Lecture 13 - Molecular Systematics Flashcards
Molecular trees can resolve both _____ and _____ divergence
ancient, recent
How can molecular trees resolve diverge?
by using molecules that evolve at different rates
What resolves deep divergences?
conserved sequences
What is an example of a conserved sequence?
ribosomal RNA
What is a benefit of using additional genes?
gives a more complicated view
What resolves more recent divergence?
mitochondrial DNA
What are the two types of homologous genes that molecular phylogenies rely on?
- orthologous
2. paralogous
What is orthologous?
found in different species as a result of speciation (product of speciation)
What is paralogous?
found in the same genome as a result of gene duplication (within a species)
How do molecular phylogenies track evolutionary time?
if we assume a molecular clock
What is a molecular clock?
- using phylogenies to estimate evolutionary time of divergence
- molecular yardstick
What is the basis of the molecular clock?
- yardstick for measuring absolute time of an evolutionary change
- based on observation that some genome regions appear to evolve at constant rates
What is the Neutral Theory?
- states that much evolutionary change in genes/proteins has no effect on fitness
- therefore not influence by Darwinian selection
- states that rate of molecular change in genes/proteins should be regular like clock
Who was Motoo Kimura?
developed the Neutral Theory
What are 3 flaws to molecular clocks?
- imprecise
- rates vary among genes and among species
- clock rates need to be calibrated with independent data
What are 5 practical applications of phylogenetics?
- The origin of HIV
- Source of SARS
- MERS source + transmission
- Source of 2009 H1N1 outbreak
- Zika Virus
_____ combined with _____ suggests that HIV-1 M originated in the 1930s
phylogeny, molecular clock analysis
What was evidence that the 6 medics accused of infecting infants with HIV were innocent?
- many children co-infected with hepatitis (suggests dirty needles)
- at least one child infected with HIV after medics were arrested
- strongest evidence from phylogeny
What does phylogeny suggest about SARS?
supports hypothesis that virus originated in bats
What was the source of MERS? Why?
- bats
- bats have higher metabolic rate that may keep viruses at bay
Where did swine flu derive from”
avian, swine, and human strains all circulating in pigs
What does molecular clock analysis suggest about the 2009 outbreak?
- phylogeny proved it was recombinant virus of viral DNA
- ancestors of the 2009 outbreak have been ciruculating undetected for between 9 and 17 years
Did the world cup fans introduce Zika to Brazil?
no, phylogenetic and molecular clock analyses show single introduction to Americas in 2013
