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BIOEE 1780: Prelims 2
Plantae
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Domain Eukarya; Supergroup under Bikonts (2 flagella); also known as Archaeplastida. All members contain primary chloroplast
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Chloroplasts of Plants
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- All derived from primary endosymbiosis of cyanobacteria
- Plant chloroplasts are bound by double membranes
- Photosynthetic membranes = arranged in stacks (grana) in higher plants
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Photopigments in primary chloroplast and cyanobacterium
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Chlorophyll a = absorbs violet-blue and orange-red light
Carotenoids = (eg beta carotene) absorb blue light
Phycocyanin = absorbing orange and red light
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Eukaryotes Characteristics
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Red Algae, Green Algae, Land Plants = all have primary chloroplasts
Those three + Unikonts, Excavates, Rhizaria, Chromalveolates = all have mitochondria
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Eukarya --> Plantae Phyla
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Glaucophytes, Red Algae, Green Algae (various types, mostly chlorophytes), Land Plants (Embryophytes)
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Glaucophytes
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- Single celled, marine; only 13 spp!
- Chloroplasts are called cyanelles
- Membranes are not arranged into stacks
- Peptidoglycan layer under outer membrane
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Red Algae
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- Red Pigment = phycoerythrin
- Almost all are multicellular, marine
- Chloroplasts lack peptidoglycan
- Membranes are not stacked
- Store special starch granule
- Sushi, nori, agar
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Green Algae
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- Freshwater, marine, symbionts
- Single-celled, filaments, sheets
- Experiment with multicellularity
--- Volvox: 50,000 sterile vegetative somatic cells retain cytoplasmic connections and flagella; reproductive (germ) cells are protected on the inside
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Problem with Plants Moving to Land
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1. Desiccation
2. Physical support
3. Movement of nutrients
4. Increased UV radiation
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Land Plants - Liverworts
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- Sheets of cells (1n) on the ground
- Spore bearing structures (2n)
- Evolved metabolic pathway for anthocyanidin pigments
- Anthocyanidins are deposited facultatively in cell wall when
the plant is exposed to sun
- Pigment absorbs UV (240, 280,330nm) and blue (495nm); protects the plant from UV damage
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Land Plants - Mosses
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- Spore bearing structures (2n) stand up
- Carpet of haploid (1n) plants
- Membranes start to appear in stacks, but plastid still requires peptidoglycan gene MurE, for proper division
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Mosses and all Higher Plants have... (2)
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Stomata = control water loss during gas exchange
Waxy suberin in cuticle = reduces desiccation
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Alternation of Generations
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- Within the life cycle, organisms may alternate between a diploid phase (2n) and a haploid phase (1n)
- Similar in plants: 2n phase = sporophyte ; 1n phase = gametophyte
- Plants evolved to have the sporophyte as the dominant phase
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Selective benefits of plants having evolved to have the sporophyte phase as dominant?
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1. Sporophyte is diploid, thus may be buffered against deleterious mutations
2. Big diploid sporophyte nurtures tiny haploid gametophyte
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Earliest vascular plants
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- Sporophytes found in late Silurian (420 mybp) deposits in Britain reveal vascular tubes
- These also contain stomata, as with sporophytes of mosses
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Hierarchy of Land Plants
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Land Plants (mosses, liverworts + vascular&seed plants) --> Vascular Plants (lycophytes, horsetails, lepto ferns + seed plants)--> Seed Plants (angio and gymno sperms)
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Lycophytes (club mosses)
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- Land Plants --> Vascular Plants
- Common in moist woodland understory
- Comprised vast forests in Carboniferous Period
- Unlike the roots of higher plants, roots of lycophytes always
bifurcate evenly
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Horsetails
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- Land Plants --> Vascular Plants
- Common in moist areas
- Gametophyte is small, sporophyte is big
- Flagellated gametes need to swim
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Ferns
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- Land Plants --> Vascular Plants
- Common in moist areas; can be HUGE or tiny
- Gametophyte is small, but still photosynthetic. Sporophyte is big.
