Lecture 12- Bacterial genomics II - Population Genomics of bacterial pathogens

Question 1

theories of different ways molecular evolution can occur

Answer 1

neutral diversification
ecotypes
divided-genome model

Question 2

neutral diversification

Answer 2

suggests that most variation can be explained by drift, and clumping patterns are because of transmission barriers

Question 3

ecotype model

Answer 3

adaptation to specific environments shapes evolution

Question 4

divided-genome model

Answer 4

multiple colonising genotypes can acquire an adaptive trait, leading to sweeps and convergence even with different genomic backgrounds

Question 5

important factors in population genetic structures

Answer 5

mutation, HGT rates

Question 6

what is hypermutation and what is its impact

Answer 6

accumulation of mutation- can be due to niche hostility, and often causes disease, but can allow quick adaptation to the bad niche

Question 7

example of clonal and non-clonal populations

Answer 7

m tuberculosis is exclusively clonal, h pylori is entirely non-clonal (recombining)

Question 8

3 genetic mechanisms of HGT

Answer 8

transformation (uptake from environment), conjugation (pili), transduction (viruses)

Question 9

types of recombination

Answer 9

homologous- replacement of existing genes at the same point
non-homologous- novel insertion

Question 10

what might cause genetic changes that are non-adaptive

Answer 10

bottlenecking and drift

Question 11

what are dN/dS methods

Answer 11

looking at the relative rates of change at non-synonymous (dN), amino acid changing vs synonymous (dS) sites

Question 12

what does dN/dS>1 mean

Answer 12

positive selection

Question 13

issues with dN/dS methods

Answer 13

-selection operates on things which don’t impact the ratio, such as on gene order and GC content
-complex traits involve too many genes to be easily detected- linkage disequilibrium can skew estimates for example
-frameshifts can lead to non-synonymous SNPs being read as synonymous, not enough detection of positive selection
-polymorphisms that will be purged due to being mildly deleterious may be counted, and this could lead to thinking these are positive

Question 14

what is a PAI

Answer 14

pathogenicity island- parts of a bacterial genome which suggest virulence evolution, have functions such as host immune defence

Question 15

homoplasty

Answer 15

traits developed by unrelated species in response to the same thing- result of convergent evolution

Question 16

use of genome-wide association studies

Answer 16

testing of many genomes to find the parts which seem to be statistically associated with a trait/disease

Question 17

example of how genome-wide association studies have been useful

Answer 17

analysis of S aurelius genomes, can look at genes specifically associated with disease in poultry to identify evolutionary events