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2B - Genetics & Evolution > week 9 > Flashcards

week 9 Flashcards

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Biology 101 flashcards
1
Q

What does natural selection require?

A
  1. There is variation amongst individuals
  2. Some of that variation is heritable
  3. Variation effects survival and reproduction
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2
Q

What is an adaptation?

A

a trait currently favoured by natural selection, and previously shaped by natural selection. traits that allow individuals to leave more offspring than individuals without that trait

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3
Q

What other forces affect evolution of traits? do they lead to adaptation?

A
  • other forces affect the evolution of traits (e.g. genetic drift, allele frequencies change upon chance which affects the traits)
  • but only natural selection leads to adaptation
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4
Q

Adaptive vs Maladaptive

A

Adaptive: A trait that enhances fitness

Maladaptive: A trait that reduces fitness

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5
Q

What is adaptionist program and what are the dangers of uncritical adaptionist program?

A
  • create and test hypotheses based on these questions
  • adaptive story telling = providing a plausible story for the adaptive significance of a trait without demonstrating adaptation.
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6
Q

What is exaptation? Give an example.

A

when a trait evolves for one purpose but is later co-opted for another.

Example: Feathers initially evolved for heat retention, not flight.

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7
Q

Why is blood red, and how does this illustrate a non-adaptive explanation?

A

Blood is red because hemoglobin uses iron to bind oxygen, a physical/chemical property. This is not necessarily an adaptation.

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8
Q

Chance is also not an adaptive trait. give an example.

A

Why can some humans roll their tongues
This ability likely arose by chance through genetic variation, not as an adaptive trait.

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9
Q

Why does the flu virus make us sneeze, and what alternative explanation exists?

A

Adaptive Explanation: Sneezing spreads the flu virus.
Alternative: Sneezing expels foreign objects, a side-effect of immune defenses.

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9
Q

Not all traits are adaptations. list the alternatives.

A
  1. exaptation
  2. chance
  3. side-effect of other adaptation
  4. historical constraint
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10
Q

What are some methods to tell us about the heritability of a trait

A
  • Trait correlation between parents and offspring
  • Comparing monozygotic and dizygotic twins, if mono> di then it tells us smt abt heritability
  • Looking at associations between phenotypes and genotypes
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11
Q

In a low-starch diet population, why do individuals have fewer copies of the amylase gene?

A

Low selective pressure for increased starch digestion results in fewer copies of the gene.

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12
Q

How do we determine if variation in the amylase gene affects fitness?

A

Feed individuals with different genotypes high-starch diets.
Measure offspring production as a fitness indicator.

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13
Q

What was biology’s main focus before phylogenetics?

A

Systematics, the classification of organisms into fixed categories (e.g., Linnaean taxonomy).

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14
Q

Why are fixed taxonomic ranks considered arbitrary?

A

They imply a simple tree structure, but molecular phylogeny reveals more detailed evolutionary relationships.

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15
Q

What is the significance of Darwin’s idea of phylogenetic trees?

A

They model evolutionary ancestry and genetic inheritance over time, replacing fixed hierarchical systems.

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16
Q

How are phylogenies reconstructed from trait data?

A

matrix fo pair wise distance of sequences

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17
Q

how to perform UPGMA

A

Create a distance matrix of pairwise distances.
Merge the pair with the smallest distance.
Update the matrix by averaging distances to the new cluster.
Repeat until all taxa are clustered.

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17
Q

What is UPGMA (unweighted pair group method with arithmetic mean)

A

combining taxas with most similar average to construct tree

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18
Q

4 amino acids in the sodium potassium pump has changed.. leading to…

A

changes evolved independently

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19
Q

What is the principle of maximum parsimony in phylogenetics?

A

Focuses on reconstructing evolution rather than using similarity measures.
Assumes traits arise on the simplest path (fewest evolutionary events).
A parsimonious explanation minimizes repeated or independent trait evolution.

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20
Q

What are the 2 problems regarding parsimony reconstruction?

