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BIO3A: Processes 2 Patterns > S1: W3 (Prof. Kelsey) > Flashcards

S1: W3 (Prof. Kelsey) Flashcards

1
Q

Types of heterozygosity? (2)

A

• Observed heterozygosity.
• Expected heterozygosity.

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2
Q

Observed heterozygosity?

A

= alleles observed in the population (polymorphic).

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3
Q

Expected heterozygosity?

A

= uses the HWE (2pq).

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4
Q

Population?

A

= group of individuals that interbreed

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5
Q

Population properties? (2)

A

• Density.
• Dispersion.

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6
Q

Density?

A

= number of individuals in a given area.

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7
Q

Dispersion?

A

= pattern of the distribution of individuals in a population.

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8
Q

Types of dispersion? (3)

A

• Clumped.
• Spaced.
• Random.

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9
Q

Metapopulation structure?

A

= population of subpopulations/patches.

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10
Q

2 things to consider when talking about metapopulation structure?

A

• Patch.
• Patch size.

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11
Q

Two pressures that play a large role in dispersion?

A

• Gene flow.
• Drift.

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12
Q

What does the level of population differentiation depend on? (2)

A

• Gene flow.
• Drift.

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13
Q

Consequences of metapopulations? (2)

A

• Bottlenecks.
• Odd patterns of genetic diversity & differentiation.

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14
Q

What do you mean by odd patterns of genetic diversity?

A

We mean that genetic diversity is high or low.

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15
Q

Eg of Odd patterns of genetic diversity & differentiation?

A

Guppies

  • downstream guppies have low genetic differentiation but high genetic diversity due to downstream flow.
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16
Q

Genetic diversity vs Gentic differentiation?

A

● Genetic diversity
= number of alleles.

● Genetic differentiation
= comparison between composition of alleles in populations.

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17
Q

Causes of population differentiation? (3)

A

• Reduced gene flow.
• Local adaptation (slxn).
• Vicariance (geographic isolation).

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18
Q

Why do we care about population differentiation? (3)

A

• Conservation.
• Population divergence.
• Evolution.

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19
Q

How do we measure population differentiation?

A

By estimating genetic diversity & looking at how it’s distributed (variation = heterozygosity).

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20
Q

Why do populations diverge? (4)

A

• Migration of individuals.
• Local adaptation (slxn).
• Habitat fragmentation.
• Limited dispersal abilities & philopatry.

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21
Q

Philopatry?

A

= the tendency to go back to a specific area habitually.

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22
Q

Eg of philopatry?

A

Salamanders going back to ponds that they were born in.

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23
Q

Indications of subpopulations in data?

A

Via the Wahlund effect.

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24
Q

Wahlund effect attributes? (3)

A

• Reduced heterozygosity due to structure of data.
• Both subpopulations in HWE.
• Two or more populations have different allele frequencies, but are in HWE.

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25
Q

Why care about subdivisions? (3)

A

• Gender diversity.
• Conservation.
• Range of trait/behaviour sampling.

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26
Q

Eg of Consersation in Importance of subdivisions?

A

Erica vertiallote.

  • brought back at the brink of extinction.
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27
Q

Key part of subpopulation genetic differentiation?

A

Gene flow.

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28
Q

How do alleles/genes move?

A

Dispersal.

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29
Q

Dispersal?

A

= movement of individuals between discrete populations/locations.

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30
Q

Dispersal attributes? (3)

A

• Disperse to share alleles.
• Ofen good intentions, but not always a successful endeavor.
• Surrogate for gene flow.

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31
Q

Eg of Dispersion?

A

Calopteryx splendens

  • discriminate against immigrant females & kill them.
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32
Q

Migration?

A

= the periodic movement to & from a geographic area.

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33
Q

Migration attributes? (2)

A

• Doesn’t contribute to gene flow/movement of alleles.
• Eg is Monarch butterflies.

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34
Q

Dispersal & Migration attributes? (2)

A

• Both precede gene flow.
• Neither result in gene flow until reproduction takes place.

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35
Q

Eg that shows why it matters how/when alleles are shared?

A

Malaria mosquitoes.

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36
Q

Barriers to dispersal & gene flow? (2)

A

• Man-made.
• Natural.

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37
Q

Egs of Man-made barriers? (3)

A

• Roads.
• Farms.
• Turbines.

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38
Q

Egs of Natural barriers? (5)

A

• Mountains.
• Rivers.
• Salinity.
• Nutrient gradients.
• Ocean upwelling.

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39
Q

Interspecific interactions?

A

= where organisms rely on each other to disperse alleles (for gene flow) through dispersal mechanisms, host-parasite interactions & hybridization.

