bio pt2 mt 2

Natural selection

  • Catastrophism: earth and life on it are primarily shaped by major, sudden events

  • Gradualism: earth and life on it are primarily shaped by long, slow processes


Friday, October 18 2024 lecture


Natural selection

  • Descent with modification

    • The same limb bones in all tetrapods, adapted to different purposes 

  • Homologous and analogous traits

    • Homologous

      • Descent with modification produces homologous traits

      • Similar in different organisms because they inherited from common ancestors

    • Analogous

      • Convergent evolution produces analogous traits

      • Similar in different organisms because of similar selective pressure

  • Vestigial structure

    • A structure or trait that is rudimentary, atrophied, or no longer “serves an obvious purpose”

  • Evolution

    • Changes in the frequencies of a trait in a population over generations

    • No obvious end goal

    • No individual or population is less evolved

  • Development 

    • Changes within an individual during a lifetime

  • Conditions for natural selection

    • Variation: individuals vary in their traits

    • Inheritance: individuals pass on some of their traits to their offspring

    • Differential success: individuals with different traits differ in their survival or reproductive success

  • Patterns of natural selection

    • Stabilizing selection: phenotypes nearest the mean have the highest fitness. The mean stays the same, variation is reduced

    • Directional selection: phenotypes at one extreme have the highest fitness. Mean trends toward that extreme

    • Disruptive selection: phenotypes at both extremes have higher fitness than the mean. Variation is increased, and a bimodal pattern emerges

    • Frequency-dependent selection: rarer phenotypes have the highest fitness. The frequency of a given phenotype oscillates


Monday 21 October 2024 lecture

Natural selection

  • Sexual selection

    • Natural selection on traits that affect the likelihood of obtaining a mate

    • Intrasexual selection: within the same sex (territory, status)

    • Intersexual selection: one sex is ‘choosy’ aka mate choice

  • Constraints of natural selection

    • Laws of physics

      • Environmental change

      • Optimal trait might change

      • Evolutionary history

      • Natural selection acts on the existing variation in the population

      • Tradeoffs

      • Lack of variation in population

        • Small populations end up losing genetic variation

        • Historically there were many more haplotypes (distinct genetic types in the population)

        • Variation in survival/reproduction is a core driver of evolution by natural selection, so condor populations will struggle to adapt to a changing environment 

    • Explaining altruism: kin selection

      • Altruism: a behavior that reduces an individual's fitness and increases the fitness of other individuals

      • Kin(relative) selection: favors behaviors that increase the reproductive success of relatives

      • Inclusive fitness: the sum of an individual’s own fitness, and it’s contribution to the success/survival of relatives

    • Hamilton’s rule

      • rB>c

      • r: coefficient of relatedness

        • The fraction of genes shared between relatives

      • B: benefit to relative

        • The increase in offspring for the relative

      • c: cost to Altuist

        • The loss of offspring for the altruist


Wednesday, October 23, 2024

Inheritance I: Mendelian Genetics

  • Structure of DNA

    • Gene: a section of DNA that codes for a particular function/trait

    • Gene expression

      • The central dogma: information in genes is transcribed (DNA→RNA) and then translated (RNA→proteins)

    • Organisms function and interact using proteins

    • Transcription: DNA→RNA, occurs in the cell nucleus

    • Translation: RNA → protein, occurs in the cytoplasm with the help of tRNA

      • Condons to amino acids

      • Triplets of RNA are translated to particular amino acids

    • Alleles, genotypes, and phenotypes

      • One base pair on the DNA strand (gene) is different

      • Different alleles produce different phenotypes of the same trait

      • Allele: a particular variant of a gene (within a population there may be many alleles for a gene)

      • Genotype: an individual’s particular alleles at a gene/locus

      • Phenotype: an individual’s observable trait

      • Homozygous: two identical alleles

      • Heterozygous: two different alleles

  • Mendels laws

    • Gametes= sperm and eggs(more generally, the result of meiosis)

    • Law of segregation: when any individual produces gametes, the two copies of a gene separate so that each gamete receives only one copy

    • Law of independent assortment: alleles of different genes assort independently of one another during gamete formation