A
  1. not all changes are equally likely
  2. we could have to check a frightening large number of trees to be sure we have found the best one
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21
Q

A phylogeny is a hypothesis about…

A

shared ancestry

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22
Q

Why are all changes not equally likely?

A

diff mutation rates, diff substitution rates

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23
Q

Which is more frequent? transitions or transversions?

A

transitions

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24
Q

Which codon is the one that diverges fastest?

A

3rd codon substitution is most likely synonymous so it diverged fastest (2nd is non-synonymous)

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25
Q

What is the solution for ‘not all changes are equally likely’?

A

use a substitution model, find tree that maximises probability (maximum likelihood tree)

assuming rate of 0.3 substitutions per million years allows maximum likelihood reconstruction

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26
Q

What is the solution for “checking large number trees”

A

only look at plausible trees, use algorithm to search tree space

27
Q

What are some examples for when taxonomic groups do not reflect evolutionary relationships?

A

Falcons and eagles, both raptors with high similarity, were once classified as “falcon-like things.”
However, their most recent common ancestor was something else, making this classification incorrect.

28
Q

What do phylogenetic trees reflect?

A

Inheritance and the flow of genetics over time.
A model of evolutionary change.

29
Q

Why does UPGMA sometimes give the wrong topology?

A

pair wise is agnostic to what events take place

30
Q

What is midpoint rooting?

A

Midpoint rooting is a method to root a phylogenetic tree.
The root is placed at the midpoint of the longest branch, assuming an unrooted tree.
It helps estimate the root when no outgroup is available.

31
Q

What do branch lengths in phylogenetic trees measure?

A

Sometimes nothing; trees without branch length info are cladograms, where branches usually have equal lengths.

Often, branch lengths represent sequence divergence, with units typically indicating the number of mutations (e.g., 1 mutation length).

32
Q

How do you calculate the mutation rate in a sequence alignment? If 13 mutations are observed in a 100-base alignment

A

divide 13 by 100.
This gives a mutation rate of 0.01 per base (1% mutation rate).

33
Q

Assuming an alignment of 100 bases and a substitution rate of 0.01 per million years, what is the age of the most recent common ancestor of A and B? (one has 1 one has 3)

A

best guess is average so 2

34
Q

Why may phylogenetic branches differ in length?

A

Substitution rates vary between branches.

Samples differ in age, affecting the molecular clock.

Mutations occur at different rates: transitions are more frequent than transversions (Kimura 2-parameter model).

35
Q

Biodiversity is not evenly distributed. how is each of the factors shown?
- space
- time

A

space : mammal richness (hotspots in tropics)
through time : fossil records

36
Q

How can we study long term patterns of diversification?

A
  1. fossil data
  2. molecular phylogenies (dated with molecular clock and calibrated with fossil dates)
37
Q

What is the formula for diversification rate (D)?

A

D = S – E, where S is the speciation rate and E is the extinction rate.

38
Q

What does a positive diversification rate (D > 0) indicate?

A

It indicates exponential growth in species diversity.

39
Q

What limits species diversity accumulation?

A

There may be a limited number (K) of ecological niches, which restricts further diversification.

40
Q

What is an LTT plot?

A

An LTT (Lineage Through Time) plot shows the number of lineages over time, derived from a dated phylogeny.

41
Q

What does an LTT plot reflect about surviving lineages?

A

The number of surviving lineages in an LTT plot is less than the actual number of lineages due to extinction.

42
Q

What does the steepness of the number of lineages in an LTT plot represent?

A

The steepness on a log scale is given by the diversification rate (D).

43
Q

What does the up-turn in the recent past of an LTT plot indicate?

A

“Pull of the Present” refers to a phenomenon where the number of surviving lineages appears to increase more steeply in the recent past on an LTT plot. This effect is caused by the speciation rate (S) being higher than the extinction rate (E) in more recent times.
The ratio S/E (speciation rate to extinction rate) helps explain this observed up-turn. If S > E, more lineages are being formed than going extinct, leading to the increase in lineages visible in the recent part of the plot.

