EE Lecture 9: Molecular Ecology and Evolution

Question 1

how can you measure variation among individuals

Answer 1

microsatellites

Question 2

what are microsatellites

Answer 2

simple sequence repeates of 2-6bp eg.CGTCGTCGTCGT
highly variable due to copying areas
co-dominant: can detect heterozygotes

Question 3

why are microsatellites highly variable

Answer 3

due to coping errors

Question 4

what is the method for detecting variation among individuals

Answer 4

1. extract DNA
2. primers to amplify microsats
3. amplify microsat by PCR -mills of copies
4. run on gel

Question 5

on what levels can variation be measured among individuals

Answer 5

through identifying individual
family relationship
genetic variability and inbreeding in pops

Question 6

what case study has been done to identify individuals

Answer 6

Pyrenean brown bears

Question 7

what did the brown bear case study involve

Answer 7

used genetic and field data
genetic - SRY gene for sex&microsats
field-fur and scat samples

Question 8

what genetic and field data can be used to identify individuals

Answer 8

genetic: SRY gene for sex + microsats
field: fur and scat samples

Question 9

why are pyrannean bears problematic

Answer 9

have low genetic variation compared to bears in other pops,this is due to inbreeding

Question 10

how are people trying to maximise pyrannean bear genetic variation

Answer 10

guid reintroduction of new bears

Question 11

to identify family groups of cheetahs in algeria, what sequences were used

Answer 11

Cytb and mtDNA

also for 9dinucleotide microsatellite loci

Question 12

what is kinship analysis based on

Answer 12

the pattern of alleles

Question 13

what’s the use of microsatellites

Answer 13

identify relationship among individuals-pedigree,genealogy

Question 14

what can be used to identify relationship among individuals eg.pedigree +genealogy

Answer 14

microsatellites

Question 15

what can be used to infer popn history

Answer 15

pattern of genetic variation

Question 16

how can pattern of genetic variation be used to infer popn history

Answer 16

eg.popn bottlenecks,expansion, fragmentation

Question 17

why might it be useful to analyse popn history

Answer 17

for popn viability analysis

extinction risk

Question 18

what factors affect genetic variation in pops

Answer 18

pop size
mutation rate
level inbreeding
pop subdivision-gene flow
pop history-bottlenecks

Question 19

what is mtDNA

Answer 19

maternally inherited marker

mitochondrial DNA

Question 20

how can mtDNA be tested for

Answer 20

1. extract DNA
2. amplify marker region using primers eg. cytochrome oxidase 1
3. clean up the PCR product
4. cycle sequencing

Question 21

what DNA can be used to test variation in humans

Answer 21

mtDNA

Question 22

what are the results from using mtDNA to test for variation in humans

Answer 22

1. other continents nested within African variation
2. signature of pop expansion
3. lineages coalesce back to SCA:mitochondrial Eve ~200k

Question 23

what do mitochondrial lineages coalesce back to

Answer 23

a single common ancestor; Mitochondrial Eve ~200kya

Question 24

what is reverse simulation

Answer 24

reconstructing the past

Question 25

assuming random sample from a constant pop, random mating, discrete genes, what is the probaiblity that 2 individuals share a mother

Answer 25

[1/Nf] * [1/Nf] * Nf

Question 26

what is the expected time till coalescence to a single ancestor

Answer 26

2Nf * (1 - 1/k) generations

Question 27

discuss the popn history of the giant panda

Answer 27

2 pop expansions due to warmer climate 2 pop declines:colder climate final reduction to extreme low numbers: human cause subdivision of pops in 3 areas, but with some gene flow

Question 28

what are alternatives to using the model to explain variation

Answer 28

compare fit of the model to the data (1000s SNPs) | choose the model that best explains the data

Question 29

what is to blame for endangered giant panda

Answer 29

climate hotter:pop expand twice climate colder:pop decline twice final threat:humans

Question 30

which DNA sequence markers can be used to test species relationships

Answer 30

mtDNA | nuclear

Question 31

how can you reconstruct a phylogeny

Answer 31

align sequences of species, so comparing homologous sites

Question 32

how do you get from DNA sequences to a phylogenetic tree (what 2 methods)

Answer 32

1. distance methods 2. Parsimony methods 3. likelihood methods (most likely based on models and data)

Question 33

what problems do you face when trying to get from sequences to trees

Answer 33

rooted/unrooted? | DNA evoln is not parsimonious

Question 34

in what way is DNA evoln not parsimonious

Answer 34

multiple subs transitions vs. transversions codon positions synonymous/non synonymos

Question 35

how can you obtain a dated tree

Answer 35

use molecular clock | use fossil/biogeographical calibrations

Question 36

what is a molecular clock

Answer 36

neutral subs occur @ constant average rate (proportional to the muatoin rate)

Question 37

what value on tree shows measure of tree support

Answer 37

bootstrap value

Question 38

what can phylogeny tell us

Answer 38

``` identification DNA barcoding diet of chamois trnL intron of plastid DNA from faeces history of speciation events leading to a set of species broad history of life ```

Question 39

what can neutral markers be used for

Answer 39

to reconstruct individual, popn and species history

Question 40

for the following level, which markers and analyses can be tested: INDIVIDUAL

Answer 40

microsatellites SNPs analyses:pedigree,pop genetics

Question 41

for the following level, which markers and analyses can be tested: POPN

Answer 41

mtDNA SNPs analyses: phylogeography, coalescence

Question 42

for the following level, which markers and analyses can be tested: SPECIES

Answer 42

mtDNA nuclear DNA analyses: phylogenies

Question 43

what markers can be used to test phylogenies

Answer 43

mtDNA | nuclear DNA

Question 44

what analyses can SNPs be used for

Answer 44

pedigree, pop genetics, phylogeography, coalescence

Question 45

whar analyses can mtDNA be used for

Answer 45

phylogeography, coalescence, phylogenies

Question 46

at which levels can SNPs be used to create analyses

Answer 46

individual or species