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Unit 9: Change in Organisms Over Time Honors Biology Honors Biology In historical context Other people’s ideas paved the path for Darwin’s thinking competition: struggle for survival population growth exceeds food supply land masses change over immeasurable time Some Important Contributions Carolus Linneaus (1707-1778) was a Swedish naturalist in the field of taxonomy: developed a binomial system of nomenclature (two-part names for each species [e.g., Homo sapiens]). believed in the ideas of special creation-- each species had an "ideal" structure and function fixity of species -- each species had a place in the scala naturae, a sequential ladder of life. Jean-Baptiste de Lamarck (1744-1829) Organisms adapted to their environments by acquiring traits change in their life time Disuse organisms lost parts because they did not use them — like the missing eyes & digestive system of the tapeworm Perfection with Use & Need the constant use of an organ leads that organ to increase in size — like the muscles of a blacksmith or the large ears of a night-flying bat transmit acquired characteristics to next generation Charles Darwin 1809-1882 British clergyman and naturalist Proposed the idea of evolution by natural selection Collected clear evidence to support his ideas Who Was Darwin? LaMarckian vs. Darwinian view LaMarck in reaching higher vegetation giraffes stretch their necks & transmits the acquired longer neck to offspring Darwin giraffes born with longer necks survive better & leave more offspring who inherit their long necks Darwin’s study of geology and Fossils Darwin took only a few books with him on the 5 year journey (no TV; no computer; no radio. Books.) In Principles of Geology, Charles Lyell presented arguments to support a theory of slow but continuous geological change proposed by James Hutton. Darwin took Lyell's book on the voyage of the HMS Beagle. And the Bible, being a clergyman. And Milton’s Paradise Lost. Some of Darwin’s fossil observations: Ocean shells occurred far inland and at great heights (12,000 feet) in the Andes. Fossils of huge sloths and armadillolike animals suggested modern forms were descended from extinct forms with change over time. Succession of types Armadillos are native to the Americas, with most species found in South America. Why should extinct armadillo-like species & living armadillos be found on the same continent? Glyptodont fossils are also unique to South America. Mylodon (left) Giant ground sloth (extinct) Modern sloth (right) “This wonderful relationship in the same continent between the dead and the living will…throw more light on the appearance of organic beings on our earth, and their disappearance from it, than any other class of facts.” The Galápagos Islands Volcanic islands off the South American coast Fewer types of organisms than mainland. Island species varied from the mainland species, and from island-to-island. Each island had a variation of tortoise; long and short necked tortoises correlated with different vegetation. More observations… Correlation of species to food source Whoa, Turtles, too! Darwin's Finches Finches on the Galapagos Islands resembled a mainland finch but there were more types. Galapagos finch species varied by nesting site, beak size, and eating habits The finches posed questions to Darwin: did they descend from one mainland ancestor ? did islands allow isolated populations to evolve independently ? could present-day species have resulted from changes occurring in each isolated population? Natural Selection and Adaptation Darwin decided adaptations develop over time, and sought their mechanisms Natural selection was proposed by both Alfred Russel Wallace and Darwin as a driving mechanism of evolution caused by environmental selection of organisms most fit to reproduce, resulting in adaptation Because the environment is always changing, there is no perfectlyadapted organism. Why Does Evolution Matter Today? Preconditions for natural selection members of a population have random but heritable variations in a population, many more individuals are produced each generation than an environment can support (Malthus) some individuals have adaptive characteristics that enable them to survive and reproduce better Consequences of natural selection More individuals in succeeding generations have the adaptive characteristics The result of natural selection is a population more adapted to its local environment Natural selection can only utilize variations that are randomly provided; therefore, there is no directedness or anticipation of future needs. Organisms Differ in Fitness Organisms whose traits enable them to reproduce to a greater degree have a greater fitness. Fitness is a measure of an organism’s reproductive success ex: Black pocket-mice are more likely to survive on dark lava flows; lighter-colored pocket-mice are more likely to