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40
Q

Host-parasite interactions attributes? (2)

A

• Host dispersal to avoid infection.
• Parasites also manipulate host dispersal.

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41
Q

Eg of Host dispersal to avoid infection?

A

Cliff swallows

  • will abandon a colony to avoid parasites.
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42
Q

Eg of Parasites also manipulating host dispersal?

A

Fire ants.

  • Fungi took over a fire ant (no a zombie) to move towards an ideal condition for fungal growth.
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43
Q

Implications of host-parasite interactions for evolution? (2)

A

• Affects gene flow/dispersal of alleles.
• Study protein changes in cells that alter behaviour.

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44
Q

Eg of Implications of host-parasite interactions?

A

Toxoplasma gondii (cats & rats).

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45
Q

Hybridization attributes? (4)

A

• On a continuum.
• Can lead to unique evolutionary lineages.
• Can lead to divergence.
• Can lead to homogenization of species.

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46
Q

Lay out Hybridization continuum for me? (3)

A

● Left side
= species divergence.

● Middle
= maintenance of hybrid swarm.

● Right side
= species homogenization.

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47
Q

How to measure Hybridization?

A

By measuring introgression.

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48
Q

Introgression?

A

= movement of genes from one species to another by recurrent/repeated backcrossing of a hybrid to parent species.

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49
Q

Backcrossing?

A

= crossing of a hybrid with one of its parents or an individual genetically similar to its parent, to achieve offspring with a genetic identity closer to that of the parent.

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50
Q

Eg of introgression?

A

Finches.

  • Bill depth changes due to introgression of G. fortis & G. fuliginosa finches on Island Daphne Major.
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51
Q

Subsume adaptively radiated taxa?

A

= where a generation of genetic diversity enables rapid evolutionary change in new environments.

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52
Q

What causes radiations in subsume adaptively radiated taxa?

A

Gene duplications.

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53
Q

Eg of Subsume adaptively radiated taxa?

A

Cichlids.

  • More on the homogenous side of the Hybridization continuum.
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54
Q

Why is experimental design important? (2)

A

• Develop an efficient way to test a hypothesis.
• Ensures a conclusion due to a real pattern & not researcher error.

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55
Q

Steps for testing ideas? (5)

A

• Resesrch question & hypothesis.
• Experimental approaches.
• Marker choice.
• Sampling.
• Data analysis.

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56
Q

List the experimental approaches? (2)

A

• Observational.
• Experimental.

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57
Q

Observational approach attributes? (2)

A

• Use natural variation to test for correlation between variables.
• Infer cause-effect relationship.

58
Q

Eg of Observational approach?

A

Do sable horn curves differ between sexes?

  • You would observe the difference in males & females, and see whether it gives males a sexually selective advantage.
59
Q

Experimental approach attribute?

A

Manipulate one variable in a system to measure effects on other variables.

60
Q

Eg of Experimental approach?

A

Alter predator context/content to test for selection pressure on guppies.

61
Q

Marker choice attributes? (3)

A

• Links back to your question (What scale?).
• Inheritance patterns (eg nDNA; mtDNA; cpDNA).
• Variability of marker.

62
Q

How to quantify genetic diversity? (2)

A

• Based on the number of variants.
• Based on the frequency of variants.

63
Q

Based on the number of variants attributes? (4)

A

• Polymorphism or rate of polymorphism (Pj).
• Proportion of polymorphic loci.
• Richness of allelic variants (A).
• Average no. of alleles per locus.

64
Q

Based on frequency of variants attributes? (2)

A

• Effective no. of alleles (Ae).
• Average expected heterozygosity (He; Nei’s genetic diversity).

65
Q

Importance of quantifying genetic diversity?

A

Helps in estimating composition of alleles in the population (= diversity) [using microsatellites].

66
Q

Sampling attributes? (5)

A

• How many individuals do you need to sample?
• How many populations do you need to visit?
• Who?
• Where?
• What tissue?

67
Q

Data analysis components? (2)

A

• Basic morphologies of microsatellites.
• Genalex files.

68
Q

Basic morphologies of microsatellites attributes? (3)

A

• Translate gel to chromatographs.
• 1 peak (1 gel band) = homozygous.
• 2 peaks of similar same peak height = heterozygous.

69
Q

Genalex files attributes? (2)

A

• Chromatograph to table.
• Eg: 322 to 324 = heterozygous.

70
Q

Ways to test for population differentiation using molecular data? (4)

A

• Non a prior approach.
• Individual-based analyses.
• Multi-variate statistics.
• TESS & Geneland.

71
Q

Individual-based analyses?

A

= used to test for structure in your dataset.

72
Q

Multi-variate statistics kinds? (2)

A

• PCA.
• MDS.

