Learning Objectives: Biology 1130

Biology 1130 Topic 1: The Scientific Method 1. Define science and explain the scientific method and why it is important. - Science: The systematic study of the structure and behavior of the physical and natural world through observation, experimentation, and the testing of theories against the evidence obtained. - The scientific method is an approach to learning to ensure that our understanding is based on evidence. - This is important because it enables us to form theories based on the world around us. This helps us understand our universe. 2. Distinguish the types of science, and types of reasoning, and outline both of their roles in the scientific method. - Descriptive science: Wants to characterize patterns or similarities, and provides the gist for hypothesis testing because it may suggest possible explanations to life. - Hypothesis- testing: Concerned with testing 1+ causal explanations for an already existing pattern, interprets patterns, and provides direction as to the next patterns to look at. 3. Differentiate between hypothesis vs. prediction vs. theory - Hypothesis: A causal explanation for a given pattern, needs to be refutable. - Prediction: A statement of what will be observed under specified conditions, if the hypothesis is true. - A failure to observe the prediction falsifies the hypothesis. - Theory: Plausible or scientifically acceptable general principle or body of principles offered to explain a phenomenon. 4. Explain why science proceeds via rejecting, not proving, hypotheses - A hypothesis is never the only potential cause of a prediction. - Observing the prediction supports the hypothesis, but never proves it. - We have to disprove every hypothesis until there is only one left, the correct one. 5. Summarise the characteristics that distinguish science from non-science - Science: A systematic and empirical approach to studying the natural world, knowledge is evaluated on the quality and quantity of empirical evidence that supports it, minimizing error and bias. - Non-science: Seeks to explore the meaning and significance of human experience, evidence is based on coherence with beliefs, values, and traditions. 6. Explain confounding variables and the role of controls in addressing them - Manipulative studies are better for controlling confounding variables and, therefore have better inferential strength. - Confounding variables: A separate variable that is often unknown, that may be responsible for the pattern observed. - Can have a negative or positive effect. 7. Explain the concept of inferential strength and extrapolation, and how these relate to observational vs. manipulative studies. - Inferential strength: The measure of how strongly the results support the conclusions. This is higher in manipulative studies. - Extrapolation: Estimating something by assuming that existing trends will continue or will remain applicable, lowers the inferential strength. 8. Outline the four requirements for science to result in knowledge acquisition - (1) Has to be rational, and employ the scientific method to ensure inferences are based on the evidence. - (2) Has to remain skeptical of hypothesis and evidence. - (3) Has to strive to be objective or unbiased. - (4) Has to be methodologically materialistic or restrict assumptions to the material world. 9. Demonstrate concepts from above via the case study on the evolution of human skin color. - Causal observation and more rigorous descriptive studies show geographic variation in skin color. Why? - Observations: Humans and chimpanzees shared a common ancestor 6-7 Mya. Chimpanzees are light-skinned but covered by dark hair. Evidence suggests that early humans left the cover of trees for the open savannah where there is little shade. Humans lost much of their body hair. UV light causes DNA mutations. Melanin absorbs UV light, shielding cells from UV-induced DNA damage. - Hypothesis 1: Variation in human skin color evolved from selection for increased melanin in areas of high UV exposure because this reduces UV-induced DNA damage (skin cancer). - Observational study: Evidence is consistent with the hypothesis, it remains possible that another hypothesis makes the same prediction, and continues to remain skeptical and objective. - Problem 1: Skin cancer occurs later in life and is usually not fatal. Jablonski and Chaplin (2000) argued that selection for increased melanin resulting from decreased cancer risk will, therefore, be very weak and that the cancer-protecting function of melanin is not likely to be the primary selective agent for melanin. - Problem 2: Folate or folic acid is an essential nutrient for DNA synthesis and is especially beneficial during pregnancy. Melanin protects against UV-induced breakdown of folate in the skin. - Hypothesis 2: Humans evolved increased melanin (hence darker skin tones) in areas of high UV exposure because this protected them from UV-induced degradation of folate. - Problem 3: This can explain the evolution of darker skin in humans with hair loss, but not the evolution of light skin. - New observation: UVB is critical for the synthesis of vitamin D3, which starts in the skin, dark skin can cause D3 deficiency. - Hypothesis 3: Selection in more extreme latitudes favors lighter skin to increase vitamin D production. - Support: The association between skin color and latitude is consistent, females require more D3 during pregnancy and while breastfeeding (females have slightly lighter skin than males do), D3 is also gained through certain foods popular at extreme latitudes (they usually have darker skin). Topic 2: Darwin and the Theory of Evolution 1. Summarise the history of evolutionary thinking up to Darwin, including the ‘argument from design’ - Before Darwin, people all around the world had many stories as to how the world worked and how it was created. - Greek philosophers sought out natural explanations on the natural world, instead of the supernatural. They viewed it as incompatible with evolution. - Aristotle emphasized the importance of direct observation and that the principles must agree with the facts/observations. - Lots of what was observed was related to Christianity. - Watchmaker analogy: Argues that complex structures of living things and the adaptations of plants/animals are evidence of an intelligent designer. - Carl Linnaeus developed a taxonomic system where all organisms are organized in hierarchical groupings based on similarity. He said this represented a divine plan (still used today). - By the 1700s, it was found that rocks had been laid down under ancient oceans. This explained that things must have operated over very long periods in a slow and controlled manner (uniformitarianism). - Fossils played an important role in finding out about extinction. This opens to the fact that change is a thing and that it can happen over long periods. - Unfortunately, times were extremely sexist towards women. They weren’t allowed to gain scholarships and many discoveries were infiltrated by men. Progress is being made, but it is nowhere near perfect. - Mary Anning: She knew so much about fossils (which she learned about because her family collected and sold them), and she made many discoveries. She knew more about fossils and geology than most geologists and scholars around the world. She would often help researchers but never get mentioned in their papers. She was named one of the most influential women in the history of British science. 2. Explain how changing views of geology and fossil evidence set the stage for Darwin. - The change in views of fossils and geology helped set the stage because it showed that different species, over time, went through transmutation, meaning they looked different several years later. 3. Outline Lamark’s theory of evolution, including his mechanism of acquired characters. - Lamark was an expert on plants and invertebrates. - He provided the first detailed theory of evolution: natural mechanism. - He proposed that complex species descended gradually from older, less complex ones. - He suggested (he wasn’t right) that this occurred because of the inheritance of acquired characters. So, traits that were useful to the parents were passed down to their offspring, and so on. - He was influential because he suggested this theory, even though he was wrong, and he connected it to environmental fit. 4. Describe the key observations Darwin made during his voyage on the Beagle and how they influenced his thinking. - He spent most of his time on land, collecting fossils of extinct organisms, observing and preserving local fauna and flora, etc. - He began his expeditions believing in catastrophism: the theory that the change in the Earth’s crust came from unusually big disasters. - He found an archipelago of around 21 volcanic islands around the equator, and the fauna on each island was similar but had some distinct features that were to adapt to each separate island. They resembled a species in South America. - He also found many tortoises, each with different shell types (which depended on the environment) that differed from island to island. - He collected and preserved birds from these islands, thinking that they were all different species, but found out that they were all the same species (of ground finches). Their beaks were different shapes to adapt to what food was on what island. - He also saw sea lions that were similar to those in California. - He concluded that these observations were inconsistent with creationism. - He got home, convinced that the planet was extremely old and that the current geological patterns were the result of slow and ongoing processes. 