- Gametes lack flagella, but still need water
- Spores are produced in clusters on the underside of fronds
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Vascular/support systems: Xylem
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- Lycophytes and all higher plants have true roots to anchor themselves and move water/minerals from the soil up into the plant
- In all vascular plants xylem cells die and become hollow for
transport of water and minerals
- Dead vascular tissue also provides structural support. In
higher vascular plants, new xylem grows yearly, increasing strength
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Vascular/support systems: Phloem
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- Even primitive vascular plants have tubes of dead cells, tracheids, that carry the products of photosynthesis from leaves to sinks that have high energy demands, such as growing shoots, leaves, etc.
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Why get big? [Plants] (2)
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- Competition for sunlight
- Enlarged surface area for photosynthesis (eg leaves)
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Seeds and pollen
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- Characterize the seed plants and contribute to their success
- Pollen is the MALE gametophyte that is composed of 3-4 cells that disperse
- The seed is desiccation resistant and packed with nutrients
- Seeds comprise three generations
1. A coat from a sporophytes
2. Nutritive gametophyte tissue
3. The next sporophyte zygote
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Gymnosperms
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- Land Plants --> Vascular Plants --> Seed Plants
=- "Naked seeds"
- Gametophyte is multicellular, but no longer photosynthetic
- Cycads = tropical, spiny, most are short, female plants produce large spore-bearing structures
- Ginkgo = "Living fossil tree"
- Conifers = all are woody trees; dominant in Boreal forests.
Includes the largest and oldest living land organisms, eg redwoods, Great Basin Pine
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Angiosperms
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- Land Plants --> Vascular Plants --> Seed Plants
- What makes them special:
1. Double Fertilization
2. Flowers
3. Fruit
- One sperm fertilizes the egg resulting in diploid sporophyte
- Second sperm combines with 2 haploid egg nuclei to form
the highly nutritious triploid (3n) endosperm (wheat, rice, barley, corn, beans)
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Flowers
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- Inconspicuous in some species (wind pollinated)
- co-evolved with animal pollinators, showy to advertise nectar reward
- petals provide a landing platform, UV absorbing patterns point to nectar
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Fruit
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- Swollen ovarian tissue surrounding the seed(s)
- Some co-evolved with seed dispersers, others simply provide fertilizer for the seed
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Two Major Radiations within Angiosperms
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MONOCOTS
- seed sprouts; a single cotyledon (seed leaf)
- grasses, include grains, orchids, palms, lillies, sedges
EUDICOTS
- seed sprouts; two cotyledons
- legumes, including beans, most non-coniferous trees and nuts, crucifers, citrus
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Fungal Structure
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- Fungal cell walls contain chitin (a beta 1,4 polysacc)
- Fungal bodies are composed of tubular filamentous hyphae perforated by septa that allow passage of organelles: mass of hyphae called a mycelium
- Acquire nutrition by absorptive heterotrophy = hyphae secrete digestive enzymes and absorb nutrients. Their biochemical range rivals that of prokaryotic organisms (digest cotton, cellulose, uniforms, tents, kerosene, jet fuel)
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Fungi reproduce... (2)
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1. Asexually (1n)
- mitosis; identical spores
2. Sexually (2n or n + n)
- mating of different strains; meiosis: fusion of nuclei and cytoplasm.
