Bio 1111 Exam 1 - Exam 1 Prep PDF

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Biology 1111 Chapters 22 - 26 Study Guide

Chapter 22 - Introduction to Evolution and Natural Selection Important People: Aristotle (384 BC) ● Rejected Evolution along with Plato, species were fixed ● Scala naturae Great chain of being, arranged by increasing complexity ○ Impacted evolutionary ideas with bias ○ EX/ No such thing as a lesser or greater animals C. Linnaeus (1707) ● Developed binomial naming system (Homo sapiens) ● Adopted a nested classification system, groups similar in same genus, similar genera in the same family, etc. G. Cuvier (1769) ● Father of Paleontology ● Noted that the older the stratum, the more dissimilar the fossils were to current life forms ● Inferred extinctions must have occurred where fossils stopped appearing ● Denied the idea of evolution J. Hutton (1726) ● Concept of geological gradualism ○ Erosion and other processes change the landscape over time C. Lyell (1797) ● Expanded Hutton’s work ● Geological processes are and have been slowly changing the land over a long period of time - a slow cycle Lamarck (1744) ● Use and Disuse (Not true) ○ Part of the body used extensively become larger and stronger, while those parts that do not deteriorate ● Acquired Characteristic (Also not true) ○ Organisms have the ability to pass on characteristic acquired through their life ● Perfectibility of Organisms

Darwin (1882) ● Influenced by Lyell/Henslow/Malthus ● Spent much time on land collecting and observing plants/animals/fossils ○ Plants/animals were not similar to those from similar environments in different locations ● Theory of Evolution or descent with modification ● Adaptations and Natural/Artificial Selection

Important Terms: Evolution - Descent with modification Fossils - Remains or traces of organisms from the past Strata - Layers of rocks Paleontology - Study of Fossils Adaptations - Inherited characteristics of organisms that enhance their survival and reproduction in specific environments Natural Selection - a process in which individuals that have certain inheritable traits tend to survive and reproduce at higher rates than those who do not because of those traits Artificial Selection - A process of selecting and breeding certain individuals that possess desired traits, large changes occur over a “short” period of time Homology - Similarity resulting from common ancestry Homologous Structures - Structures that represent variations on a theme that was present in a common ancestor (similar ancestry not necessarily same function) Vestigial Structures - Remnants of features that served a function in the organism’s ancestors Evolutionary Tree - A means of representing the pattern of descent from common ancestors Convergent Evolution - Independent evolution of similar features in different lineages Analogous - Similarity resulting from similar environment/convergent evolution (similar function different ancestry)

Notes: Natural Selection ● Differential reproductive success = higher fitness ○ Leads to adaptation of organisms ● Population variation arises by chance ● Not a CHANCE EVENT ○ Environment selects for those with criteria for reproductive success

● Variation and Overproduction common to all species ● NS occurring over time could account for diversity of life ● Population ○ Groups of interbreeding individuals belonging to a particular species and share a common geographic area ○ Population is smallest unit capable of evolving ● INDIVIDUALS DO NOT EVOLVE ○ Measured as a change in relative proportions of variations in populations of several populations ○ NS can only amplify or diminish heritable differentiations ○ Organisms can adapt to changes in their environment and can be modified by life experiences - but these acquired characteristics can not be passed down ○ Must distinguish between acquired adaptations and inherited ones Traits and Adaptations ● Adaptation is not perfect ○ Previous evolutionary history determines types of traits ○ No all traits are adaptive ● Selections cannot optimize all traits in organisms ○ Acts on multiple traits at one ○ Leads to tradeoffs

