imprints or traces of animals or plants that lived in the past. * Fossils provide convincing evidence of Earth’s evolutionary past * Overall the life that existed more than 500 million years ago was vastly different in appearance from life today. * Although planet Earth has had extensive oceans for most of its existence, fish fossils have been found in rocks 500 million years old or younger (less than 15% of the 3.5 billion year existence of life on our planet). * One conclusion that can be drawn from studying fossils is that life of Earth is constantly changing. * Most of the changes have occurred over huge timescales (hundreds of thousands or millions of years) that humans find difficult to grasp. Fossil Record: * The sequence in which fossils appear within layers of sedimentary rocks-provides some of the strongest evidence of evolution. * The fossil record reveals the historical sequence in which organisms evolved. * The chronological fossil record gives us the history of life in general and allows us to trace the decent of a particular group. * Reveals a succession of fossil forms in layers of sedimentary rock that differed from the current life forms. It allows for the study of similarities between modern day forms and ancient forms. MISSING LINK: * The existence of fossils is very difficult to explain without evolution. An example of this is Acanthostega. * It has similarities to other vertebrates, with a backbone and four limbs, but has eight fingers and seven toes so it is not identical to any existing organism. This suggests that vertebrates and other organisms change over time. * Acanthostega is an example of a “missing link”. Although it has four legs, like most amphibians, reptiles, and mammals, it also had a fish-like tail and gills and lived in water. This shows that land vertebrates could have evolved from fish via an aquatic animal with legs. * Another series of fossils can trace the evolution of whales from four legged animals. Whales living today have forelegs in the form of flippers but lack hind legs. * Additional fossils show that Pakicetus and Robhocetus had a type of anklebone that is otherwise unique to the group of mammals that include pigs, hippos, cows, camels and deer. The anklebone similarity strongly suggests that whales (and dolphins and porpoises) are most closely related to this group of land mammals. BIOGEOGRAPHY: Biogeography is the study of the distribution of plants and animals throughout the world. * The distribution of organisms on Earth is explainable by assuming organisms originated in one location. * Darwin observed animals in the Galapagos Islands resembled species on the South American mainland more than they resembled animals on islands that were similar but much more distant. * The logical explanation was that the Galapagos species evolved from animals that migrated from South America. These immigrants eventually gave rise to new species as they became adapted to their new environments. The Cretaceous Period At the end of the Cretaceous Period, mammals split into 3 groups: 1. Monotremes (most primitive) eg. Duckbill platypus and Australian Spiny Anteater 2. Marsupial (species has a pouch in which young live for a short time) eg. Opossum, kangaroo, wombats, koalas 3. Placental (live birth from uterus and placenta) pangea eg. Cats, dogs, whales, elephants, humans, etc… * The breakup of the world-continent Pangaea, which began to disperse during the Jurassic period, continued. This led to increased regional differences in floras and faunas between the northern and southern continents. * As Pangaea began to split 220 million years ago, mammals were evolving, and continued to evolve on separate continents. QUESTION: Marsupials and Monotremes only exist in Australia and New Zealand ……WHY? * Australia split from the super continent early and it is believed that it was the place of the ancestors to monotremes and marsupials. These two groups were out competed and did not flourish anywhere else in the world. * Placental mammals are worldwide except Australia and New Zealand. * Australia separated before placental mammals arose, so only monotremes and marsupials diversified in Australia * Comparable forms throughout the world was troubling and revealing because they suggested common ancestry if not a common origin. 2. HOMOLOGOUS ANATOMICAL STRUCTURES: * Other evidence for evolution comes in the form of HOMOLOGOUS ANATOMICAL STRUCTURES, which are body structures that are similar in form but are found on seeming dissimilar species and often have different functions. * Similarity in characteristics that result from common ancestry (same evolutionary origin) in known as HOMOLOGY. * Organisms have anatomical similarities when they are closely related because of common descent. * There are remarkable similarities between some groups of organisms in their structure. EXAMPLE OF HOMOLOGOUS STRUCTURE * Pentadactyl forelimb is the “five” digit comparison. The forelimbs of several vertebrates all have the same basic arrangements of bones, yet they may be modified into wings, arms, legs, and fins. * The most likely explanation for these structural similarities is that organisms have evolved from a common ancestor. * All these animals descended from common ancestors, and the same bones were put to different uses. The bones in all these animals have the same developmental origin, yet may differ in structure and function of the forelimbs. * The same skeletal elements make up the forelimbs of humans, dogs, dolphins, bats and all other mammals, although the appendages have different functions. All of these forelimbs show the same basic skeletal pattern. In different vertebrate groups, the various bones have been modified as the limbs became specialized for different functions. homologous VESTIGIAL ORGANS Are anatomical features that are fully developed in one group of organisms but reduced and maybe even non-functional in similar groups. * The oldest homologous structures are vestigial organs that do not perform any function within the organism, but had important functions in ancestors. Vestigial organs are thought to occur because organisms inherit their anatomy from their ancestors; therefore, vestigial organs are traces of an organism’s evolutionary history. * These organs are no longer essential today. Appendix, tail bone, male nipples, ear muscles, and wisdom teeth in humans, pelvic bones in whales and snakes. https://laidbackgardener.files.wordpress.com/2018/09/20180919a-eng-mashtalegypt-com1.jpg?w=800 ANALOGOUS STRUCTURES: Some structures may have a similar appearance (superficially) and the same function but may come from an entirely different structure. These structures are said to be ANALOGOUS * In contrast to homologous structures, similar structures often evolve within organisms that have developed from different ancestors. Such as body parts or organs called analogous structures, they have a similar form and function but have different evolutionary origins. homologous-analogous * Both plants and animals show analogous structures Examples: * birds, bats, and insects all adapted wings for flight * shark fins and whale fins, and trout fins all adapted for swimming * cacti, euphorbs, and milkweed all have developed thick, barrel-like fleshy stems that store water as an adaptation to the desert environment. * Bird and bat wings are analogous — that is, they have separate evolutionary origins, but are superficially similar because they have both experienced natural selection that shaped them to play a key role in flight. Analogies are the result of convergent evolution. * Interestingly, though bird and bat wings are analogous as wings, as forelimbs they are homologous. Birds and bats did not inherit wings from a common ancestor with wings, but they did inherit forelimbs from a common ancestor with forelimbs. 3. EMBRYONIC DEVELOPMENT (EMBRYOLOGY): * The study of embryonic development reveals homology shared by vertebrates not apparent in adult species. Closely related organisms go through similar stages in their embryonic development. embryology * For example: all vertebrate embryos go through a stage in which they all have gill pouches on the sides of their throats, notochord (stiff dorsal rod), tails, and four limbs. * Similarities between fish, frogs, snakes, birds, humans and all other vertebrates are much more apparent than differences. * Scientists have observed that early embryonic development stages of many different organisms are similar. * Eg fish, frog, turtle, bird rabbit, and human were all similar. This provides evidence that similar genes are used to determine body structures in organisms. This shows that these organisms had a common ancestor or origin. * As development progresses, the various vertebrates diverge more and more, taking on the distinctive characteristics of their classes. 4. BIOCHEMISTRY: Almost all living organisms use the same basic biochemical molecules, including DNA, ATP, and many identical or nearly identical enzymes and same 20 amino acids in their proteins. Closely related species show unmistakable similarities in their DNA and proteins. * Organisms with similar biochemistry can be explained by decent from a common ancestor. * All organisms have certain biochemical molecules in common. The degree of similarity between DNA base sequences and amino acid sequences is thought to indicate the degree of relatedness. * Those organisms with more similar molecules are more closely related (they became two distinct species more recently) * We know mutations are a product of chance and occur at regular intervals. * Changes in DNA cause changes in the physical expression of genes. Therefore evolutionary changes are due to an accumulation of genetic changes. * As the DNA mutates (which it does on a regular basis), it causes physical changes, and eventually enough physical changes lead to the formation of a new species 🡪 EVOLUTION * Therefore the number of mutations between 2 species may be used to determine the time that has elapsed since the two diverged. Example: Human and chimpanzees: the number of differences in certain proteins indicates we split from the common ancestor about 5 million years ago. THE HISTORY OF LIFE: LOOKING AT THE PATTERNS * Life began 3.8 billion years ago * The central ideas of evolution are that life has a history, it has changed over time and that different species share common ancestors. * Evolutionary change and evolutionary relationships are represented in "family trees” * Evolutionary trees are hypotheses reflecting our current understanding of patterns of evolutionary descent. Phylogeny The evolutionary history of life, can be analyzed through cladistics, a method of assessing evolutionary relationships by comparing shared traits. UNDERSTANDING PHYLOGENIES 34_38PrimatePhylogeny * Understanding a phylogeny (or sometimes called a cladogram) is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time. * When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages. * Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages. * Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors. Referring to the figure shown on the board, determine if the CROCODILES are more closely related to LIZARDS (# 4) OR BIRDS (#6). Explain your answer. MISCONCEPTIONS ABOUT HUMANS It is important to remember that: 1. Humans did not evolve from chimpanzees. Humans and chimpanzees are evolutionary cousins and share a recent common ancestor that was neither chimpanzee nor human. 