BIO120 Notes PDF

Chapter 2 Topic: Darwin's Big Idea Paley: The Argument From Design: There is a creator. Mistake was design-based Lamarck: Proposed the theory of inheritance of acquired characteristics, suggesting that organisms could pass on traits acquired during their lifetime to their offspring (giraffe necks...

Chapter 2 Topic: Darwin's Big Idea Paley: The Argument From Design: There is a creator. Mistake was design-based Lamarck: Proposed the theory of inheritance of acquired characteristics, suggesting that organisms could pass on traits acquired during their lifetime to their offspring (giraffe necks). Darwin ARW: Natural Selection. Did not know how traits were inherited. Malthus: populations grow exponentially while resources grow linearly, leading to competition for limited resources. Weismann: inheritance only occurs through germ cells (sperm and egg), not somatic (body) cells. Lyell: uniformitarianism—the idea that geological processes occurring in the present also occurred in the past, at similar rates. Chapter 3 Topic: The Evidence for Evolution Sources of Evidence for Evolution: Geology Homology Biogeography Domestication Evidence from Geology: Earth is very old Evidence from homology Homology: a term used to describe similarity in the traits of two or more organisms due to same ancestors Vestigial Structure: features inherited from an ancestor, but reduced in morphology and function Examples of Vestigial Structures in Humans: ear muscles, appendix, tailbone, goosebumps, etc. Not every homologous trait is a vestigial trait. Vestigial traits provide evidence of the evolutionary past Evidence from Domestication: Vast amounts of heritable variation found within species This variation can be selected on, leading to dramatic changes over generations Chapter 4 Topic: The Evolutionary Significance of Genetic Variation Genotype: Genetic constitution of an organism (Aa, AaBB) Phenotype: Any feature of the organism that is observed ( Genome: All of the DNA in the organism Sources of Genetic Variation Mutation Independent assortment Recombination Mutation: Any stable change in DNA sequence Stable means any change to any nucleotide level that will later not be fixed in DNA repair mechanism Possible effects of mutations on fitness are neutral, beneficial, and harmful Characteristics of Mutation: Mutation is inevitable. It will happen no matter what Mutation is not directed. It happens without respect to what the organism wants or don't wants Environment can affect mutation rate as well as mutagen such as heavy metal or radioactivity Mutation and the Structure of DNA (Types of Mutations): Point Mutation: is taking any one of the nucleotides and swapping it out with something else Insertion: adding one nucleoid into a existing sequence (adding one letter) Deletion: is removing one letter from an existing sequence Changes in repeat number: makes it harder for DNA replication to occur Chromosomal rearrangements/Inversions: you get a continuous stretch of DNA, you flip it and reinsert it Theory of blending inheritance: is taking phenotypes from paternal and maternal lineage and mixing them together like paint. Once you got this mix you can't reverse it. Preformationist: believed only one parent contributed to inheritance Mendel's Conclusions: Traits are determined by discrete units (genes). Organisms carry two alleles for each gene (dominant and recessive). Gametes combine to form offspring, with one allele inherited from each parent at random. Discrete is like flower color and continuous is skin color and height (varies) Particulate Inheritance: The concept that traits are inherited as discrete units (genes) rather than blended. This explains why traits can skip generations and why offspring can resemble their grandparents more than their parents. Chapter 5 Topic: Genetic Variation: Models and Measurements What Forces Influence Patterns of Genetic Diversity and Evolution? 1. Mutation - ultimate source of genetic variation and is caused by errors during replication (IGV) 2. Recombination - creates new combinations of mutations (IGV)  3. Genetic Drift - change in frequency of an allele leading to certain genes becoming more ore less without regard to how it affects their survival. Happens in small populations (DGV) 4. Negative selection removes mutations that reduce fitness (DGV) Positive selection keeps beneficial mutations which will eventually become fixed in a population (DGV) Selection favoring diversity can maintain diversity over the long term (IGV) 1. Migration (Gene flow) Metrics of Genetic Variation: Heterozygosity Polymorphism 2 Schools of Thought: Classical: populations have low generic variation, most individuals in a population are genetically similar, harmful mutations get removed quickly because they reduce he chances of survival. Balance: lots of different traits in a population, having 2 different alleles can be better for survival than having the same, and different alleles can be favored at different times and places so trait can exist together. Allozymes - different allelic forms of the same protein Neutral Theory: Negative selection quickly removes bad mutations Positive selection fixed beneficial mutations Only mutations left the create genetic variation are neutral Chapter 6 Topic: Sex, Reproductive Systems, and Evolution Reproductive Modes Reproductive System: Asexual or Sexual Sexual System: Dioecious or Hermaphrodite  Dioecious organisms two different sexes and one sex has a bigger gamete the other one has a smaller gamete during reproduction. Hermaphrodites are individual organism that have both male and female reproductive parts to produce both types of gamete. Can produce sperm and eggs in animals, and for plants pollen and ovule. Most plants are hermaphrodites. Mating System in Hermaphrodite: Self-fertilization or Cross-fertilization Self-fertilization is reproducing with themselves and taking both of their gametes and forming a single zygote. Not the same as asexual reproduction. Fusion of two different gametes from the same parent. Has female and male parts and mixes with another organism. This is called cross-fertilization or Outcrossing. Two ways of asexual reproduction Parthenogenesis is which an embryo develops from an egg without fertilization Clonal propagation is asexual reproduction not involving an egg The Costs and Benefits of Sex Costs: Two-Fold Cost of Meiosis is sexual female only gives 50% of her gene copies to the next generation, whereas asexual female gives all her gene copies. This is called transmission bias. More genetic fitness for the asexual lineage. Sexual reproduction gives us combinations of alleles that we might not want. Some other costs include: Time and energy to find and attract mates Increased energetic cost Risk of predation Benefits: Can form good combinations of alleles Gets rid of the bad variants by bringing together favourable mutations and ending the harmful ones. (Independent assortment and recombination) Hypotheses for the Advantages of Sex  Spatially heterogenous environments (Tangled Bank hypothesis) Space Temporally heterogenous environments (Red queen hypothesis) Time Cause & Consequences of Inbreeding & Outbbreeding Outbreeding is mates that are less closely related than random Inbreeding is mates that are more closely related than random Lots of potential for inbreeding in nature. Inbreeding is common in plants. Inbreeding Avoidance Traits in Plants: Timing offsets in which plants will produce pollen at a different time then it produces ovules so those will not come together Self-incompatibility Spacing of anther and stigma Inbreeding Avoidance Traits in Animals: Dispersal by one sex Delayed Maturation (by the time offsprings are mature, the parents are no longer reproducing) Extra pair copulation (cheating) Actually recognizing your kin and avoiding mating Population Genetic Effects of Inbreeding: Main issue with inbreeding is that it repackages the alleles in a population in a way that produces more homozygosity and decreases heterozygosity. Does not change frequency of alleles or polymorphism. Inbreeding Depression: When the loss of heterozygosity start to have really nasty effects on the organism, leading to lower fitness. This causes the organism to have lower fertility and survival. Inbreeding depression can change allele frequency. Why do we get this reduction of fitness? In populations we have super rare alleles but they are recessive. When the bad alleles are heterozygous and we start inbreeding in the population, it's going to make them homozygous. Consequences of Inbreeding:  Heterozygosity is reduced by 50% per generation Inbreeding depression Overall: Asexual: Lack of genetic diversity but fast and efficient reproduction with only one parent Sexual: Slower and only 50% of each parent's genetic material is passed. But increases genetic diversity Chapter 7 Topic: Natural Selection & Adaptation Fitness - organism's ability to survive and reproduce in its environment. Selective advantage - traits that give an organism better chance of surviving compared to others without that trait Adaptation - any trait that contributes to fitness by making an organism better able to survive and reproduce (in given environment) Artificial Selection - selection by humans towards a goal Natural Selection - selection by nature. No goal. Modes of Natural Selection Natural Selection on Alleles: Positive selection: favours beneficial alleles increasing in frequency Negative selection: eliminates harmful alleles from a population Balancing selection: maintains genetic diversity by favoring multiple alleles Many Phenotypic Traits Are Polygenic and Show Continuous Distributions Disruptive selection leads to trait divergence which can lead to trait divergence Directional Selection: favors individuals at one extreme trait Stabilizing Selection: favors individuals with average traits Disruptive Selection: favors individuals at both extremes of traits while being against the average Chapter 8 Topic: Population Structure: Genes & Phenotypes Genetic Differentiation of Populations Population: a group of individuals from a single species occupying a space at a given time Migration: movement of individuals from one population to another Gene flow: movement of alleles from one population to another Populations are held together by gene flow and separated by genetic drift and natural selection Gene Flow: How to Measure Gene Flow? Experiment - establish 2 populations , fixed for alternative alleles and separated by a given distance. Score heterozygotes in offsprings for estimate gene flow. Genetic Drift Random in Evolution: Stochastic - mutation, recombination, and genetic drift Deterministic - natural selection Genetic drift decreases diversity. Special cases of genetic drift include: Population Bottlenecks: sharp reduction in genetic diversity from one generation to the next. Causes a loss of diversity Founder Events: small number of individuals from one population colonizing a new area. Genetic drift is more pronounced in small populations. More fluctuations in allele frequencies in smaller populations. Geographic Patterns of Variation Isolation by distance: accumulation of local genetic variation due to geographically limited dispersal Phenotypic Population Differentiation Phenotypic Plasticity: ability of a genome to modify its phenotype in response to a particular environment Example: Arrowhead plant can have 2 difference shapes of its leaves because it can grow in water and land. Reciprocal Transplant - taking organisms from different populations and placing them in each other's environments