EB11

Question 1

What are the deviations from the SNM due to

Answer 1

selection

Question 2

what are the two types of variation

Answer 2

1. within spp: polymorphism

2. between spp: divergence. *between two species originates as varaition within, which becomes fixed in two species.

Question 3

what does neutral theory assume about DNA sequences

Answer 3

all sites are subject to equal mutation and drift, synonymous and non synonymous.
all genes in same demography are subject to same effects.

Question 4

what can we assume if a small pi is found for a small populations

Answer 4

that population size is causative

Question 5

what can we assume if two regions in the same demography have different pis (one is much larger than the other)

Answer 5

suggest due to selection

Question 6

what is the rate of sequence divergence between species equal to

Answer 6

d = 2Tu

2 x generation between x mutation rate

Question 7

what might faster dviergence between two lineages indicate

Answer 7

evolution in response to a new challenege: adaptaiton

Question 8

what might slower divergence between two lineages indicate

Answer 8

purifying selection atgainst deleterious changes at a functionally important region/site.

Question 9

what comparisons can be made to cancel out affect of demography
why is this the case

Answer 9

1. coding vs. non coding vs pseudogene
2. coding expressed vs silent
3. functional vs non functional protein parts``

demography is usually shared between regions of the same genomea nd tehrefore cancel out

Question 10

which regions of the genome do not share the same demopgraphy as the rest

Answer 10

maternally inherited mitochondria
horizontally transferred selfish elements
differences in mutation rates

Question 11

what are the three degrees of degeneracy

Answer 11

1. 0 fold degenerate: non synonymous- intolerant to site changes.
2. 2 fold degenerate: partly silent
3. 4 fold degenerate: silent

Question 12

give an example of a 2 fold degenerate

Answer 12

Leu can start with U or C

Question 13

give an example of 0 fold degenerae

Answer 13

central codon for Leu must be U or will not get Leu

Question 14

give an example of a 4 fold degnerate

Answer 14

silent

usually thirs mutation in codon is unlikely to change the AA.

Question 15

how are homolgous sequences compared

Answer 15

1. line sequences up to ensure homologous. *esp difficult with gene duplications
2. count no. of AA changes per site
3. no. of nt changes can be tagged by changes
4. rate of evolution degree of degeneracy calculated

Question 16

what can you combine 0 fold and 2 fold into

Answer 16

non synonymous

Question 17

what is dN/dS

Answer 17

ratio of nonsynymous to synonymous

Question 18

what is neutral expectation for dN/dS

Answer 18

1:1

Question 19

What does dN/dS >1 imply

Answer 19

positive selection

Question 20

what does dN/ds<1 imply

Answer 20

purifying or stabilizing selection

Question 21

What is dN

Answer 21

no. of non-synonymous changes/ total no. of nonsynonymous sites

Question 22

what is dS

Answer 22

no. of synonymous changes/ total no. of synonymous sites.

Question 23

what is pN/pS

Answer 23

the within species equivalent of dN/dS

the polymorphism ratio

Question 24

Give an example of deviations within lineages

Answer 24

evolution of new function of lysozyme

Question 25

what is a lysozyme

Answer 25

enzyme that attacks bacterial cell walls functioning as an antibiotic in tears, saliva and egg whties

Question 26

what does AA alignment of lysozyme proteins from diffferent species show

Answer 26

a no. of AA substitutions along branches during evolution of lysozyme intro two different clades

Question 27

what does the Languar/cow/deer lysozyme branch show, what does this suggest

Answer 27

faster rate of change

due to change in function

Question 28

how does lysozyme change in languar, deer, cows and cloven hoofed animals

Answer 28

acquied new function, digests bacterial remains in stomach, functions in acidic environment and resists degradation by digestve enzymes in cloven hoofed animals
(cows, deers, leaf eating monkeys (languars)

Question 29

What is BRAC1

Answer 29

encodes a protein involved in DNA reapira nd regulation of programmed cell death (apoptosis) during neural development

Question 30

What did analysis of BRAC1 evolution show in mammals generally and in humans and chimps

Answer 30

** exon 11 was sequenced

mammals dN/dS <1 = neual
humans and chimps >1 = positive selection

Question 31

what does dN/dS of BRAC1 in chimps and humans show

Answer 31

as greater than 1 shows not evolving neutrally, evidence of faster rate of evolution in this lineage, implying positive selection in ancestor leading to human and chimp