Biology Exam II --> Molecular Evolution

Phylogeny

parent to offspring transmission of genes (gene history)

gene history can be used to infer evolutionary relationships among species

Phylogenetic techniques can be used to reconstruct…

morphology, behavior, nucloetide & amino acid sequences of ancestral species

Ancestral Function

infers ancestral gene sequences & evolutionary history of gene function

Genome Evolution

infers evolutionary history (structures, additions, deletions of genes

Population Structure

infers levels of gene flow among populations & history of population expansion & contraction

Ancestry

trace own lineage back into deep evolutionary time

Molecular Evolution

evolution of DNA & protein sequence

Neutral Theory

gene & protein sequence evolution is dominated by genetic drift of NEUTRAL mutations

Neutral Mutations

mutations are neither beneifcial nor detrimental to the organism

Synonymous base changes

silent mutations that occur in introns, pseudogenes, noncoding & non regulatory regions

mutations that occured in 3rd position

Non-synonymous Base changes

base changes that don’t affect protein function

Genetic drift applies mostly to…

genes with little or no selective effects

Small populations

gene fixation is more likely & mutations are less likely; fewer new mutations

Large populations

gene fixation is less likely and mutations are more likely; holds more genetic variety

genetic drift does not affect

genes that are coding or under selection

it is greatest in small populations (mutations are random)

Population bottlenecks & founder effects

high change of losing genetic variety

Kimura’s Neutral Theory

vast majority of nucleotide subsitutions have no effect on fitness

genetic drift dominates evolution @ a molecular level

molecular evolution rate = neutral mutation rate

Pseudogenes evolve..

neutrally and faster than sequences constrained by selection

rate of substitution is faster in pseudogenes

Synonymous sites evolve…

faster than nonsynonymous sites

nonsynonymous sites are more harmful to the function of the gene so removed from population faster via natural selection

Rate of fixation of new neutral mutations by genetic drift is

independent of population

pop size = N , neutral mutation rate = µ

#of new mutations = 2Nµ

• 2N gene copies abialbe to mutate in a population of diploid organisms

Probability of given mutation being fixed by drift is its frequency:

½(N)

M = 2Nµ (1/2N) = µ

M = µ

rate of fixation of netural mutations depnd on neutral mutation rate

New mutations are more likely in

large populations

— fixation more likely in smaller population so if mutation = short time of fixation

Drift Selection

Synonymous Change = Nonsynonymous change
describe genetic drift

Purifying Selection

Synonymous Change > Nonsynonymous Change

harmful genetic variations are removed from a population, essentially acting as a filter against deleterious mutation

Positive Selection

Synonymous Change < Nonsynonymous Change

beneficial genetic variations become more common in a population

Molecular Clock

used to figure out when divergences happened by sequencing 2 different organisms

average at which species genome accumulates mutations

• measures evolutionary divergence

• rate of evolution depending on mutation rate

Calibration Point

• reasonable amount of time where the change occured

Assumptions for Molecular Clock

1. Nucleotide changes are constant

2. Error rates of DNA can be calibrated

Genes evolve at a

constant rate

Molecular clock uses

average rate at which gene accumulates changes to gauge time of divergance

Origin of HIV Hypothesis

transmission early

transmission causes epidemic

parallel late transmission

Transmission early

in person for long time prior to explosion

transmission causes epidemic

just immediately started and exploded

parallel late transmission

WHO spread HIV bc vaccines

which origin of hiv was correct?

transmission early

Why is HIV perfect for MC analysis

HIV beginning coincided with end of colonial rule in Africa, civil wars, needle reusing, sex revolution, increase travel to Africa

Variation comes from

gene duplications and divergence

Orthologs

copies of same gene in different species descended from common ancestor due to speciation

Paralogs

copies of same gene in same genome due to gene duplication event

Xenologs

horizontal transfer of genetic materials between a distantly related species (no evolutionary history)

Analogs

different genes in different species that have converged to have same function

Globin genes

hemoglobin is related to myglobin

globin genes in humans are closely related to globin genes in mice

Why are genomes big?

Most are nonfunctional or noncoding genes
accumulation of pseudogenes