EEOB 3310 Exam 2025

EEOB 3310 Exam 2025 What is Scientific Inquiry? - -Deliberate and hypothesis-driven investigation into something that has already happened. Even 'discovery-based' scientific inquiry uses what is known to predict the identification of something new but related to that known phenomenon. Scientific Method - -1) Observation 2) Hypothesis 3) Experimental Design + Implementation 4) Data Analysis 5) Conclusion Carefully designed experiments to test well-reasoned hypotheses can yield information rich data that, if analyzed with appropriate statistical methods, support or refute hypotheses that inform subsequent conclusions that then can inform careful design of experiments to test well-reasoned hypotheses...etc. Evolution: Defined Over Time - -...development of an individual, from the Latin word meaning 'unrolling', Albrecht von Haller (18th cent.) ...preformation, Charles Bonnett (18th cent.) ...transformation of a species/population, Robert Grant, Charles Lyell, and Charles Darwin (19th cent.) ...descent with modification (19th-20th cent.) Biological evolution explains the forces, and their impacts, that give rise to heritable modifications over time within species. Evolution As A Science - -Can experiments be designed and performed that demonstrate the evolution of a species? YES! Evidence: -Surveys of moth collections over time -Predation rates -Genetic testing -Experimental manipulations -Policy examinations -Experimental (Antibiotic resistant bacteria) -Epidemiological (Antibiotic resistant bacteria) -Genetic testing, behavioral, anthropological EEOB 3310 EEOB 3310 Evolutionary biology derives evidence from many disciplines for supporting or refuting hypotheses about biological phenomena. Evolution As A 'Theory' - -Is Evolution a Theory or Fact? It is both. But that answer requires looking more deeply at the meanings of the words "theory" and "fact". A 'theory' colloquially refers to opinion or speculation, often a conclusion based on speculation or inconclusive evidence. A formal scientific theory is 'a comprehensive explanation of some aspect of nature that is supported by a vast body of knowledge'. Examples: Cell theory; heliocentric theory; theory of gravity; germ theory A formal scientific theory can be used to make predictions. Examples: movement of the moon; disease transmission; transitional forms between fishes and limbed terrestrial animals in sediments 375Myo. A 'fact' in science refers to a 'scientific explanation that has been tested and confirmed multiple times that there is no longer a compelling reason to keep testing it'. Abundant data collected from across many fields about many species all supports the existence of biological evolution...and WE will examine this evidence throughout this course. What 'Evolves'? - -Individuals can be acted on by 'evolutionary forces', like natural selection, but it is the population of individuals, each with variable reproductive success, contribute to each generation of a species...and how each generation changes, dramatically or subtly, reflects how the species evolves. Individuals that survived long enough to have offspring passed those traits on to the next generation, and those individuals represented the species. Living at high-altitudes for prologued periods can lead to diminished health and low birth rates due to low oxygen availability (hypoxia). Tibetian and Andean populations have exhibited mutations around genes that are linked to survival at elevated altitudes that aren't common in populations residing at low altitudes. The frequency of these mutations are much higher in Andean and Tibetian human populations than in... EEOB 3310 EEOB 3310 Individual peppered moths did not change but the frequency of different phenotypes changed over time due to evasion success. Therefore, the population of peppered moths changed over time. The Best Traits Are Only 'The Best Under Current Conditions' - -Huntington's Disease: -neurodegenerative disorder affecting muscle coordination and cognitive ability. -onset in 35 yo. -persists because it doesn't show up until later in life, post-reproductive maturity. -Protein components associated with the disease are associated with lower cancer and tumor rates. -People with Huntington's disease also have higher fecundity. 18th Century--Evolution As Progress! - -Transmutation is the improvement through human effort. Blending of social views and scientific speculations. No great abundance of empirical evidence (e.g. fossils, comparative anatomy, genetics, etc.) to refute or support transmutation. 