- diverse looking fruiting bodies
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Fungi Phylogeny = Microsporidia
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- Reduced mitochondria, polar tube
- Very small; all are intracellular parasites and infect via polar tube
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Fungi Phylogeny = Chytrids
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- Probably paraphyletic; still retained flagellated (unikont) zoospore
- Infects skin, especially of frogs: causes severe electrolyte imbalance --> cardiac arrest
- Caused 90-120 amphibian extinctions since 1980
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Fungi Phylogeny = Zygomycota
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- Probably paraphyletic
- Most are microscopic, except for sporangium
- Most have a zygospore (diploid repro stage) (orgiastic karyogamy and meiosis)
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Types of Zygomycota
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- Black bread mold and tempeh (fermented soybeans)
- Trichomycetes are gut symbionts that digest cellulose for termites
- Entomophthorales are specific pathogens
of many groups of insects
- Glassy Hat Thrower = grows on dung of herbivores, sporangia are phototrophic; launch spores onto grass, herbivores eat it, poop out spores in nutrient medium
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Glomeromycota (arbuscular mycorrhizae)
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- Form mycorrhizae with 90% of plants, esp herbacious species
- Penetrate cell wall but not the plasma membrane
- Fungus gets photosynthate, Plant gets increased surface area for acquisition of soil nutrients, moisture, fungal nutrients
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Dikarya
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- Sexual life stage with two unfused nuceli
- +90% of all fungi
- Ascomycota = sac/cap fungi: produces spores as an ascus
- Basidiomycota = club fungi: produce spore in basidium
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Ascomycota include...
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- Cup/sac fungi = sexual reproduction and meiosis produces 8 ascospores within an ascus; discharged by turgor pressure
- Morels = conglomerate of cups lined with asci
- Truffles = Ectomycorrhizal; asci no longer shoot spores
- Yeast = many single-celled fungi; asexual budding, ferments sugars to ethanol and CO2
- Lichens = as a whole reproduces by fragmentation or by soredia; fungal partners may reproduce independently by ascospores
- Nematode wranglers = specialized structures to capture nematodes (eg three cell lassos) or just sticky hyphae
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Basidiomycota
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- Sexual reproduction and meiosis produce 4 basidiospores on a basidium; spores are discharged passively
- Rust and smut = serious pathogens of plants; some life cycles are very complex with several hosts
Brackets = grow on live or dead wood
Mushrooms !
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Genetic Definition of Evolution
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- Evolution is any genetic change in a population. Genetic change may occur through natural selection, genetic drift, migration and/or mutation.
- Evolution is any change in allele frequency of a population over time.
- Microevolutionary and macroevolutionary processes are fundamentally similar = microev IS macroev drawn out over longer time scales
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Population Genetics : definition
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The study of evolutionary processes within populations over small time scales.
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Phenotype can be determined by:
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- an individual's genes
- environmental conditions (phenotypic plasticity)
- interactions between genes and environment
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Define: population, gene, locus, allele
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- Population = group of interbreeding individuals
- Gene = a functional segment of DNA
- Locus = any defined segment of DNA
- Allele = variant version of a gene or another genetic locus: can always be identified by DNA differences, sometimes from single-gene traits.
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Define: polymorphism, monomorphism, genotype
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- Polymorphism = multiple alleles segregating the population, passed between generations
- Monomorphism = only one allele in the population
- Genotype = particular combination of two alleles carried by a diploid individual; genetic makeup of an organism vs. the actual physical characteristics (phenotype)
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Mutation
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- Where genetic variation comes from
- Any heritable changes to DNA
- Variants shuffled by meiotic recombination, moved around by dispersal
- Can be inconsequential, deleterious or advantageous
- Genetic mutations aren't THAT rare... 10/individual/gen
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Types of Mutations
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- Point Mutations
-- Synonymous
-- Nonsynonymous
- Insertions and Deletions
- Regulatory Mutations
-- Gain of function
-- Loss of function
- Aneuploidies
- Polyploidies
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Point Mutations
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- Any mutation that alters a single nucleotide base
- Synonymous/Silent Mutations = substitutions that do not cause aa changes: no functional consequence
- Nonsynonymous/Replacement Mutations = substitutions that DO cause aa changes
- Progeria, Hemophilia, Sickle Cell Anemia = Point Mutation Diseases
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Insertions and Deletions
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- Insertions or deletions that aren't multiples of 3 bases = FRAME SHIFT mutation
- Insertions or deletions that are multiples of 3 bases = preserve reading frame, cause insertion or deletion of an aa
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Regulatory Mutations
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- Mutations in the upstream regulatory region of a gene can change its expression level
- 'Gain of function' mutations
-- does not destroy allelic function, creates a novel function or expression pattern
- 'Loss of function' mutations
-- frameshift insertion/deletions; large deletions,
-- some point mutations at critical nucleotide sites
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All microevolutionary change can be explained by 4 basic processes (what causes allele freqs to change):
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- Mutation = raw material for evo change; mechanism of evolution that changes allele frequencies
- Natural Selection = advantageous alleles will increase in freq over time in a population
- Genetic Drift = chance events can alter allele freqs in pops
- Gene Flow/Migration = movement of individuals
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Hardy Weinberg Equilibrium (Equation + Null Hypothesis)
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- p^2 + 2pq + q^2 = 1
- use to predict genotype frequencies in next generation
- H-W Equilibrium serves as a 'null model' that allows
us to explore the effects of these evolutionary
mechanisms.