2. Humans are not "higher" or "more evolved" than other living lineages. Since our lineages split, humans and chimpanzees have each evolved traits unique to their own lineages. SELECTIVE BREEDING OF DOMESTICATED ANIMALS * The breeds of animals that are raised for human use are clearly related to wild species and in many cases can still interbreed with them. * These domesticated breeds have been developed from wild species by selecting individuals with desirable traits, and breeding from them. * The striking differences in the heritable characteristics of domesticated breeds give us evidence that the species can evolve rapidly. http://toolbox-4-websites.com/wp-content/uploads/2011/12/dog_history_tree.jpg QUESTION SET #2 - EVIDENCE OF EVOLUTION QUESTIONS ________________ POPULATION GENETICS AND EVOLUTION * 1800’s- Darwin developed his theory of natural selection without knowing about genes. * 1900’s- genetics was used to explain the variation among individuals of a population * Today- genetics and evolutionary theory are inseparable. Fitness, adaptations, species, and the process of evolutionary change are defined in genetic terms. POPULATION GENETICS: Studies of the complex behavior of genes in populations of plants and animals. Population sampling: Is important as it allows us to use a random sample of the population to study changes in certain characteristics within a population. It allows researchers to determine trends or frequencies of genes (alleles) and characteristics of a population without measuring the entire population. Population: * Is all the members of a single species occupying a particular area at the same time. Members of the population can breed with one another. * Ie. All gold fish in a pond are one population. Those in another pond are another population. * Because all members of a population can interbreed, the offspring share a common group of genes called a GENE POOL. * Each gene pool contains a number of alleles (forms of each gene: recessive or dominant alleles) for each inheritable trait. * Recall for each gene: * Individuals may be homozygous recessive or dominant (two identical alleles) or heterozygous (two different alleles) * Many genes have different alleles. In a typical interbreeding population, some alleles will be more common than others. How common an allele is can be assessed using allele frequency. ALLELE FREQUENCY: * The number of times an allele occurs in the gene pool, compared to the number of times other alleles for the same gene occur. * Relative frequency of the alleles in a gene pool may change over time. * IE: Peppered moths relative frequency of dominant and recessive alleles changed during the Industrial Revolution. Sexual reproduction ALONE does not change the relative frequency of alleles in a population. * Therefore Evolution can now be defined as any change in the relative frequencies of alleles in a gene pool of a population which changes the genetic composition of that population. * Microevolution: evolution occurring on a small scale with small changes to the gene pool. How can the O be the most common of the blood types if it is a recessive trait? * If Huntington’s disease is a dominant trait, shouldn’t three fourths of the population have Huntington’s while one fourth have the normal phenotype? Why don’t the recessive genes gradually disappear from a population? * These questions reflect on the common misconception that the dominant allele of a trait will always have the highest frequency in a population and the recessive allele will always have the lowest frequency. Gene frequencies can be high or low no matter how the allele is expressed and can change. It is the changes in gene frequencies over time, that result in evolution. GENETIC EQUILIBRIUM and the HARDY WEINBERG PRINCIPLE * If the allele frequencies in a population remain the same from one generation to the next, and over several generations, the population is in GENETIC EQUILIBRIUM. If the allele frequencies change, the genetic equilibrium is altered and evolution has taken place. HARDY WEINBERG PRINCIPLE: * Hardy-Weinberg is named after two scientists who derived the principle in 1908. G.H. Hardy was an English Mathematician and W. Weinberg was a German doctor. * The Hardy Weinberg Principle provides a baseline to determine whether or not gene frequencies have changed in a population and therefore whether evolution has occurred. * An important way of discovering why real populations change with time is to construct a model of a population that does NOT change. Hardy-Weinberg described a hypothetical situation in which there were NO changes in the gene pool and NO evolution. Hardy Weinberg Principle: * States as long as certain conditions within a population were met, the gene pool would remain unchanged generation after generation, and allele frequency in a sexually reproducing population would reach genetic equilibrium. FIVE CONDITIONS NECESSARY FOR GENETIC EQUILIBRUM 1. LARGE POPULATION SIZE The population must be very large, and changes in the allele frequencies due to change alone are insignificant and do not alter the gene pool 2. NO MUTATIONS Allele changes DO NOT occur 3. RANDOM MATING Individuals pair by chance and not according to their genotypes or phenotypes 4. NO GENE FLOW Population is isolated; NO migration of individuals into or out of the population 5. NO NATURAL SELECTION No selective force favors one genotype over another. All individuals have equal reproductive success. QUESTION: The general population of the United States is growing taller. Assuming height is a genetic trait, does this observation violate the Hardy Weinberg Principle? ANSWER: YES, it violates Hardy-Weinberg. The United States is not in genetic equilibrium because new genes enter the population, mating is not random, and natural selection affects the trait of human height. HARDY WEINBERG FORMULA: SUM OF FREQUENCIES: The Hardy Weinberg equation is applied to populations with a simple situation: dominant and recessive alleles controlling a single trait. The frequency of all the dominant alleles and all the recessive alleles equals the total genetic complement and adds up to 1 or 100% of the alleles present. Variables: p= frequency of dominant allele q = frequency of recessive allele so p + q = 1 (to represent 100% of the alleles) RECALL: 2 alleles represent one gene (genotype) so we end up with this formula (p + q )2 = 1 DETERMINING FREQUENCIES OF GENOTYPES IN A POPULATION: A a A AA Aa a Aa aa Frequency of AA = represented by p2 Frequency of Aa = represented by 2pq Frequency of aa = represented by q2 THEREFORE: (p + q )2 = p2 + 2pq + q2 = 1 STEPS HOW TO SOLVE HARDY-WEINBERG PROBLEMS: 1. Determine what piece of information you have been given about the population. In many cases, this is the percentage or frequency of the homozygous recessive phenotype (q2). 2. The first objective is to find the value of p or q. If this is achieved, then every other value in the equation can be determined by simple calculation. 3. Take the square root of q2 to find q 4. Determine p by subtracting q from 1 (p = 1- q) 5. Determine p2 by multiplying p by itself (p x p = p2) 6. Determine 2pq by multiplying 2 times q times p (2)(p)(q) 7. Check that your calculations are correct by adding up the values so that the sum is equal to 1 or 100% EXAMPLE 1: Suppose that in a population of pea plants 42 plants are recessive for the short trait (tt) out of 120 plants. 1. Determine the allele frequency of offspring that will be tall and the allele frequency that will be short. 2. Determine the number of heterozygous pea plants. SOLUTION: GIVEN: Recessive phenotype: q2 = 42/ 120 = 0.35 Recessive allele q = √ 0.35 = .59 Dominant allele p = 1 - .59 = .41 Homozygous dominant phenotype p2 = (.41) 2 = 0.17 (17%) Heterozygous phenotype 2pq = (2)(.41)(.59) = 0.48 (48%) CHECK: p + q = 1 .41 + .59 = 1 CHECK: p2 + 2pq + q2 = 1 .17 + .48 + .35 = 1 RECALL 2 pq = .48 or 48% 48% out of 120 plants are heterozygous 58 plants EXAMPLE 2: An investigator has determined by inspection that 12% of the population has a straight hairline (recessive trait (h)). Find the values of p, q, p2, q2, and 2pq provided the conditions for Hardy- Weinberg are met. SOLUTION: EXAMPLE 3: When studying the population of iguanas, two varieties exist that differ in foot webbing. Allele for non-webbed feet (W) is completely dominant to the allele for webbed feet (w). The frequency for the dominant allele is 0.8 and the gene pool for the population contains 500 individuals, determine the actual number of alleles that are recessive. Solution: EXAMPLE 4: In a fruit fly population, 44% express the dominant trait of red eyes, determine the values of p, q, p2, q2, and 2pq provided the conditions for Hardy- Weinberg are met. SOLUTION: HARDY-WEINBERG PRINCIPLE QUESTIONS - Worksheet # 3_____________________ MECHANISMS OF EVOLUTION POPULATIONS, NOT INDIVIDUALS EVOLVE: * Can individuals evolve? NO * Natural selection acts on the range of phenotypes in a population not the individual within the population. * The population’s genes change over time. CHANGES IN GENETIC EQUILIBRIUM: What are the mechanisms that cause changes in genetic equilibrium? What causes evolution? 1. MUTATIONS: Mutations are changes in the genetic material (DNA) of an organism. * Mutations provide new alleles, and therefore underlie all mechanisms that produce variation, the raw material for evolutionary change. * Most mutations are minor, such as changing the color of the scales of a butterfly’s wings, but they provide the variation that can be acted upon by natural selection. * Mutations occur constantly as chance events, causing changes in the gene pool. These changes are difficult to detect because many mutations are recessive and are seldom expressed in the phenotype of individuals. * Eventually a recessive mutation may appear in the phenotype and natural selection can act upon it. If the mutation is harmful, the individual may die. The mutation is then removed from the gene pool. * All other mechanisms of evolution merely shuffle the genetic material that is already present. 