5. Detail Darwin and Wallace’s key insights – i.e., evolution AND natural selection – and the evidence presented for each (you should be able to define evolution and explain what natural selection is) - Before publishing his findings, Darwin was sure that evolution was based on slight changes over time. - He had the basic findings of his theory in place, but it took him 23 years to finally publish his findings. - While Darwin was working, he got a letter from Wallace, who ironically came up with almost the same theory. - Wallace was a historian, a geographer, and a collector who identified many new species of birds and insects. - He kept many records of everything he saw and his thoughts on them, and he came to the same explanations and conclusions as Darwin did. - Wallace asked Darwin to forward the paper to Lyell and for it to be presented to the Linnean Society if he thought it was worthy. - They published the paper together and they became friends. The book was called The Origin. - They had 2 main points: Common descent (the fact that all species evolve from pre-existing species) and Natural selection (the way that characteristics change over time and fit to their environment). - Populations evolve, but individuals do not. 6. Summarise the evidence for common descent that comes from homology, vestigial organs, fossils, and biogeography. - Darwin said that humans and all other species are related like individuals in a family tree. We’re all linked to one common ancestor. Think of Russian nesting dolls. - Homology: Originally refers to the strange similarities in structure despite the difference in function. Darwin explained that this is very hard to explain via “special creation”, but it makes sense if the species descended from a common being. So widely accepted that this became the new definition ➔ Structural homology: “What could be more curious than the hand of man formed for grasping, that of a mole, for digging, the leg of a horse, the paddle of a porpoise and the wing of a bat, should all be constructed on the same pattern and should include similar bones and in the same relative positions?” (Darwin) ➔ Developmental homology: When similar traits are present in different species at a particular stage of their development. This is why chick embryos will look super similar to human embryos. - Vestigial structures: Remnants of structures that served a function in an ancestor (ex: human appendix, the pelvic bone of a snake, and the wings of land birds). - Fossils: Come from extinctions, show that species change through time, more rare to find and evaluate. - Biogeography: The fact that living species tend to be similar to others geographically nearby and to fossils in that area (due to a common ancestor). - Evidence is overwhelming for this, basically a scientific fact at this point. 7. Explain what experimental evolution is and how it provides evidence for evolution. - Experimental evolution is the study of evolutionary processes occurring in experimental populations in response to conditions made in the lab. - This provides evidence for evolution because things can be seen in a lab and recreated, to show that this wasn’t any other reason. 8. Differentiate between artificial and natural selection. - Darwin and Wallace realized that all organisms must experience the same thing. - Animals and people must compete for resources, to survive and reproduce. - Observation 1: There must be a fierce struggle to exist among members such that only a small portion of offspring survive to reproduce. - Observation 2: Success for existence is not random, but depends on the trait. This is natural selection. - Observation 3: Across many generations, traits that increase in success will become more popular. - Deductive reasoning is when there is a process that occurs when certain conditions are met. - Artificial selection is not natural. This happens when someone manipulates traits to get a desired outcome. 9. Be able to counter several common misconceptions about evolution - Misconception 1: Natural selection is not goal-driven or progressive. It is very complex and specialized, there is no goal, it is simply a process that happens when certain conditions are met, it makes organisms better because it shapes them to their environment. - Misconception 2: Natural selection does not act for the good of the species. Selection comes from variation and not absolute fitness, natural selection tends to favor traits that are detrimental to a population. - Misconception 3: Natural selection does not result in perfection. Natural selection does improve the survival of species, but there are many reasons as to why the outcome is not perfect. 10. Outline how Müllerian and Batesian mimicry work and explain their differences. - Herman Muller proposed that selection would favor shared warning signals in 2 distasteful butterfly species because it spreads the selective burden of educating predators. - Observational studies and theories supported the idea, but nothing like this had been demonstrated in the wild. - Kapan provided a great test by taking advantage of the unusual polymorphism of Heliconius cydno alithea. - He used a manipulative experiment. - Hypothesis: The resemblance of H. cydno to different local co-models is due to preferential predation of morphs that don’t match the local co-model compared to those that do. - Experiment: He captured yellow butterflies and put them with the whites and vice versa, to track their survival. - Results: Predators eliminated rare morphs more rapidly when they deviated from the local co-model, consistent with the hypothesis. 11. Explain why creationism and intelligent design are not scientific - Many people don’t believe in evolution even now. This is more pronounced for those who interpret sacred texts literally (ex: the Bible). - To deny evolution on this ground requires rejecting much of science (physics, astronomy, geology, biology), as well as the scientific method itself. - They aren’t scientific because they can’t be refuted. Such an explanation adds nothing to our understanding. Topic 3: Genetics and the Modern Evolutionary Synthesis 1. Compare/contrast blending vs. particulate inheritance - Blending inheritance: The theory that phenotypes in offspring are an average or a blend of the two parents. - Particulate inheritance: The theory found by Mendel, proposes that genetic information is transmitted from one generation to the next in particles so that the character of the offspring is not a blend of essences from the parents. 2. Outline the core ideas in Weismann’s germ plasm theory - Weismann was a German theorist. He developed a germ plasm theory for multi-cellular organisms, proposing that heritable information was transmitted only by the reproductive cells. - Germ cells produce somatic cells (the soma) each generation. Information flows from one germ cell to somatic cells, but not vice versa. Somatic cells are disposable, but the germplasm is (maybe???) immortal. - The situation is different in plants, corals, and sponges. In them, the germ cells are produced by somatic cells and changes in those cells can affect subsequent germ cells and can then go across generations. 3. Explain Mendel’s three ‘laws’ of inheritance using modern genetic terminology and outline the core tenant of Mendel’s that remains true despite inheritance usually being more complex. - Mendel’s law of dominance: Says that if 2 alleles at a locus differ, then the dominant one determines the phenotype and the recessive one has no effect. - Mendel’s law of segregation: Says that only one of the two gene copies present in an organism is distributed to each gamete (egg or sperm) that it makes, and the allocation of the gene copies is random. - Mendel’s law of independent assortment: Says that the allele a gamete receives for one gene does not influence the allele it receives for another gene. 4. Map phenotype to genotype under different scenarios of dominance - Draw Punnett squares for this. 5. Draw a Punnett square to determine genotypes of offspring from specific crosses of two parental genotypes. - Draw a 2x2 or 4x4 square, depending on if you’re looking at 1 or 2 genes. - Name the alleles involved, if not already named. - Check the parents’ genotypes. - Label the rows with one genotype and the columns with the other genotype. - Have each box inherit letters from its row and column. - Interpret and describe the Punnett square. 6. Use the addition and product rules of probability, and Punnett squares, to calculate probabilities of specific genotypes from given crosses. - Multiplication (product rule): The probability that 2+ independent events will both occur is the product of their individual properties. - Pr (A and B) = Pr (A) x Pr (B) - Addition (sum) rule: For mutually exclusive outcomes (only one can occur), the probability that any one of them occurs is the sum of their independent probabilities. - Pr (A or/either B) = Pr (A) + Pr (B) 7. Be familiar with modern genetic terms (e.g., locus, gene, allele, heterozygote, homozygote, phenotype, genotype) - Gene: A specific sequence of DNA (or RNA in viruses) that encodes the synthesis of a gene product. - Locus: Plural is loci, a broader term meaning a specific location on a chromosome, that may or may not contain a gene. - Allele: A unique variant of a gene that differs in nucleotide sequence. - Heterozygote: An individual with 2 different alleles at a given locus. - Homozygote: An individual with 2 copies of the same allele at a given locus. - Phenotype: Any quantifiable trait of an organism (morphological, behavioral, physiological). - Genotype: The genetic makeup of an individual in terms of the identity of the alleles it carries. 8. Explain the ways in which inheritance is often more complex than a simple ‘one locus-2 allele’ Mendelian model. - (1) Mendel’s law of dominance is far from universal. Incomplete or partial dominance is a thing. Co-dominance is also a thing. - (2) Alleles don’t always segregate independently within a locus. The meiotic drive is when a locus manipulates meiosis to favor the transmission of one allele over another. - (3) Addition is complicated for single genes. There can be more than 2 alleles at a gene/locus. Pleiotropy is when one gene affects multiple phenotypes, it is very common. - (4) Assortment of alleles at one locus is often not independent of those at another locus. This happens because of physical linkage when the genes are close together on a chromosome. Alleles of physically linked genes tend to be inherited together. - (5) Epistasis happens when one locus alters the effect on the phenotype of another, separate locus. You can’t just add up the effects of the various alleles at the two loci. - (6) Many traits are quantitative, meaning they vary continuously. Variations here arise from the individual’s environment and the multiple loci that affect the trait. 9. Describe the two reasons why many traits exhibit continuous variation. - (1) The individual’s environment can differ depending on how much that trait shows. The worse the environment, the less it is shown. - (2) The fact that multiple, often many, loci affect the trait. 10. Calculate allele frequencies from genotype/phenotype frequencies or the reverse (by assuming HW). - Allele frequency: total number of alleles looking for / total number of alleles (x100). 