Introduction to Evolution: Chapter 1

Chapter 1: Introduction to Evolution

• Charles Darwin, often credited as the father of modern evolutionary theory, served as a naturalist on the HMS Beagle.
• Darwin's observations led to a coherent theory of evolution, as detailed in "The Origin of Species".
• The biogeography of species reveals that similar species cluster geographically rather than being randomly distributed worldwide.
• Armadillos and glyptodonts existing exclusively in South America provide evidence of common ancestry.
• Darwin's key insight of common ancestry suggests that tracing lineages back far enough reveals shared ancestors.
• Darwin presented four types of observations to support the common ancestry hypothesis.
• Hummingbirds' restriction to the Americas and penguins' to the southern hemisphere despite suitable habitats elsewhere supports common ancestry through biogeography.
• Homologies, structures with underlying similarities between species, indicate common ancestry.
• Vertebrate forelimbs with similar bone structures for running, digging, flying, or climbing illustrate homology and descent from a shared ancestor.
• Transitional fossils, sharing traits with both ancestral and living groups, support descent from common ancestry.
• The nested structure of taxonomic groups, with groups within groups, aligns with a diversifying process originating from a common ancestor.
• Molecular similarities, including DNA/RNA, nitrogenous bases (A, C, G, T, U), 20 amino acids of left-handed variants and ATP use, across all life forms, support a single common ancestor beyond reasonable doubt.
• Polymorphic populations with change in the frequency of genetic variants constitute evolution.
• Polymorphic populations with changes in the frequency of variants continuing until one variant becomes fixed is also evolution.
• Mutation can introduce new variants, sustaining evolution indefinitely.
• Natural Selection implies that genetic variants better equipped for their environments increase in frequency in populations over time.
• Three core ideas of evolution: common ancestry unites all life, populations evolve with ongoing genetic variation, change is adaptive due to natural selection.

Chapter 2: Tree Thinking

• Phylogenetic trees use the tree metaphor to represent evolutionary relationships, with the root indicating the deepest ancestry.
• Branches connect the root to the tips (leaves, taxa) that represent biological groups (taxon).
• Branches representing population lineages experienced extensive gene flow
• Lineage splitting is depicted at the nodes in a tree diagram.
• Nodes separates two "sister" lineages.
• Lineage splitting is a population event that stops gene flow, and allows for accumulation of genetic differences
• Speciation is when lineages accumulate differences, and can then be classified as different species.
• Geographic isolation causes lineage splitting which leads to speciation and diverging traits over time.
• A clade is a grouping containing all descendants of a single ancestor with no more, and no less members.
• Clades can be identified because they can be removed from the root with a single cut.
• (land plants, red algae, fungi, animals) or(land plants, red algae) are an example of taxa to indicate clades by grouping them in parentheses.
• All taxa within a clade are more closely related among themselves than to any taxa outside the clade.
• Tree topology represents relationships among clades, allowing for varied expressions of relationships.
• The (B,C) clade is the same because the two trees in figure 2-4 show the same topology.
• Tree diagrams are commonly misinterpreted with one being that diagrams are a story of progress.
• Good tree-thinking skills involves extracting and interpreting information in diagrams to convey evolutionary history.
• Every living species is equally advanced and has been evolving for the same amount of time.
• Common ancestry, evolution, and natural selection are the three main concepts behind Tree Thinking.

Chapter 3: Trait Evolution

• If a change gets fixed in a population lineage will be retained by its descendants
• A lineage with dewlaps splits into two on separate landmasses, different traits evolve
• Horns evolved later in right-hand lineage and the backs of the lizards on the left-hand lineage.
• Clades descended from that clade are expected to carry both dewlaps and the new trait.
• Sum of traits over evolution history is found at branch tips in the Phylogenetic tree.
• Traits do not evolve at steady rates
• Number of evolved traits cannot be evaluated by the topology shown on a phylogenetic tree.
• External morphology on branch leading to birds changed a lot more traits, crocodile still closely related to the bird
• More similar to second cousin but more closely related to the first cousin
• Common ancestry hypotheses can be found evaluating distribution of traits among species
• Distribution of traits among species tends to have a nested or hierarchical pattern.
• Biological classifications (taxonomy) are based on traits that evolved along tree
• Long before Darwin, taxa recognize based on certain traits
• Cat species exist as a member cat family, carnivoran order, and mammal class.
• Nesting pattern exceptions to the common ancestry model involves trait could evolve dependently a few times and one or more lineages.
• A non-nested pattern turns out to be wrong
• Nested structure arising fro phylogeny is strong and concrete kind of evidence
• Proven in Chapter 2 with common ancestry being beyond reasonable doubt
• Common ancestry we can refine into homology
• The principle of parsimony is that many hypotheses simplest are the most likely to assume
• Occam’s Razor and that the explanation is correct
• Evolutionary biologists method for inferring the relationship for living species.
• Estimate set of taxa what varies among the tips
• Two competing trait his is what is most likely true, with character state state
• Evolves so long the trait (changes state) rarely

