Lecture 12

Question 1

Is rapide adapation(phenotypic change) due to coding sequence change or gene regu;atory changes?

Pelvic?
Tall/short?
White/purple?

Answer 1

In stickleback pelvic spins are lost due to a gene regulatory changes; round/wrinkled and tall/short peas due to coding sequences changes.

white and purple was a splicing mutation

Question 2

Parallel vs neutral divergence topologies

Answer 2

parallel not random and the tree is bunched

Question 3

In the study of domestic dog lineages?

Answer 3

WGS(whole genome sequences)-1171
SNP-3090

Question 4

What is depth in a read?

Answer 4

average number of reads per nucleotide position.

Question 5

What does AA|0.9546 mean in the SNP data from the WGS alignments.

AB
BB

Answer 5

AA is the allele that this dogs has which is the most common

B is the rare allele

Question 6

What are SNP arrays or Genechips

Answer 6

SNP chips is when we know the SNPs exist and want to genotype many indiduals at these know loci

Question 7

How long is each probe in the SNP chips

Answer 7

25bp long

Question 8

Then probe and chips are____ to a certain genome

Answer 8

complementary

Question 9

Photo #1
-____is washed over the array for 14 to 16 hours. All of the____strands are swimming around looking for______.If this happens then_____

Answer 9

DNA samples are washed…

DNA strands are swimming
their perfect complement
the DNA matches the probe and will stick to the probe

Question 10

Phot0#2
explain

Answer 10

Fluorescent stain washes over the array then the glow in the dark molecules(red ball) stick to the biotin glue(purple cup). The fluorescent molecules are shaken away and only the stain only sticks to where the DNA is bound. Then shine a laser light on the array causing the stain to glow. Photo shows heterozygous

Question 11

Illumina single beadchip
-photo #3
____bp probes that encode the DNA adjacent to the ___. Fragmented genomic DNA is hybridized to it. Then___. If the sample DNA is from a heterozygote the the signal is____

Answer 11

50
to the SNP locus.
then a single base addition (using DNA polymerase) takes place.

yellow

Question 12

There were ____loci on the SNP chip and data were collected for ____dogs

Answer 12

173,662
3090

Question 13

PHATE- the distal-most portions of the trajectories represent_____genetic states in the data( the most divergent genomes within the dataset)

Answer 13

endpoint

Question 14

What is the difference between a tree-based approach and the PHATE?

Answer 14

the indiduals in the PHATE are not at the tides of the branches but each spot is an individual.