- A single generation of random mating is required to return the population genotypes to HW proportions after alteration of a population by an evolutionary force
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Assumptions underlying HWE
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• No mutation
• No selection
• No migration
• Infinite population size (no genetic drift)
• Random mating
(• Diploid, sexually reproducing organism )
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Natural Selection
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- Happens when individuals (genotypes) vary in fitness, due to some having higher rates of survival and/or reproduction.
- There must be phenotypic variation in the population, and that phenotypic variation has to affect fitness.
- The phenotypic variation that affects fitness must be inherited from parent to offspring. (Non-genetic phenotypic variation does not contribute to evolution.)
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Fitness and 2 Ways of Considering It
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- Depends on genes and environmental context.
- 1. Absolute fitness (R) = the raw 'success' of each genotype; Ri
2. Relative fitness (wi) = The fitness of genotype i relative to some reference genotype (usually the genotype with the highest absolute fitness)
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Relative Fitness (wi)
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wi = Ri / Rref
- Relative contribution made, on average, to the next generation by individuals of a particular genotype.
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Selection Coefficient
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- Degree to which a given genotype has lower relative fitness than the reference. Selection coefficients apply to GENOtypes
- It is arbitrary that we focus on selection against less fit genotypes rather than selection for more fit genotypes.
- si = wref - wi
- si is a measure of the strength of selection against genotype i
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Two common modes of natural selection:
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Ways in which selection can act on PHENOTYPES:
- Purifying (stabilizing) selection = selection against deleterious alleles; strong purifying selection can cause a
departure from Hardy-Weinberg Equilibrium.
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Why isn't purifying selection perfectly effective
at removing deleterious alleles?
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- not all phenotypic variation has a simple genetic basis
- deleterious recessive alleles can be 'sheltered' in heterozygotes
- mutation continually introduces genetic variation into populations; much of it is deleterious
- Even weak purifying selection leaves a 'footprint' at the DNA level
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Mutation-selection balance
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If mutation is continuously producing an allele "a" and selection is continuously trying to eliminate it, there must be
an equilibrium frequency, qeq, when selection and mutation
are operating with the same efficiency!
- for a purely recessive mutation: qeq ≈ sqrt(µ/s)
- for a lethal recessive mutation where s = 1.0: qeq = sqrt(µ)
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Even weak purifying selection leaves a 'footprint' at the DNA level
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1. Most mutations that cause an amino acid change are deleterious
2.Purifying selection will be stronger against deleterious mutations than against neutral (inconsequential) mutations
3.Therefore most polymorphism in coding regions will be synonymous (non=amino acid changing)
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Directional (positive) Selection
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- genetically simple directional selection
- the advantageous allele p eventually reaches a frequency of 1.0: no further evolution - becomes fixed for advantageous allele
- rate of fixation depends on whether the positively selected allele is dominant, recessive, or co-dominant.