Chapter 23 - The Evolution of Populations Important Terms: Microevolution - Evolution in its smallest scale, within a single population Genetic Variation - Differences among individuals in the composition of their genes and DNA Mutation - A change in the nucleotide sequence of an organism's DNA Neutral Variation Gene Pool - all copies of every type of allele at every locus of all members of a population Population - a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring Hardy - Weinberg Equilibrium - A population that is not evolving, where allele and genotype frequencies will remain constant from generation to generation Adaptive Evolution - A process in which traits that enhance survival or reproduction tend to increase over time Genetic Drift - Allele frequencies fluctuate randomly from one generation to next due to chance Bottleneck Effect - Sudden decrease in population size that allows for a disproportionate effect of genetic drift Founder Effect - When individuals become isolated from a larger population and establish a new population whose gene pool differs from the original Gene Flow - the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes Relative Fitness - the contribution an individual makes to the gene pool of the next generation relative to the contribution of the other individuals Types of Selection Disruptive - Conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes. Directional - Conditions favor individuals exhibiting one extreme of a phenotypic range, shifting the curve in one direction Stabilizing - acts against both extremes and favors intermediate traits Sexual Selection - Individuals within population differ in ability to attract mates ○ Favored individuals will produce more offspring ○ Favored traits will increase in frequencies Sexual dimorphism - Traits differing between males/females of same species, sexually selected traits often differ sharply Balancing Selection - Maintains alleles within a population two types

Frequency-dependent Selection - The fitness of a phenotype depends on how common it is within a population Heterozygote Advantage - Heterozygous individuals at a particular locus have a greater fitness than homozygous individuals

Notes: Five Conditions for Population to be in HW equilibrium 1. No natural Selection 2. No genetic drift 3. No gene flow - immigration/emigration 4. No mutation 5. Random Mating Tips for HW 1. Estimate genotype frequencies 2. Calculated observed allele frequencies 3. Used observed info to get genotype expected 4. Compare observed vs. expected Sources of Genetic Variation ● Sets stage for natural selection ● Sources ○ Formation of new alleles - mutations ○ Altering gene # or location - chromosomal ○ Rapid Reproduction - mutations rates constant / generation time not constant ○ Sexual Reproduction - recombination of chromosomes Gene Flow ○ Individuals move from one population to another ■ Increase variation ■ Reduced genetic differences among populations over time ○ Can lead to reduced fitness for SOME populations ● Mutations ○ Restores genetic diversity

■ Creates new alleles ■ Random with respect to fitness i.e. not always helpful ■ Slow compared to other evolutionary processes ■ Essential for evolution ○ Most result in deleterious alleles ■ Lowered fitness - eliminated by natural selection ○ Rarely Produces beneficial alleles Inbreeding ● Can lead to inbreeding depression ○ Loss of fitness due to increased homozygosity and decreased heterozygosity ○ Increased homozygous recessives (aa) which are usually deleterious/loss of function mutations (can kill them) ● Increases rate by which natural selection eliminates deleterious recessive alleles ● Could result in an extremely well tailored population but is unlikely

Chapter 24 - The Origin of Species Important Terms: Speciation - process by which one species splits into to two or more species Biological Species Concept Species - a group of populations whose members have the potential to interbreed in nature and produce viable offspring Reproductive Isolation - existence of biological factors that impede members of two species from interbreeding Hybrids - offspring that results from an interspecific mating Prezygotic Barriers - Prevented from mating Habitat Isolation - different environments Temporal Isolation - different breeding times Behavioral Isolation - different mating rituals Mechanical Isolation - just can't mate physically Gametic Isolation - egg and sperm are not released at same time Postzygotic Barriers - Can mate but offspring have low fitness/die/are sterile Reduced Hybrid Viability - fails to develop or dies after birth Reduced Hybrid Fertility - offspring is sterile Hybrid Breakdown - fertility in first generation but subsequent generations are sterile Polyploidy - A species may originate from an accident during cell division that results in extra sets of chromosomes Autopolyploid - an individual that has more than two sets of chromosomes that are all derived from a single species Allopolyploid - Fertile when mating with themselves but cannot interbreed with either parent species Hybrid Zone - a region in which members of different species meet and mate, producing at least some offspring of mixed ancestry Reinforcement - Reducing formation of hybrids, strengthening reproductive barriers Fusion - breakdown of reproductive barriers Stability - continued production of hybrids Punctuated Equilibria - periods of apparent stasis punctuated by sudden change