19th Century-Lamarckism - -Marine invertebrate and botanical taxonomist. Transmutationalist; change is inherently good. Spontaneous generation. Organisms 'ascend' levels of improvement over time in an upward-rising 'Chain of Being'. Extant forms aren't related but reflect various stages of progress. Inheritance of acquired characteristics. Mechanisms unknown at the time. (Modern giraffes had long-necked ancestors 25Mya.) Foreshadowed environmental epigenetics to a degree. Epigenetics is the study of how changes in organisms by the modification of gene expression genetic code itself. Environmental epigenetics focuses on whether or not factors external of the organism can drive the emergence, stabilization and maintenance of changes in gene expression. 19th Century Pre-Evolutionists - -Immanuel Kant was hostile to evolutionary theory, but Georges Cuvier reflected optimal adaptation as fundamental and the periods between as ultimately maladaptive. Foreshadows adaptive landscape theory. 19th Century Natural Selection - -Reverent Malthus' reflections upon population growth outstripping resource availability leading to the 'struggle for existence'. Alfred Russell Wallace. Inspired by Malthus to propose natural selection as the "long-sought-for law of nature that solved the problem of the Origin of Species". EEOB 3310 EEOB 3310 Wallace inspired Darwin to (finally) publish his ideas. Charles Darwin () - -Inspired by Charles Lyell's extensive geological examinations. Gathered considerable empirical data while on HMS Beagle (5 years). -fossil data: ground sloth, mastodon and horse teeth. --extinctions, ecological changes. -minerology/geology: volcanoes yielding different 'species' of rock reflecting current, dynamic processes. -movement of landmasses. -morphological data: separate, original generation or common origin with recent adaptations. -John Gould hypothesized the finches were of the genus... -Impact of geographic isolation, foraging behaviors suggests the latter. Framing Origin of Species - -Darwin used animal breeding (artificial selection) to introduce the idea of natural variation and how specific varieties could be favored under given conditions. Origin of Species - -Malthusian thought was integrated as 'struggle for existence' that drives the fixation of natural variants that lead to better individual survival and reproductive success (sexual selection)! Origin of Species--The Tree Analogy - -"As buds give rise by growth to fresh buds, and these, if vigorous, branch out and ovretop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fill with its dead and broken branches the crust of the earth and covers the surface with its ever branching ramifications." Initial Criticisms of Origin - -Mivart's "half a wing"--the adaptive value of intermediate forms--incipient forms of complex features couldn't have adaptive value and thus would be under negative selection. Unambiguous age of the Earth -Dr. John Lightfoot calculated a ~4,000 y.o. Earth. Lord Wm. Thompson Kelvin asserted that the planet would cool from its primitive state at a constant rate that could be measured and he estimated 20-100 M.y.o. Earth. Mendelian Genetics - -Gregor Mendel (). -unsuccessfully tested for a teaching certificate, considered a nervous student who "lacked insight and the requisite clarity of knowledge". EEOB 3310 EEOB 3310 Principle of Segregation--single traits segregate into separate gametes in a predictable fashion. Principle of Independent Assortment--alleles for different traits not linked and thus can segregate independently, giving rise to variations. -Mendel (luckily) selected traits that independently sorted, because many traits, and their alleles do 'travel' together. Genes - -Particulate theory of inheritance (William Bateson, Ronald Fisher). -offspring are representative of characteristics of parents that can independently assort. Chromosomal Theory (Sutton and Boveri). -particles of inheritance is located on chromosomes. -Morgan demonstrated how the frequency of genetic recombination is related to the distance between genes on a chromosome. --that these were physical objects. Major Factors Affecting Allele Frequency - -Allele--an expression of a gene. Mutation--changes in genetic code that are fixed and can have phenotypic consequences. Migration--movement of alleles by geographic isolation or between populations by way of emi/immigration of individuals. Nonrandom Mating--self-fertilization and sexual selection. Random Effects--small populations are particularly sensitive to these. -Genetic drift. -Population bottlenecks. -Founder's effects. Natural Selection--culling of alleles that disadvantageous (negative selection) or enrichment of adaptive alleles (positive selection). Natural Selection--Major Components - -Variation--individuals in a population differ from one another, but they can still reproduce! Inheritance--some differences are heritable. Differential reproductive success--not only do offspring survive, but they also have lots of babies. Variation - -Mutation is a major source of difference between individuals within a population, and different organisms fix mutations at different rates. EEOB 3310 EEOB 3310 Mutations arise largely due to molecular and physical