survive on desert soil. Pocket Mice Artificial Selection Darwin noted that humans carry out artificial selection Humans selectively bred many varieties of pigeon, dog, chicken, cattle, horse, etc. In nature, interactions with the environment and predators determine which members reproduce more. Evolution by artificial or natural selection occurs when more fit organisms reproduce and leave more offspring than the less fit Artificial selection This is not just a process of the past… It is all around us today Selective breeding the raw genetic material (variation) is hidden there Selective breeding Hidden variation can be exposed through selection! Organisms Become Adapted An adaptation is a trait that helps an organism be more suited to its environment. Because of differential reproduction, adaptive traits increase in each succeeding generation. (in other words, those with the traits best suited to an environment will live and reproduce more successfully; therefore, their traits are passed on to the next generation in a higher proportion than poorly adapted members of the same species) Essence of Darwin’s ideas (1) Variation exists in natural populations (2) Many more offspring are born each season than can possibly survive to maturity (from Malthus) (3) As a result, there is a struggle for existence - competition (4) Characteristics beneficial in the struggle for existence will tend to become more common in the population, changing the average characteristics of the population - adaptations (5) Over long periods of time, and given a steady input of new variation into a population, these processes lead to the emergence of new species Adaptation Vs. Acclimation A mutation or combination of mutations that causes an adaptation may occur tens of thousands of years before the trait becomes adaptive When environmental conditions change within the range of tolerance for an organism, the organism may acclimate to new surroundings or conditions within its lifetime. Evidence supporting evolution Fossil record transitional species Anatomical record homologous & vestigial structures embryology & development Molecular record protein & DNA sequence Artificial selection human-caused evolution Fossil Evidence The fossil record is the history of life recorded by remains from the past. Fossils include skeletons, shells, seeds, insects trapped in amber, and imprints of leaves. Fossils can be dated in a wide variety of ways; location in rock strata; several radiometric measurements, etc. Living organisms resemble the most recent fossils in the line of descent; underlying similarities allow us to trace a line of descent over time. Fossil evidence supports the common descent hypothesis; fossils can be linked over time because they reveal a similarity in form, despite observed changes. Fossil Record Comparing Relative and Absolute Dating of Fossils Can determine Is performed by Drawbacks Relative Dating Absolute Dating Age of fossil with respect to another rock or fossil (that is, older or younger) Age of a fossil in years Comparing depth of a fossil’s source stratum to the position of a reference fossil or rock Determining the relative amounts of a radioactive isotope and nonradioactive isotope in a specimen Imprecision and limitations of age data Difficulty of radioassay laboratory methods Water carries small rock particles to lakes and seas. Dead organisms are buried by layers of sediment, which forms new rock. The preserved remains may later be discovered and studied. Fossil record A record showing us that today’s organisms share common ancestors with ancestral species Evidence for Evolution: The fossil record Archaeopteryx and modern pigeon Archaeopteryx Compsognathus Transitional Species Transitional forms between fossil remains and /or modern day species reveal links between groups. Caudipteryx is between dinosaurs and birds. This Chinese fossil shows some dinosaurs had feathers on arms, tail and probably body. Advantages during running and escape gave rise to birds once lift-off occurred. Eustheopteron is an amphibious fish. Seymouria is a reptile-like amphibian. Therapsids were mammal-like reptiles. Many mollusks and fish have transitional fossil forms 2006 Fossil Discovery of Early Tetrapod Tiktaalik “missing link” from sea to land animals Land Mammal ? ? ? ? Biogeography Biogeography is the study of the geographic distribution of life forms on earth Darwin's comparison of the animals of South America and the Galápagos Islands caused him to conclude that adaptation to the environment can cause diversification, including speciation. The location of continents influence where a population can spread. cacti are restricted to North American deserts and euphorbia grow in African deserts. marsupials arose when South America, Antarctica, and Australia were joined; Australia separated before placental mammals arose, so only marsupials diversified in Australia. Evidence for Evolution: Biogeography Toucan (Neotropics) Hornbill (SE Asia) Anatomical Evidence Organisms have anatomical similarities when they are closely related because of common descent Homologous structures in different organisms are inherited from a common ancestor. Vertebrate forelimbs contain the same sets of bones organized in similar ways, despite their dissimilar functions. Analogous structures have come to resemble each other because they serve a similar function (not related to common descent) wings on bats, birds, butterflies Homologous structures spines leaves succulent leaves needles colored leaves tendrils Convergent evolution Fish: aquatic vertebrates Dolphins: aquatic mammals similar adaptations to life in the sea not closely related Vestigial Structures Remains of a structure that was functional in some ancestor but is no longer functional in the organism in question. Most birds have well-developed wings; some bird species have reduced wings and do not fly. Humans have a tailbone but no tail Whales have a pelvis with attachment sites to support lower limbs Presence of vestigial structures is explained by the common descent hypothesis; these are traces of an organism's evolutionary history. Embryology During development, all vertebrates (this would include YOU) have a post-anal tail and paired pharyngeal pouches. In fishes and amphibian larvae, the pouches become gills In humans, few are born with visible gill slits, instead: The first pair of pouches becomes a cavity of middle ear and auditory tube second pair becomes tonsils third and fourth pairs become thymus and parathyroid glands. Above features are explained if fishes are ancestral to other vertebrate groups. Biochemical Evidence Most organisms use the same basic biochemical molecules, e.g., DNA, ATP, and many identical or nearly identical enzymes Organisms utilize the same DNA triplet code and the same 20 amino acids in their proteins. Early example: analysis of degree of similarity in amino acids for cytochrome c among organisms. cytochrome c was originally chosen because it is a mitochondrial protein present in all organisms that use aerobic respiration; this protein is essential to life on Earth for most living organisms Life's vast diversity has come about by only slight differences in the same genes. Genes for the same characteristics are found in organisms as diverse as yeast and humans DNA from two species can be cut and the degree to which the two reattach can be measured and quantified Animals, including roundworms and insects are used for molecular studies in part because they use the same molecules we do Many disorders are more easily studied in non-human animals they can be selectively bred they have genes for the same characteristics they have a shorter generation time Theory? In science, the term “theory” is reserved for those conceptual schemes that are supported by a large amount of experimental evidence over a long period of time and has not been found lacking. Much different from the way the word is used in common language A scientific theory is never a hunch, guess, or idea Theories never become laws; (laws are very narrow mathematical truths) the details of all theories are modified over time Because it is supported by so many lines of evidence, evolution is no longer considered a hypothesis; it is a theory Evolution is one of the great unifying theories of biology. Equivalent scientific theories: Cell theory: all organisms are made of cells. Gene theory: organisms contain coded information that determines their form and behavior. Atomic theory: all matter is composed of atoms Kevin Padian: Paleontologist UC Berkley Population Genetics Population genetics studies the genetic variation in a population. The gene pool is the total of all the alleles in a population, described in terms of gene frequencies. Neither allele dominance nor sexual reproduction changes allele frequencies. Get Your CLICKERS! The Hardy-Weinberg Law This is a tool used by population genetics to determine whether a change in a population (evolution) has occurred This law states an equilibrium of allele frequencies in a gene pool (using the formula p2 + 2pq + q2 ) remains in effect in each succeeding generation of a sexually reproducing population if five conditions are met. No mutation: no allelic changes occur. No gene flow: migration of alleles into or out of the population does not occur. Random mating: individuals pair by chance and not according to the genotypes or phenotypes. No genetic drift: the population is large so changes in allele frequencies due to chance are insignificant. No selection: no selective force favors one genotype over another. Note that the converse is also true: if equilibrium is not maintained, then evolution has occurred by one of those five conditions In reality, conditions of the Hardy-Weinberg law are rarely, if ever met, and allele frequencies in the gene pool of a population do change from one generation to the next, (which is evolution) Any change of allele frequencies in a gene pool of a population signifies that evolution has occurred. The Hardy-Weinberg law tells us what factors cause evolution-- those that violate the conditions listed. The Hardy-Weinberg equilibrium provides a baseline by which to judge whether evolution has occurred. 