Notes: Speciation Allopatric ● Genetic Isolation ○ Populations become physically separated (vicariance) ○ Isolated populations begin to diverge ○ Finish with two populations isolated from each other ■ EX Mountains, Rivers, ■ Leads to no gene flow ● Natural Selection and genetic drift ○ May result in rapid divergence ● Dispersal - like founder effect ○ Individuals leave and begin new population in another area ○ Darwin's finches Sympatric ● No physical barrier preventing gene flow ● Isolation based on habitat preferences ○ EX/ Apple + Hawthorne flies ■ Prefer Scent of respected fruits (mating occurs there) ■ Prezygotic barriers - habitat isolation ■ Not breeding at same trees --- so don’t breed ■ Apples mature more quickly ■ Temporal Isolation of different breeding times Morphological Species Concept ● Identifying on morphological differences ○ Useful for fossils Phylogenetic Species Concept ● Based on reconstructing history of populations ● Monophyletic groups ○ Common ancestor and all descendants ● Species are smallest monophyletic group on tree ● Disadvantages ○ Only a small number of phylogenies available ○ Could lead to recognition of many more species than other species concepts Ecological Species Concept ● Species defined on ecological niche

● Applies to asexual and sexual species ● Disruptive selection is important Rates of Speciation ● Rapid or slow ○ 4,000 years (Rapid) ○ 40 million years (Slow) ○ Average 6.5 million years Punctuated vs. Gradual ○ Recognized via ■ Fossils ■ Morphological data ■ Molecular data Polyploidy ○ Duplication of chromosomes ○ Usually from multiple closely related species ■ Have different number of chromosomes ● Can't Breed - offspring die or are infertile ○ Instantaneous Speciation

Chapter 25 - The History of Life on Earth Important Terms: Endosymbiosis - Mitochondria and plastids (chloroplast and related structures) were formerly small prokaryotes that began living within larger host cells Serial Endosymbiosis - Mitochondria evolved before plastids Cambrian Explosion - Present day animal phyla appear in fossils formed suddenly around 525 million years ago Mass Extinction - a large number of species become extinct world wide Adaptive Radiations - periods of change in which groups of organisms form many new species whose adaptations help them fill roles or niches

Notes: Abiogenesis ● Primary pseudo-argument against evolution ○ How do you get biological structures from nothing? ● Organic molecules have been synthesized spontaneously ○ Oparin - Haldane experiments ○ Miller - Urey experiments ● Protocells and self replicating RNA Fossil Records ● Collection of fossils that have been found throughout the world ● Provides the only direct evidence of what organisms looked like and when/where they existed ● History of Evolution ○ However is highly incomplete and biased ■ Fossilization is rare ■ Some habitats preserve better than others ■ Organisms with hard parts are more common as fossils ■ Recent fossils are more common than earlier than ones ■ Abundant organisms are more common Making fossils ● Need sedimentary rocks ○ Fossils between layers of different rocks ● Only a small proportion of organisms left fossils ● Limitations of records ○ Habitat Bias

■ Organisms that live in areas were sediments are deposited are more likely to fossilize ○ Taxonomic Bias ■ Some organisms (with hard parts) are more likely to leave evidence ○ Temporal Bias ■ Recent fossils are more common than ancient ones ○ Abundance Bias ■ Abundant, widespread and present on earth for long periods of time leave more fossils ● Rarity and Types ○ Trace fossils ■ Footprints, trails, tracks, etc ■ Behavior of organisms ○ Body fossils ■ Preservation of parts or entire body Uses for fossils ● Correlate rock layers from different locations ○ Similar fossils --- similar ages ○ Correlation fossils called index or guide fossils ● Sedimentary rock accumulates in layers ○ Law of superposition ■ Higher up in layers you go, the younger the rocks ● Records then give a scale of the relative age of fossils ● Shows the order and relative time various groups evolved ● Used to create geological time scale ○ Broken into several segments of interest Time Scale ● Precambrian --- Hadean, Archean, and Proterozoic eons ○ Most life was unicellular ○ Very little oxygen (anaerobic) ● Phanerozoic --- Paleozoic, Mesozoic and Cenozoic era ○ Most modern taxonomic groups first appeared in Paleozoic era ● How is age determined ○ Radiometric Dating ■ Measures concentration of ratios of parent to daughter nucleotides

