Coalescent Theory

Question 1

Why can it be argued only mutation causes genetic variation

Answer 1

• recombination is just shuffling

- everything else removes DNA = less variation

Question 2

Describe microsatellite markers

Answer 2

10,000 per genome
- repeat motifs in tandem: 10-100 times
Vary in freq in alleles
Co dominant = can tell if homo or hetero
High mutation rate but neutral as often in non coding
Need specific primers to amplify via PCR

Question 3

How do you view microsatellites

Answer 3

Separated by size via polyacrylamide gel electrophoresis

Or, same concept using automated DNA sequencer

Question 4

DNA slippage mechanism

Answer 4

DNA polymerase dissociates from the nascent strand (the one being created) often at hairpin structures
Then realigns at a different point causing an expansion or deletion of the nascent strand
Often occurs during sections of small repeats e.g. microsatellites

Question 5

Coalescing branches

Answer 5

Branches coming together

Question 6

How would you suppose bottle necks/no expansions in population from histogram

And then for a phylogenetic tree

Answer 6

‘Gappy’ distribution w/ missing alleles
Leptokurtic distribution

Short branches

Question 7

Leptokurtic distribution

Answer 7

Where the tails of a bell curve are still quite high..not steep curve

Question 8

How would you suppose a population does have expansion occurring from a histogram

And then for a phylogenetic tree

Answer 8

The central peak is surrounded by alleles of low frequency

All deep branches

Question 9

Describe the Komodo dragon case study

Answer 9

Found on 5 islands in Indonesian archipelago
Some were connected during last Galician but not komodo island
- they are strong swimmers
-populations stable on some islands but not on others
Created genealogical model using allele size differences w/ stepwise model and allele freq differences
Results:
- komodo v divergent
- other islands formed single genetic unit
Because they were recently connected and dragons can swim

Question 10

What is coalescent theory

Answer 10

Mathematical model to determine genealogy of sample

• looking at recent history to determine its evolutionary path
• seeing when alleles coalesced
• only need a small sample size to see lots of genealogy