11. Understand the conceptual basis of HW expected genotype frequencies – i.e., Why are they p2, 2pq, q2? What assumptions are necessary for this to be true, and what does it mean if genotype frequencies differ from this? - Use the equation 1 = p^2 +2pq + q^2 - (AA) = p^2, (aa) = q^2, (Aa) = 2pq - For this to be true, you need to assume that there was: ➔ Diploid organisms that reproduce sexually ➔ Random mating concerning the locus ➔ No natural selection at the locus ➔ No mutation at the locus ➔ No migration (individuals moving in or out) ➔ No genetic drift (population is HUGE) - If genotype frequencies are not the same as originally, it means that one or more of the assumptions have not been met. 12. Conduct a test for HW genotype frequencies for a locus with two alleles: calculate the expected # of individuals of each genotype under HW, compare these with the observed # of individuals, and make an appropriate inference. - Lab 2. Topic 4: Microevolution 1. Distinguish between micro vs macroevolution and enumerate the processes causing the latter and the various ‘sources’ of genetic variance. - Microevolution: A change in allele frequency in a population across generations, that requires genetic variation. There is a focus on the variation within populations and evolutionary change over short periods. - Macroevolution: The evolution above the species level, focuses on variation among species and questions across long periods. - Macroevolution is the result of microevolution. - Caused by: mutation, gene flow, genetic drift, and natural selection. 2. Contrast random vs. non-random mating and explain the effects of the different forms of these on allele and genotype frequencies. - Random mating: Also called panmixia, when anyone mates with anyone, causes zero predictability in genotype. - Non-random mating: When the mating of animals is manipulated, it is calculated. This can happen because: ➔ Chance (not on purpose) ➔ May self-fertilize less or more often than expected ➔ May mate more often with other individuals that are more or less similar to them - Non-random mating affects how alleles are organized into genotypes. Allele frequencies are not affected. 3. Define inbreeding and inbreeding depression, outline the causes of the latter, and identify mechanisms that have evolved to reduce the likelihood of inbreeding. - Inbreeding: When mating happens between related individuals, causes an increase in the frequency of homozygotes across the genome and a deviation from expected genotype frequencies. - Inbreeding depression: The increase in homozygosity as a result of inbreeding that tends to decrease fitness. The decrease in fitness, in the body as a whole, is substantial. - This is widespread and can exacerbate the loss of genetic variation and the biology/health of humans. - This could be because the alleles are almost all recessive, which makes the population against them. - This could also be because some heterozygotes have a higher fitness level than homozygotes. 4. Identify the different types of mutations and how they are classified in terms of their effects on fitness (i.e., beneficial, neutral, deleterious); discuss the relative frequencies of these different types (i.e., fitness spectrum of new mutations). - Substitution mutation: A mutation that happens when a single nucleotide is replaced with another. These can be silent (when the effect is unnoticed) or replacement (when the effect is noticed). - Insertion/deletion mutation: A mutation that happens when one or more nucleotides are added or removed. They can alter the frameshift, usually making more consequences as it goes on. - Mutations are rare on a nucleotide-site basis but vary more among taxa. - Every new generation contains 5x10^10 more mutations than the previous one did! 5. Discuss the effects of mutation on allele frequencies and its role in creating genetic variation. - Most mutations are deleterious (reduce fitness). The beneficial ones are much rarer. - Many mutations have little to zero effect on someone and are lost by drift. However, the combination of mutations and drifting can maintain this genetic variation in a population. 6. Define gene flow and compare/contrast it with mutation in terms of their roles in altering allele frequencies and as sources of genetic variation in a population. - Gene flow or migration is the movement of alleles between populations. It introduces and removes alleles from a given population, the effect of this is higher than mutations. - It homogenizes populations, reducing the genetic difference between them. If the gene flow is high, the population differences are abolished. 7. Outline how gene flow and spatially varying selection can interact to impact local adaptation. - Local adaptation happens when a population adapts to its local environment. - Divergent selection is the selection that happens due to local adaptation. - Gene flow can hinder local adaptation because it introduces maladaptive alleles from other populations into the mix. - But, it can also promote adaptation by helping spread beneficial alleles among those same populations. 8. Define genetic drift and explain how it varies with population size and the impacts it has on allele frequencies, genetic variation, and population divergence. - Genetic drift is when finite (or countable) populations are subject to varying degrees of random change in allele frequencies across generations. This occurs due to sampling variation, which is the difference between the value in a finite sample and the actual population size. - Genetic drift reduces genetic variation because alleles can be lost, so heterozygosity decreases. - In smaller populations, the drift can overwhelm selection such that deleterious alleles may rise in frequency. - The drift will cause populations to diverge from each other, in the absence of gene flow. 9. Summarize the effects of population bottlenecks/founder events. - A population bottleneck is a severe and usually rapid decrease in population size that reduces genetic variation and enhances genetic drift. Environmental factors, human activities, disease, etc., can cause this. - This can also be caused by a founder event, which is when a small group colonizes a new geographic area and isolates it from other populations. This can have consequences for population persistence and future adaptation. 10. Outline the human health implications of drift (via a founder event) on the frequency of a deleterious mutation and how subsequent gene flow (isolate breaking) can alter this. - Bottleneck events can result in increased frequency of a deleterious (causes harm or damage) in an isolated population. This can have human health implications, for example, look at Tay-Sachs disease in Ashkenazi Jews or EVC syndrome in Pennsylvania Amish. 11. Be comfortable interpreting the output of the drift simulation we discussed. - Interpreting the output of a drift simulation often involves analyzing how a system evolves due to some kind of systematic or random change. 12. Define natural selection and fitness, outline the different components of fitness that can be involved and the different forms of natural selection that can take. - Natural selection is a process that occurs when certain conditions are met. The conditions are that the individual must vary in a trait, there is a non-random association between the trait and their reproductive success, and the trait is heritable. This needs to happen to produce evolutionary change. - Fitness is the absolute contribution of an individual to the next generation. Its reproductive success is measured as the number of offspring it produces. - Natural selection arises from variation in relative fitness. 13. Summarize the different approaches to detecting natural selection and the associated problem of correlated traits. - There are 3 forms of selection, linear, stabilizing, and disruptive. - You can detect it with direct measurement, which is an observational study. - Traits are often correlated, which can be produced on one trait with direct selection, in response to another trait. - Because traits are often correlated, we cannot assume that: because a trait changed, it must have been a direct target of selection, selection favored a change in the direction observed, or that because a trait didn’t evolve selection, it must not have acted on it. 14. Outline how genetic variation can be maintained, including the role of the processes discussed in this topic. - Genetic variation arises ultimately from mutations and sometimes gene flow. - It can be maintained by balancing selection, the mutation and drift selection, and ensuring that there is spatial and/or temporal variation in selection. Topic 5: Adaptation 1. Define adaptation in its different usages and distinguish it from acclimation. - Adaptation has two different meanings: ➔ A heritable phenotype that allows individuals to perform some function that enhances their survival and reproduction in their current environment. ➔ The evolutionary process that makes adaptation, or when natural selection causes the evolution of traits that improve the fit between an organism and its environment. - This is different from acclimation (which is when an individual adjusts to a change in its environment to minimize stress and keep its performance), because adaptation is a population, while acclimation is one singular individual. 2. Explain how exaptations are a form of adaptation and what characterizes them. - Exaptations are structures that are currently adaptations but were originally evolved for a different purpose. These are adaptations that arose after a change in its function. - They don’t imply that evolution is goal-oriented or that it can anticipate its future needs. 3. Outline what an adaptationist fairy tale is, why they are problematic, and how they can be avoided. - An adaptationist fairy tale is an untested and unsupported explanation for the adaptive value of a phenotype. They arise from the assumption that most traits are adaptations that evolved via natural selection, for their current function. - They are not as common in science, but they are very popular among the general public. - They are problematic because they can be misleading. They can lead people to believe something that has no correct evidence to approve or disapprove it. Scientists need to remain skeptical and be guided only by evidence. - They can be avoided by remaining skeptical and only being guided by evidence. 4. List the criteria necessary to demonstrate that a trait is adaptative. - You need to find the function of the adaptation and you need to demonstrate that this function correctly increases fitness in its current environment. 