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Biol 221 > Topics 4-8 > Flashcards

Topics 4-8 Flashcards

1
Q

What are the principles of the Hardy Weinberg Equilibrium?

A
  1. Infinitely large population
  2. Random mating
  3. No selection for/against phenotypes
  4. No net migration
  5. No net mutation
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2
Q

Is allele variation greater in small or larger pops?

A

“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?

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3
Q

How does drift affect genotypic ratios?

A

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)

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4
Q

What is the expected number of heterozygotes?

A

2pq(1-F) (recall F means autozygous, so remove any potential for heteros)

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5
Q

What does inbreeding do to allelic frequencies?

A

nothing, but will increase chance of autozygosity (recall grandpa example, you may be less diverse than grandpa)

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6
Q

How to calculate the inbreeding coefficient?

A

2pq-observed(heterozygotes)
/
2pq

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7
Q

What does polygenetic mean?

A

Trait influenced by many loci

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8
Q

What is the difference in broad sense vs narrow sense heritability?

A

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.

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9
Q

What does hertability measure?

A

Proportion of phenotypic variances attributable to genetics

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10
Q

When the selection differential is larger, what does this mean?

A
  1. Selective pressure is stronger(strength of selection)
  2. 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

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11
Q

What is the formula for intensity of selection?

A

Za-Zb/SD(phenotype)

Note”Za and Zb are the mean sizes of the traits(ie means)

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12
Q

What is the formula for the selection variance?

A

j=Va-Vb/Vb
j is selection on variance

Where V is the variance, a and b are after and before

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13
Q

What are the important conclusions of the experiment on Daphne Major?

A
  1. Intensity of selection may vary
  2. Direction of selective presure can change
  3. Evolution in morphology can be quite fast!
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14
Q

What is ecological character displacement?

A

Evolution is driven by competition in a way such that the species involved evolve to reduce overlap in resource use/niche

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15
Q

What is selective sweep?

A

Very strong selection for favourable alles to be fixed

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16
Q

What is hitchhiking?

A

Loci on either side of allele (being selected for) increase in frequency due to another gene undergoing a selective sweep

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17
Q

In particular, what causes the loss of armour in freshwater 3 spined sticklebacks?

A

Lack of nutrients
Lack of predation (predators less common in lakes)

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18
Q

What does the selection gradient measure?

A

The degree to which selection is occuring

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19
Q

What are orthologs?

A

Homologous sequences separated by speciation

Occur in different species

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20
Q

Where are paralogs found?

A

Within the same species, due to duplication event

Paralogs are homologous sequences

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21
Q

What are the pros and cons of molecular phylogenies?

A

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)

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22
Q

Outline the principles for the common methods of molecular phylogenetic construction

A
  1. Maximum Parsimony
    - simplest tree is best
    - give greater weight to trees less prone to homoplasy
    -
  2. 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
  3. 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

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23
Q

True or False:
Human genetic variation is greatest outside of Africa because the evolutionary background?

A

FALSE:
Greatest variation is IN AFRICA

This is a benefit of molecular phylogenies,

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24
Q

Define neutral evolution

A

Much of variation observed in genome was due to drift, rather than natural selection

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25
What are the predictions of neutral evolution?
1. Rate of mutation is constant/predictable 2. Mutations should accumulate more rapidly in areas of genome that **dont** influence phenotype (synnonymous mutations occur more rapidly then non-synonymous) | e.g pseudogene
26
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
27
What is some evidence for neutral theory?
Linear relationship of mutation accumulation of cytochrome c gene in pairs of mammals, with time
28
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!
29
When are *molecular* clocks **inaccurate**?
- When determining relations among species that are long diverged - Reversals can occur too -
30
# ;....................................................................... 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
31
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
32
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_
33
How can we measure selection?
1. Survivorship comparison 2. Selection gradient measurements
34
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)
34
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*
35
What explains how Hox gene cluster has such diverse function?
Duplication events, allow for one gene to be tinkered on, while one remains functional
36
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?
37
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
38
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
39
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
40
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
41
Why is variation in reproductive success among males so large in species where males take harems?
Only the largest males mate, thus contribute greatly,
42
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
43
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)
44
Why do peacocks look so different from peahens?
The variation in the males reproductive success generates intense selection resulting in great dimorphisms
45
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
46
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
47
Why is inbreeding **bad**?
Inbreeding could **increase** *homozygosity*, which could bring deleterious recessive alleles forward, this is *inbreeding depression*
48
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
49
What is the difference between narrow sense heritability and broad sense heritability?
h2=Va/Vp H2=Vg/Vp
50
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.
51
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
52
Bootstrapping is done to all trees?
No, only to the most parsimonious, then build the best tree using the randomly sampled traits
53
Neighbor joining requires a lot of computing power?
No! It is very quick
54
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
55
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
56
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
57
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
58
Is eukaryotic genome correlated with # of protein encoding genes
No, our genomes are very bloated, compared to bacteria who have streamlined genomes
59
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
60
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
61
How did bacteria develop the ability to metabolize citrate?
Duplication in a regulatory area of a cis element allowed CitT expression
62
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)
63
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)
64
In grey tree frogs (lec 8) what do females prefer?
Long, **more** complex call in males
65
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
66
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
67
What were the examples of horizontal gene transfer resultijng in novel characteristics?
Must **remember**: Carotenoid biosynthesis in arachnids Antifreeze proteins in some vertebrates
68
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
69
What are Darwinian demons and why do they not exist?
Because there are trade offs, both physiologically, and in their life history strategy
70
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
71
Define ***stabilizing*** vs ***disruptive***/diversifying selection
**Stabilizing**: Selection for mean trait value, or **against** **extremes** **Diversifying**/disruptive: Selection for extremes/ **against** **mean**
72
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)
73
What is the mnemonic device to remember orthologs vs paralogs?
Ortho: orhter species (other species) means homologous sequences separted by speciation event
74
Molecular phylogenetics showed that HIV was monophyletic?
False, it was polyphyletic | Also: Recall how mol. phylos are important for humans, tetrapods
75
What actually is EVO DEVO?
Infers how traits evolved from comparison of developmental processes
76

Biol 221 (3 decks)

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