EVE100 MT1

Jasen UC Davis UCD SS2 2024

Phylogeny

A hypothesis of the relationships among species, populations, or genes

Paraphyletic group

Includes common ancestor and some, but not all, of the ancestors descendants

Polyphyletic group

Does not include the common ancestor of the group

Monophyletic group

includes the common ancestor of the group

Can a monophyletic group be removed from a tree with a single “cut?”

yes

monophyletic group

triangle cut on a phylogenetic tree at the end; clade

non-monophyletic group

rectangular cut on a phylogenetic tree in the middle

Solve

B

T/F: It’s possible to rotate branches around nodes without changing the evolutionary relationships depicted?

True

Solve

A

Polytomy

Used to indicate uncertainty in the correct branching pattern

T/F: Phylogenies can be drawn with fewer species

True

Solve

D

Cladogram

Only represents branching pattern; branch lengths meaningless

Phylogram

Branch lengths proportional to amount of character change

What are five common misconceptions on phylogenetic trees?

1. Reading across the tips

2. Ladder thinking

3. Similarity=relatedness

4. Long branch implies no change

5. different lineage ages for modern species

Misconception #1: Reading across the tips

• order of terminal nodes is meaningless

• only the branching order provides information about relatedness

• Taxa that share more recent common ancestors are more closely related

Solve

B

Misconception #2: Ladder thinking

• no currently existing species is ancestral to any other species

• there’s no higher or lower organisms

• there are no main lines and side tracks

• trees depict evolutionary relationships, not evolutionary progress

Solve

C

Misconception #3: Similarity=relatedness

phylogenies portray relatedness (common ancestry), not similarity

Misconception #4: Long branch implies no change

• The meaning of branch lengths depends on the type of tree (cladogram, phylogram, chronogram)

• Long branches can be made to appear shorter by having more taxa

Solve

D

Misconception #5: Different lineage ages for modern species

The lineage of any modern species is just as old as the lineage of any other modern species that shares a common ancestor

Solve

D

Which is the rooted tree? (1 or 2)

1

Solve

B

Parsimony

Based on traits or DNA sequences; phylogeny

How do we construct phylogenies?

• Historical (simple method): parsimony

• Modern methods based on DNA sequences:

  1. Maximum likelihood, 2: Bayesian inference

Why would modern methods be used to construct phylogenies?

Allows for the estimation of uncertainty

Character

A feature or trait (no specificity)

• ex. Number of toes on a hindlimb

• ex. Each site on one strand of DNA

Character state

One of the variant conditions of a character

ex. 5(humans), 1(horse), 3(rhinos)

ex. Identity of the nucleotide base (A,T,C,G)

Homology

possession by two or more species of a character state derived, with or without modification, from their common ancestor

Plesiomorphy

ancestral character (having eyes)

Apomorphy

derived character state (trait loss or gained often by adaptation); (eyelessness)

Homoplasious character (Homoplasy)

similar or identical character states that were not derived from a common ancestor (convergence)

solve

2

Why are phylogenetic trees important?

• used to classify organisms (Myxozoan classification)

• Understand the origins of infectious agents (Cholera in Haiti)

• Infer the history of character evolution

• Estimate the timing and order of divergence

• Understand patterns of evolution

Gustatory receptor (GR) function

heritable trait with variation

GR frequency changing

GR allele frequency changing

Variation in GR affects likelihood of eating poison

variation affects fitness

how do we know when evolution is occurring via natural selection

variation is heritable, affects fitness, and is changing

allele frequencies

proportion of a specific allele among all alleles at that loci within the population

biallelic loci

2 alleles at a locus

fixation

when an allele reaches 100% frequency in the population (indicates no genetic variation at that locus)

biallelic loci equation

p + q = 1

• p is the frequency of allele 1

• q is the frequency of allele 2

natural selection

consistent differences in fitness among different classes of biological entities (e.g. alleles, genotypes, populations, species)

fitness

number of offspring an individual leaves to the next generation (reproductive success)

What are the 4 conditions for evolution by natural selection?

• reproduction

• variation

• inheritance

• differential success

reproduction

individuals reproduce to create the next generation

variation

individuals vary in their traits

inheritance

individuals pass on some of their traits to their offspring

differential success

individuals with different traits differ in their survival or reproductive success (fitness)

Why do the best possible variants fall short of perfection often?

trade-offs (energy spent on one things must be spent on others)

What is a key limitation of natural selection in evolving traits?