5. Explain the methods that can be used to demonstrate adaptation, including quantifying selection, reciprocal transplants, and the comparative method. - The comparative method is a method that seeks to correlate trait differences among populations or species with variation in a presumed selective agent. - A reciprocal transplant is a method to see if an adaptation or a species is well adapted. The idea is to grab two groups of the population you wanna look at and swap their environments, to see if they live or die. - Quantifying selection has the goal of understanding how certain traits increase in frequency within a population due to the selection advantage they give. 6. Discuss how adaptation and complexity are related (are adaptations necessarily complex?). - Adaptations do not have to be complex, but natural selection can and does produce complex structures. - Complex adaptation often consists of interdependent parts that can’t work on their own. This leads to the idea of divine creation (ew.). - Complex adaptations can be co-opted from already existing structures or molecular/developmental pathways. 7. Explain how complex adaptations can evolve via gradual, advantageous steps regarding an example (e.g., the eye). - Complex adaptations can evolve gradually. - An example of this is the helmets of treehoppers. Treehoppers are a group of insects that have weird helmet structures on their heads. These resemble wings in certain ways and they have similar genes to wings. Wings were originally found on the insect but were suppressed at some point, leading to the co-opting of these developmental pathways for protection. 8. Outline how exaptation may also contribute to the evolution of complex adaptations. - Exaptation can contribute to complex structures by allowing natural selection to reuse and repurpose already-existent traits, making it easier to develop complexity. 9. Summarize a Darwinian demon and describe the different factors that may constrain, or result in non-perfect, adaptation (i.e., explain why we don’t see Darwinian demons). - A Darwinian demon is an ideal organism that would maximize every fitness aspect, like breeding right after birth and making large and healthy offspring, with no decline in performance, forever. - We don’t see any of these organisms because: ➔ Selection acts on existing variation. So, variation may be lacking for some phenotypes or adaptions, suggesting a waiting game. ➔ Natural selection modifies phenotypes that are a product of past evolution, meaning an organism’s evolutionary history can impact future evolution. Look at the mammalian laryngeal nerve. ➔ Traits can have many functions and the optimal design for one function may differ from that of another function. Traits are also costly to produce and maintain because organisms have only a certain amount of energy and resources. Resources invested in one make it inaccessible to another. ➔ Natural selection lacks foresight. It grows from variation in survival and reproduction in the current environment. We have to remember that there are many organisms in one current environment. Natural selection acts on all organisms, sometimes favoring traits that allow them to win interactions and diminishing adaptation in other species. ➔ Gene flow may prevent local adaptation. The founder event may cause a loss of genetic variation (which hampers adaptation) and even cause a dangerous mutation to spread. And, genetic drift may increase the frequency of a negative allele or diminish that of a good one. Topic 6: Speciation 1. Define speciation, reproductive barriers, and reproductive isolation. - Speciation: The process where one species splits into 2+ species. This makes species related to one another, because they share characteristics from each other. - Reproductive barriers: Distinguished by whether they occur before (prezygotic) or after fertilization (postzygotic). ➔ Prezygotic: Blocks fertilization by reducing the likelihood of mating by preventing an attempted mating from being successful or impeding fertilization. Can be due to habit isolation, temporal isolation, behavioral isolation, mechanical isolation or gametic isolation. ➔ Postzygotic: Reduces the survival and/or reproductive success of hybrids. Can be due to genetic incompatibility or ecologically-dependent postzygotic location. - Reproductive isolation: When there is a set of barriers that exist between different species that makes them unable to reproduce and make offspring. 2. Outline the different species concepts, list their advantages and disadvantages, and discuss why, when speciation is considered as a process, they may not always agree. - Biological (BSC): Most useful, groups that actually or potentially interbreed and produce offspring in nature, which don’t form fertile offspring with members of other groups (reproductive compatibility). This makes gene flow possible and prevents accumulation of genetic differences. But, they evolve independently. This can’t be applied to asexuals or fossils, reproductive barriers. - Morphological: Defines species based on morphological similarities, can be applied to fossils and asexuals, misses cryptic species. - Ecological: Defines species based on their ecological niche, can be applied to asexual taxa, but not fossils. - It’s hard to agree on things because these different ways of categorizing them are so different. 3. Describe the various forms of pre- and postzygotic barriers and be able to classify examples correctly. - Prezygotic: ➔ Habitat isolation: When a population of a species changes habitats and lives somewhere that no longer overlaps with other populations of the same species. ➔ Temporal isolation: When the timing of reproduction between populations doesn't happen at the same time. They only mate with those at that same time. ➔ Behavioural isolation: When mates are isolated from each other due to differences in behavior. ➔ Mechanical isolation: When the shape and size of genitalia don’t work with each other. ➔ Gametic isolation: When gametes come into contact, but no actual fertilization happens. - Postzygotic: ➔ Genetic incompatibility: When genes of the parents interact in ways that reduce the viability of their offspring, it does not matter what location, can arise due to any microevolutionary process. ➔ Ecologically-dependent isolation: When a hybrid has redacted fitness between its phenotype and location, can be produced by divergent natural selection. 4. Define allopatric and sympatric with respect to the geography of populations and of speciation. - Allopatric: Happens in separate, non-overlapping geographic areas, gene flow is interrupted making populations evolve independently. The evidence is that many species have geographic ranges that are separated by geographical barriers, isolated habitats often contain endemic species. - Sympatric: Happens in separate, overlapping geographic areas, no geographical behavior, difficult to overcome the initial gene flow, is more rare to happen, can occur via strong disruptive selection. 5. Explain the different mechanisms of speciation (i.e., how/why does reproductive isolation evolve under each) and the geographic context in which each can occur. - Ecological: Happens when isolation arises due to adaptation of different habitats, can occur under any geographical context. - Polyploidization: Increases the entire set of chromosomes, can be instantaneous, happens in sympatry, common in ferns and flowering plants, type autopolyploid (from a single species), type allopolyploid (from different species) - Reinforcement: The strengthening of prezygotic barriers by natural selection due to the postzygotic barriers, can complete a speciation event, requires secondary contact 6. Summarise the technique of experimental evolution and discuss how lab experiments can employ it to provide insight into our understanding of speciation. - We study them as an ongoing process in real time. - Lab studies: Experimental evolution is a technique where multiple and replicate populations are derived from a common ancestor and their evolution is tracked under lab conditions. - Speciation in nature: Testing for ecologically-dependent postzygotic isolation, which happens when hybrid fitness is reduced due to a mismatch in phenotype and environment, can be tested via reciprocal transplant or parents and hybrids. 7. Outline conceptually how the existence of ecologically-dependent postzygotic isolation provides evidence for ecological speciation and explain how to test for this via a reciprocal transplant experiment. - For the reciprocal transplant experiment, we wanna test if hybrids between 2 populations are less fit in either parent’s environment. - Hypothesis: Hybrids will have lower fitness compared to parent populations in both environments. - If the hypothesis is supported, it proves strong evidence for ecological speciation. If not, then some other explanation should be considered. Topic 7: Systematics 1. Define systematics and its two components (taxonomy and phylogenetics). - Systematics: Science of classifying organisms and finding their relationship, evolutionary-wise - Taxonomy: Scientific discipline of naming and classifying organisms - Phylogenetics: Study of evolutionary relationships - Phylogenetic tree: A diagrammatic hypothesis of the relationship, evolutionary-wise, of different organisms 2. Write genus and species names of an organism following the Linnaean nomenclature. - Created by some scientist called Carl Linnaeus - His system groups species in a hierarchy of shared characteristics (homologous traits) (think russian nesting dolls) - Taxon: A group of any level of the classification hierarchy, different ones aren’t necessarily comparable - Uses binomial nomenclature, combines the genus and species name (unique to every species!) - Genus name has a capital and both names are italicized (underlined during final and midterm) 3. Distinguish between homologous vs. analogous traits and explain why it is important to do so. - Homologous traits: Traits that are similar due to their shared ancestry - Analogous traits: Traits that are similar due to their shared environments - Important to do so to make classification clear, simple and as close to the truth as possible 4. Explain how analogous traits can evolve. - Natural selection 5. Interpreting phylogenetic trees and inferring the evolutionary relationships based on its branching patterns. - Starting organism is called the root, most recent is called the tip - Sister taxa are 2 species that came from the same event - Every time some lines join up, it shows that that is the ancestor of those species - You can draw them in different way, proximity of taxa at the tips does not indicate relatedness - Trees are not ladders (duh.) and no taxa are more advantageous than others - Not more or less evolved - LUCA: Last Universal Common Ancestor 6. Define common terminology used in phylogenetic tree reconstruction (e.g., root, branch, tip, common ancestor, clade, mono/para/polyphyletic, taxon/taxa, sister taxa, ingroup/outgroup, etc.). - Root: Primary ancestor - Branch: A graphical representation that shows the