Final exam - LM4 Flashcards
How is genetic variation measured
polymorphisms
Measures of genetic diversity
- allele frequency
- heterozygosity
Forces which can act on allele frequency
- mutation
- selection
- migration
- random sampling/genetic drift
What does inbreeding change
genotype frequency but not allele frequency
Hardy weinberg
p2 + 2pq + q2 = 1
What does it mean if expected > observed in hardy weinberg
indicates inbreeding as loss of heterozygosity
Conditions of hardy weinberg
- no mutations
- no inbreeding
- no random genetic drift
- no gene flow
- no selection
Inbreeding on heterozygosity and homozygosity
- increases homozygosity
- decreases heterozygosity
Inbreeding coefficient
the probability of homozygosity by descent
Unrelated parents inbreeding coefficient
0
parent-offspring or brother-sister inbreeding coefficient
1/4
half sib inbreeding coefficient
1/8
first cousin inbreeding coefficient
1/16
Relative risk
F/q
Inbreeding deepression
- increased homozygotes for deleterious and lethal alleles
- decreased adaptiveness
- can only tolerate small range of environmental conditions
What does genetic drift cause
- loss of heterozygosity
- change in allele frequency
what does a loss of heterozygosity cause
decreased variation in allelic polymorphism
Selection
- differential rates of survival and reproduction resulting in changes of allele frequency
- successful individuals leave more copies of their alleles for next generation
fitness
observed/expecred
Types of natural selection
- directional
- stabilising
- disruptive
directional selection
- fitness of one homozygote is larger than other possibilities
stabilising selection
heterozygotes have greatest fitness
disruptive selection
homozygotes have greater fitness than heterozygotes
heterozygotes > homozygotes
- balanced polymorphism
- overdominance
- heterozygote advantage
- stabilising selection
homozygotes > heterozygotes
- unstable
- selection against heterozygotes
- underdominance
- disruptive
Discrete traits
few genes for phenotype
Quantitative traits
continuous phenotype, many genes acting together
What is a quantitative trait described by
mean and standard deviation
Familial variation
- relatives resemble one another more than randomly selected individuals
- shared genotypes
- relatives tend to have similar enviro conditions
Heritable
variation in phenotype caused by variation in genotypes
Additive gene action
combination of alleles contribute to trait
Phenotypic variance
genetic variance and enviro variance
Genetic variance
additive gene variance and dominance variance
Broad sense heritability
- genetic variance/phenotypic variance
- proportion of variance due to genetic differences rather than enviro
Narrow sense heritability
- additive genetic variance/ phenotypic variance
- used to compare offspring and parents
Why is narrow heritability used rather than broad heritability
parents pass a single allele so dont pass dominance effect on so only additive effects
Heritability in a stable environment
higher heritability as enviro variance is low
Selection differential
- difference between optimum (parents) and mean of population
- selected parents - average
selection response
- difference between mean trait value for off spring and previous generation
- narrow x selection differential
How is the location of major genes inferred
association mapping with gene markers
Quantitative trait locus
a gene affecting a complex phenotype
2 methods of detecting a major QTL
- linkage mapping for families
- association mapping in populations
How to know if something is a QTL
different genotypes have different mean phenotypes
Genetic markers
- RFLP
- Microsatellites
- SNPs
Linkage disequilibrium
- non random association of alleles across nearby loci in genome
- marker is a good prediction of causative agent
- marker must be very tightly linked so isnt broken up during meiosis
Linkage equilibrium
random association
3 types of information in molecular archive
- approximate time of existence of a molecular ancestor common to the sequences that are being compared
- probable AA sequence of ancestral protein
- lines of descent along which given changes in AA occured
Pan selectionist view
- speed and direction of macroevolution determined by natural selection and not mutation
- neutral mutations are rare so random genetic drift plays no role in evolution
Neutral theory
-diversity from evolution greater than just that from selection
- alleles have equal fitness
- most diversity is from random mutation and random genetic drift
challenges in identifying neutral mutations
- estimation of fitness
- distinguishing neutral from deleterious or beneficial
Why do different proteins evolve at different rates
depends on how any changes can be made without affecting function
Rate of clock
D/2T
complications of molecular clock
- relative rate isnt constant between all species as influenced by metabolism, generation time, DNA repair
- calculation of rate is dependent of correct phylogeny
Phylogenetic tree
evolutionary history of a group of organisms can be represented as a branching diagram
3 types of homology
- orthologous
- paralogous
- xenologous
Orthologous homology
homologous gene that diverge via speciation
Paralogous homology
gene that diverge via gene duplication events
Xenologous homology
genes that diverge via lateral gene transfer between genomes
Manuka species
- native in both NZ and AUS
- using molecular clock with 12 fossils diverged 16MYA
- whole genome sequencing found that NZ manuka arrived 9-12MYA
- species are distinct with different chemical compositions and morphological differences
- regional differences are genetic
speciation
the evolutionary process by which populations evolve to become distinct species
Allopatric speciation
- species seperate as reproductively isolated
- unique mutations will eventually occur in each species making them genetically different
Stochastic lineage sorting
- divergence between gene sequences can occur at different time than speciation
- random due to genetic drift but eventually an allele gets fixed
modern phylogenetics
have become phylogenomics which is a comparison of whole genome sequences which averages out the stochastic sorting of individual genes
Hybridisation
- can be random or non random
- makes gene sequences look more similar between species
- non random = selection
Human evolution
- homo erectus evolved 2MYA and migrated out of Africa
- modern humans arose in Africa 200,000YA then migrated out of africa to replace homo erectus
- neanderthals appeared 400,000YA and likely hybridised with modern humans
- neanderthal hybridisation occcured randomly and non randomly of the lipid catabolism genes
- also seen denisovan hybridisation
Problem with ancient DNA
degrades fast so there is an effective time limit
Nuclear DNA via mitochondrial DNA
- nuclear DNA has less copies
- amplification of nuclear DNA via PCR is vulnerable to contamination
3 requirements for evolution via natural selection
- variation in trait must exist
- variation must be heritable
- differential survival and reproduction on the basis of the variable trait
What is adaptive evolution
the incorporation of beneficial alleles
purifying selection
remove negative mutations and keep positive mutations
Adaptive evolution in australian sheep blowfly
- introduced to NZ
- lay eggs in sheep flesh
- develped resistance to insecticide by 2 changes in amino acids
Adaptive evolution in E.coli
- order in which the antibiotic resistant alleles are important to giving the E.coli fitness
Evo devo
regulatory genes affecting the timing and distribution of gene expression throughout an organisms development
Adaptive regulatory evolution in drosophila
- melangaster and biarmipes have different phenotype
- biarmipes has a black patch on its wing
- in biarmipes the regulatory sequence in the wing for the gene is upregulated so increased melanin deposits
adaptive regulatory evolution in stickleback fish
- in deep water they will have pelvic spines
- shallow fish have no pelvic spines
- deep water fish keep spines as similar selection pressures as ancestors
- in shallow fish the regulatory gene is off
Types of gene duplication
- polyploidy = whole genome duplication
- misalignment of DNA during meiosis
- retrotransposition
Types of duplicated genes
- neofunctionalization =genes evolve to a new function
- deleterious will be deactivated = pseudogene
- subfunctionalization = function split between 2 copies where each copy performs only part of function
