EB22

Question 1

How are mosquitos collected

Answer 1

human landing catches/spray
landing catches; ethically dubious: catch them on skin at feeding time
Spray collections: spray houses in the morning and put sheet outs to catch insects

Question 2

how is mosqutio DNA collected

Answer 2

max 1ug per mosquito could be limiting for some applications.
*rapid tech means able to sequence genome of single mosquito

Question 3

what markers can be used for genome comparisons

Answer 3

1. allozymes and chromosomal banding patterns used ot be uysed.
2. mtDNA easy to amplify (many copies)
3. microsatellites
4. AFLPs: amplified fragment length polymorphisms
5. Nuclear gene sequences
6. SNPs

Question 4

what are the pros and cons of using mtDNA

Answer 4

Pro: easy to amplify, easy to get sequence data
con: essentail 1 locus so selection could obscure demography

Question 5

what are the pros and cons of using microsatellites:

Answer 5

pros: many developed in anopheles, easy to amplify, multi locus
cons: limited no. can be processed, no good model of evolution.

Question 6

what are the pros and cons of nuclear gene sequences

Answer 6

pros: multilocus, sequence data
cons: practically limited to a small no. and must be careful of selection in coding regions.

Question 7

What are the various methods of stat analysis of population diversity and structure

Answer 7

1. Nt diversity: effective population size
2. Neutrality tests: selection or demographic changes
3. HWE: assortative mating or selection
4. Fst:differentiation between populations (divergence)

Question 8

What are examples of more complex analysis of population strucutre and population hisotry

Answer 8

1. Haplotype networks: similar to phylogeny reconstruction
2. Clustering analysis: cluster data to try and identify whether two popualtions/three/four/five are linked and then find cluster to best fit the data
3. Linkage: `

Question 9

what is the challenge in population history

how can this be done

Answer 9

to tease apart ongoing gene flow from popualtion history

done by modelling genetic data under different demographic scenarios (Lamarc, SPATCH, dadi, ms ABC.

Question 10

What is an example of a rapidly spread resistance gene

Answer 10

kdr

*single pathotype shared across Africa and between species

Question 11

how we infer the source (single or multiple origins) or a mutation

Answer 11

looking at the flanking DNA around the mutation can help infer the source, if it spread from one source than that flanking DNA would spread with it.

Question 12

What was found to be the origin of Kdr

why is this info useful

Answer 12

multiple origins of this mutation
followed by wide georgraphical spread, giving info about gene flow
this info and that of the time series data can tell us how our transgene might spread through content wide mosqutio populations

Question 13

What are the 4 types of spread of a transgene that need to be taken into account

Answer 13

1. spatial spread: physical barriers to gene flow
2. temporal spread: across dry seasons?
3. spread between closely related species
4. resistant genotype

Question 14

What could the potential pitfalls be of the spatial spread of a transgene

Answer 14

potential stopped by areas with no humans
genetic data showed no barriers between large parts of Africa, spatial spread is possible. (via numerous mtDNA and microsat studies)
** rift valley could be a potential barrier

Question 15

What could the potentially pitfalls of temporal spread of a transgene

Answer 15

experiment: same population measured before and after dry season
found they woukld not be at risk in dry season

Question 16

whats the potential for spread between closely related species

Answer 16

gambiae and arabiensis have shown ability to hybridise

higher gene flow in arabiensis than gambiae

Question 17

what is the potential for resistant genotypes

Answer 17

transgene is put into specific DNA sdequence if there is variation in this sequence in the wild population than thsoe moswutios will be resitance to transgene.

Question 18

Desribe the gene flow of An. scaloni in Thailand

what is this thought to be due

Answer 18

mtDNA haplotype data from An. scaloni showed clustering of lineages found in different regions
*lack of gene flow thought to be due to high mosquito association with lime stone cast caves, which have a patchy distribution, meaning mosquitos will not move far from caves

Question 19

what is the mtDNA dsitribution of gambiae and arabiensis in Africa

Answer 19

across Africa showed haplotypes occur in both kenya and Senegal in a large network of gene flow

Question 20

What is hypothesized spread of transgene in gambiae and colluzii

Answer 20

should spread between them due introgression

*mapped chromosome divergence between the two groups ascertains regions not to put the transgene.

Question 21

How was chromsome position of fertility gene tracked

Answer 21

various info from 16 anopheles species, to look at genes of interest and observe amount of variation at each place in genomes.

Question 22

Why is it important to know effective population size of mosqutios

Answer 22

to know how many mosquitos to release, allow monitoring of success and failure

Question 23

how was effecitve population size calcualted

Answer 23

different methods to estimate effective population size from genetic data: genetic diversity, allele frequencies, linkage d, runs of homozygosity

Question 24

How can the population history be inferred

Answer 24

using allele frequency spectrum
*distribution of alelle frequencies from a set of loci (often SNPS) in a population or sample. each entry in frequency spectrum records total no. of loci with corresponding derived alelle frequency
shape of spectrum can tell you about population history.

Question 25

what is the Dadi demographic fit model

Answer 25

bayesian methods to check models and give different scenarios of exponential growth or sudden grwoth etc. can work out the best model for the data

Question 26

What can linkage D tell us

Answer 26

* with no recombination, all SNPs on a chromosome are linked * with recombination, expectation of degree of linkage. * deviations/variations in amount of linkage due to population size, selection, demographic history, variation in recombination rate etc.

Question 27

How can diversity be measured

Answer 27

Tajimas D: ratio of diversity measures (pi(nt diversity)/s (no. of segregating sites) pi/s value of zero reflects steady neutral population with no selection. negative value reflects excess of low frequency of polymorphisms consistent with population expansion or selection. positive value reflects a deficit in low frequency polymorphisms consistent with a recent decline in population size.

Question 28

what is the population recombination rate?

Answer 28

p - estimated from LD between SNPS p= 2Ne*r theta - 4ne*u at neutrality p/theta = r/2u = ~10

Question 29

what did LD in kilifi in Kenya show

Answer 29

LD decay in gambiae showed Kilifi gambiae in kenya had higher LD than other populations

Question 30

why do kilifi gambiae mosquitos have a smaller population with a large tajimas D.

Answer 30

correlated with high bed net distribution and mosquito control, which have reduced no. decline can be observed in genetics.

Question 31

what are cryptic speceis

Answer 31

often revealed by genomics | eg. colluzi and gambaie