2 p + 2pq + 2 q Yes, you have to know this and be able to use it. Yes, you will need calculators. Get over it. Going back to genetics, this equation is looking at allele frequency 2 Homozygous dominant individuals, AA = p Heterozygous individuals, Aa = 2pq Homozygous recessive individuals, aa = q2 Example In a population of 10,000 rats, there are 36 albinos How many total alleles at the albinism locus are in the population? A. 36,000 B. 20,000 C. 10,000 What are the possible genotypes for the albinism locus in this population? A. AA, Aa, aa C. AA and Aa only B. AA only D. Aa and aa only Which part of the Hardy – Weinberg equation goes with which genotype? AA = A. q2 Aa = A. q2 aa = A. q2 B. p2 C. 2pq B. p2 C. 2pq B. p2 C. 2pq What is the frequency of homozygous recessive individuals in this population? A. 0.36 B. 0.6 C. 0.0072 D. 0.0036 36 / 10,000 (36 per 10,000) = 0.0036 What is the frequency of the albinism allele in this population? A. 0.0036 B. 0.072 C. 0.06 q2 = 0.0036 = 0.06 That means 6% of the alleles in this population are a. What are the possible genotypes in the gametes of this population? A and a ; p + q = 1 What is the frequency of the A allele in this population? A. 0.06 B. 0.94 C. 0.8836 D. None of these p = 1 – q; so 1 – 0.06 = 0.94 So 94% of the alleles in this population are A What is the frequency for homozygous dominant individuals in this population? A. 0.94 B. 0.36 C. 0.8836 D. None of these AA = p2 p2 = 0.942 = 0.8836 ; so 88.36% of this population is homozygous dominant, AA What is the frequency of carriers, Aa in this population? A. 0.0564 B. 0.0282 C. 0.0032 D. None of these Aa = 2pq 2(0.94 x 0.06) = 0.1128; so 11.28% of this population are heterozygotes What is the frequency of aa in this population? A. 0.094 B. 0.0036 C. 0.06 D. none of these q = 0.06 so q2 = 0.062 = 0.0036 Reality check: Does this make sense? Yes, the original question said the number albinos in the population was 36/10,000, or .36% Detailed explanations of each of the Hardy-Weinberg conditions follow: #1 Genetic Mutations Natural populations contain high levels of allele variation Analysis of Drosophila (fruit fly) enzymes indicates have at least 30% of gene loci with multiple alleles Similar results with other species indicates that allele variation is the rule in natural populations. Gene mutations provide new alleles, and therefore are the ultimate source of variation. A gene mutation is any change in the DNA sequence Mutations can be beneficial, neutral, or harmful ex: a seemingly harmful mutation that requires Daphnia to live at higher temperatures becomes an advantage when the environment changes. a change that occurs in an area of DNA that does not code for a gene is a neutral mutation a change that occurs in a gene, but still codes for the same amino acid is a neutral mutation #2 Gene Flow Is the sharing of genes between two populations though interbreeding Gene flow moves alleles among populations by migration of breeding individuals. Gene flow can increase variation within a population by introducing new alleles produced by mutations from another population. Continued gene flow decreases diversity among populations, causing gene pools to become similar. Gene flow among populations can prevent speciation from occurring. #3 Nonrandom Mating Random mating involves individuals pairing by chance, not according to genotype or phenotype. Nonrandom mating involves individuals inbreeding, assortative mating, and sexual selection Inbreeding is mating between relatives to a greater extent than by chance. Inbreeding decreases the proportion of heterozygotes and increases homozygosity at all gene loci. Inbreeding increases the frequency of recessive genes, many of which are abnormalities. Note that these were always in the population, they are just being uncovered If there were no recessive abnormalities; none would show up by inbreeding Assortative mating occurs when individuals mate with those that have the same phenotype. Assortative mating divides a population into two or more phenotypic classes with reduced gene exchange Homozygotes for gene loci that control a trait increase , and heterozygotes for these loci decrease Sexual selection occurs when males compete for the right to reproduce and the female selects. #4 Genetic Drift Genetic drift refers to changes in allele frequencies of a gene pool due to chance Genetic drift causes isolated gene pools to become dissimilar; some alleles are lost and others are fixed If a tsunami were to split an island in two, pink haired yaks may have just happened to