Topics 4-8 Flashcards
What are the principles of the Hardy Weinberg Equilibrium?
- Infinitely large population
- Random mating
- No selection for/against phenotypes
- No net migration
- No net mutation
Is allele variation greater in small or larger pops?
“Greater in smaller
Consider the impact of killing 30 humans from a population of 200, vs 30 in a pop of 1 million, what impact does this have on allele frequency?
How does drift affect genotypic ratios?
Any change in allele frequency results in very large change in pheno frequencies, but drift may result in more bad homozygosities (since non selectional, bad phenotypes aren’t selected against)
Drift may decrease diversity as well (could also increase it), or cause fixation (e.g kill all the remaining 10 smart humans by accident and youll fix the stupid genes)
What is the expected number of heterozygotes?
2pq(1-F) (recall F means autozygous, so remove any potential for heteros)
What does inbreeding do to allelic frequencies?
nothing, but will increase chance of autozygosity (recall grandpa example, you may be less diverse than grandpa)
How to calculate the inbreeding coefficient?
2pq-observed(heterozygotes)
/
2pq
What does polygenetic mean?
Trait influenced by many loci
What is the difference in broad sense vs narrow sense heritability?
Broad sense heritability
reflects all of the genetic contributions to a trait’s phenotypic variance, including additive, dominant, and epistatic gene effects. It also includes influences of the parent phenotype (maternal and paternal effects) on the environment of offspring that can cause siblings to resemble each other.
Narrow sense heritability
more accurately reflects the contributions of specific, additive components of genetic variation to offspring.
What does hertability measure?
Proportion of phenotypic variances attributable to genetics
When the selection differential is larger, what does this mean?
- Selective pressure is stronger(strength of selection)
- Individuals who differ more from the mean have higher reproductive success
REcallselection intensity is different, it is a measure of the change in mean value/phenotypipic standard deviation
What is the formula for intensity of selection?
Za-Zb/SD(phenotype)
Note”Za and Zb are the mean sizes of the traits(ie means)
What is the formula for the selection variance?
j=Va-Vb/Vb
j is selection on variance
Where V is the variance, a and b are after and before
What are the important conclusions of the experiment on Daphne Major?
- Intensity of selection may vary
- Direction of selective presure can change
- Evolution in morphology can be quite fast!
What is ecological character displacement?
Evolution is driven by competition in a way such that the species involved evolve to reduce overlap in resource use/niche
What is selective sweep?
Very strong selection for favourable alles to be fixed
What is hitchhiking?
Loci on either side of allele (being selected for) increase in frequency due to another gene undergoing a selective sweep
In particular, what causes the loss of armour in freshwater 3 spined sticklebacks?
Lack of nutrients
Lack of predation (predators less common in lakes)
What does the selection gradient measure?
The degree to which selection is occuring
What are orthologs?
Homologous sequences separated by speciation
Occur in different species
Where are paralogs found?
Within the same species, due to duplication event
Paralogs are homologous sequences
What are the pros and cons of molecular phylogenies?
Pros:
- Character state identification is unambigious
(compared with morphology)
- Millions of states available to construct trees
Cons:
- Require extant taxa
-DNA only lasts approximately 100k years, and will be fragmented
- Harder to determine homology vs homoplasy (since independent mutation can causef same change, and sequence may appear ancestral)
Outline the principles for the common methods of molecular phylogenetic construction
- Maximum Parsimony
- simplest tree is best
- give greater weight to trees less prone to homoplasy
- - Neighbor joining
- build trees based on genetic distance of taxa (do not need to know ancestral derived traits)
- needs lots of data
3.Maximum likelihood
- takes advantage knowing mutations are more likely to occur in certain DNA regions - Bayesian
- uses inverse probability
- tweak a tree until you reach its maximum probability
Note: ML and Bayesian in particular can require days, and lots of comput
True or False:
Human genetic variation is greatest outside of Africa because the evolutionary background?
FALSE:
Greatest variation is IN AFRICA
This is a benefit of molecular phylogenies,
Define neutral evolution
Much of variation observed in genome was due to drift, rather than natural selection
What are the predictions of neutral evolution?
- Rate of mutation is constant/predictable
- Mutations should accumulate more rapidly in areas of genome that dont influence phenotype (synnonymous mutations occur more rapidly then non-synonymous)
e.g pseudogene
What is neutral theory?