Natural selection can only "choose" from existing genetic variants in a population at a given time. It cannot select the best possible traits if they haven't arisen yet.

“greedy algorithm”

natural selection operates to maximize fitness locally, but does not have an “end goal”

• simplified: natural selection focuses on what's most helpful right now for survival and reproduction without aiming for a specific future goal.

solve

G

Cancer cell

a cell lineage that has evolved a high rate of replication compared to other lineages, at the expense of host fitness

Selfish genetic elements

genetic segments that can enhance their own transmission at the expense of other genes in the genome

Transposable elements (TEs)

DNA sequence that can change its position within a genome

Segregation distorters

alleles that distort normal segregation in their own favor

Prion

“Proteinaceous infectious particle”

What does prion act as?

a highly stable misfiled protein that acts as an infectious agent

How do prions propagate?

transmitting a misfolded protein state, causing other proteins to misfold in the same way

What diseases are caused by prions?

mad cow disease; Creutzfedt-Jakob disease in humans

What is the methodology for prions in cell culture?

• “grow” a single strain in cell culture

• Impose selection: drug inhibiting protein aggregation

What does the exposure of prions to drugs in culture lead to?

evolution of drug-resistant strains

Heritable information

structure of the protein

variation in fitness example

strains grown in the presence of the drug outperform susceptible strains when exposed to the drug

fitness

the currency of selection

We often use ____ components as a proxy for absolute fitness

fitness

How to get W? (absolute fitness)

(Probability that an individual survives to maturity) x (expected # of offspring if the individual does survive)

solve

• AA: 0.72

• Aa: 1

• aa: 0.12

(divide by highest percentage)

selection coefficient

measure of differences in relative fitness among genotypes

Solve:

What is the selection coefficient?

S22= 1 - w22 = 1 - 0.4 = 0.6

S12 = 1 - w12 = 1 - 0.8 = 0.2

Positive selection

selection for an allele that increases fitness

__ affects the evolutionary trajectories of beneficial alleles

dominance

(- or + ?) selection tends to reduce genetic variation

positive

Linkage Disequilibrium (LD)

measure of non-random associations between alleles at different loci- high LD just after a sweep

*simplified: measure of how certain genetic variants (alleles) at different locations (loci) on a chromosome are inherited together more often than would be expected by chance.

How does positive selection reduce genetic variation?

By driving adaptive alleles to fixation

How can selection maintain genetic variation? (balancing selection)

• over dominance (heterozygotę advantage)

• negative frequency-dependent selection

selective sweeps

process by which a new advantageous mutation eliminates or reduces variation in linked neutral sites as it increases in frequency in the population

Positive selection at the genomic level-selective sweeps (explanation of what the image depicts)

• Left Side: This shows a population with a variety of genetic variants (different colored dots) at different locations on the chromosome (each horizontal line represents a chromosome).

• An Adaptive Mutation Arises: A new beneficial mutation appears (represented by the red star). This mutation gives the organisms carrying it an advantage, making them more likely to survive and reproduce.

• Right Side: Because this mutation is so beneficial, it spreads rapidly through the population (this process is called a "selective sweep"). As it spreads, it drags along the nearby genetic variants (light blue and greenish alleles) because they are close to the beneficial mutation on the chromosome.

Overdominance (heterozygotę advantage)

occurs when heterozygote has a higher fitness than either homozygote

Solve

0.878

Negative frequency-dependent selection

the fitness of an allele/genotype/phenotype decreases as it becomes more common (rarity is favored)

mutation description

production of new alleles

mutation effect on genetic variation

increase by introducing new alleles

mutation effect on average fitness

most mutations with phenotypic effects lower fitness

natural selection description

certain alleles are favored and spread

natural selection effect on genetic variation

can lead to maintenance, increase, or reduction

Natural selection effect on average fitness

can increase, but not always

Pick the correct answer: Selection should (remove/introduce) deleterious alleles but mutation is always (removing/introducing) new alleles.

remove; introducing

Mutation-selection balance describes what?

equilibrium frequency q of a deleterious allele that we would expect to observe in a population

solve

recessive: sqrt((6 × 10^-6)/(0.9)) = 0.0026

Dominant: (6 × 10^-6)/(0.9 × 0.5) = 1.33 × 10^-5

evolution

heritable change in populations over generations

How do we know when evolution has occurred?

If there is change in a population’s genetic composition over time

Locus

physical location in on a chromosome

Gene

a DNA sequence that encodes a product with a distinct function

Allele

variant