Evolutionsbiologie
ETH Zürich
ETH Zürich
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Phylogeography
How did species get from one part of the world to another? 1. They were there when the supercontinent split 2. They got there on little rafts
Co-evolution and co-speciation
Predation, parasitism, mutualism can lead to co-evolution, Ex: Aphids and endosymbiotic bacteria mutualism, Aphids need amino acids and bacteria need nutrients
Watching co-option happen
Allows re.evolution of social complexity in Myxococcus xanthus; drives swarming on soft sugar and requires pili; can it regain the ability to swarm on soft agar? Gene for pili is removed but regain the ability to swarm... Another gene mutated and now has a similar function to the required=> ECM = evolved cooperative swarming
Co-option of a pre-existing trait for new function
Genetic mutation
Source of ultimate genetic variation? Mutation: Any change in DNA base-pair sequence; Recombination during meiosis? Reshuffling of existing variations into new combinations
Different kinds of mutation
Point mutation: change in a snigle base pair; Complementary base pairs: A-T, G-C; Linkage: tendency for alleles of different genes to be inherited together; Chromosome inversion: chromosome segment flips, changes linkage; Transitions (A => G, C => T) and Transversions (all other); silent site (synonymous) substitution; Point muation but no change; Loss-of-function mutations: inactivate a gene; Replacement (non-synonymous) substitutions: point mutations that lead to amino acid change; Polymorphism: different expression of gene in phenotype => chromosome with & without inversion exist; Polyploidy: more than 2 sets of chromosome; Indels: Insertion or deletion of a small number of bases; Selection Coefficient: difference in fitness caused through mutations; Nautral alleles: alleles without effect on fitness; Unequal crossing over: chromosomes trade unequal long sequences; Pseudogenes: nonfunctional loci => loss of function mutations; Paralogs, paralogous: homologous genes that are duplicated and then diverge in sequence; Othologs, orthologous: homologous genes that have diverged after speciation => found in different species
Mutation rates
Base-pair matching is amazingly accurate; 99'999'999/100'000'000 times without unrepaired mismatch; Mutations can decrease fidelity
Number of mutations in humans
6*10^9 bp per human diploid genome; 1.8*10^-8 mutaions per bp per generation => 100 mutations per baby; 7*10^9 on planet => 7*10^11 mutations in one replacement generation => 117 average muations per bp site in human population
Mutation accumulation lines in roundworm
Mutation Accumulation Treatment: transfer one randomly chosen worm per generation (individuals with reduces fitness survive); Cotrol Treatment: transfer many worms per generation
Most mutations lower fitness
Calculating mutation rates from mutaion accumulation lines: 25 replicate lineages, 500 generations, 130'000'000 base-pairs chromosome, total of 35'000 mutations among 25 terminal individuals => total # mutations / (# bp * # generations * # lineages) = 2.1*10^-8 mutations per bp per generation => 2.1*10^-5 mutations per gene per generation
Mutations rates & effects
Most mutations have a small negative effect on fitness; Selection coefficient is a quantitative measure how a mutation affects fitness
Does natural selection mold mutational rates?
Traditional loss-of-function studies indicate similar per genome per generation mutation rates for many species; Recent studies indicate significant variations => Heritable variation in DNA polymerase accuracy and DNA mismatch repair rate
De novo vs. standing variation
Life and reproduction => less than perfect copy of hereditary indorfmation; Most changes deleterious; De novo mutation: new alelles; Reshuffling of alleles (recombination) relies on standing variation
Mechanisms of gene dupliaction
1. Retro-transposition (mRNA without Introns transcribed into DNA) => duplicated genes without introns/regulatory regions in eukaryotes 2. Un-equal crossing over during meiosis => new copies with introns and regulatory regions 3. Whole chromosome/genome duplications
Mechanisms of gene introduction (horizontal gene transfer)
1. Free DNA transfer (transformation and conjugation) 2. Viral transfer (transduction)
Rates of gene duplication
Lynch/Conery: documented number of genes duplicated in each species, compare to age of species => average rate of gene duplications 0.01 per gene per mil. years; Higher frequency (by selection, drift) every several thousand years; Ex: 100 new genes in 1'000'000 years; Human-chimpanzee divergence estimated at 7.5 mil. years => 2.7% of genomes represent lineage-specific duplication
What happens to new gene copies over evolutionary time?