Null hypothesis for no natural selection
(most variation has no impact on fitness)
If rates of mutation differ -> null hypothesis rejected -> selection could be taking place
What is some evidence for neutral theory?
Linear relationship of mutation accumulation of cytochrome c gene in pairs of mammals, with time
What is the point behind a molecular clock
Give an example of its use
Since neutral mutations accumulate at constant rate as per neutral theory, can look at mutation differences to estimate divergence time of taxa
e.g more mutations between species indicates longer time since divergence
Clock tells you how much time has passed, you must also have anchor!
When are molecular clocks inaccurate?
- When determining relations among species that are long diverged
- ## Reversals can occur too
;……………………………………………………………..
What is the relation of differentiation between two closely related species?
Differentiation slope will be great, but will eventually plateau because mutations will begin to overwrite old sequences
Why is neutral theory not correct?
Note: Still use it as a hypothesis
Sequence divergence rates are negatively correlated with bozy size, metabolic rate (endotherms diverge faster than ectotherms)
Ie sequence differences are less among larger organisms
How do you calculate the selection intensity i?
Note:
Selection differential is S
Selection gradient B:
Selection Intensity i:
i=Zbar,before-Zbar,after/Sqrt(Vp)
Ie i is the difference in means/SD(phenotype_
How can we measure selection?
- Survivorship comparison
- Selection gradient measurements
What is saturation in molecular clocks?
When taxa diverge, initally BP difference slope is great, however after ~10-20 million years, mutations overwrite, reversals occur causing slope to plateau (ie differences accumulate slower, less informative)
Broadly describe the role of Hox genes
They are a patterning gene (during early devoplment, patterns embryo for later developlment)
- acts as a master switch for gene cascading
What explains how Hox gene cluster has such diverse function?
Duplication events, allow for one gene to be tinkered on, while one remains functional
What are the costs of sex?
- Costs associated with finding mate
- Chance of STIs
- Beneficial combinations of alleles may be lost (reduced relatedness)
e.g maybe blonde hair is beneficial but having sex may mean children may not be blonde
-males cannot produce offspring?
What are the benefits of sex?
- You look cool man
- You are cool
- Feels good
JK
- genetic variation
- potential to create novel combination of alleles (create the ultimate child!)
- more variation = more chance for evolution
- clearance of deleterious alleles (note: without sex it is essentially impossible to clear bad alleles, this is called Muller’s Ratchet
- If not clearance of bad alleles, then at least they can be outbred
Compare the male and female sexual reproductive strategy
Females:
If gamete is larger: female
-Females are choosier
-It is rarely beneficial for females to mate often (choosy)
Males:
- It is rarely beneficial to be choosy
- Mating with substandard female rarely reduces reproductive success
- The only thing that limits male success is availability of eggs/mates
Generally speaking, do females invest as much into deterence, showyness?
No!
Females tend to have their reproductive success tied to their individual fecundity
MORE EGGS= MORE OFFSPRING
What sort of development occurs for males, when a female can or cannot be monopolized
If the female can be monopolized:
- characters selected for include:
- size, agression, horns (generally deterrants)
If females cannot be monopolized (e.g female is stronger, rare)
-intrasexual selection acts to increase sperm output, quality
Why is variation in reproductive success among males so large in species where males take harems?
Only the largest males mate, thus contribute greatly,
True or false:
Great variance in reproductive success enables intense selection
TRUE!
Only a few mate (with desired characteristic)
while the rest do not pass down genes leads to great evolution
If a female is polygamous, how much energy should be invested into quality or quantity of sperm?
More then if the female was monogamous
e.g testis weight relative to body size is related to polygamy, monogamous species have smaller testes (also reduces dimorphism)
Why do peacocks look so different from peahens?
The variation in the males reproductive success generates intense selection resulting in great dimorphisms
When will the overall sex ratio of a population be equal?
Note: In sexual pops, will generalyl be 50:50
but to be specific:
Population should be entirely sexual and biparental
Larger pops have less or more genetic stability?
More! Larger pops have less allelic variation, smaller pops have more allele variation and thus are genetically unstable as a result of genetic drift
Caveat Drift can cause nonselective fluctuation but also cause fixation
Why is inbreeding bad?