history between species over a period of time - Tip: The most recent version of the ancestor - Common ancestor: An ancestor that one or more species come from - Clade: A group of organisms, including a single ancestor and all of his descendents - Mono/para/polyphyletic: A single group of organisms that have one common ancestor to come from, para and poly have more groups - Taxa/taxon: Represents the evolutionary relationships between a set of organisms - Sister taxa: Pairs of taxa that are closely related - In/outgroup: Out is more distantly related, in is more related, in is closer 7. Explain the basic principle of cladistics. - Cladistics: An approach to systematics where you need to know common ancestry, uses homology - Taxonomy should reflect this history of ancestors - Evidence came from the study of shared derived characters - Clades are monophyletic, but many groups are not monophyletic 8. Explain the use of morphology or molecular data in the construction of phylogenetic trees. - Phylogenies are more built from molecular data (more accurate) or from morphological data (less accurate) - Help with construction by obtaining the nucleotide sequences of the species (molecular data) - Morphology helps with addressing the phylogeny of fossils and their relationship to living species 9. Distinguish ingroups and outgroups. - Ingroup: Group of interest - Outgroup: Groups out of interest 10. Distinguish shared derived vs. shared ancestral characters. - Shared ancestral traits are traits that are directly from the ancestors of that/those species - Shared derived traits are traits that are present in the current version of the species, but absent in the ancestors 11. Define parsimony and explain how it is used in the construction of phylogenetic trees. - Parsimony is the most likely scenario of a phylogenetic tree, involves the least amount of evolutionary steps - Used in phylogenetic trees to help simplify, be more accurate (in theory) and more calculated because it takes a while for a trait to change in a species 12. Reconstruct a simple phylogenetic tree based on molecular data and following the principle of parsimony. - 13. Discuss the difference between a cladogram and a phylogram. - Cladograms show only the branching patterns without information about timing or the amount of change that has occurred - Phylograms show branching pattern and branch length that are proportional to either the amount of genetic change or the timing of the branch points 14. Explain two methods by which dates can be added to trees. - Fossils combined with radiometric dating and/or stratigraphy (study of rock layers) - Molecular clocks assumes that the rate of nucleotide substitutions per unit of time is constant for a given gene Topic 8: Tree of life 1. Describe the 7 properties of life using an organism as an example. - Cellular organization - Ability to have or make energy and metabolism - Able to reproduce - Able to have heritable traits to evolve - Able to grow and develop - Able to regulate and do homeostasis - Able to respond to stimuli 2. Justify the importance of the C, H, N, and O in organic molecules. - C: Highly abundant in the atmosphere and on Earth, bind to 4 other atoms (with carbon too), can be covalent and have multiple bonds (strong one) - All help with the making of the carbohydrates, proteins, fatty acids, nucleic acid, etc, contribute to 96.3% of all a - Without these atoms, we would never be alive. 3. Explain how specific properties of life emerged during the formation of protocells. - Protocells: Droplets with membranes that have maintained an internal chemistry that is different from its environment, not living, lack genetic material - From research, we know that they can divide, they have internal metabolism, they can grow, they can regulate through selective permeability, they respond to the environments (ALIVE) - To make protocells, we need to (1) make small organic molecules (monomers), (2) add these up into bigger molecules (polymers), (3) we then pack these into protocells (cells without some components), (4) make the origin of inheritance through transmission of self-replication - Stanley Miller’s experiment: Wanted to check the artificial and spontaneous synthesis of organic matter by mimicking the early Earth’s atmosphere and lightning, he made formaldehyde, hydrogen cyanide, amino acids and hydrocarbons - Replications showed that you could synthesize amino acids by simulating volcanoes - Formation of molecule: From monomers into oligomers or polymers, we need precursor molecules, thermal energy and a catalyst 4. List some advantages of ribonucleic acid molecules for the emergence of life. - RNA has all 4 organic atoms (C, H, N, O), can be found as ribozymes, can copy themselves, natural selection can favor them, constitute inheritance, creates evolution 5. Explain how the fossil record can provide evidence for the evolution of organisms. - Helps us understand the evolutionary relationships between organisms - Helps find similarities (morphologic, anatomic or genetic sequencing) - Gives us tree topology - Fossils belong to species that have changed or gone extinct - Helped with first cells (prokaryotes), increasing of O2 concentration in atmosphere, endosymbiosis, sexual reproduction, multicellularity and colonization of land 6. Compare two methods used to date fossils. - Biostratigraphy: Determines the relative age, imprecise and usually inaccurate, from sedimentary rocks, looks at wide geographical distribution and specific habitats with large morphological diversity, often well preserved - Radiometric dating: Determines the absolute age, much more precise, from magnetic rocks, uses changes of isotope composition - Faunal succession helps with this because it gives a specific vertical sequence of fossilized flora and fauna that can be later identified - Specific fossil compositions help to define biozones (intervals of geological strata) - For radiometric dating, we look at the atmosphere (has equal composition of C12 and C14), when an organism dies and it doesn't make CO2 anymore, the C14 will decay into an isotope (N14) at a constant rate, C12 will stay for the fossil - Half-life: Amount of time it takes for 50% of the parent isotope to decay into its daughter isotope 7. Describe how the Burgess Shale has contributed to our understanding of the evolution of animals. - Burgess Shale is a paleontological site in BC where many sediments were found, found different lifestyles (benthic (on sediments), endobenthic (in sediments), nektonic (in water)), helped with a huge chunk of our fossil, evolution and animal knowledge - We found evolutionary success of bilateral symmetry with anterior sensing organs (nervous system), anterior predation appendages (prey capturing and feeding) and posterior appendages for movement - Found adaptive radiation: Periods of change where groups of organism form many new species where adaptations allow them to survive anywhere 8. Define mass extinction, and provide an example. - Mass extinction: When a large number of species become extinct - Can be caused by changes in temperature, meteorites, volcanoes, etc. - Always followed by a new adaptive radiations and many new families - Examples: Permian extinction, we lost 96% of all species, followed with hotter temperatures and CO2 levels and lower oxygen levels / Paleogene, all dinos left us, lost 75% of species 9. Define adaptive radiations, and provide an example. - Adaptive radiations are processes where organisms diversify quickly from an ancestral species into many new forms, think of the Darwin finches 10. Analyse graphical data to infer major changes in taxonomic diversity. - 11. List different characteristics of L.U.C.A. - All organisms synthesize and use only Left optical isomers of amino acids - Genetic code is universal - LUCA wasn’t the first living thing, but simply the one that we know of today (there could be one farther) - 355 genes were present in LUCA - Likely lived near deep-sea vents, was deprived of O2 but rich in CO2 and H2 12. Name characteristics that differ between the 3 domains. - Bacteria - Archaea - Eukarya 13. Give examples of organisms for each of the 3 domains. - Mitochondria or gram-positive bacteria - Euryarcheotes or crenarcheotes - Plants or algae or animals (us!!) 14. Explain the evolution of eukaryotes from endosymbiosis. - Endosymbiosis is a symbiotic relationship where one organism lives inside of another - Eukaryotes were possible (in theory) by genome fusion, via endosymbiosis, with archaea and bacteria, to have made a eukaryote 15. Explain the evolution of multicellularity. - The first known organism appeared 3.5 billion years ago, first multicellular appeared 600 million years ago - We start with cell proliferation (increasing the number of cells), then cell specialization (giving a specific function to a cell), then cell interaction (interacting with other cells), then cell movement Topic 9: Prokaryotes 1. Differentiate bacteria and archaea based on morphological and anatomical characteristics. - Bacteria: Lack histones (proteins), cell wall made of peptidoglycan - Archaea: Contain histones, cell wall made of pseudomurein 2. Classify specific structures into Gram (+) and Gram (-) bacteria. - Gram-negatives tend to be more resistant to antibiotics (the outer membrane blocks water-soluble [by proteins] antibiotics), appear pink/red when stained - Gram-positives only have their plasma membranes and their cell walls, negatives have another cell membrane on top of the cell walls, and positives appear purplish 3. Defend the importance of bacteria using quantitative or qualitative examples. - Bacteria play a HUGE portion in our body and making sure that it functions correctly - Helps with abundance and diversity in the microbiome (community of microorganisms) in the human body - Commensalism: Symbiotic relationship where another organism benefits from another (without harming it) - Humans are chemoheterotrophs (get energy from chemical compounds) 4. Classify organisms based on nutritional requirements. - Organisms can be classified into phototrophs (eat light) or chemotrophs (eat chemical compounds) - If the carbon source is organic: photoheterotroph or chemoheterotroph, it is inorganic: photoautotroph or chemoautotroph 5. Provide arguments for the importance of prokaryotes in the ecosystem. - They help absorb energy from outside the ecosystem - Photoautotrophs can convert carbon dioxide into sugars that enter the food chain, produce oxygen used by chemoheterotrophs during respiration, fix atmospheric N2, and produce proteins/nucleic acids - Helps to assimilate minerals into biomass that is passed on to the upper trophic levels, recycles elements to