Thursday October 24 2024

Genetics + inheritance

  • Meiosis

    • Meiosis I: end with 2 cells containing duplicates of 1 chromosome

    • Meiosis II: end with 4 cells containing 1 chromosome each

  • Types of dominance

    • Complete dominance: a single dominant allele produces the dominant phenotype. The homozygous dominant and heterozygous genotypes have the same phenotype

    • Incomplete dominance: the heterozygote phenotype is intermediate between the two homozygous phenotypes

    • Codominance: the heterozygote shows both of the homozygous phenotypes

  • Pedigrees

    • A pedigree tracks individuals’ phenotypes, as well as their mating and the resulting offspring

    • Often used to track diseases, called the shaded phenotype “affected”

    • Only recessive traits can skip a generation


Friday October 25 2024

Inheritance 2: complex inheritance

  • Pleiotropy

    • When one gene affects multiple traits

  • Polygenic inheritance

    • One trait is additively controlled by many genes

  • Environmental influences

    • Acclimations are examples of environmental influences on phenotypes

  • Quantitative traits: gene and environment

    • Continuous phenotypes with both genetic and environmental influences

    • Changes in diet (environment) have led to changed in average height

    • Height is also affected by genetics

  • Epistasis

    • When multiple genes interact in a non-additive way to determine the phenotype

Monday, October 28, 2024 lecture

Population Genetics I: Hardy-Weinberg Equilibrium 

  • Natural selection acts on individuals 

  • Population evolve

    • Changes in allele frequencies

    • Changes in mean and variance of traits

  • Frequencies

    • Allele frequencies: the proportion of dominant allele. q = frequency of recessive allele

    • More generally, fA1, fA2,FA3 for frequency of alleles A1, A2,A3….

  • Genotype frequencies: the proportion of individuals with a particular genotype in a population

  • Hardy-Weinberg equilibrium: as long as allele frequencies remain the same and mating is random, genotype frequencies will remain the same across generations

    • In a non-evolving population, genotype and allele frequencies reach equilibrium after one generation and remain constant at specific values/frequencies in subsequent generations

    • Assuming:

      • No mutations

      • No natural selection

      • No gene flow (no migration)

      • No genetic drift

      • Random mating

    • Violations of any of the requirements can cause allele and genotype frequencies to deviate from expectations

Wednesday October 30th, 2024

Population genetics II: drift, non-random mating, selection

  • Genetic drift: 

    • Chance events that cause allele frequencies to fluctuate unpredictably from one generation to the next, especially in small populations

    • Generation: average difference in age between parent and offspring

    • Genetic variation has been lost

    • Small populations lose diversity more quickly

    • Genetic drift is the strongest in small populations 

    • Genetic drift is Weakest in large populations

    • Cause allele frequencies to change randomly through generations

    • Extreme causes of genetic drift:

      • Founder effect: a new population is created with few individuals from the initial population

      • Alleles common in the founders will be high frequency, even if uncommon in the original population

      • Genetic bottlenecks: when population size is severely reduced due to biotic or abiotic factors 

        • Or due to environmental impacts

  • Non-random mating

    • Positive assortative mating: mating preferentially happens between individuals with similar genotypes

    • outbreeding/ negative assortative mating: mating preferentially happens between unrelated individuals with dissimilar genotypes

Friday November 1st 2024 lecture

Speciation I: species concepts and reproductive barriers

  • Species: a group of actually or potentially interbreeding natural populations that are reproductively isolated from other groups

  • Hybrid offspring: the result of interbreeding between individuals of 2 different species/types

  • Biological species: a species group of actually or potentially interbreeding natural populations that are reproductively isolated from other groups

    • Pro: simple to understand, clearly linked to gene flow

    • Cons: does not apply to some organisms,  do not always have mating data

  • Lineage species concept: a common species is a group of organisms that shares a common ancestor and can be disguised from other organisms by particular traits

    • Pro: includes historical/evolutional context, applies to all organisms which genetic data are available

    • Cons: requires modern genetic and computational tools

  • Morphological species concept: a species is a group of organisms that similar physical traits