processes and not with the interest of the organism in mind. Not all mutations have immediate phenotypic consequences. What are the implications of this phenomenon? Natural selections acts on individuals while populations evolve. Genes that negatively impact individual fitness are lost as individuals harboring those genes do poorly in their respective environmental and population contexts. Mutations Acquired During Replication - -Mutations acquired during replication can impact: -correct expression regulation. -accurate mRNA transcription All can impact phenotype. MutLHS-DNA mismatch repair system is responsible for repairing erroneous insertion of deletion mutations. Mutation On Speed! - -Mutations in genes responsible for DNA repair and error corrections (e.g. mutS, mutL, mutH, uvrD, mutU) can lead to hypermutator strains. -mutations in 1/100,000 cells instead of 10^-9. -prevalent in disease-causing bacteria. N. meningitidis strains with high infectivity and Rif-resis. exhibited high mutability that would be reduced with the introduction of wild-type mutS or mutL. Adaptation - -An inherited trait that confers a fitness advantage to individuals in environment that has arisen due to natural selection. Humans/Yao honey-hunters subdue honeybees. Birds (honeyguides) eat wax left behind by humans. Exaptations - -Traits originally selected for one purpose but later co-opted to serve a different, selectively advantageous function. Jasmonic acid (JA), a compound stimulated by herbivory in plants, is upregulated in the snap-trap of Venus fly trap and is a chemical trigger of the secretion of digestive enzymes in gland cells. Trap insect processing build on JA-based touch/wound sensing. EEOB 3310 EEOB 3310 Plant-Insect Interaction--Insect--Force--Excitation--Signaling--Molecular Response--Global Response--Survival. (These are the same whether the plant is doing it for 'Defense' Herbivory or 'Offense' Carnivory.) Natural Selection--Limitations - -Acts upon available material--no spontaneous generation. Coevolution or 'evolutionary arms race'. -compensatory modifications between interacting species. -"Cyclical coevolution wherein predator phenotypes continually 'chase' prey phenotypes are expected" (Feldman et al. 2010). -rapid variation in Nav1.4 (Thamnophis) and toxin production (Tarichia). -azithromycin. -antibiotic enhancers. Lacks foresight and intentionality. -current adaptations aren't necessarily the best forever. Time...is not always on your side. Devil facial tumor disease (DFTD), a transmissible and nonviral disease, decimating highly social Tasmanian devil populations. In 20 years, DFTD-resistant individuals have emerged and they have up to seven mutations in genes related to cancer and immune function that may be protective. -small changes having HUGE impacts! Reconstructing the phylogenetic relationships between genes is a crucial first step towards understanding their evolution. -Page and Holmes, Molecular Evolution - -Mendel and Darwin's 'heritable factors' are genes, which are made up of deoxyribonucleic acid (DNA). Important to evolutionary biologists because: 1) it's the instructions. 2) they are replicated. -but the replication isn't 100% perfect leading to mutations. Mutations acquired during replication in transcriptional regions can disrupt: -regulation. -accurate mRNA transcription. Mutations are generally problematic because the current gene set is likely representative of those conferring most success under the current conditions, but not all mutations are created equally. Types of Mutations - -Point mutations: -nucleotide change. EEOB 3310 EEOB 3310 -undisturbed reading frame. Insertion/deletion (indel) mutations: -nucleotide change. -disturbed reading frame (frameshift mutation) Point Mutations In Protein Coding Regions - -Synonymous mutations (silent): no amino acid change. -mostly due to drift. -frequent. -2nd and 3rd position. Nonsynonymous mutation: amino acid change. -relaxed (tolerance) selection or novel benefit. -less frequent due to being likely deleterious. -1st and 2nd position. CC(UCAG)=proline CA(UC)=histidine CA(AG)=glutamine GC(UCAG)=alanine 3rd2nd1st position -different mutation frequencies. Testing For Selection - -Synonymous mutations [silent, Ks]: no amino acid change. Nonsynonymous mutation [Ka]: amino acid change. Ka/Ks: pairwise comparisons for types of selection. Purifying selection: selection for conservation of ancestral state (Ka/Ks 1). Near neutrality (Ka/Ks = 1). Positive selection: selection for beneficial, derived state (Ka/Ks 1). Fixation of dN (Ka) in endos due to drift, founder's effects and host-isolation. Novel species? Mutations - -Frameshift mutations can cause major amino acid changes, resulting in genetic diseases. -thalassemia. -Tay-Sachs. -Crohn's disease. -Hypertrophic cardiomyopathy. -Cystic Fibrosis. Chromosomal mutations that affect copy number ('ploidy') and rearrangements