2. GENETIC DRIFT * Genetic Drift is the change in allele frequencies of a population as a result of chance processes. * In nature two situations lead to small populations in which genetic drift drastically affects the gene pool frequencies: Founder Effect and the Bottleneck Effect Founder Effect: * Occurs when a few individuals found a colony and only a fraction of the total genetic diversity of the original gene pool is represented. Which particular alleles the founders carry is dictated by chance alone. Example: * The Amish of Lancaster, Pennsylvania, is an isolated religious sect descended from German founders. Today, as many as 14 individuals in this group carries a recessive allele that causes an unusual form of dwarfism (affects only legs and arms) and polydactylism (extra fingers). In the non-Amish population, only 1 out of 1000 individuals have this allele. founder Bottleneck Effect: bottleneck * Occurs when a population is subjected to near extinction because of a natural disaster, or human interference. The disaster acts as a bottleneck preventing the majority of genotypes from participating in the production of the next generation. Example: * Large genetic similarities found in cheetahs is believed to be due to a bottleneck effect. In a study of 47 enzymes, each of which can come in several different forms, all the cheetahs had exactly the same form. This demonstrates that genetic drift can cause certain alleles to be lost from a population. 3. GENE FLOW * Gene flow is the movement of alleles between populations by migration of breeding individuals from one population to another. * Gene flow between two populations keeps their gene pools similar. It also prevents close adaptation to a local environment. 4. NONRANDOM MATING * Nonrandom mating occurs when individuals pair-up, not by chance, but according to their genotypes or phenotypes. * Inbreeding or mating between relatives are examples of nonrandom mating. * Inbreeding decreases the proportion of heterozygous individuals and increases the proportions of both homozygous dominant and recessive individuals. In human populations, inbreeding increases the frequency of recessive abnormalities. 5. NATURAL SELECTION * Natural selection is the process by which populations become adapted to their environment. Recall: Darwin’s explanation of natural selection. * In evolution by natural selection, the fitness of an individual is measured by how reproductively successful its offspring are in the next generation. * Evolution by natural selection requires: variation, inheritance, differential adapted-ness, and differential reproduction QUESTION SET #4 - MECHANISMS OF EVOLUTION QUESTION SPECIATION WHAT IS A SPECIES? Definition: A species is defined as a group of interbreeding organisms that occupy a certain geographical range that share a common gene pool and that are isolated reproductively from other species. The mating of different species results in 1. no offspring 2. Sterile offspring i.e. horse and donkey = mule (sterile) SPECIATION is the origin of new species. * It occurs when two groups of the same species within a population become geographically isolated or separated from each other, they develop into two separate groups. * Isolating a group of organisms separates its gene pool from the gene pool of the rest of the species. Through evolution, a different gene pool will evolve in each group. * It is believed that speciation is a two-step process: 1. geographical isolation (allopatric speciation) 2. reproductive isolation (sympatric speciation) GEOGRAPHICAL ISOLATION: (Allopatric Speciation) * Occurs when a natural barrier, (mountain, desert, river) divides a population, or landslide caused by an earthquake, or a species migrate to a new area, forming a population that is geographically isolated from the rest of the species. Interbreeding becomes impossible. * Geographical isolation acts as a barrier between the gene pools of the populations. * The gene pool of each group becomes isolated and can no longer intermix. Over a period of time each group becomes adapted to its particular environment. When differences between the isolated groups become great, they can no longer interbreed. * Example: The Albert Squirrel and Kaibab Squirrel each live on opposite sides of the Grand Canyon. Due to the geographical barrier the population that once occupied the entire area was divided. It is believed that these two squirrels evolved from a common ancestor. They are similar in appearance but are different species because they cannot interbreed. REPRODUCTIVE ISOLATION: (Sympatric Speciation) * Occurs when two varieties of a species live in the same geographical area, but do not interbreed. * Occurs when formerly interbreeding groups of organisms are prevented from producing fertile offspring. * There are many types of reproductive isolation as seen in the chart. Barriers between gene pools can also occur by hybrid infertility, often due to POLYPLOIDY. * Polyploidy is an increase in the number of chromosomes beyond the usual diploid (2N) number forming a tetraploid. * can occur as a result of nondisjunction or during mitosis or meiosis when chromosome number doubles but cytokinesis does not occur. * polyploidy offspring can interbreed only among themselves. They are considered a new species. Many species of plants arise by polyploidy. QUESTION SET #5 - SPECIATION PATTERNS OF EVOLUTION Large scale evolutionary patterns help to outline the probable evolutionary history of life on Earth. Patterns that occur on a more local scale can demonstrate how processes of change among species may have contributed to and been influenced by these large-scale events. DIVERGENT EVOLUTION * Occurs when a group of one species becomes isolated from the rest of the same species. The isolated species may follow a different line of evolution due to different selective pressures. * By becoming adapted to different ecological roles, the different species avoid competition with each other. * At first the new species is similar to the ancestral species, but as time goes on, the new species each become adapted to their environments and become less and less alike. This is called divergent evolution. Example: polar bears may have split from the Brown bears when the population became isolated. ADAPTIVE RADIATION: * If species in a group diverge rapidly and evolve into a number of different species, each occupying a new environment, this process is called adaptive radiation. * This spreading or radiation, of the organisms into different environments is accompanied by adaptations. This can happen when the group has a characteristic that gives it a competitive advantage over the existing species or where there are opportunities that no other species are utilizing. l_016_02_l * Darwin’s finches on the Galapagos Islands are examples of adaptive radiation. An ancestral type of finch first arrived on the Galapagos Islands and then radiated into a variety of habitats and ways of life. The initial radiation involved living on the ground or in trees. Further radiation occurred on the basis of food. Without competition from other birds, the finches slowly radiated into and adapted to the various types of environments that were present. NOTE: Mammals are another group that demonstrate adaptive radiation. The mammalian pentadactyl limb, derived from one ancestral mammal. CONVERGENT EVOLUTION * If natural selection acts in the same way, in different parts of the world, species can become very similar, despite NOT being closely related. The process by which unrelated taxonomic groups become more similar and begin to resemble one another is called convergent evolution. * This pattern of evolution is shown when two groups of unrelated species adapt to the same kind of environment. Unrelated species show striking similarities. * Convergent evolution produces analogous structures that produce resemblances that are only “skin deep”. Example: birds and bats, whales and sharks, koala and bear, cacti and euphorbs Marsupials in Australia resemble placental mammals in the rest of the world. They evolved in isolation after Australia separated from other continents. Resulting in species that appear similar occupying similar ecological niches. CO-EVOLUTION * Two or more species also can evolve in response to each other through cooperative and competitive adaptations. * Two different populations that interact so closely that each other act as a strong selective pressure to the other Example: Relationship between flowers and their pollinators * Some species of flowers have developed adaptations that attract bees. Other flowers are adapted for birds or bats to feed on and act as pollinators. Coevolution reduces competition between species and benefits both species. EXTINCTION: * A study of the fossil record reveals that many fossils come from species no longer living today. * In fact, it has been estimated that, of all the species that ever lived, less than 1% exist today. * When the last individual of a species has died, the species is said to be extinct. * The fossil record showed that on several occasions many species became extinct at the same time. * Best known example of this is the dinosaurs at the end of the Cretaceous period, 65 million years ago. * What ever caused this mass extinction, has played a major role in the course of evolution. RATE OF EVOLUTION * What is the rate of evolution? There has been much discussion among biologists about rates of evolution. * One view, called GRADUALISM, is that evolution proceeds very slowly, but large changes can gradually take place over long periods of time. Darwin believed in this rate of evolution. * If evolution is gradual, there should be evidence of many intermediate forms of all species in the fossil record. Scientists have found remains of some of these intermediate forms, but the fossil record also shows that most species remain largely the same for hundreds of thousands of years. * Therefore gradualism does not fit with the fossil record, which shows periods of stability, with fossils showing little evolution followed by periods of sudden major change. The periods of stability may be due to equilibrium where living organisms have become well adapted to their environment so natural selection acts to maintain their characteristics. * The periods of sudden change that occasionally occur, may correspond with rapid environmental change, caused by volcanic eruptions or meteor impacts for example. New adaptations would be necessary to cope with changed environmental conditions, therefore strong directional selection and rapid evolution. This view of the pace of evolution is called PUNCTUATED EQUILIBIUM. * Then suddenly in a span of 1000 years or less, a new species is formed. This step-like pattern of evolution in the fossil record is called punctuated equilibrium. WORKSHEET #6 - PATTERNS OF EVOLUTION QUESTION Summary:

HOW DID EVOLUTIONARY THOUGHT EVOLVE?
* Early biological thought did not include the concept of evolution
* Prior to the 18th century, the church heavily influenced science.  
* The acceptable theory was that all organisms were created simultaneously by God (CREATIONISM) and that each distinct life form remained fixed and unchanging from the moment of its creation
* This view reigned unchallenged for nearly 2000 yrs.
* By the 18th century, however several lines of new emerging evidence began to erode the dominance of this static view of creation
* As early European naturalists explored the newly discovered lands of Africa, Asia, and America they found that the number of species or different types of organisms was much greater than anyone had suspected.
* They also observed that some species closely resembled one another yet differed in some characteristics.
* These observations led some naturalists to consider that perhaps species could change after all.  Some of the similar species might have developed from a COMMON ANCESTOR.

COMMON ANCESTORY
Definition: 
* an organism, which is the shared ancestor of two (or more) different descendant groups of organisms. Image result for common ancestry 
* A group of organisms have common descent if they have a common ancestor.
* According to modern biology, all living organisms on Earth are descended from a common ancestor or ancestral gene pool.

THEORIES OF EVOLUTION
   * Evolution is something that happens to living organisms.  It is the alteration of life throughout history.
   * Important scientists that helped to explain evolution are: 
  JEAN BAPTISTE de LAMARCK (French Naturalist) 
1st evolutionary theory to propose species evolve over time (early 1800’s)
Believed organisms changed for THREE REASONS: 
   1. Universal Force willing organisms to change:
   * Organisms had an “imaginary” force or “desire” to change themselves for the better.  Organisms had the ability to produce new parts to satisfy their needs and become better adjusted to their environment. 
   * ie. birds can fly because they wanted to
   2. Use and disuse of body parts:
   * Use and disuse of certain body parts could be passed onto offspring.  Organs that were regularly used became stronger and more developed to perform their function, and organs not used withered away.    
   * ie. Giraffes necks became longer because they used them extensively for feeding
      3. Acquired Characteristics:
      * Species modification is the result of acquired characteristics, which are passed from generation to generation, and eventually these changes make permanent changes to a species.
      * Ie. One giraffe acquires a larger, longer neck and will produce longer, larger necked babies

Even though Lamarck’s theories were incorrect, they did attempt to explain adaptations.  He showed that evolution is adaptive, and that evolution of life is the result of adaptations.  He helped set the stage for Charles Darwin.

CHARLES LYELL: (1820)
a geologist who studied the changing Earth  Image result for charles lyell 
      * Wrote the book “Principles of Geology”
      * influenced Darwin’s thinking because he believed the earth was an ancient arena in which rock formations slowly appeared, changed, and disappeared.
      * demonstrated that Earth’s surface changed over time by wind, water, ice, volcanoes, etc…
      * He recognized that competition between species leads to a “struggle for existence” and even discussed the extinction of species caused by humans.

THOMAS MALTHUS: (1798’s) Image result for THOMAS MALTHUS 
      * an economist who influenced Darwin’s thinking with his Malthusian Doctrine: every human population must eventually outgrow its food supply; stated that more babies would be produced than people dying off.  This would lead to over population, which would be rectified by disease, famine, or war.
      * he realized his theory applied to all living things

CHARLES DARWIN and EVOLUTION BY NATURAL SELECTION
Darwin’s Research was based on:  
At the age of 22, Darwin makes a 5-year scientific exploration on board the H.M.S. Beagle ship to chart stretches of the South American coast. Image result for charles darwin 
      1. Observations of South American plants, animals and fossils
      2. Galapagos Islands, a chain of volcanic islands located about 900 km off the Pacific coast of South America studying diversity of species of animals such as blue-footed boobies, giant tortoises, marine iguanas and many species of finches.
      3. Carried out work of Domestic Breeding with pigeons
      4. Work of other Scientists:
                Population Studies: Malthusian Work 
                Geologist Charles Lyell
      5. Developed the theory of evolution by Natural Selection

How Darwin accomplished his research:
      * Darwin explained his theory in the Origin of Species published in 1859. 
      * Darwin delayed publication of his ideas for many years, fearing a hostile reaction.  He might never have published them if another biologist, Alfred Wallace, had not written a letter to him in 1858 suggesting very similar ideas.
      * Darwin believed that the Earth’s many species are descendants of ancestral species that were different from those living today. This is due to the many accumulation of adaptations to various environments.
      * In Darwin’s book he said: In the process of NATURAL SELECTION, organisms best suited to their environment reproduce more successfully than other organisms.  Therefore, over generations the proportion of organisms with favorable traits increases in a population. 
      * Darwin proposed that environment may affect individual organisms in a population in different ways because individuals of a species are not identical.  
      * Some organisms have traits that make them better able to cope and survive within their environment.  Organisms that have a greater number of these favorable traits tend to leave more offspring than organisms that do not have favorable traits.

Note: if the trait both increases the reproductive success of an organism and is inherited, then the trait will be passed on to many offspring.  (A population of organisms adapt to their environment as their proportion of genes for favorable traits increases).

Fitness of an Organism:
      * In an evolving population, a single organism’s genetic contribution to the next generation is termed FITNESS.  
      * Definition: Fitness is a measure of how well suited an organism is to survive in its habitat and its ability to maximize the number of offspring surviving to reproductive age.  
      * Therefore, an individual with high fitness is well adapted to its environment and reproduces more successfully than an individual with low fitness.
      * Natural selection acts on the phenotype, or the observable characteristics of an organism, but the genetic (heritable) basis of any phenotype, which gives a reproductive advantage, will become more common in a population. 
      * Over time, this process can result in adaptations that specialize populations for particular ecological niches and may eventually result in the emergence of new species.
      * In other words, natural selection is an important process (though not the only process) by which evolution takes place within a population of organisms.

NATURAL SELECTION 
Natural Selection: (Nature selects)
      * NATURAL SELECTION is a passive process; organisms do not purposefully acquire traits that they may need.  
      * The environment “selects” those traits that will increase within a population.  
      * The kinds of traits that are favorable depend on the demands of the environment. The environment acts as a sieve through which only certain variations can pass.
      * Natural selection is an ongoing process in nature, and is the single most significant factor that disrupts genetic equilibrium.  
      * As a result of natural selection, some members of a population are most likely to contribute their genes to the next generation than are other members. 
      * Natural selection is uneven reproduction.  Individuals whose traits are best suited to the environment (better enable them to obtain food or escape predators or tolerant physical conditions) will survive and reproduce more successfully; passing these adaptive traits to their offspring.

Example: 
Walking Stick insect blending in with its environment, sunflowers bending toward light, antibiotic resistant bacteria allow them to survive when exposed to certain chemical.  An organism that may be able to run fast, or it may be strong or have coloring that act as camouflage from predators. These characteristics make the organism better suited to their environment and nature favors them.

It is important to recognize three key points about evolution by natural selection:
      1. Natural selection occurs through interactions between individual organisms and the environment, individuals do not evolve. Rather it is a population (group of organisms) that evolves over time as adaptive traits become more common in the group and other traits change or disappear.
      2. Natural selection can amplify or diminish only heritable traits, NOT acquired traits.  Unless the trait is coded for in the genes of an organism’s gametes, it cannot be passed onto offspring. 
      3. Evolution is not goal directed; it does not lead to perfectly adapted organisms.  Natural selection is the result of environmental factors that vary from place to place and over time.  A trait that is favorable in one situation may be useless in another circumstance.

Natural selection is contingent on time and place.  It favors those heritable traits in a varying population that fit the current, local environment.

6 MAIN IDEAS OF DARWIN’S THEORY
      1. OVERPOPULATION
      * All species are capable of producing more offspring than the environment can support. 
Examples:
Fish lays millions of eggs annually, but only a few survive and reproduce, thus preventing overpopulation.

2. COMPETITION
      * There is a struggle for existence in which some individuals survive and some die.

3. VARIATION
      * Living organisms vary.  They may differ in the exact size, shape of a body part, in strength, running speed, resistance to diseases and so on. These differences are called variations. 
      * If the variations are positive and increase the successfulness of the organism, the traits are passed onto the next generation.

4. SURVIVAL OF THE FITTEST (NATURAL SELECTION)
      * Those individuals in a species with traits that give them an advantage are better able to compete, survive, and reproduce.  
      * All others will die off without leaving offspring.  The phase “survival of the fittest” is used to summarize this idea.
      * Since nature selects the organisms to survive, the process is called NATURAL SELECTION.  
      * The results of natural selection therefore accumulate.  As one generation follows another, the characteristics of the species gradually change- the species evolves.

5. ADAPTATION
      * All living organisms are “adapted” in the sense that their appearance, behavior, structure, and mode of life made them well-suited to survive in a particular environment
Examples: 
Snail shells with more stripes may improve camouflage and therefore reduce predation.
      6. SPECIATION (ORIGIN OF NEW SPECIES) 
      * Over numerous generations, new species arise by the accumulation of favorable, inherited variations.  
      * If the range of inherited adaptations in one population of a species becomes so extreme that it prevents breeding with other populations of the same species, the “changed population” is effectively a “NEW SPECIES”.