Inbreeding could increase homozygosity, which could bring deleterious recessive alleles forward, this is inbreeding depression
What is variation due to interactions?
Variance due to interactions
This variance is a result of expression of one gene being tied to expression of another:
Note Va is additive variance: due to additive affects of alleles
Example of episatic/interactions: albinism
What is the difference between narrow sense heritability and broad sense heritability?
h2=Va/Vp
H2=Vg/Vp
What is indicated by a change in the range of phenotypic values within a generation?
This change in the variance of phenotypic values, could indicate stabililizing or diversifiying selection, and can indicate a selection on the variance, represented by j.
Which molecular phylogenetic technique involes giving greater weighting to genes less prone to homoplasy?
Maximium parsimony,
also involves bootstrapping to test most parsimonious tree branching
Bootstrapping is done to all trees?
No, only to the most parsimonious, then build the best tree using the randomly sampled traits
Neighbor joining requires a lot of computing power?
No! It is very quick
Which molecular phylogenetic methods require the most computing power, and are based on prior knowledge?
ML and Bayesian
Recall
NJ: Look at character states and build tree
MP: Build trees based on character states
Outline the principle of maximum likelihood
Given a sequence, computer calculates a model (based on some mutations being more likely)
Given each tree, the probability of observing the date set given the tree and model are calculated, the tree is then assigned a maximum likelihood
Restate the predictions of neutral theory
1.Mutation rate is constant
2. Mutations should accumulate more rapidly in areas of genome that don’t influence phenotype (no selection)
e.g silent mutations accumulate more rapidly then non silent
If the rate of silent mutations is greater than non silent, what is happening?
If the mutations which don’t affect phenotype are accumulating, then extreme phenotypes are being selected against, ie variation from the mean is selected against, so STABILIZING SELECTION
Is eukaryotic genome correlated with # of protein encoding genes
No, our genomes are very bloated, compared to bacteria who have streamlined genomes
What explains how small some bacteria genomes are?
They have abandoned some of their genes in favour of their host’ functions
AlsO: Less time to multiply if smaller genome
True or false:
Variation in eukaryotic genome can be easily explained
No, it really makes no sense, corn has a massive genome size for no reason
How did bacteria develop the ability to metabolize citrate?
Duplication in a regulatory area of a cis element allowed CitT expression
How did snake venom evolve?
A defensin gene was duplicated, resulted in a change of regulation and location of expression (venom may have evolved in a common ancestor of snakes)
What did we use the red queen analogy for?
Parasite and host are constantly trying to out evolve each other (explains why parasite needs to be diverse)
In grey tree frogs (lec 8) what do females prefer?
Long, more complex call in males
Iteroparity is accompanied by?
Lower survival for reproducing at younger age,
Less than 100% reproductive effort in that moment
Lower reproduction trade off
High survivorship in offspring
Iteroparity means mating more than once in life cycle
Give an example and define semelparity
One mating season before death
example, annual flowers
Accompanied by:
lower survivorship in offspring
100% reproductive effort in breeding session
High trade off between survival and reproduction
Uncertainty in future reproducrtive success
What were the examples of horizontal gene transfer resultijng in novel characteristics?
Must remember:
Carotenoid biosynthesis in arachnids
Antifreeze proteins in some vertebrates
Outline the origin of snake venom
Duplication event results in copy of defensin gene
Change in gene reuglitation leads to expression in mouth rather than pancreas
What are Darwinian demons and why do they not exist?
Because there are trade offs, both physiologically, and in their life history strategy
Consider two species, one has large range, one has a small range, which species will show greater genetic distance between members of species?
The one with smaller ranger since there will be less overlap in populations
Define stabilizing vs disruptive/diversifying selection
Stabilizing: Selection for mean trait value, or against extremes
Diversifying/disruptive: Selection for extremes/ against mean
Stupid question:
But she refers to big s and S as?
s is sample standard deviation
“BIg S” refers to selection differential (mean in trait value of succesful vs. pop)
What is the mnemonic device to remember orthologs vs paralogs?
Ortho: orhter species (other species)
means homologous sequences separted by speciation event
Molecular phylogenetics showed that HIV was monophyletic?
False, it was polyphyletic
Also: Recall how mol. phylos are important for humans, tetrapods
What actually is EVO DEVO?
Infers how traits evolved from comparison of developmental processes