be used again 6. Explain how cellular mechanisms in bacteria can influence populations' dynamics and evolution. - They go through asexual reproduction (binary fission), requiring the replication of the genome, the 2 daughter cells are clones of the mother, exponential growth curve - Lag phase: The synthesis of the components needed for growth - Log phase: Rapid growth through cell divisions by a factor of 2^n - Stationary phase: Population stops to grow (lack of things), activates stress response - Death phase: Exponential loss of viability due to lack of things 7. Describe mechanisms that can lead to the evolution of antibiotic resistance. - Mutations alter gene coding for proteins that the antibiotics target (genetic variation) - Resistance can be transmitted vertically through inheritance (heritability) - Only the resistant strains can grow (selection) - At this point, antibiotics are synthesised to inhibit new cellular targets 8. Explain three processes that can lead to the formation of a recombinant bacteria - Conjugation: When bacteria from the same species donate DNA to others, happens when two cells are connected through a pilus (that shortens the distance between them), establishes a mating bridge, gives off a plasmid (small circle of chromosomes) that is transferred, F factor (fertility factor contains genes that make this pilus), selfish DNA is DNA that enhances its own transmission, genes that carry the R plasmid confer antibiotic resistance - Transduction: Exchanging DNA through a virus (bacteriophage) (we saw this in high school) - Transformation: Release of DNA (after the cell death) that is taken up by another bacteria directly from the extracellular environment, occurs naturally, used in molecular biology lab to make new strains and clone a gene, used for COVID-19 vaccine Topic 10: Eukaryotes 1. Compare prokaryotes and eukaryotes based on cellular characteristics. - Eukaryotes have multiple cells, they have a nucleus and genome, originate from a common ancestor that did endosymbiosis, tend to be bigger on average - Prokaryotes are the opposite. 2. Associate cellular structures of eukaryotes with their functions. - Has a plasma membrane, which is a selective barrier with the environment - Has cytoplasm, which is basically everything but the nucleus, contains cytosol (internal fluid), organelles and inclusions (particles of insoluble substances) - Has a nucleus, which contains the genetic information, made of chromatin - Has ER (a membranous network), contained of rough ER (filled with ribosomes and makes proteins) and smooth ER (no ribosomes, makes lipids, carbohydrates, metabolism, steroids, etc) - Has a Golgi apparatus, which gets proteins and modifies them (adding sugars or removing things), prepares proteins for their job, modify the phospholipids - Has a mitochondria, which performs cellular respiration - Has a cytoskeleton, which is a network of microtubules, microfilaments and intermediate filaments, can send important signals for cell life - Has peroxisome, which is an oxidative organelle that transfers hydrogen from substances into oxygen, makes H2O2, a cleaning organelle - Has lysosome, which is a digestive organelle - Has a flagellum, which is a long cellular appendage that is used for locomotion 3. Justify why the evolution of multicellularity and sexual reproduction were key innovations. - This helped make life as diverse as it is - Helped create many efficient species, with large diversity in nutrition and reproduction - Also helps with life cycles 4. Explain the benefits of both sexual reproduction and asexual reproduction. - Disadvantages: Takes time and energy to look for someone, the individual starts to dilute over time, reproductive output is decreased by half - Advantages: New genetic combos that can be beneficial for changing environments, eliminate deleterious alleles (can speed adaptation) 5. Place on a life cycle the ploidy level (n or 2n), mitosis, spores, meiosis, gametes, fertilization, zygote. - A life-cycle is a sequence of stages in the reproductive history of an organism, has a haploid phase and a diploid phase - Can be a diplontic, haplodiplontic or haplontic - MAKE SURE TO BE ABLE TO DRAW THE LIFE CYCLES ON THE MIDTERM 6. Differentiate between the three types of life cycles. - 7. Name examples of protists. - Diatoms: Unicellular algae with hard walls made of silica - Plasmodiums: Parasite that causes malaria, comes from mosquitos - Dinoflagellates: Have 2 flagella, can have explosive population growth - Myxomycetes: Unicellular, can be cut into many pieces, can learn and move, almost immortal, over 720 sexes - Fungi and yeast does both asexual and sexual reproduction 8. Explain the heterozygote advantage against malaria for individuals that have sickle cell anemia. - Those who have sickle cell anemia have a higher chance of survival against malaria - This is because it stops the parasite from inhibiting the host - It gives a heterozygote advantage and a higher frequency of the ‘S’ allele in those regions 9. Draw mutualistic beneficial relationships between a fungus and a plant, or between a fungus and an algae. - Fungi gives water, protection and minerals to the plants - Plants give sugars to the fungi Topic 11: Evolution of plants 1. Identify the main plant groups based on key characteristics. - They are eukaryotes, multicellular, embryophytes, and photoautotrophs. - They also have cell walls made of cellulose, chloroplasts with chlorophylls with beta-carotenes and xanthophylls. - They go through sexual reproduction and asexual reproduction (more common) - The embryo developed is dependent on the parent. - They were the first photosynthetic organisms that lived only on land. 2. Place the main plant groups on a phylogenetic tree. - There can be flowers, fruits, trees, bushes, etc. 3. List physical, chemical and biological problems faced by plants during land colonization; and their solutions. - If living above the water line (problems): Dry environment Strong gravity effect No nutrients in the atmosphere Rapid changes in temperatures - If living above the water line (advantages): Brighter sunlight, unfiltered water and phytoplankton More CO2 in the atmosphere than in the water Abundance of nutrients on the shore lines - Adaptations made: Protection of spores, gametes, zygotes, embryos Maximizes photosynthesis Growth can compensate the lack of movement towards resources 4. Explain the causes and consequences of indeterminate growth. - Indeterminate growth: Plant growth where the main stem continues to elongate indefinitely without being limited by a terminal inflorescence or other reproductive structures. - Can respond to the environment, maximizes exposure to nutrients, water, sunlight and CO2 - Happens when most individuals don’t survive long enough to reach zero growth or if the reproduction occurs before zero growth occurs. - Consequences are increased survival and reproduction, phenotypic plasticity (how well organisms cope with stress), competition between vegetative and reproductive growth, variable maturing times or demographic consequences. 5. Explain the expression “reduction of the gametophyte”. - This refers to the evolutionary trend in plants to have a smaller and less independent gametophyte generation. - The gametophyte is a haploid generation and the sporophyte is the diploid generation. In most plants, the sporophyte is more dominant. 6. Associate a plant structure with its ploidy level. - Ploidy level is the number of chromosomes sets in a plant’s somatic cells. You can find this by counting the number of chromosomes in cells under a microscope. You can also estimate this by comparing the number of chromosomes in a reference sample with DNA content. - In diploid plants, guard cells have a ploidy level of 2C, tetraploid plants have a level of 4C, octoploid plants have a level of 8C. - Pavement cell area increases with ploidy levels. - Polyploid plants tend to have larger leaves, stems, roots and flowers. 7. Provide arguments for the importance of vascularization in plants. - Vascularization is the presence of lignified tissues that transport water, nutrients and sugars through the plant. - Helps with structural support (allows plants to grow larger), nutrient and water delivery, long-distance communication with the plant and coordination of physiological and developmental processes 8. Explain the advantages of heterospory in plants. - Heterospory is the production of 2 different-sized spores in the same plant. - Increases the likelihood of getting successful offsprings - Helps with reproductive control (controls size of gametophyte) - Helps with natural selection by producing more variations - Leads to more outcrossing or mixing around - Helps with shared habitats and nutrient reservation 9. Justify the evolutionary importance of five key innovations in plants. - A really reduced gametophyte (microscopic) is protected from environmental stressors, from UV and from desiccation, and is directly nourished from the sporophyte. - Ovules are a structure that contains the megaspore, which fertilizes without needing much water from the environment. - Seed plants are heterosporous, either microspore (female, can disperse farther) or megaspore (male, nourishes the developing embryo). - Pollen grain is in microspores (since they are enclosed in a pollen wall), which can travel very far. - To make a seed, we have to increase the survival of plants during the reproduction and make sure the embryo is nourished and can resist droughts or low temperatures. 10. Contrast key characteristics of gymnosperms and angiosperms. - Gymnosperms: Have unprotected seeds, usually pollinated by wind, don't have flowers, don't go under double fertilization, used for decorations or ornaments. - Angiosperms: Have protected seeds (in the ovaries and surrounded by fruit), can be pollinated by wind or animals, have flowers, go under double fertilization, more diverse growth habits and ecological roles, have conducting tissues, used for paper and plywood and lumber. 