be in abundance on the north side of the island, while green haired yaks happened to be mostly on the south side Over time, if there is no migration between these two islands, the gene frequencies will become more dissimilar, even though there may have been an equal number of each color morph of yak on the original island Genetic drift occurs when founders start new population, or after a genetic bottleneck with interbreeding. The bottleneck effect prevents most genotypes from participating in production of the next generation. Bottleneck effect is caused by a severe reduction in population size due to natural disaster, predation, or habitat loss Bottleneck effect causes severe reductions in total genetic diversity of the original gene pool. The cheetah bottleneck causes relative infertility because of the intense interbreeding when populations were reduced in earlier times. The founder effect is genetic drift where rare alleles or combinations occur in higher frequency in a population isolated from the general population. This is due to founding individuals containing a fraction of total genetic diversity of the original population. Which particular alleles are carried by the founders is dictated by chance alone So, a boy and girl yak get lost at sea, but manage to grab hold of a piece of floating debris. They hold on until they reach an island uninhabited by yaks, but with plenty of preferred food, water and shelter. They can only mate with each other, and later the yaklettes can only mate with each other. The alleles available to this population are due to chance. #5 Natural Selection Natural selection is the process that results in adaptation of a population to the environment. Natural selection requires variation inheritance of the variable traits differential adaptedness differential reproduction Relative fitness compares the fitness of one phenotype to another. Types of Selection: Directional Selection Directional selection occurs when extreme phenotype is favored; the distribution curve shifts that direction. Increases in insecticide-resistant mosquitoes and resistance of malaria agent to medications are examples of directional selection. The gradual increase in the size of the modern horse, Equus, correlates with a change in the environment from forest-like conditions to grassland conditions. Stabilizing selection occurs when extreme phenotypes are eliminated and an optimum phenotype is favored. The average human birth weight is near optimum birth weight for survival. The death rate is highest for infants at the extremes of the ranges of birth weights. Disruptive selection occurs when extreme phenotypes are favored and can lead to more than one distinct form British snails (Cepaea nemoralis) vary because a wide range causes natural selection to vary. In forest areas, thrushes (a bird) feed on snails with light bands. In low-vegetation areas, thrushes feed on snails with dark shells that lack light bands. Speciation the splitting of one species into two or more species or the transformation of one species into a new species over time; speciation is the final result of changes in gene pool allele and genotypic frequencies. A biological species is a category whose members are reproductively isolated from all other such groups. Reproductive isolation occurs when members of one species can only breed successfully with each other Reproductive Isolating Mechanisms For two species to be separate, gene flow must not occur between them. A reproductive isolating mechanism is any structural, functional, or behavioral characteristic that prevents successful reproduction from occurring. Two types: Prezygotic and Postzygotic Prezygotic Isolating Mechanisms anatomical or behavioral differences between the members of two species that prevent mating or make it unlikely fertilization will take place if mating occurs. Habitat isolation occurs when two species occupy different habitats, even within the same geographic range, so that they are less likely to meet and to attempt to reproduce. Temporal isolation occurs when two species live in the same location, but each reproduces at a different time of year, and so they do not attempt to mate. Behavioral isolation results from differences in mating behavior between two species. Mechanical isolation is the result of differences between two species in reproductive structures or other body parts, so that mating is prevented. Postzygotic Isolating Mechanisms prevent successful development after mating has taken place. Gamete isolation includes incompatibility of gametes of two different species so they cannot fuse to form a zygote; an egg may have receptors only for the sperm of its own species or a plant stigma prevents completion of pollination. zygote mortality is when hybrids (offspring of parents of two different species) do not live to reproduce. hybrid sterility occurs when the hybrid offspring are sterile (e.g., mules).