Molecular phylogenies 2 Flashcards
Bootstrapping
Bootstrapping is used to measure the uncertainty of the estimate of the phylogenetic tree.
It involves the permutations of the original data to create a large number of pseudoreplicates data sets.
A tree is generated from these data sets and the frequency with which clusters occur in these replicates is a measure of reliability.
> 70% is considered robust.
Long branches tend to be more robust as there has been more change so there is more power.
Molecular clock hypothesis
Molecular changes in genetic material (such as DNA or protein sequences) occur at a relatively constant rate over time.
This based on the theory of molecular evolution which assumes a more constant rate of molecular change compared to the selectionist model.
-> In moden molecular clocks the variation in evolutionary rates can be modelled
This means they can be used to work out the divergence dates and the date of the common ancestor.
Why can’t we look at morphological data?
There is a dramatic variability in morpholical evolution compared to molecular evolution.
Example:
Dog breeds: huge variation in the last 5000 years
Domesticated plants: huge variation in appearance (e.g. huge tomato vs small purple tomato)
Coalacanths: Little variation in the last 100,000,000 years.
Opposing theories of molecular evolutions: Neutralist positions and the selectionist position
What causes the molecular variations that can be seen?
Neutralist: Observed molecular variations are due to neutral mutations which do not confer a fitness advantage/ disadvantage, so they accumulate over time via drift.
Selectionist: Observed molecular variations are a result of natural selection where beneficial mutations increase in frequency and deleterious mutations decrease -> balancing, directional and frequency dependent selection.
These theories are not mutually exclusive, and both cases occur
But there is evidence that genes within an genome evolve at different rates and that species also evolve at different rates.
- Also even if all molecular variation was neutral and there was a constant mutation rate, substitution rate would not be constant due to varying population sizes.
What are modern molecular clocks used for?
1) Understanding why some genes/ gene regions/ species evolve faster than others.
-> compare the rate of evolution of different genes and look at their function.
2) To estimate timescale for phylogenies and evolutionary history
Different rates of evolution within the genomes
- Genes evolve at different rates depending on their evolutionary constraint
- Different regions of genes evolve at different rates (e.g. haem binding regions vs surface residues of haemoglobin or peptide binding vs non peptide region in MHC)
- Species evolve at different rates (e.g. Virus DNA vs plant DNA, lack of evolution in some species like crocadiles)
Why do we have different rates of evolution? (overview)
Substitution rate (rate of evolution = mutations rate x probaility of fixation x population size)
Probability of fixation is determined by the type of muations
- Neutral mutation: 1/N
- Advatageous mutation: 2 x N x u x S
- Deleterious mutation: 0
Different mutations rates
- varying metabolic rates
- Varying generation time
- Varying repair mechanisms
Different probability of fixation
- population size
- selective pressure
Substitution rate vs mutation rate
Mutation rate: the rate of error during replication
Substitution: the rate at which sequences in different populations diverge
Rate variation: selective pressures determining P
The type of mutation effects the selective pressure and therefore the probaility of fixation.
Neutral: p=1/N probability of fixation (genetic drift)
beneficial: p=2S probability of fixation (positive selection)
deleterious: p=0 probability of fixation (negative selection)
The region where the mutation occurs effects the selective pressure
- The more constraint the site/ gene the greater the selective pressure and lower substitution rates
- Example: Cytochrome is highely conserved enzyme important for respiration -> Highely conserved so can be compared to understand evo relationship between species.
Rate variation: population size
The smaller the population size, the more likely mutations are fixed by genetic drift and the substitution rate increases.
- deleterious mutations fixed by drift in small populations
- Purged by negative selection in large populations
But small popualtions often have longer generation times which counteract this.
Rate variation: mutation rate
Generation time: faster generation time, more opportunity for mutation. Some generations result in more mutations than others (Sperm production has more cell divisions than egg production)
-> Male mutations bias (e.g great apes show the highest rates and male germline goes through approximately 2.95 times more rounds of cell divisions (DNA replications) per generation than does the female germline in monotremes
Metabolic rate: Higher metabolic rate, more aerobic respiration leading to more free radicals and more mutations.
Efficiency of DNA repair: Highly transcribed genes have more efficient DNA repaire and therefore lower mutation rate (RNA viruses use a different polymerase which are error-prone to allow fast rate of evolution)
- E.g. INFLUENZA has approx one error per replication so each cell can produce 10,000 new viral mutants to infect neighboring cells
Turning genetic distances into divergence time
Genetic distances = evolutionary rate x (2x divergence time)
Calibrating phylogeny
Fossils: A node is fixed in time from a fossil and this is used to calibrate
Biogeography: Using life biogeographic data to estimate nodes of evolutionary event.
Example, genetic distance and island age on Hawaiian islands to decipher drosophila phylogeny.
Example: The formation of Panama, which isolated the tropical western Atlantic and eastern Pacific oceans between north and south america, is frequently used to infer rates of nucleotide sequence divergence (3.1–3.5 MYA)
Example: During the glacial maxima sea levels dropped leading to river systems across the shelf connecting the river basins of Southeast Asia and Western Indonesia. -> used to date cyprinoid fish populations
co-evolution: If two groups have co-evolved, then a timescale for one phylogeny can be used to calibrate the other.
Example: Dating feline virus phylogeny against cat phylogeny.
Example: Symbionts. Fig tree and fig wasps
Measurably evolving population: Rapidly evolving pathogens. Sample pathogen at different time points and use this to calibrate the tree -> knowing rate of evolution now, we can work backwards.
Making molecular clocks more realistic in terms of varying evolutionary rates
Strict clock: all branches have the same evolutionary rate
Local clock: Rate varies but is inherited, so adjacent branches have more similar rate
Relaxed clock: Rate varies among lineages with no restriction
Can create different trees for different parts of the genome which have evolved at different rate.
Overview:
Bootstrapping is a statistical method used test the robustness of a tree.
The branches of phylogenetic trees can represent time using a molecular clock.
Genetic distance = (2x divergence time) x evolutionary rate
The clock can be calibrated using different methods to work out then the time of divergence events and common ancestors.
It is important to understand molecular evolution to reliably carry out molecular clocks as they assume a constant rate of evolutionary change.
Two theories:
- Neutralist approach
- Selectionist approach
They are not mutually exclusive, and both neutral evolution and natural selection occur.
The molecular clock is based on the neutralist approach, as it assumes a constant rate of evolutionary change. Molecular clocks are often constructed by looking at neutral alleles where neutral evolution has occurred.
In modern models, evolutionary rates can be varied between lineages to make it more accurate (relaxed clock, relaxed clock).
Molecular clocks shows us:
1) Divergence time and most recent common ancestor
2) Helps us understand the variation in rates of evolution within genes, among genes, between species.
Substitution rate= mutation rate x population size x selective pressure
mutations rate
- metabolic rate
- generation time
- Repair mechanism
Selective pressure
- Type of mutations
- Position of mutation
Population size