11. Explain the process of double fertilization and its biological importance. - Double fertilization is a process that happens in angiosperms, that involves the fusing of two sperm cells with different parts of the same plant’s female reproductive cell. - Important because it restores the plant’s diploid state, initiates seed development and stimulates the plant. Topic 12: Evolution of animals (part 1) 1. List and define characteristics that are shared by all animals. - They have molecules of cholesterol (only produced by animals). - They are multicellular and soft-bodied eukaryotes. - They are heterotroph (with some exceptions like a kleptoplast), breathe oxygen with aerobic and oxidative respiration. - They can move, reproduce either sexually or asexually, organized tissues by cells. - They develop through the blastula stage (a cavity made of cells), no cell wall (but thy do have an extracellular matrix) 2. Demonstrate how genetic data can help determine the position of animals within the phylogeny. - When we build phylogenetic trees, we need to classify them by order of evolutionary traits. - Knowing the data of the species can help by limiting down which species are missing a certain trait. - This creates the order of the phylogenetic tree. 3. Identify various modes of asexual reproduction in animals. - Budding: Happens in jellyfish, when a new organism develops from a bud of an already existing organism. - Fragmentation: Happens in sponges and flatworms, happens when the body of the organism is chopped up, each part turns into another organism. - Parthenogenesis: Happens in zebra sharks, happens when the female can produce an offspring from an unfertilized egg. 4. Justify the benefits of bilateral symmetry. - Gives more mobile directional movement, keeps the balance in the organism, allows for both females and males. 5. Explain how homeotic genes can affect the resemblance between different animal body plans. - Controlled by Hox genes (control more that 100 genes), they control the placement and spatial organization of body parts by controlling the developmental fate of group cells - They create the order of genes and that somehow relates exactly to the order of working on the body 6. Define key words in animal embryogenesis and development. - Cell divisions can undergo either: Spiral cleavage: Get an oblique axis of the body (more twisted) Radial cleavage: Get a parallel axis of the body Determinate cleavage: Each cell defines a specific part of the embryo (don’t remove the cells!!) Indeterminate cleavage: Each cell has the potential to make a complete embryo - Gastrulation is the formation of a gastrula (embryonic tissues that will develop into adult body parts) through infolding. - Those with radial symmetry have ectoderm and endoderm (diploblastic), and can form the jaws, teeth, pituitary gland, nervous system and the epidermis system. - Those with bilateral symmetry also ectoderm and endoderm with mesoderm (triploblastic). - Ectoderm can form the jaws, teeth, pituitary gland, nervous system and the epidermis system. - Mesoderm can form the musculoskeletal system, circulatory system, adrenal cortex and more. - Endoderm can form the thyroid and epithelial linings. - The infolding of the neural plate forms the neural tube and many other nervous system functions - Notochord is a dorsal and longitudinal rod along the axis of a chordate, helps with structural support 7. Associate each embryonic tissues with the organs they form. - Archenteron represents the primitive gut (external environment) - Blastopores represent the opening of the archenteron, forms the mouth (by protostomes) and the anus (deuterostomes) 8. Illustrate differences between the development of protostomes and deuterostomes. - Protostomes: Develops in spiral and determinate, solid masses of mesoderm split and form the coelom, forms the mouth - Deuterostomes: Develops in radial and indeterminate, forms the archenteron from the coelom, forms the anus - Coelom: The cavity lined by tissues derived from the mesoderm between the digestive tract and the outer body layer, helps with structural support, transport and diffusion, allows growth of organs, lost in some triploblastic animals 9. Calculate, compare and explain the consequences of different surface-to-volume ratios. - This ratio influences heat conservation, metabolic activity and exchanging. - As the ratio decreases, the size of the organism increases, the surface area is proportionally smaller and heat loss is decreased. 10. Define the different modes of thermoregulations. - Endothermy: For animals that generate their own body heat internally, mostly through metabolic processes. Shivering: Involuntary muscle contractions to generate heat Non-shivering thermogenesis: Increase of metabolic activity to generate heat Vasodilation/constriction: Adjusts blood flow to help with heat loss or heat retention - Ectothermy: For animals that rely on external factors for temperature regulation. Behavioral thermoregulation: Moving between the sun and shade, burrowing, basking in the sun Postural adjustments: Changing the body orientation to maximize or minimize exposure to heat - Heterothermy: Animals that have characters of both endothermy and ectothermy. Daily heterothermy: Organisms that may drop their temperature at night and rewarm during the day Seasonal heterothermy: Organisms that lower their body temperatures due to seasons changing - Poikilothermy: For animals whose body temperature changes with the environmental pressure. 11. Determine the modes of thermoregulation based on graphical data. - Endothermy: Body temperature remains constant, even with external temperatures changing. - Ectothermy: Body temperature closely tracks the external temperature, if one increases, so does the other. It shows that the body temperature is not regulated. - Heterothermy: Body temperature can either be constant or fluctuating, look at time of day or season for indication. - Poikilothermy: Body temperature fluctuates in direct relation with the external environment. 12. Explain and provide examples of adaptations in response to physical/physiological problems that animals face on land. - Water conservation: Waterproof exoskeletons: Many terrestrial arthropods, like insects, have waxy and waterproof exoskeletons that help reduce water loss. Concentrated urine: Many terrestrial animals, like reptiles and birds, have evolved to excrete highly concentrated urine to minimize water loss. Behavioral adaptation: Some animals avoid water loss by being nocturnal or burrowing underground to escape heat and dry air. - Temperature regulation: Insulating fur or feathers: Mammals and birds have developed thick fur or feathers that provide insulation, to help retain body heat in cold conditions, like polar bears. Behavioral thermoregulation: Many animals adjust their behavior to regulate their body temperature, like lizards that bask in the sun. Evaporative cooling: Mammals and birds use sweat or panting to cool down in hot environments, like the African elephant. - Structural support: Limb modifications: Land vertebrates evolved stronger and more supportive limbs, like giraffes. Exoskeletons: Terrestrial arthropods, like grasshoppers and beetles, have rigid exoskeletons made of chitin that provides support against physical stress. Vertebral column: Mammals and reptiles have strong spines with specialized vertebrae that provide support against the force of gravity, like camels. - Respiration: Lungs: Most terrestrial vertebrates have evolved lungs, which are adapted to extract oxygen from air rather than water, like humans. Tracheal systems: Insects have developed a network of tubes called tracheae, which delivers oxygen to tissues. Breathing mechanisms: Many terrestrial animals, like amphibians, have created specialized breathing mechanisms. - Reproduction: Amniotic egg: Some animals, like sea turtles, lay eggs with a protective amniotic membrane that prevents desiccation. Internal fertilization: Most terrestrial animals have this, like mammals, where fertilization occurs inside the female’s body, protecting the eggs or embryos from environmental threats. - Locomotion: Specialized limbs: Land animals have specialized limbs that help them move effectively on land, like cheetahs have longer legs and flexible spines to get them to run faster. Muscle power: Many animals, like kangaroos, have powerful hind limbs for hopping, which helps conserve energy. - Sensory adaptation: Eyesight: Many land animals, like eagles, have evolved with better eyesight for large distances or low light. Hearing: Many land animals, like owls, have adapted their hearing to be more directional. Topic 13: The evolution of animals (part 2) 1. Define key characteristics of invertebrates. - Have no backbone (spine), 95% of all known species, many traits that have been lost, evolved from deuterostome invertebrates. 2. Classify invertebrate organisms into clades based on embryological or anatomical characteristics. - Porifera (sponges): Is diploblastic, have radial symmetry, sessile (don’t move) and no true tissues. - Ctenophora: Are diploblastic, have radial symmetry, contain a sensory epidermis and a networked nervous system. - Cnidaria: Are diploblastic, hav radial symmetry, contain a sessile polyp and a swimming medusa, have a hydrostatic skeleton with a gastrovascular cavity contraction. - Ecdysozoa: Produce an exoskeleton that is periodically molted (helps grow the animal), made of proteins and chitin, segmented in functional units, presence of ganglions (clusters of nerve cell bodies). - Lophotrochozoa: Contain a lophophore (crown of tentacles around the mouth) or a trochophore (a specific larvae stage). - Echinodermata: Have bilateral symmetry, is a deuterostome, has a water circulatory system. - Chordata: Has a notochord and muscles that attach to it, a dorsal nerve cord, have pharyngeal slits behind the mouth and a post-anal tail Cephalochordates: Feeds through filtration in the pharynx, has lateral movement for locomotion Urochordates: Have a larva evolved the ability to reproduce before metamorphosis, loss of 4 hox genes. 3. Place the evolution of body symmetry and the embryological formation of the mouth on a phylogeny. - Body symmetry: Basal organisms (like sponges) lack symmetry entirely. Then, radial symmetry evolved in Cniaria and Ctenophora because they are sessile and free-floating. Then, the rest of the groups evolved with bilateria. - Mouth: Happens with bilateria, protostomes have blastopore that develop into the mouth, deuterostomes have an anus that then forms a tube and a mouth. 4. Justify the importance of the notochord in the evolution of vertebrates. - It provides structural support, maintains body shape and rigidity. - Plays a vital role in the development of the central nervous system, forming the neural tube which becomes the brain and the spinal cord. - Is the precursor to the vertebral column in vertebres. - Allows for axial movements and flexibility. - Is an important factor in diversity and organization of species. - Helps guide the development of other organ systems, like the digestive and circulatory systems. 