TYPES OF ADAPTATIONS
      1. STRUCTURAL:   changes to an organism’s anatomy or physical characteristics. (camouflage, fur, fat layers, mimicry)
STRUCTURAL EXAMPLES:
      * Mammals have the same basic limb design.   Humans however, have forelimbs that are well adapted for grasping and holding things and opposable thumbs.
      * Plants have become adapted to feeding on insects to increase protein.  (Venus fly trap and pitcher plant). Leaves have become adapted in different ways to capture prey.
      * Monarch butterflies have a bitter taste and are avoided by birds.  Viceroy butterflies look and act like Monarch butterflies, but are not bitter tasting, tricking birds into thinking they are Monarch butterflies to avoid been eaten.

2. PHYSIOLOGICAL:   changes to the metabolic processes occurring within the body (chemical changes, temperature regulation, production of toxins sexual attractants, alarm signals).   Production of enzymes that control body functions such as temperature, respiration, circulation, and muscle coordination can also help the organism adapt and survive.
PHYSIOLOGICAL EXAMPLES:
      * Mutant strains of bacteria that are resistant to penicillin have evolved.  Some strains of bacteria can produce an enzyme that inactivates penicillin, others have cell walls that block the penicillin molecule from entering.
      * Secretion of venom by snakes and the production of toxins by certain plants are also examples of physiological adaptations.

3. BEHAVIORAL:  Are inherited behavioral patterns that allow an organism to survive in an environment, avoid danger or enable them to reproduce successfully. (hibernation, migration)
BEHAVORIAL EXAMPLES:
      * Migration of Canada Goose.  Hibernation of certain mammals.  Storage of nuts by squirrels 
      * Broken wing behavior of bird to draw enemy away from nest
      * Plant movement toward light called phototropism
      * Courtship behaviors to increase reproductive success. These allow species to recognize and attract members of the opposite sex of their own species.

SCIENTISTS CAN OBSERVE NATURAL SELECTION IN ACTION
CASE STUDY: Finches on Galapagos Islands Image result for finches natural selection 
The beak sizes of ground finch species were measured.  Ground finch eats mostly small seeds.
      * In dry years, when all seeds were in short supply, birds must eat the larger seeds.
      * Birds with larger, stronger beaks have a feeding advantage and greater reproductive success.  This lead to an increase in the average beak depth for the population.

* In wet years, small seeds were abundant.
      * Birds with small beaks were more efficient in eating the small seeds, and now have greater reproductive success. This lead to a decrease in average beak depth.

CASE STUDY: Peppered Moths in England pepfig1b.gif - 22175 Bytes 
      * During 1800’s, there were two kinds of peppered moths in England: 
-a common light brown colored variety
-a rare dark colored variety
      * The Peppered Moth spends much of its day resting on the bark of oak trees (light coloured bark). 
      * Light brown variety had an advantage and could camouflage against the trees and avoid predatory birds. 
      * This variety had greater reproductive success. This lead to an increase in numbers of the light coloured variety of Peppered Moths.
      * When the Industrial Revolution began in England, the air became full of smoke and soot from burning coal.  This extreme pollution of the air settled on the tree trunks and stained the tree trunk bark dark brown.
      * By the end of the century, the dark coloured variety of Peppered Moth population in England had the advantage of camouflage, and was able to avoid the predatory birds. 
      * This variety now had greater reproductive success. This lead to a decrease in the light brown colored moths.
      * Therefore, in each environment the moths that were better camouflaged (adapted) had the highest survival rate.
      * Scientist observed light and dark moths in both industrial and rural areas to determine if natural selection had caused the dark variety of moths to become more numerous.
      * Rural areas: Birds ate more dark colored moths on light tree trunks
      * Industrial areas: Birds ate more light brown colored moths on dark tree trunks
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CASE STUDY: Antibiotic Resistance in Bacteria
      * A well-known example of natural selection in action is the development of antibiotic resistance in microorganisms. Since the discovery of penicillin in 1928 by Alexander Fleming, antibiotics have been used to fight bacterial diseases.   
      * Natural populations of bacteria contain, among their vast numbers of individual members, considerable variation in their genetic material, primarily as the result of mutations. 
      * When exposed to antibiotics, most bacteria die quickly, but some may have mutations that make them slightly less susceptible. If the exposure to antibiotics is short, these individuals will survive the treatment. This selective elimination of maladapted individuals from a population is natural selection.
      * These surviving bacteria will then reproduce again, producing the next generation. Due to the elimination of the maladapted individuals in the past generation, this population contains more bacteria that have some resistance against the antibiotic. 
      * At the same time, new mutations occur, contributing new genetic variation to the existing genetic variation. Spontaneous mutations are very rare, and advantageous mutations are even rarer. However, populations of bacteria are large enough that a few individuals will have beneficial mutations. If a new mutation reduces their susceptibility to an antibiotic, these individuals are more likely to survive when next confronted with that antibiotic.
      * Given enough time, and repeated exposure to the antibiotic, a population of antibiotic-resistant bacteria will emerge. This new changed population of antibiotic-resistant bacteria is optimally adapted to the context it evolved in. 
      * At the same time, it is not necessarily optimally adapted any more to the old antibiotic free environment. The end result of natural selection is two populations that are both optimally adapted to their specific environment, while both perform substandard in the other environment.
      * The widespread use and misuse of antibiotics has resulted in increased microbial resistance to antibiotics in clinical use, to the point that the methicillin-resistant Staphylococcus aureus (MRSA) has been described as a "superbug" because of the threat it poses to health and its relative invulnerability to existing drugs. Response strategies typically include the use of different, stronger antibiotics; however, new strains of MRSA have recently emerged that are resistant even to these drugs.

Resistance to antibiotics is increased though the survival of individuals which are immune to the effects of the antibiotic, who’s offspring then inherit the resistance, creating a new population of resistant bacteria.

________________

TYPES OF NATURAL SELECTION
STABILIZING SELECTION: http://img.sparknotes.com/figures/A/a3aa6bb95c7d70781cc0089d17f9160f/stable.gif 
         * Encourages the formation of average traits
         * Individuals with the average form of a trait have the highest fitness.  The average represents the optimum for most traits. 
         * Example: larger than average lizards might be easily seen, captured and eaten by predators or smaller than average lizards are not able to run as fast as average and might not be able to escape predators.

DIRECTIONAL SELECTION: http://img.sparknotes.com/figures/A/a3aa6bb95c7d70781cc0089d17f9160f/direct.gif 
         * Encourages the formation of one extreme trait, such as a very long tongue in anteaters
         * Individuals that display a more extreme form of a trait have greater fitness than individuals with an average form of the trait.
         * Example: Anteaters with longer than average tongues would have an advantage obtaining termites in very deep nests.

DISRUPTIVE SELECTION: http://img.sparknotes.com/figures/A/a3aa6bb95c7d70781cc0089d17f9160f/disrupt.gif 
         * Selects for both extreme traits rather than average traits
         * Individuals with either extreme variation of a trait have a greater fitness than individuals with the average form of that trait.
         * Example: Studying shell color on marine animals called limpets shows that the white and dark variation have an advantage camouflaging themselves against rocks and barnacles compared to the average intermediate colored limpets in both the white and dark backgrounds.

Practice Questions Set #1 - THEORIES OF EVOLUTION QUESTIONS

EVIDENCE OF EVOLUTION
1. FOSSIL RECORD and BIOGEOGRAPHY
The best clues scientists have about what life was like thousands or millions of years ago comes from fossils.

Fossils: 
Are the petrified remains or imprints or traces of animals or plants that lived in the past.  
         * Fossils provide convincing evidence of Earth’s evolutionary past
         * Overall the life that existed more than 500 million years ago was vastly different in appearance from life today.
         * Although planet Earth has had extensive oceans for most of its existence, fish fossils have been found in rocks 500 million years old or younger (less than 15% of the 3.5 billion year existence of life on our planet).
         * One conclusion that can be drawn from studying fossils is that life of Earth is constantly changing.
         * Most of the changes have occurred over huge timescales (hundreds of thousands or millions of years) that humans find difficult to grasp.

Fossil Record:
         * The sequence in which fossils appear within layers of sedimentary rocks-provides some of the strongest evidence of evolution. 
         * The fossil record reveals the historical sequence in which organisms evolved.
         * The chronological fossil record gives us the history of life in general and allows us to trace the decent of a particular group. 
         * Reveals a succession of fossil forms in layers of sedimentary rock that differed from the current life forms. It allows for the study of similarities between modern day forms and ancient forms.

MISSING LINK:
         * The existence of fossils is very difficult to explain without evolution. An example of this is Acanthostega.    
         * It has similarities to other vertebrates, with a backbone and four limbs, but has eight fingers and seven toes so it is not identical to any existing organism.  This suggests that vertebrates and other organisms change over time.
         * Acanthostega is an example of a “missing link”.  Although it has four legs, like most amphibians, reptiles, and mammals, it also had a fish-like tail and gills and lived in water.  This shows that land vertebrates could have evolved from fish via an aquatic animal with legs.
            * Another series of fossils can trace the evolution of whales from four legged animals. Whales living today have forelegs in the form of flippers but lack hind legs.
            * Additional fossils show that Pakicetus and Robhocetus had a type of anklebone that is otherwise unique to the group of mammals that include pigs, hippos, cows, camels and deer. The anklebone similarity strongly suggests that whales (and dolphins and porpoises) are most closely related to this group of land mammals.

