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HELENP EE Evolution and Natural Selection > EE Lecture 9: Molecular Ecology and Evolution > Flashcards

EE Lecture 9: Molecular Ecology and Evolution Flashcards

1
Q

how can you measure variation among individuals

A

microsatellites

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2
Q

what are microsatellites

A

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

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3
Q

why are microsatellites highly variable

A

due to coping errors

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4
Q

what is the method for detecting variation among individuals

A
  1. extract DNA
  2. primers to amplify microsats
  3. amplify microsat by PCR -mills of copies
  4. run on gel
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5
Q

on what levels can variation be measured among individuals

A

through identifying individual
family relationship
genetic variability and inbreeding in pops

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6
Q

what case study has been done to identify individuals

A

Pyrenean brown bears

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7
Q

what did the brown bear case study involve

A

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

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8
Q

what genetic and field data can be used to identify individuals

A

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

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9
Q

why are pyrannean bears problematic

A

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

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10
Q

how are people trying to maximise pyrannean bear genetic variation

A

guid reintroduction of new bears

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11
Q

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

A

Cytb and mtDNA

also for 9dinucleotide microsatellite loci

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12
Q

what is kinship analysis based on

A

the pattern of alleles

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13
Q

what’s the use of microsatellites

A

identify relationship among individuals-pedigree,genealogy

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14
Q

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

A

microsatellites

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15
Q

what can be used to infer popn history

A

pattern of genetic variation

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16
Q

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

A

eg.popn bottlenecks,expansion, fragmentation

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17
Q

why might it be useful to analyse popn history

A

for popn viability analysis

extinction risk

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18
Q

what factors affect genetic variation in pops

A 
pop size
mutation rate
level inbreeding
pop subdivision-gene flow
pop history-bottlenecks
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19
Q

what is mtDNA

A

maternally inherited marker

mitochondrial DNA

20
Q

how can mtDNA be tested for

A
  1. extract DNA
  2. amplify marker region using primers eg. cytochrome oxidase 1
  3. clean up the PCR product
  4. cycle sequencing
21
Q

what DNA can be used to test variation in humans

A

mtDNA

22
Q

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

A
  1. other continents nested within African variation
  2. signature of pop expansion
  3. lineages coalesce back to SCA:mitochondrial Eve ~200k
23
Q

what do mitochondrial lineages coalesce back to

A

a single common ancestor; Mitochondrial Eve ~200kya

24
Q

what is reverse simulation

A

reconstructing the past

25
Q

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

A

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

26
Q

what is the expected time till coalescence to a single ancestor

A

2Nf * (1 - 1/k) generations

27
Q

discuss the popn history of the giant panda

A

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

28
Q

what are alternatives to using the model to explain variation

A

compare fit of the model to the data (1000s SNPs)

choose the model that best explains the data

29
Q

what is to blame for endangered giant panda

A

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

30
Q

which DNA sequence markers can be used to test species relationships

A

mtDNA

nuclear

31
Q

how can you reconstruct a phylogeny

A

align sequences of species, so comparing homologous sites

32
Q

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

A
  1. distance methods
  2. Parsimony methods
  3. likelihood methods (most likely based on models and data)
33
Q

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

A

rooted/unrooted?

DNA evoln is not parsimonious

34
Q

in what way is DNA evoln not parsimonious

A

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

35
Q

how can you obtain a dated tree

A

use molecular clock

use fossil/biogeographical calibrations

36
Q

what is a molecular clock

A

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

37
Q

what value on tree shows measure of tree support

A

bootstrap value

38
Q

what can phylogeny tell us

A 
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
39
Q

what can neutral markers be used for

A

to reconstruct individual, popn and species history

40
Q

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

A

microsatellites
SNPs
analyses:pedigree,pop genetics

41
Q

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

A

mtDNA
SNPs
analyses: phylogeography, coalescence

42
Q

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

A

mtDNA
nuclear DNA
analyses: phylogenies

43
Q

what markers can be used to test phylogenies

A

mtDNA

nuclear DNA

44
Q

what analyses can SNPs be used for

A

pedigree, pop genetics, phylogeography, coalescence

45
Q

whar analyses can mtDNA be used for

A

phylogeography, coalescence, phylogenies

46
Q

at which levels can SNPs be used to create analyses

A

individual or species

HELENP EE Evolution and Natural Selection (14 decks)

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