Chapter 26 - Phylogeny and the Tree of Life Important Terms: Phylogeny - Evolutionary history of species Taxonomy - Two Part name of species, groups species into increasingly broad group Naming System (Most specific to least) Species Genus Family Order Class Phyla Kingdom Domain Taxon - a taxonomic unit at any level of the hierarchy Cladistics - Common ancestry is the primary criterion used to classify organisms Clades - a group of species, which contains an ancestral species and its descendants Phylogenetic Tree A branching diagram that represents evolutionary history of a group or organisms Branch points - represent divergence of two taxa Branch - population through time Sister Taxa - groups that share an immediate common ancestor Rooted - common ancestor of all taxa in tree is represented Basal - taxon that diverged near common ancestor of group (minimal divergence) Node - point where two branches diverge Tip (terminal node) - end point of branch (represents species or larger taxon) Polytomy - node from which more than two groups emerge Homologies - phenotypic and genetic similarities due to shared ancestry Analogy - Similar characteristics that are NOT a result of common ancestors Monophyletic Group - Single common ancestor and all descendants Paraphyletic Group (systematic error) - Single common ancestor but not all descendants Polyphyletic Group (systematic error) - Species with different common ancestors Outgroup - Species or group that diverged before the group of interest Ingroup - Species being studied

Notes:

Phylogenetic Trees ● Depict evolutionary relationships ○ Morphological/molecular/other data used to determine ● Can be used to predict ○ Adaptive radiations -- rapid speciation as result of new niches ○ Mass extinctions Constructing Phylogenies ● Use morphological, biochemical and/or genetic characteristics ● Homologies --- phenotypic and genetic similarities due to shared ancestry ○ Predicts organisms that share characteristics should be more closely related ● Analogous Characters ○ Homoplasy --- analogous characters ○ Similar characteristics that are NOT a result of common ancestors ■ Convergent evolution due to similar environments ■ EX/ Ichthyosaurs vs. Dolphins ■ Look Similar ■ Not due to common ancestor Convergent Evolution ● Natural selection produces similar adaptation in unrelated organisms ● Look similar but very different ○ Internal anatomy ○ Physiology ○ Reproduction ● Wings in pterosaurs, bats and birds ○ Homologous as forelimbs ○ Analogous as wings ■ Wings evolved independently from forelimbs of flightless ancestors ● Homology generally more complex that analogies Molecular Homologies ● Molecular systematics ○ Uses DNA and other molecular data to determine relationships ● DNA may be similar due to coincidence alone ● Use computer programs and algorithms to identify molecular homoplasy Cladistics ● Group organisms by common descent ○ Clade or lineage --- group of species that includes common ancestor and all descendants (monophyletic group) ● Synapomorphies --- shared derived characteristics

○ Define monophyletic grouping ○ Shared because common ancestor had them ● Shared ancestral characters ○ Character that originated in ancestor of taxa ○ Found in further back than common ancestor of group Tree Building ● Many possible trees ○ Determine which tree is best for data ● Method 1 - Max parsimony ○ Tree that requires fewest evolutionary changes is probably correct ○ Occam's Razor - simplest explanation is usually the best ● Method 2 - Max likelihood ○ Tree reflects most likely sequence of evolutionary events given certain "rules" about how DNA changes with time Patterns in Phylogeny ● Morphology based trees put whales as an outgroup to artiodactyls ○ Based on ankle bone shape ● However DNA comparisons shows whales are a sister group with hippos ● Trees can also take on different forms ○ For example, cladograms share same info in a different form...