BIOGEOGRAPHY: 
Biogeography is the study of the distribution of plants and animals throughout the world. 
            * The distribution of organisms on Earth is explainable by assuming organisms originated in one location.
            * Darwin observed animals in the Galapagos Islands resembled species on the South American mainland more than they resembled animals on islands that were similar but much more distant. 
            * The logical explanation was that the Galapagos species evolved from animals that migrated from South America.  These immigrants eventually gave rise to new species as they became adapted to their new environments.

The Cretaceous Period
At the end of the Cretaceous Period, mammals split into 3 groups: 
1.        Monotremes (most primitive) 
eg. Duckbill platypus and Australian Spiny Anteater
2.        Marsupial (species has a pouch in which young live for a short time)
eg. Opossum, kangaroo, wombats, koalas
3.        Placental (live birth from uterus and placenta) pangea 
eg.        Cats, dogs, whales, elephants, humans, etc…
            * The breakup of the world-continent Pangaea, which began to disperse during the Jurassic period, continued. This led to increased regional differences in floras and faunas between the northern and southern continents.
            * As Pangaea began to split 220 million years ago, mammals were evolving, and continued to evolve on separate continents.

QUESTION: 
Marsupials and Monotremes only exist in Australia and New Zealand ……WHY?
            * Australia split from the super continent early and it is believed that it was the place of the ancestors to monotremes and marsupials. These two groups were out competed and did not flourish anywhere else in the world.
            * Placental mammals are worldwide except Australia and New Zealand.
            * Australia separated before placental mammals arose, so only monotremes and marsupials diversified in Australia
            * Comparable forms throughout the world was troubling and revealing because they suggested common ancestry if not a common origin.

2. HOMOLOGOUS ANATOMICAL STRUCTURES:
            * Other evidence for evolution comes in the form of HOMOLOGOUS ANATOMICAL STRUCTURES, which are body structures that are similar in form but are found on seeming dissimilar species and often have different functions.  
            * Similarity in characteristics that result from common ancestry (same evolutionary origin) in known as HOMOLOGY.
            * Organisms have anatomical similarities when they are closely related because of common descent. 
            * There are remarkable similarities between some groups of organisms in their structure.

EXAMPLE OF HOMOLOGOUS STRUCTURE
            * Pentadactyl forelimb is the “five” digit comparison. The forelimbs of several vertebrates all have the same basic arrangements of bones, yet they may be modified into wings, arms, legs, and fins.
            * The most likely explanation for these structural similarities is that organisms have evolved from a common ancestor. 
            * All these animals descended from common ancestors, and the same bones were put to different uses.  The bones in all these animals have the same developmental origin, yet may differ in structure and function of the forelimbs.
            * The same skeletal elements make up the forelimbs of humans, dogs, dolphins, bats and all other mammals, although the appendages have different functions.

All of these forelimbs show the same basic skeletal pattern.  In different vertebrate groups, the various bones have been modified as the limbs became specialized for different functions. homologous

VESTIGIAL ORGANS 
Are anatomical features that are fully developed in one group of organisms but reduced and maybe even non-functional in similar groups. 
            * The oldest homologous structures are vestigial organs that do not perform any function within the organism, but had important functions in ancestors.  Vestigial organs are thought to occur because organisms inherit their anatomy from their ancestors; therefore, vestigial organs are traces of an organism’s evolutionary history.
            * These organs are no longer essential today. Appendix, tail bone, male nipples, ear muscles, and wisdom teeth in humans, pelvic bones in whales and snakes. https://laidbackgardener.files.wordpress.com/2018/09/20180919a-eng-mashtalegypt-com1.jpg?w=800

ANALOGOUS STRUCTURES: 
Some structures may have a similar appearance (superficially) and the same function but may come from an entirely different structure.
These structures are said to be ANALOGOUS
               * In contrast to homologous structures, similar structures often evolve within organisms that have developed from different ancestors.  Such as body parts or organs called analogous structures, they have a similar form and function but have different evolutionary origins.  homologous-analogous 
               * Both plants and animals show analogous structures
Examples:
                  * birds, bats, and insects all adapted wings for flight 
                  * shark fins and whale fins, and trout fins all adapted for swimming
                  * cacti, euphorbs, and milkweed all have developed thick, barrel-like fleshy stems that store water as an adaptation to the desert environment.   
                  * Bird and bat wings are analogous — that is, they have separate evolutionary origins, but are superficially similar because they have both experienced natural selection that shaped them to play a key role in flight. Analogies are the result of convergent evolution.
                  * Interestingly, though bird and bat wings are analogous as wings, as forelimbs they are homologous. Birds and bats did not inherit wings from a common ancestor with wings, but they did inherit forelimbs from a common ancestor with forelimbs.

3. EMBRYONIC DEVELOPMENT (EMBRYOLOGY):
                  * The study of embryonic development reveals homology shared by vertebrates not apparent in adult species. Closely related organisms go through similar stages in their embryonic development.   embryology 
                  * For example: all vertebrate embryos go through a stage in which they all have gill pouches on the sides of their throats, notochord (stiff dorsal rod), tails, and four limbs.  
                  * Similarities between fish, frogs, snakes, birds, humans and all other vertebrates are much more apparent than differences.
                  * Scientists have observed that early embryonic development stages of many different organisms are similar.  
                  * Eg fish, frog, turtle, bird rabbit, and human were all similar.  This provides evidence that similar genes are used to determine body structures in organisms. This shows that these organisms had a common ancestor or origin.
                  * As development progresses, the various vertebrates diverge more and more, taking on the distinctive characteristics of their classes.

4. BIOCHEMISTRY:
Almost all living organisms use the same basic biochemical molecules, including DNA, ATP, and many identical or nearly identical enzymes and same 20 amino acids in their proteins. Closely related species show unmistakable similarities in their DNA and proteins.
                     * Organisms with similar biochemistry can be explained by decent from a common ancestor.
                     * All organisms have certain biochemical molecules in common.  The degree of similarity between DNA base sequences and amino acid sequences is thought to indicate the degree of relatedness.
                     * Those organisms with more similar molecules are more closely related (they became two distinct species more recently)
                     * We know mutations are a product of chance and occur at regular intervals. 
                     * Changes in DNA cause changes in the physical expression of genes. Therefore evolutionary changes are due to an accumulation of genetic changes.
                     * As the DNA mutates (which it does on a regular basis), it causes physical changes, and eventually enough physical changes lead to the formation of a new species 🡪 EVOLUTION
                     * Therefore the number of mutations between 2 species may be used to determine the time that has elapsed since the two diverged.

Example:
Human and chimpanzees: the number of differences in certain proteins indicates we split from the common ancestor about 5 million years ago.

THE HISTORY OF LIFE: LOOKING AT THE PATTERNS
                        * Life began 3.8 billion years ago
                        * The central ideas of evolution are that life has a history, it has changed over time and that different species share common ancestors.  
                        * Evolutionary change and evolutionary relationships are represented in "family trees”
                        * Evolutionary trees are hypotheses reflecting our current understanding of patterns of evolutionary descent.

Phylogeny
The evolutionary history of life, can be analyzed through cladistics, a method of assessing evolutionary relationships by comparing shared traits.

UNDERSTANDING PHYLOGENIES 34_38PrimatePhylogeny 
                           * Understanding a phylogeny (or sometimes called a cladogram) is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time.
                           * When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.
                           * Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.
                           * Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.

Referring to the figure shown on the board, determine if the CROCODILES are more closely related to LIZARDS (# 4) OR BIRDS (#6).   Explain your answer.

MISCONCEPTIONS ABOUT HUMANS
It is important to remember that:  
                           1. Humans did not evolve from chimpanzees. Humans and chimpanzees are evolutionary cousins and share a recent common ancestor that was neither chimpanzee nor human.
                           2. Humans are not "higher" or "more evolved" than other living lineages. Since our lineages split, humans and chimpanzees have each evolved traits unique to their own lineages.

SELECTIVE BREEDING OF DOMESTICATED ANIMALS
                           * The breeds of animals that are raised for human use are clearly related to wild species and in many cases can still interbreed with them.
                           * These domesticated breeds have been developed from wild species by selecting individuals with desirable traits, and breeding from them.
                           * The striking differences in the heritable characteristics of domesticated breeds give us evidence that the species can evolve rapidly.

http://toolbox-4-websites.com/wp-content/uploads/2011/12/dog_history_tree.jpg

QUESTION SET #2 - EVIDENCE OF EVOLUTION QUESTIONS

________________

POPULATION GENETICS AND EVOLUTION
                           * 1800’s- Darwin developed his theory of natural selection without knowing about genes.
                           * 1900’s- genetics was used to explain the variation among individuals of a population
                           * Today- genetics and evolutionary theory are inseparable.  Fitness, adaptations, species, and the process of evolutionary change are defined in genetic terms.