Chapter 4: Population Thinking

• Evolution is a population-level and not an individual-level process.
• The understanding of the roles of genetic and environmental variation in explaining frequencies of different characteristics.
• It serves as the basis for scientific flaws of eugenics, a misguided attempt to improve humans as a species
• “Evolution” change or specifically change for the better, is how it is used in common speech.
• Change of properties of populations over time is related to evolution.
• Biological evolution: A change in the frequency of gene variants (or traits caused by genes) in a population over generations.
• Phenotypic plasticity is not relevant to long term change
• Survey of Queen Elizabeth Nat’l park showed only 1% of adult elephants lack tasks, end of 20th century 30% lacked
• Change in freq of tasks leads to change in freq of tuskless allele over time
• change doesnt apper to be selection against a or B alleles, genetic bottlenecks removed these
• Genetic, not environmental change is considered Evolution.
• Phenotype of an organism, all it measurable attributes, interaction between genotype and environment for development.
• Allele is a varient of gene that is present in a population
• Locus is a place in chromosome, allele’s are encoded
• Diploid have two sets of chromosomes, and thus and individual carries two alleles
• Population has genetic variation, but always amount of phenotype expression
• Minority traits that show of of variation, length hair density.

5. Allele Frequency

• traits controlled by alleles of many loci, end to show bell-shaped distribution.
• Genetic changes of one or more alleles through genome is precise
• Can provide more precise evolution over change in allele frequencies over generation.

Hardy & Weinberg

• G.H. Hardy and Wilhelm Weinberg discover the relationship between allele and genotype frequencies in early 20th century
• Key Assumptions include no new alleles, mating happen randomly, alleles have equal fitness, population is infinitely large
• Individual in next generation always parented by people of this generation.
• Allele A1 has a frequency pin a population, what's the frequency of A1Sperm?
• Genotype frequency that we had was that established earlier, the probability that the father.

Chapter 5: Directional Natural Selection

• Directional selection favors enhanced fitness caused by one allele within a population
• Long-term outcome is fixation of favored (beneficial) alleles, and loss of disfavored (deleterious) alleles.
• Peppered moth in Britain shows classic Direction Selection
• Melanistic moths is a dominant allele which reduced odds of survival
• A scientist named Bernard Kettlewell pinned both dark and light dead moths onto trees covered with Lichen and soot.
• Fitness depends on the environment highlights important principle
• That direction depends relative success with reproducing or producing offspring.

Chapter 6: Genetic Drift

• Genetic drift is one important evolutionary mechanism and it interacts with directional selection.
• Key insight of what genetic drift affects randomness to evolution.
• Genetic drift violates the key of what Hardy - Win Berg is violation. all populations are finite. means that chance is sampling from generation to generation means that allele frequencies is always changing or that evolution is always happening.

Chapter 7: Genetic disorders and human health

• Genetic disorders are disease states caused by a location or loci
• Genetic disorders reduce fitness, so their deleterious alleles can be passed on.
• Strength selection depends on if alleles have a mild effect
• Determined by genetic disorder affects effective
• Selection acts against recessive alleles right away.
• Inbreeding and Founders affect the expected disease.
• Overdominant Selection, a few genetic disorders appear can often be explained by greater.

Chapter 8: Selection on Continuous Variation

• Many polymorphic loci can yield a bell-shaped distribution of trait variation
• Heritability is the fraction of phenotypic variation in a population
• Using the breeders equation we can predict the response to direction selection
• List scientific flaws of the movement and correlating it between parents
• Disruptive selection is based on the relative fitness of different trait
• Continuous traits are often characterized by a long scale with single Locis.

Chapter 9: Origins of Complexity

• Distinguish adaptation from exaptations based on function from the start
• Recognize the role of reproductive in explain that
• Explain how selection result in exagreate
• Explain the selection unit

Chapter 10: Species and Speciation

• The recognition of species concept
• Explain variety between biological species.

Chapter 11: The Origin and Early Evolution of Life

• List evidence to support common ancestry
• Summarize the traits and evvolutionary relationships between Bacteria, Arcahea and Eucarya
• List the evidence to support endosymbiotic relationships to orgin to miitchondria
• Summarize differences between outside and inside in the Nucleus

Chapter 12: Human Evolution

• Hominids share skeletal traits, loss of tails
• Adapted to better locomotion