73
Q

Multi-variate statistics attributes? (2)

A

• Qualitative.
• Only shows whether data is clustered or not.

74
Q

TESS & Geneland?

A

= helps you incorporate geographic data, therefore helping you to relate species based on geographic regions.

75
Q

Thing to note about the methods for testing population differentiation?

A

They require careful sampling to reduce potential biases in data.

76
Q

How to estimate population differentiation? (2)

A

• Direct measures.
• Indirect measures.

77
Q

Direct measures of estimating population differentiation? (3)

A

• Mark recapture.
• Radio transmitters.
• Parentage analyses.

78
Q

Pro of Direct measures to estimate population differentiation?

A

Provides direct evidence of dispersal.

79
Q

Cons of direct measures of estimate population differentiation? (4)

A

• Expensive.
• Time consuming.
• Need at least 1 parent.
• No evidence of gene flow.

80
Q

Indirect measures to estimate population differentiation? (4)

A

• Non a priori approach.
• Individual-based analyses.
• Multi-variate statistics.
• TESS & Geneland.

81
Q

3 things that the indirect measures to estimate population differentiation fall under?

A

• Assignment tests.
• Nei’s genetic distance.
• F (ST).

82
Q

Assignment tests?

A

= where individuals are allocated in a group due to genotypic similarities.

83
Q

Assignment tests attributes? (3)

A

• Based on allele frequencies.
• We try to achieve HWE with this by allocating individuals with similar genotypes into a group to achieve HWE within that group.
• Enables clusters to be in HWE.

84
Q

Aim of Assignment tests?

A

To understand population structure.

85
Q

Structure file things to look for? (4)

A

• Abo A205; A205 = individual.
• 2 rows/individual.
• Abo L74, L87 = loci.
• Loci with both homozygous & heterozygous information is informative + polymorphic locus.

86
Q

Why 2 rows/individual?

A

It’s because you’re dealing with diploids.

87
Q

Nei’s genetic distance for population differentiation?

A

= genetic distance is based on allele frequencies.

88
Q

Structure graph attributes? (3)

A

• Read from left to right.
• Has individual bars.
• HWE is violated & we’re trying to figure out whether it’s because of hybrids, backcrossing or gene flow.

89
Q

Why are structure bars important? (3)

A

• Help us figure out where individuals are from.
•
•

90
Q

Admixture/Admixed individuals?

A

= individuals that are either hybrids, backcrossed individuals or as a result of gene flow.

91
Q

Eg of structure bar?

A

Zebra population structure.

92
Q

Lorenzen et al. 2008 summary? (3)

A

• Speaks on zebra population structure.

• k = 2 means 2 populations.
• k = 3 means 3 populations.
• k = 4 means 4 populations.

93
Q

Nei’s genetic distance (D) steps? (2)

A

● Know I.

● Calculate D.

94
Q

D equation?

A

D = -ln I

95
Q

I? (2)

A

• Nei’s estimate of similarity.
• Based on frequency of alleles in two or more populations.

96
Q

D range?

A

0 –> infinity

97
Q

D approaches zero? (2)

A

• I approaches 1.
• 2 populations are similar.

98
Q

D approaches infinity? (2)

A

• I approaches zero.
• 2 populations don’t share alleles.

99
Q

Important thing to note regarding Nei’s genetic distance (D)?

A

This is different from genetic distance calculated with MEGA! It is based on allele frequencies NOT sequence comparisons.

100
Q

Factors affecting heterozygosity (F(ST))? (2)

A

• Drift or NS.
• Inbreeding.

101
Q

F-statistics attributes? (2)

A

• Quantification of the genetic variation in metapopulations (population structure).

• Measure the heterozygosity (genetic variation) deviation from HWE using 3 different measures of H.

102
Q

F(ST) attributes? (2)

A

• Identifies population differentiation.
• Range: 0 - 1.

103
Q

How to partition variation?

A

Combine different sources of reduction in expected heterozygosity into one equation:

1 – F(IT) = (1–FST)(1–FIS)

104
Q

1–FIT?

A

= overall deviation from HW expectations.

105
Q

1–FST?

A

= deviation due to subpopulation differentiation.

106
Q

1–FIS?

A

= deviation due to inbreeding within a population.

107
Q

Equation that partitions variation?

A

= a means to characterize evolutionary processes acting on a population.

108
Q

Evolutionary processes for FST? (2)

A

• Selection.
• Gene flow.

109
Q

Evolutionary processes for FIS? (2)

A

• Random & Non-random mating.
• Inbreeding.

110
Q

Estimating heterozygosity?

A

= partition variation to the total metapopulation (HT), subpopulation (HS), individuals (HI).

111
Q

HT?

A

= expected heterozygosity of total population level.

112
Q

HS?