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Heterozygote inferiority (underdominance)
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- Selection will ultimately "fix" one or the other allele, with the other allele completely lost.
- Genetic polymorphism is short-lived within populations.
- Perhaps underdominance was important in early human evolution...
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Genetic Drift
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Random Genetic Drift is more pervasive than the consequences of rare events.
- Real populations are finite in size.
- Random sampling of gametes from the gene pool does not assure accurate replication of allele frequencies in the resulting zygotes.
- The smaller the population, the more random error is expected when gametes are sampled to make a new
generation.
- Drift is evolution, but is not adaptive.
- Drift reduces genetic variation within populations and causes divergence among isolated populations.
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Independent probabilities are ________.
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Multiplicative.
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The probability that an allele will ultimately
become fixed is equal to ...
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- Its current frequency in the population.
- A brand new mutation that arises in a population of N diploid individuals has an ultimately probability of fixation equal to 1/(2N).
- Probability of fixation has no memory
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Genetic Drift vs Mutation
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- Genetic drift is a force that reduces genetic variation
in populations. Mutation is a force that increases genetic variation in populations.
- There is an equilibrium between drift and mutation that predicts the level of heterozygosity expected in a population.
- In very small populations genetic drift is strong. It can either reinforce or counteract the effects of selection. In very large populations, drift is minimal and selection is more powerful.
- The relative importance of genetic drift versus selection depends on the effective population size
(Ne) and the selection coefficient(s).
-- If Ne *s < 1, drift rules
-- If Ne *s >> 1, selection rules
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Population Bottlenecks
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- Temporary reductions in population size
- Often due to stochastic events: hurricanes, lava flows, reduction in habitat, etc.
- Alleles change in frequency due to chance sampling; accelerated random change in allele frequencies during bottleneck
- Loss of genetic variability, especially if the population stays
small for many generations
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Founder effect
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- Special case of population bottleneck
- A small population is founded by just a few individuals.
- Allele frequencies will be different (due to sampling error) from "parent" population.
- Founded populations will have lower genetic diversity.
- Allele frequencies will continue to drift in the founded
population, exacerbating the founder effect.
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Effective population size
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- Ne as the "genetic size" of the population; Ne is not the same as the census population size, N.
- They do not all make equivalent genetic contributions to the next generation. That variance in reproductive success usually causes Ne << N.
- Ne determines the amount of genetic drift and the effectiveness of natural selection.
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Several Modes of Selection
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1. Selection reducing variation within populations
• purifying (negative) selection
• mutation-selection balance
• Positive selection
• Heterozygote inferiority
2. Selection increasing variation within populations
• Heterozygote superiority
• Frequency dependent selection
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Heterozygote superiority (overdominance)
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- eg sickle cell anemia
- over time, the frequencies of the A1and A2 alleles find an equilibrium at intermediate frequency. When the two homozygotes have the same fitness, the equilibrium frequency p = q = 0.5, when they are different the
equilibrium frequency will NOT be p = q = 0.5.
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Frequency dependent selection
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- The fitness of an allele or genotype is not constant, but depends on its frequency in the population.
- Negative frequency dependence: rare alleles/genotypes have higher fitness than common ones.
- With two alleles, negative frequency dependent selection has the same equilibrium properties as heterozygote superiority.
- Self-incompatibility in plants
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Genetic Drift Mechanisms
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• Tree falls and other sudden calamities
• Alleles frequency changes each generation due to chance
sampling of gametes
• Population bottlenecks and founder effects
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Migration
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- Causes genotype frequencies to deviate from Hardy-Weinberg expectations.
- For "migration" to have an evolutionary impact, immigrants must reproduce successfully
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Gene Flow
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- The movement and incorporation of genes from one population into the gene pool of another population.
- Causes homogenization of populations and therefore opposes diversifying evolution due to selection and genetic drift
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Isolated island populations
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- often genetically distinct from the mainland
- Strong genetic drift due to founder effects and/or continually small population size
- Different selection pressures than on mainland
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