BIO113 Exam 2

How do genome’s change overtime?

Mutations that are subjected to Natural Selection, Genetic Drift

Mutation

Base substitutions, deletions, insertions, DNA rearrangements

Natural Selection (for mutation)

a base substitution in the genome could be:

- selected for (organism becomes more fit). The substitution becomes “fixed in the population/species.”

- selected against (causes a mutation and the organism becomes less fit). The substitution is “eliminated from the population/species

Genetic Drift (for mutation)

A substitution is neutral (no effect on fitness). The substitution is usually eliminated, but some will become fixed.

Genetic drift is caused by sampling error, and if the population is larger, then it will take longer, but neutral alleles will still go to fixation.

New neutral mutations become fixed in a population at a frequency of…

1/2N (4N average number of generations til fixation)

rate of input of new alleles in a diploid species

2Nμ (where mew is mutation rate for a nucleotide (per generation or per year))

Who are Kimura (1968) and King and Jukes (1969) and their Neutral Theory.

Suggested that most molecular variation is neutral

The majority of evolutionary changes at the molecular level (DNA/proteins) are caused by the random genetic drift of mutant alleles that are selectively neutral or nearly neutral, rather than by natural selection.

How many of the mutations that do happen will go to fixation (replacement)? What does this mean?

2Nμ * 1/2N = μ

or just the rate of neutral mutation

The rate of accumulation of neutral DNA changes is dependent upon the neutral mutation rate (μ) and is independent of population size.

Molecular clock

Estimates the timing of species divergence by measuring the accumulation of mutations in DNA or protein sequences over time.

Rate of evolution due to random genetic drift

Independent of population size

depends solely on neutral mutation rate

What is sequence divergence = to

K = 2tμ

What are K_s, K_a, and K.

K = fixed differences in sequence between species

K_s = divergence per site at synonymous sites

K_a = divergence per site at non-syn sites

K_a/K_s ratios meaning </>/=

KA / KS = 1, No selection

KA / KS > 1, Positive Selection

KA / KS < 1. Purifying selection

Synonmyous vs non syn sites meaning

Synonymous - sequence change where a nucleotide substitution does not change the resulting amino acid

non-syn - sequence change where a nucleotide substitution does change the resulting amino acid

Taxonomy

description, naming and classification

Systematics

evolutionary history of adaptation and diversification (including biogeography and ecology) of a group.

Phylogenetics

inference of evolutionary relationships of populations, species, or genes. Basic information for systematics and taxonomy.

Phylogeny

inferred pattern of relationships, represented as a phylogenetic tree

Monophyletic group

A group that includes the common ancestor and all of it’s descendants

Paraphyletic

A group that includes the common ancestor and some, but not all of it’s descendants

Polyphyletic

A group that does not include the common ancestor of the group but only select descendants.

Parsimony

simplest explanation that fits the evidence. → A method that builds a tree that minimizes the number of changes (base changes…etc) along branches.

shared derived traits (synapomorphy)

1. Evolved in a common ancestor, and

2. Is shared by all members of a particular group,

3. But is not found in more distant ancestors.

Unique derived traits

Evolved in a lineage,

Is derived (meaning it was not present in distant ancestors),

But is found in only one species or one lineage.

Ancestral traits

as present in a distant common ancestor,

Is found in multiple groups today,

But did not evolve recently within the group being studied.

polytomy

more than two taxa whose relationship cannot be inferred (more than two brances of a node)

Phylogenetic methods

1. Parsimony

2. Maximum likelyhood methid

3. Distance methods

Maximum likelyhood method

Estimates the evolutionary tree most likely to have produced the observed DNA, RNA, or protein sequence data.

It does this by calculating the probability of the data given different possible tree structures under a specific model of sequence evolution and selecting the tree with the highest likelihood.

Distance methods (+Neighbor joining method) steps

1. Create a matrix of genetic distance between all species (taxa) – e.g., %
sequence difference for a gene.
2. Find the pair of species with the greatest similarity (lowest genetic distance)
and group them together into a single composite taxon.
3. Recalculate matrix of distances, using mean values for newly created taxon.
4. Find pair of taxa with greatest similarity and group them.
5. Continue until all taxa have been joined.