A

= expected heterozygosity of subpopulation level.

113
Q

HI?

A

= observed heterozygosity for each subpopulation.

114
Q

How to estimate heterozygosity? (4)

A

• 2 allele model.
• 2pq = observed & expected heterozygosity.
• HT = average expected heterozygosity in total metapopulation from HWE.
• 2pq –> mean p & mean q across all subpopulations.

115
Q

How does F-statistics relate to heterozygosity?

A

Via:

FIT = (HT–HI)/HT

116
Q

HT attributes? (2)

A

• Average Ho.

• p1q1 + p2q2

117
Q

FIS equation?

A

FIS = (HS–HI)/HS

118
Q

FIS large values (closer to 1)? (3)

A

• Lots of inbreeding.
• Selfing plants.
• Small animal populations of related individuals.

119
Q

FIS smaller values (& negative values)?

A

Outcrossing.

120
Q

FST equation?

A

FST = (HT–HS)/HT

121
Q

FST?

A

= reduction in heterozygosity due to population structure.

122
Q

HT in FST equation?

A

= variation between populations.

123
Q

HS in FST equation?

A

= variation within population.

124
Q

FST = 1? (2)

A

• High variation between populations (100%).
• No variation within populations (0%).

125
Q

FST = 0? (2)

A

• No variation between populations (0%).
• High variation within populations (100%).

126
Q

FST = 0.11? (2)

A

• Variation between populations (11%).
• Variation within populations (89%).

127
Q

Causes of low FST? (3)

A

• Sampling.
• Markers used.
• Taxonomic relatedness.

128
Q

In Willow leaf beetle, you’re given following data/table:

FST in different river drainage = 0.04.
FST in same river drainage = 0.02.

Interpretations? (3)

A

• Gene flow occurs at short distance.
• Nearby subpopulations are mating with each other.
• Mating is not happening often between beetles at different river drainages.

129
Q

Types of F-statistics? (2)

A

• Pairwise F-statistics.
• Global F-statistics.

130
Q

Global F-statistics?

A

= 1 F-statistic for all populations.

131
Q

Pairwise F-statistics?

A

= 2 F-statistics for all populations.

132
Q

F-statistics? (3)

A

• FIS.
• FST.
• FIT.

133
Q

F-statistics in equations? (3)

A

● FIS = (HS–HI)/HS

● FST = (HT–HS)/HT

● FIT = (HT–HI)/HT

134
Q

Scarlet Tiger Moth exercise
• Calculate Global F-statistics from data below: (6)

× Subpopulations: 1; 2; 3; 4; 5

× p : 0.86; 0.80; 0.96; 0.73; 0.91

× Ho : 0.06; 0.12; 0.03; 0.15; 0.06

A

● Use p to calculate q for each one (p+q=1)

q1= 0.14.
q2= 0.20
q3= 0.04
q4= 0.27
q5= 0.09

● Calculate HI

HI
= (Ho1 + Ho2 + Ho3 + Ho4 + Ho5)/total # population

HI
= (0.06+0.12+0.03+0.15+0.06)/5 = 0.084

HI = 0.084.

● Calculate HS

• 2pq for each subpopulation.
• HS = (2p1q1+2p2q2+2p3q3+2p4q4+2p5q5)/total # population

HS = 0.239.

● Calculate HT

• Calculate average p.
• Calculate average q.
• 2pq (with dash).

HT = 2(ave. p)(ave. q)
HT = 2(0.852)(0.148)
HT = 0.252.

● F-statistics in equations

• FIS = (HS–HI)/HS = (0.239–0.084)/0.239 FIS = 0.649.

• FST = (HT–HS)/HT = (0.252–0.239)/0.252 FST = 0.052.

• FIT = (HT–HI)/HT = (0.252–0.084)/0.252
FIT = 0.667.

● Therefore,

• FIS = 0.649.
• FST = 0.052.
• FIT = 0.667.

135
Q

Steps to calculating Global F-statistics from data given? (5)

A

● Use p to calculate q for each one (p+q=1).
● Calculate HI.
● Calculate HS.
● Calculate HT.
● Calculate F-statistics in equations.

136
Q

HI equation in Global F-statistics?

A

HI = (Ho1 + Ho2 + Ho..) /total # popn

137
Q

HS equation in Global F-statistics?

A

HS = (2p1q1 + 2p2q2 +…)/total # popn

138
Q

HT equation in Global F-statistics?

A

HT = 2 (ave. p) (ave. q)

139
Q

“Levels” of heterozygosity? (3)

A

• Individual.
• Subpopulation.
• Metapopulation.

140
Q

Types of metapopulation structure? (3)

A

• Classical.
• Mainland.
•

BIO3A: Processes 2 Patterns (12 decks)

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