    • Pros: good for groups where other data are limited ex fossil

    • Cons: similarity and difference in appearance can be misleading

  • Reproductive barriers

    • Reproductive isolation: the prevention of (viable and fertile) offspring from being created between two populations

      • fundamental driver of speciation

      • Prevention of gene flow

      • Prezygotic barrier: prevent mating or prevent fertilization if mating occurs

        • Habitat isolation: species occupy different habitats, never come into contact

        • Temporal isolation: breed during different times

        • Behavioral isolation: individuals do not recognize each other as potential mates

        • Mechanical isolation: physical differences between the organisms prevent successful mating

        • Gametic isolation: sperm is not able to fertilize the egg

      • Postzygotic barrier: prevent a hybrid zygote from developing into a viable, fertile adult

        • Reduced hybrid viability: F1 hybrid offspring do not complete development or have low survivorship

        • Reduced hybrid fertility: F1 hybrid offspring are viable, but have reduced fertility/fecundity

        • Hybrid breakdown: F1 hybrid offspring are viable and fertile, but offspring of these hybrids (F2) are inviable or sterile




Monday November 4th 2024 lecture

Speciation II: allopatry & sympatry

  • Microevolution: changes in allele frequencies across generations

  • Macroevolution: accumulation of many microevolutionary changes, such that a new group arises

  • Phylogenetic trees: a graphical depiction of the history of relationships among a group of organisms

    • Shorter the distance back to a most recent common ancestor, the more closely related

    • Time is just direct distance from tip to base, not the length zig-zagging along branches

    • speciation/reproductive isolation: creates branches, new lineages

    • Extinction: ends a branch, loss of lineages


Wednesday 6th November 2024 lecture

Speciation III: rates of speciation

  • Simple mutations can produce a diversity of flower shapes that are favored by different pollinator species

  • Core principle: rapid reproductive isolation leads to rapid speciation

  • Dicromatism/ sexual dimorphism:

    • a low dichromatism value where males and females look the same 

    • High dichromatism value = male and female look different, lots of differences in phenotypes

    • Taxa where mate choice is important may have rapid behavioral isolation when new phenotypes arrive

  • Dispersal ability

    • Low dispersal: small environmental changes can be vicariance events (habitat isolation)

  • Adaptive radiation: species adapted to particular environments and fill different ecological niches

    • Occurs when rapid speciation results in a burst of new species from a single ancestor

    • Core principle: many potential niches create opportunities for speciation

  • Polyploidy: having more than 2 sets of chromosomes

  • Allopolyploidy: the polyploid carries the combined genomes of two separate species

  • Autopolyploidy: polypoid carries the duplicate genome of a single species

Thursday November 7th 2024 discussion

speciation

Sympatric populations: populations of different species/types that are partially or completely overlapping (geographically)

Allopatric populations: populations of different species/types that do not overlap geographically

















Friday November 8th 2024 lecture

Species interactions I: predator-prey dynamics

  • Symbiosis: an interation between two species living in close association with each other

    • Does not necessarily have to be a positive interaction

  • Fundamental niche: the abiotic conditions in which a species can survive and reproduce

  • Realized niche: the real conditions in which a species occurs in the wild - it incorporates biotic conditions as well as abiotic conditions

  • Batesian mimics: look like a harmful species

  • Mullerian mimics: group of species that are well-defended and look similar to each other

Wednesday november 13th 2024 lecture

Species interactions II: competition

  • Competition: when individuals require the same shared, limiting resource

    • Competitive exclusion: Two species competing for an identical limiting resource cannot coexist. Eventually, the stronger competitor will drive the weaker competitor to extinction

    • The more two species’ niches overlap, the more likely it is that competitive exclusion will occur

    • Less overlap allows for coexistence, and natural selection can lead to less overlap over generations

  • Resource partitioning: species coexist by using resources in different ways

    • Ex: Use different physical locations in the habitat or use different “parts” of the resource

    • May arise due to natural selection reducing competition

    • Can reflect shorter-term behavioral changes

    • Character displacement: species competing for same resources may diverge in morphology due to natural selection

      • Takes place at evolutionary time scales, over generations