Can get lost; Can get deactivated and retained as pseudogene; Can diverge to serve different function; Can have (nearly) identical function by creating a (nearly) identical product
Inversions
Crossing over breaks up allele combinations and reduces linkage; Inversions can enforce genetic linkage => Genetically linked genes (super-gene) get inherited as one big gene; Inversions that lock in good allele combinations can be maintained; Breaks happen because of UV
Inversion clines
Change in frequency of an allele or an inversion over a geographic area is a cline; Ex: Drosophila fly, New World, Old World seperate populations mirror each others inversions => functional effect of inversion advantageous in colder climates => Independent Parallelism
Instant Genome Expansion: Whole Genome Duplications
Polyploidie; Common in self-fertilizers (monoecious species); More polyplod plants than animals; More than half angiosperms; Few animals, Ex: flatworms, earthworms, gold fish, salamanders; Massive input of genetic material; Leads to new species because the tetraploids and diploids offspring is not fertile, but when tetraploids mate, the offsrping is healthy
Summary of important mutations
Point mutation: Base pair substitution, chance errors in DNA synthesis, gets new alleles; Chromosome inversion: Flipping of chromosome segment, changes order of genes, breaks in DNA because of radiation, alleles inside inversion get transmitted as a unit; Gene duplication: extra copy of a sequence, unequal crossing-over in meiosis/retrotransposition, new genes acquire new functions; Genome duplications: new set of chromosomes, errors in meiosis, may create new species
Population genetics
Seeks to document: 1. Whether and how allele frequencies change 2. Why they change 3. Integration of Darwin's Theory by Natural Selection with Mendelian genetics
Calculating allele frequency
36 AA, 54 Aa, 14 aa => A: (35*2 + 54)/208 = 0.606; a (54 + 14*2)/208 = 0.394
Genetic drift
Randomly match sperms and eggs => random mating; Large sample, repeat over and over => Large population; In simulated populations allele frequencies change across generations => Evolution resulting from blind luck, genetic drift
Luck-free result of recombination
When blind luck plays no role, allele frequencies remain constant accoridng to Mendel => usually ther's no random mating, gametic equality and not all offspring survives
Hardy-Weinberg
In the absence of evolution any allele frequencies can be in equilibrium; p^2 + 2pq + q^2 = 1; No: Allele frequencies do not change, allele frequencies should be in an equilibrium (HWE), alelle frequencies are stable between 0 and 1; Yes: There's no HWE
HWE is a null model against whoch we can test if a population is evolving
Crucial assumptions for HWE
1. Infinite population size 2. Random mating 3. No Selection 4. No mutation 5. No migration 6. No chance evolution, genetic drift
HWE does not care about evolution
Signature of evolution in sexual diploid organisms
If the distribution of genotypes frequencies differs from the HWE-expectation calculated from known allele frequencies, we have evolution
Adding selection to HWE
Changes in allele frequencies; Selection coefficient proportion reproducing relative to most fit genotype = 1 - s; Ex: BB s = 0, Bb s = 0.25, bb s = 0.5; very strong selection, doesn't occur in nature
Calculating changes in genotype & allele frequencies due to selection
Ex: p(A) = 0.5, q(a) = 0.5, w(AA) = 1.0, w(Aa) = 0.7, w(aa) = 0.6; Average fitness for whole population: p^2*w(AA) + 2pq*w(Aa) + q^2*w(aa) = 0.75; Genotype frequencies after selection: f'(AA) = p^2*w(AA)*0.75 = 0.33>0.25, f'(Aa) = 0.47<0.5, f'(aa) = 0.2<0.25; Distribution of allele frequencies among gametes after selection and random mating: p'(A) = f'(AA) + 0.5*f'(Aa) = 0.57, q'(a) = 0.5*f'(Aa) + f'(aa) = 0.43; Check on significancy
Selection on recessive and dominant alleles
When s(aa) = 1 (lethal); When recessive allele common, speed of evolution is fast, when recessive allele rare, speed of evolution slow
Selection on heterozygotes
s(AA) = 1 => heterozygote superiority, stable equilibrium
Selection on homozygotes
s(Aa) = 1 => heterozygote inferiority, unstable equilibrium; One allele tends to go to fixation, the other gets lost but different populations may lose deiffrent alleles
Frequency-dependent selection
Flowers promise nectar to bumblebees; Naive bees tend to alternate between yellow and purple flowers => the rarer phenotype benefits => more visits per flower => better fitness
Selection can maintain two alleles in a population if each allele is advantageous when it's rare
Mutation fitness effects
Positive: rare, selected for increase; Neutral: more common, fate determined by drift or hitchhiking; Negative: very common, selected against; Mutation is a weak mechanism of evolution
Mutation-Selection Balance
Most mutations have negative effect => negative selection; Input rate of mutation from allele A1 to A2; Rate of decrease in population due to selection against A2; When rate of deleterious alleles that are being eliminated equals rate at which new copies are being created, the frequency is at equlibirium => Mutation-Selection Balance
q = sqrt(Mü/s); q = equilibrium frequency of mutant allele; Mü = rate of mutation to mutant allele; s = coefficient of selection against mutant allele
Example for a gene at mutation-selection balance
telSMN: Loss-of-function allele (deletion of chromosme 5 in humans) frequency q = 0.01; selection coefficient: s = 0.9 => Mü = 0.9*10^-4; Mutation-Selection balance for dominant lethal allele: q = Mü
Spinal muscular atrophy and cystic fibrosis => Mutation-selection balance?
Most common lethal autosomal recessive disease in humans; Cystic fibrosis is a hereditary, lethal disease, affected people carry two alleles of CFTR loss-of-function allele; frequency is 2% => Mü = 4*10^-4; BUT actual mutation rate is 7*10^-7; Salmonella use the missing protein to invade cells => trade-off between resistance to different intruders
Forces that cause evolutionary change
Forces affecting the fate of existing variation: slection, genetic drift, nonrandom mating migration; Forces putting in new variation: mutation, migration
Migration
It homogenizes populations if not opposed by other forces (like selection); Prevents populations from diverging; Ex: water snakes on mainland are banded, snakes on islands aren't (banded ones are eaten), some of the mainland snakes migrate to islands => banded allele to island gene pool => opposed selection
Genetic differentiation of populations
Fst values measure the degree to which seperate populations are genetically distinct; Fst = (genetic diversity across population) / (average geentic diversity within populations); Ex: Silene dioica: High Fst in youn pop, founder effect, Low Fst in intermediate pop due to gene flow, migration effect, High Fst in old pop, no longer exchanging genes
Genetic drift
Differential reproductive success that just happens (Selection happens for a reason); Genetic drift doesn't lead to adaptation, but leads to allele frequency changes; chance outcomes are most likel with little replication