POPULATION GENETICS:
Studies of the complex behavior of genes in populations of plants and animals.

Population sampling:
Is important as it allows us to use a random sample of the population to study changes in certain characteristics within a population. It allows researchers to determine trends or frequencies of genes (alleles) and characteristics of a population without measuring the entire population.

Population:
                           * Is all the members of a single species occupying a particular area at the same time.  Members of the population can breed with one another.
                           * Ie. All gold fish in a pond are one population.  Those in another pond are another population.
                           * Because all members of a population can interbreed, the offspring share a common group of genes called a GENE POOL.
                           * Each gene pool contains a number of alleles (forms of each gene: recessive or dominant alleles) for each inheritable trait. 
                           * Recall for each gene: 
                           * Individuals may be homozygous recessive or dominant (two identical alleles) or heterozygous (two different alleles)
                           * Many genes have different alleles.  In a typical interbreeding population, some alleles will be more common than others.  How common an allele is can be assessed using allele frequency.

ALLELE FREQUENCY:
                           * The number of times an allele occurs in the gene pool, compared to the number of times other alleles for the same gene occur.

* Relative frequency of the alleles in a gene pool may change over time.
                           * IE: Peppered moths relative frequency of dominant and recessive alleles changed during the Industrial Revolution.

Sexual reproduction ALONE does not change the relative frequency of alleles in a population.
                           * Therefore Evolution can now be defined as any change in the relative frequencies of alleles in a gene pool of a population which changes the genetic composition of that population.
                           * Microevolution: evolution occurring on a small scale with small changes to the gene pool.

How can the O be the most common of the blood types if it is a recessive trait?
                           * If Huntington’s disease is a dominant trait, shouldn’t three fourths of the population have Huntington’s while one fourth have the normal phenotype?

Why don’t the recessive genes gradually disappear from a population?
                           * These questions reflect on the common misconception that the dominant allele of a trait will always have the highest frequency in a population and the recessive allele will always have the lowest frequency.  Gene frequencies can be high or low no matter how the allele is expressed and can change.  It is the changes in gene frequencies over time, that result in evolution.

GENETIC EQUILIBRIUM and the HARDY WEINBERG PRINCIPLE
                           * If the allele frequencies in a population remain the same from one generation to the next, and over several generations, the population is in GENETIC EQUILIBRIUM. If the allele frequencies change, the genetic equilibrium is altered and evolution has taken place.

HARDY WEINBERG PRINCIPLE:
                           * Hardy-Weinberg is named after two scientists who derived the principle in 1908.  G.H. Hardy was an English Mathematician and W. Weinberg was a German doctor.
                           * The Hardy Weinberg Principle provides a baseline to determine whether or not gene frequencies have changed in a population and therefore whether evolution has occurred.
                           * An important way of discovering why real populations change with time is to construct a model of a population that does NOT change. Hardy-Weinberg described a hypothetical situation in which there were NO changes in the gene pool and NO evolution.

Hardy Weinberg Principle: 
                           * States as long as certain conditions within a population were met, the gene pool would remain unchanged generation after generation, and allele frequency in a sexually reproducing population would reach genetic equilibrium.

FIVE CONDITIONS NECESSARY FOR GENETIC EQUILIBRUM 
                           1. LARGE POPULATION SIZE
The population must be very large, and changes in the allele frequencies due to change alone are insignificant and do not alter the gene pool
                           2. NO MUTATIONS
Allele changes DO NOT occur
                           3. RANDOM MATING
Individuals pair by chance and not according to their genotypes or phenotypes
                           4. NO GENE FLOW
Population is isolated; NO migration of individuals into or out of the population
                           5. NO NATURAL SELECTION
No selective force favors one genotype over another.  All individuals have equal reproductive success.
QUESTION:
The general population of the United States is growing taller.  Assuming height is a genetic trait, does this observation violate the Hardy Weinberg Principle?

ANSWER:
YES, it violates Hardy-Weinberg.

The United States is not in genetic equilibrium because new genes enter the population, mating is not random, and natural selection affects the trait of human height.

HARDY WEINBERG FORMULA:
SUM OF FREQUENCIES:
The Hardy Weinberg equation is applied to populations with a simple situation: dominant and recessive alleles controlling a single trait. The frequency of all the dominant alleles and all the recessive alleles equals the total genetic complement and adds up to 1 or 100% of the alleles present.

Variables:
p= frequency of dominant allele
q = frequency of recessive allele
so p + q = 1 (to represent 100% of the alleles)

RECALL: 2 alleles represent one gene (genotype) so we end up with this formula
(p + q )2 = 1

DETERMINING FREQUENCIES OF GENOTYPES IN A POPULATION:

A
	a
	 A
	AA
	Aa
	a
	Aa
	aa
	 
Frequency of AA = represented by p2
Frequency of Aa = represented by 2pq
Frequency of aa = represented by q2

THEREFORE: 
(p + q )2 = p2 + 2pq +  q2 = 1

STEPS HOW TO SOLVE HARDY-WEINBERG PROBLEMS:
                           1. Determine what piece of information you have been given about the population.
In many cases, this is the percentage or frequency of the homozygous recessive phenotype (q2).
                           2. The first objective is to find the value of p or q.  If this is achieved, then every other value in the equation can be determined by simple calculation.
                           3. Take the square root of q2 to find q
                           4. Determine p by subtracting q from 1 (p = 1- q)
                           5. Determine p2 by multiplying p by itself (p x p = p2)
                           6. Determine 2pq by multiplying 2 times q times p  (2)(p)(q)
                           7. Check that your calculations are correct by adding up the values so that the sum is equal to 1 or 100%

EXAMPLE 1:
Suppose that in a population of pea plants 42 plants are recessive for the short trait (tt) out of 120 plants. 
                           1. Determine the allele frequency of offspring that will be tall and the allele frequency that will be short.
                           2. Determine the number of heterozygous pea plants.

SOLUTION:
GIVEN: 
Recessive phenotype: q2 =  42/ 120 = 0.35

Recessive allele                         q =        √ 0.35          = .59

Dominant allele                         p =         1 - .59                 = .41

Homozygous dominant phenotype  
p2 =        (.41) 2                 = 0.17 (17%)

Heterozygous phenotype                        
2pq = (2)(.41)(.59)         = 0.48 (48%)
CHECK:
p + q = 1        
.41 + .59 = 1

CHECK:
p2 + 2pq +  q2 = 1
.17 + .48 + .35 = 1

RECALL 2 pq = .48 or 48%
48% out of 120 plants are heterozygous 58 plants

EXAMPLE 2:
An investigator has determined by inspection that 12% of the population has a straight hairline (recessive trait (h)).  Find the values of p, q, p2, q2, and 2pq provided the conditions for Hardy- Weinberg are met.

SOLUTION:

EXAMPLE 3: 
When studying the population of iguanas, two varieties exist that differ in foot webbing.  Allele for non-webbed feet (W) is completely dominant to the allele for webbed feet (w).
The frequency for the dominant allele is 0.8 and the gene pool for the population contains 500 individuals, determine the actual number of alleles that are recessive.

Solution:

EXAMPLE 4:
In a fruit fly population, 44% express the dominant trait of red eyes, determine the values of p, q, p2, q2, and 2pq provided the conditions for Hardy- Weinberg are met.

SOLUTION:

HARDY-WEINBERG PRINCIPLE QUESTIONS - Worksheet # 3_____________________
MECHANISMS OF EVOLUTION
POPULATIONS, NOT INDIVIDUALS EVOLVE:
                           * Can individuals evolve? NO
                           * Natural selection acts on the range of phenotypes in a population not the individual within the population. 
                           * The population’s genes change over time.

CHANGES IN GENETIC EQUILIBRIUM:
What are the mechanisms that cause changes in genetic equilibrium?  What causes evolution?
1. MUTATIONS:

Mutations are changes in the genetic material (DNA) of an organism.   
                           * Mutations provide new alleles, and therefore underlie all mechanisms that produce variation, the raw material for evolutionary change. 
                           * Most mutations are minor, such as changing the color of the scales of a butterfly’s wings, but they provide the variation that can be acted upon by natural selection.
                           * Mutations occur constantly as chance events, causing changes in the gene pool.  These changes are difficult to detect because many mutations are recessive and are seldom expressed in the phenotype of individuals. 
                           * Eventually a recessive mutation may appear in the phenotype and natural selection can act upon it.  If the mutation is harmful, the individual may die. The mutation is then removed from the gene pool.
                           * All other mechanisms of evolution merely shuffle the genetic material that is already present.