5. Organize the key innovations of vertebrates on a phylogeny. - Vertebrates: Have a skeletal system formed by a vertebral column, have muscle attachments, a solidification of vertebrae and a duplication of hox genes. Cutostomes: Missing jaws (has a circular mouth), can be parasites of fish, have a cartilaginous skeleton without collagen. Gnathostomes: Have jaws, have a mandibular arch and a hyoid arch, have anterior gill slits, contain mineralization of the skeleton, duplication of hox genes. Chondrichthyes: Skeletons made with cartilage, have placoid scales, can go through oviparous (egg laying and hatching externally), ovoviviparous (embryo feeds from the egg yolk and hatches in the uterus), viviparous (embryo feeds from the placenta of mother). Osteichthyes: Bones made of calcium phosphate, have a dorsal swim bladder filled with gas, have lungs, are oviparous, can be ray-finned or lobed-finned. Dipnoi: Has functional lungs, has gills, can crawl in the mud, and has a resistance to being dry. - Tetrapodes: Have four limbs, live on land, can go against gravity, can breathe and hear, has a resistance against the dry and has a vascular system with lungs and organs. Amphibians: Have an aquatic larvae stage, goes through metamorphosis, has a terrestrial predator adult stage Amniotes: Has an insulation during embryo development and ventilation, has chorion (outer-membrane), has amnion (surrounds the cavity), has allantois (surrounds disposal sac), has a yolk sac (stock of nutrients). Reptiles: Has dry skin with scales, are ectothermic, have better locomotive abilities Birds: Are reptiles and dinosaurs, contain feathers, no bladder, one ovary, small gonads, a high metabolic rate, no teeth, a light skeleton. Mammals: Have mammary glands (makes milk), endothermic, has a large forebrain with learning abilities, has different teeth for specific functions, have hair and a fat layer, have kidneys Primates: Have opposable thumbs, large brain and short jaws, takes care of young and shows social cues, three-dwellers, overlapping visual fields. Humans: Walks on 2 legs, reduced jaw bones, short digestive tract, complex brain power. 6. Associate key innovations of vertebrates with the names of the clades they define. - Vertebral column (spine), defines Vertebrata - Jaw (Jaws and Teeth), defines Gnathostomata - Paired fins, defines Gnathostomata - Bony skeleton, defines Osteichthyes - Swim bladder, defines Osteichthyes - Lobed fins (with internal structure), defines Sarcopterygii - Tetrapod limbs (with digits), defines Tetrapoda - Lungs for respiration, defines Tetrapoda - Amniotic egg (with protective membranes), defines Amniota - Waterproof skin (keratinized), defines Amniota - Internal fertilization, defines Amniota - Endothermy (warm-bloodedness), defines Aves and Mammalia - Feathers, defines Aves - Mammary glands, defines Mammalia - Placenta (live birth), defines Eutheria 7. Describe how gill arches and rods have evolved in vertebrates. - Gill arches: In early vertebrates, gill arches were cartilaginous/fibrous structures that help support the gills for respiration. Then, when the gnathostomes came in, they had a first pair of gill arches that turned into jaws. The second pair became middle ear bones. Then, things evolved from there. - Gill rods: This started off as diffusion for gases between H2O and the bloodstream. It remains in the fish, but evolved out of the land animals. 8. Explain how specific structures found in the early tetrapods allowed vertebrates to colonize land. - Limbs with digits: They helped with supporting the body against gravity and walking/crawling. - Sturdier skeleton: Helps resist gravity and hold the body upright. This also helped transfer weight from the limbs to the rest of the body. - Lungs and enhanced breathing mechanisms: Helps adapt to breathing in the air and getting oxygen in low-oxygen water. - Desiccation-resistant skin (keratinized): Helps with protecting tetrapodes from drying out, reduces water loss and helps with cutaneous respiration. - Ear structure (tympanum and middle ear): Allows tetrapods to hear airborne sounds, detecting environmental cues and communication. - Excretion and osmoregulation (kidneys): Helps form urine with minimal water loss and store waste before excretion. - Reproductive adaptation: Helps with reproduction on land. 9. Organize the key innovations of tetrapods on a phylogeny. - Sarcopterygii: They have lobed fins with digits, rudimentary lungs, a neck and robust pectoral fins. - Acanthostega: They have limbs with digits and a stronger pelvic girdle. - Ichthyostega: They have fully formed limbs with digits, a stronger vertebral column and lungs. - Amphibia: They have moist skin, lungs, a dual life cycle and permeable skin. - Amniota: They have an amniotic egg, waterproof skin, internal fertilization and efficient kidneys. - Eurapsida: They are endothermic, have feathers, larger body sizes and highly efficient lungs. 10. Associate key innovations of tetrapods with the names of the clades they define. - Lobed fins with digits, defines Tetrapoda - Sturdier skeleton and robust limbs, defines Tetrapoda - Neck (head mobility), defines Tetrapoda - Lungs, defines Tetrapoda - Limbs with digits for terrestrial locomotion, defines Stegocephalians - Amniotic egg, defines Amniota - Keratinized and waterproof skin, defines Amniota - Internal fertilization, defines Amniota - Endothermy, defines Aves and Archosauria - Feathers, defines Aves 11. Classify adaptations based on the physical or chemical challenges faced by tetrapods on land. - Gravity and support: We adapted with a sturdier skeleton, limbs with digits and with pelvic and pectoral girdles. - Desiccation (water loss): We adapted with keratinized skin, an amniotic egg and efficient kidneys. - Respiration: We adapted with proper lungs, a rib cage and a diaphragm. - Reproduction: We adapted with getting internal fertilization, an amniotic egg and parental care. - Thermoregulation: We adapted with being endothermic or ectothermic and having insulating structures. - Locomotion: We adapted by getting limbs with digits and a flexible spine. - Sensory adaptations: We adapted with eyes and vision, and ears and hearing. 12. Define and identify exaptations. - Exaptation: A feature or trait that originally evolved for one purpose, but later became co-opted for a different function. - Examples: Feathers in birds: Was for insulation, but became for flight. Limbs in tetrapods: Was for stabilization and maneuverability, but became limbs with digits. Human larynx: Was for breathing and feeding control, but became for speech and vocal communication. Eyes in the ocella of some invertebrates: Was for detecting light and dark, but became complex eyes. Mammalian middle ear bones: Was in the jaw structure, but became the middle ear bones. Topic 14: Biosphere and Ecology 1. Determine which abiotic factors influence the presence of species in certain ecosystems and biomes. - Abiotic: Physical and chemical properties in the environment of organisms. - Climate: Temperature: Dictates the metabolic rates of organisms and limits the range of temperature-sensitive species. Precipitation: Determines water availability, influencing vegetation types and animal populations Sunlight: Impacts photosynthesis in plants and the energy availability for entire ecosystems. - Soil and substrate: Nutrient content: Soil fertility affects plant growth, herbivores and predators in the food chain. pH levels: Acidic, alkaline or neutral soils can restrict certain plant species. Texture and structure: The soil’s ability to retain water and provide support, influences vegetation types. - Water availability: Freshwater vs Salinity: Species are adapted to specific salinity levels. Hydrology: The availability and movement of water shape ecosystems. - Atmospheric conditions: Oxygen levels: Impacts aquatic species. Carbon dioxide levels: Influences photosynthetic rates in plants and aquatic algae. Wind: Affects seed dispersal, evaporation rates and microclimates. - Topography: Altitude: Higher altitudes typically have a colder temperature and lower oxygen levels. Slope and Aspect: Influences sunlight exposure, soil erosion and water drainage. - Disturbances: Natural events: Fires, floods, hurricanes and volcanic activity can reset ecosystems. Seasonality: Seasonal variations in temperature, precipitation and resource availability. - Chemical composition: Salinity: Limits species to specific osmotic tolerances. Toxins and Pollutants: Naturally occurring or anthropogenic chemicals can exclude sensitive species while favoring tolerant ones. - Availability of space: Habitat size: Determines carrying capacity and niche availability. 2. Associate biological structures, patterns or mechanisms with a specific level of ecological research. - Organismal ecology: Focuses on individual organisms and how they adapt to their environments. Bio structures: Morphological adaptations Patterns: Behavioral responses (migration or hibernation) Mechanisms: Physiological responses (thermoregulation, osmoregulation, photosynthesis) - Population ecology: Focuses on dynamics of populations in a single species. Bio structures: Reproductive organs and strategies Patterns: Population growth models Mechanisms: Competition, predation and reproduction affecting population size and genetic variation. - Community ecology: Focuses on interactions among species in a shared environment. Bio structures: Defensive structures (spines on cacti) and mutualistic adaptations (flowers and pollinators) Patterns: Predator-prey cycles or species richness gradients Mechanisms: Niche partitioning, resource competition and trophic interactions. - Ecosystem ecology: Focuses on energy flow and nutrient cycling within ecosystems. Bio structures: Primary producers and decomposers. Patterns: Biogeochemical cycles. Mechanisms: Energy transfer through trophic levels and decomposition processes. - Landscape ecology: Focuses on interactions and exchanges across ecosystems in a landscape. Bio structures: Habitat corridors or patchy vegetation that influence species movement. Patterns: Spatial distribution of ecosystems. Mechanisms: Dispersal, habitat connectivity and edge effects. - Global ecology: Focuses on the planet-wide scale of ecological processes. Bio structures: Biomes shaped by dominant vegetation types. Patterns: Global climate patterns and biodiversity hotspots. Mechanisms: Climate regulation by carbon sequestration in forests and oceans. 3. Explain how and why abiotic factors can differ between two distinct habitats. - They can change in temperature. This differs because proximity to the equator, altitude, and vegetation density influence heat absorption, retention and dissipation. - They can change in water availability. This differs because regional climate patterns like wind circulation and mountain rain shadows or consistent

Learning Objectives: Biology 1130

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