44
Q

Why might clades differ in species richness?

A
  1. diff in carrying capacity
  2. diff in D
  3. diff in age
45
Q

How can we identify traits that drive diversification?

A

By looking for traits that are associated with increased species diversity

46
Q

How are nectar spurs in Aquilegia linked to species diversity?

A

Nectar spurs are associated with pollinator isolation, which could promote speciation and increase species diversity.

47
Q

Why can’t we experiment to prove that nectar spurs drove diversification?

A

because we only have 1 instance of this trait (nectar spurs) in the clade, making it difficult to test experimentally.

48
Q

What is necessary to test whether a trait is associated with a change in diversification?

A

You need independent replicates to reliably test if a trait is linked to diversification changes.

49
Q

What is the relationship between herbivorous clades and species richness?

A

In both herbivorous clades (weevils & leaf beetles, moths & butterflies), the herbivorous groups are much more species-rich than their sister clades.

50
Q

Why could the pattern of herbivory and species richness be due to chance?

A

It could be due to chance because there are only 2 instances (N = 2) of herbivory evolution to compare.

51
Q

Phylogenetically independent contrasts are independent pairs of ____ that differ in a focal trait

A

sister clades

52
Q

What are phylogenetically independent contrasts?

A

Phylogenetically independent contrasts are pairs of sister clades that differ in a focal trait, allowing researchers to compare the evolution of that trait while accounting for their shared evolutionary history. This method helps remove the influence of common ancestry and test for associations between traits.

53
Q

How can co-evolution influence diversification?

A

Co-evolution can lead to fast change in species

54
Q

Buchnera aphidicola is an endosymbiont bacterium of aphids that supplies an essential amino acid, tryptophan. How does the phylogeny of Buchnera aphidicola compare to aphids?

A

The phylogeny of Buchnera is topologically concurrent with the phylogeny of its aphid host.

55
Q

Why is co-phylogeny often imperfect in mutualistic relationships?

A

Co-phylogeny is often imperfect because even in tight mutualisms, host switches can occur over long timescales.

56
Q

What is the relationship between figwasps and figs?

A

Figwasps are the sole pollinators of figs, forming an obligate mutualism.

56
Q

What is the co-phylogenetic pattern between figwasps and figs?

A

There is a significant but imperfect co-phylogenetic pattern due to overposition mistakes by figwasps, leading to host switches.

57
Q

Why do mutualistic relationships like figwasps and figs show imperfect co-phylogenies?

A

Over long timescales, host switches occur, leading to messy phylogenetic links despite the tight mutualism.

57
Q

on a LTT plot, what does more dots with shorter timeline?

A

diversification rate is decreasing

58
Q

What does steep uptake in an LTT plot show?

A

high extinction rate

59
Q

What is the diff between trajectories of actual and surviving lineages

A

E/S = pull of the present

59
Q

D gives the ___ of expected number of lineages on log scale

A

steepness

60
Q

What does “slow down” mean in an LTT plot, and how do clades show that?
Back:

A

“Slow down” in an LTT (Lineage Through Time) plot refers to a reduced rate of diversification, where the number of lineages increases more slowly over time.

Clades show this when the slope of the plot becomes less steep, indicating that speciation or the creation of new lineages is happening at a slower rate, possibly due to factors like limited resources or ecological constraints.

60
Q

How would you measure sexual conflicts in insects?

A

how many mates does a female have?

61
Q

How does sexual conflict relate to diversification in sister clades?

A

Each point represents a sister clade.
There is a positive association between sexual conflict and diversification.
Clades with female multiple mating (sexual conflict) tend to have more species and appear below the line on a plot, while clades above the line have fewer species.

61
Q

Compared to mutualists, which scenarios do you expect to be common for parasite?

A

antagonistic relationship = host switch
independent speciation
extinction
missing the boat
failure to speciate

2B - Genetics & Evolution (9 decks)

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