2. GENETIC DRIFT
                           * Genetic Drift is the change in allele frequencies of a population as a result of chance processes.
                           * In nature two situations lead to small populations in which genetic drift drastically affects the gene pool frequencies:    Founder Effect  and the Bottleneck Effect

Founder Effect: 
                           * Occurs when a few individuals found a colony and only a fraction of the total genetic diversity of the original gene pool is represented.  Which particular alleles the founders carry is dictated by chance alone.
Example: 
                           * The Amish of Lancaster, Pennsylvania, is an isolated religious sect descended from German founders.  Today, as many as 14 individuals in this group carries a recessive allele that causes an unusual form of dwarfism (affects only legs and arms) and polydactylism (extra fingers).  In the non-Amish population, only 1 out of 1000 individuals have this allele. founder 
Bottleneck Effect:  bottleneck 
                              * Occurs when a population is subjected to near extinction because of a natural disaster, or human interference.  The disaster acts as a bottleneck preventing the majority of genotypes from participating in the production of the next generation.
Example: 
                              * Large genetic similarities found in cheetahs is believed to be due to a bottleneck effect.  In a study of 47 enzymes, each of which can come in several different forms, all the cheetahs had exactly the same form.  This demonstrates that genetic drift can cause certain alleles to be lost from a population.

3. GENE FLOW
                              * Gene flow is the movement of alleles between populations by migration of breeding individuals from one population to another.  
                              * Gene flow between two populations keeps their gene pools similar.  It also prevents close adaptation to a local environment.

4. NONRANDOM MATING
                              * Nonrandom mating occurs when individuals pair-up, not by chance, but according to their genotypes or phenotypes.
                              * Inbreeding or mating between relatives are examples of nonrandom mating.
                              * Inbreeding decreases the proportion of heterozygous individuals and increases the proportions of both homozygous dominant and recessive individuals.  In human populations, inbreeding increases the frequency of recessive abnormalities.

5. NATURAL SELECTION
                              * Natural selection is the process by which populations become adapted to their environment.  Recall: Darwin’s explanation of natural selection.
                              * In evolution by natural selection, the fitness of an individual is measured by how reproductively successful its offspring are in the next generation.
                              * Evolution by natural selection requires: variation, inheritance, differential adapted-ness, and differential reproduction

QUESTION SET #4 - MECHANISMS OF EVOLUTION QUESTION

SPECIATION
WHAT IS A SPECIES?
Definition:
A species is defined as a group of interbreeding organisms that occupy a certain geographical range that share a common gene pool and that are isolated reproductively from other species.

The mating of different species results in
                              1. no offspring
                              2. Sterile offspring i.e. horse and donkey = mule (sterile)

SPECIATION is the origin of new species. 
                              * It occurs when two groups of the same species within a population become geographically isolated or separated from each other, they develop into two separate groups.
                              * Isolating a group of organisms separates its gene pool from the gene pool of the rest of the species.  Through evolution, a different gene pool will evolve in each group.
                              * It is believed that speciation is a two-step process:
                              1. geographical isolation  (allopatric speciation)
                              2. reproductive isolation  (sympatric speciation)

GEOGRAPHICAL ISOLATION: (Allopatric Speciation)
                              * Occurs when a natural barrier, (mountain, desert, river) divides a population, or landslide caused by an earthquake, or a species migrate to a new area, forming a population that is geographically isolated from the rest of the species.  Interbreeding becomes impossible.
                              * Geographical isolation acts as a barrier between the gene pools of the populations.
                              * The gene pool of each group becomes isolated and can no longer intermix.  Over a period of time each group becomes adapted to its particular environment.  When differences between the isolated groups become great, they can no longer interbreed.
                              * Example: The Albert Squirrel and Kaibab Squirrel each live on opposite sides of the Grand Canyon.  Due to the geographical barrier the population that once occupied the entire area was divided.  It is believed that these two squirrels evolved from a common ancestor. They are similar in appearance but are different species because they cannot interbreed.
REPRODUCTIVE ISOLATION: (Sympatric Speciation)  
                              * Occurs when two varieties of a species live in the same geographical area, but do not interbreed.
                              * Occurs when formerly interbreeding groups of organisms are prevented from producing fertile offspring.
                              * There are many types of reproductive isolation as seen in the chart. 
              
Barriers between gene pools can also occur by hybrid infertility, often due to POLYPLOIDY.
                              * Polyploidy is an increase in the number of chromosomes beyond the usual diploid (2N) number forming a tetraploid.
                              * can occur as a result of nondisjunction or during mitosis or meiosis when chromosome number doubles but cytokinesis does not occur.
                              * polyploidy offspring can interbreed only among themselves. They are considered a new species. Many species of plants arise by polyploidy.

QUESTION SET #5 - SPECIATION

PATTERNS OF EVOLUTION
Large scale evolutionary patterns help to outline the probable evolutionary history of life on Earth.  Patterns that occur on a more local scale can demonstrate how processes of change among species may have contributed to and been influenced by these large-scale events.

DIVERGENT EVOLUTION
                              * Occurs when a group of one species becomes isolated from the rest of the same species. The isolated species may follow a different line of evolution due to different selective pressures. 
                              * By becoming adapted to different ecological roles, the different species avoid competition with each other.
                              * At first the new species is similar to the ancestral species, but as time goes on, the new species each become adapted to their environments and become less and less alike. This is called divergent evolution.
Example: polar bears may have split from the Brown bears when the population became isolated.
ADAPTIVE RADIATION:
                              * If species in a group diverge rapidly and evolve into a number of different species, each occupying a new environment, this process is called adaptive radiation.
                              * This spreading or radiation, of the organisms into different environments is accompanied by adaptations.  This can happen when the group has a characteristic that gives it a competitive advantage over the existing species or where there are opportunities that no other species are utilizing.  l_016_02_l 
                              * Darwin’s finches on the Galapagos Islands are examples of adaptive radiation.  An ancestral type of finch first arrived on the Galapagos Islands and then radiated into a variety of habitats and ways of life.  The initial radiation involved living on the ground or in trees.  Further radiation occurred on the basis of food.  Without competition from other birds, the finches slowly radiated into and adapted to the various types of environments that were present.

NOTE:  Mammals are another group that demonstrate adaptive radiation. The mammalian pentadactyl limb, derived from one ancestral mammal.

CONVERGENT EVOLUTION
                                 * If natural selection acts in the same way, in different parts of the world, species can become very similar, despite NOT being closely related. The process by which unrelated taxonomic groups become more similar and begin to resemble one another is called convergent evolution.
                                 * This pattern of evolution is shown when two groups of unrelated species adapt to the same kind of environment. Unrelated species show striking similarities.
                                 * Convergent evolution produces analogous structures that produce resemblances that are only “skin deep”.  
Example: birds and bats, whales and sharks, koala and bear, cacti and euphorbs

Marsupials in Australia resemble placental mammals in the rest of the world. They evolved in isolation after Australia separated from other continents.  Resulting in species that appear similar occupying similar ecological niches.
CO-EVOLUTION
                                 * Two or more species also can evolve in response to each other through cooperative and competitive adaptations.
                                 * Two different populations that interact so closely that each other act as a strong selective pressure to the other
Example: Relationship between flowers and their pollinators 
                                 * Some species of flowers have developed adaptations that attract bees. Other flowers are adapted for birds or bats to feed on and act as pollinators. Coevolution reduces competition between species and benefits both species.

EXTINCTION:
                                 * A study of the fossil record reveals that many fossils come from species no longer living today.
                                 * In fact, it has been estimated that, of all the species that ever lived, less than 1% exist today.  
                                 * When the last individual of a species has died, the species is said to be extinct.
                                 * The fossil record showed that on several occasions many species became extinct at the same time.  
                                 * Best known example of this is the dinosaurs at the end of the Cretaceous period, 65 million years ago.    
                                 * What ever caused this mass extinction, has played a major role in the course of evolution.

RATE OF EVOLUTION
                                    * What is the rate of evolution?
There has been much discussion among biologists about rates of evolution.
                                    * One view, called GRADUALISM, is that evolution proceeds very slowly, but large changes can gradually take place over long periods of time.  Darwin believed in this rate of evolution. 
                                    * If evolution is gradual, there should be evidence of many intermediate forms of all species in the fossil record.  Scientists have found remains of some of these intermediate forms, but the fossil record also shows that most species remain largely the same for hundreds of thousands of years.   
                                    * Therefore gradualism does not fit with the fossil record, which shows periods of stability, with fossils showing little evolution followed by periods of sudden major change.  The periods of stability may be due to equilibrium where living organisms have become well adapted to their environment so natural selection acts to maintain their characteristics. 
                                    * The periods of sudden change that occasionally occur, may correspond with rapid environmental change, caused by volcanic eruptions or meteor impacts for example.  New adaptations would be necessary to cope with changed environmental conditions, therefore strong directional selection and rapid evolution.  This view of the pace of evolution is called PUNCTUATED EQUILIBIUM.
                                    * Then suddenly in a span of 1000 years or less, a new species is formed.  This step-like pattern of evolution in the fossil record is called punctuated equilibrium.

WORKSHEET #6 - PATTERNS OF EVOLUTION QUESTION

Summary:

Transcript for:Fundamentals of Evolutionary Biology

Transcript for:
Fundamentals of Evolutionary Biology