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Ecological and Conservation Genetics > Module 1 > Flashcards

Module 1 Flashcards

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1
Q

What is ecological genetics?

A

A field of science that uses genetic tools and theory to study and infer something about populations or species in natural systems.

It looks at

  • Speciation
  • Evolutionary fitness
  • Adaptive traits
  • Genetic variation
  • Landscape genetics (geneflow in the landscape, corridors etc.)
  • Phenotypic plasticity
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2
Q

What is conservation genetics?

A

A field of science which makes use of genetic theory and techniques to manage wildlife populations, however, it focuses on populations to reduce the risk of extinction and help them withstand environmental change.
Emphasis on small, declining populations.

Things such as inbreeding, genetic drift etc.

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3
Q

Why are molecular genetic markers good tools to use for wildlife populations?

A

It broadens the scope.

They tell you about the state of the animal/population now but also back in time.

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4
Q

What is effective population size?

A

The number of animals in a population that breed. The genetic material that gets carried on to the next generation.

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5
Q

Cryptic species

A

Species that look like each other (to us, but not to the animals!)

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6
Q

How is genetic diversity generated?

A

Through mutation in gametes that can be passed on

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7
Q

How does divergence among populations arise?

A

Things such as genetic drift, selection and migration influences the genetic composition of each population.

Selection: Disease, climate and competition

Chance sampling: Loss of genetic diversity

Mating selection: Affects which genomes enter the gene pool

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8
Q

What are the four micro evolutionary processes?

A

Genetic drift, selection, migration and mutation

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9
Q

What does a genome consist of?

A

The nuclear and organelle chromosomes of an organism are integrated into our phenotype

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10
Q

When do we use the word haplotype?

A

For the organelle chromosomes we use “Haplotype” since there is only one version of each gene and not two.

We also don’t call it alleles.

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11
Q

What are the ideal characteristics of genetic markers?

A
  1. We can detect variation, qualitative (present/absent) or guantitative (high/low)
  2. Same genotype irrespective of environment (i.e. there are no environmental or developmental differences)(c.f. RNA, which is NOT a genetic marker, since the expression can change with environment)
  3. Simple co-dominant inheritance (diploid: heterozygote vs. homozygote)
  4. Detect silent (synonymous) nucleotide substitution (We can’t use aminoacid sequences)
  5. Detect changes in coding and non-coding portions of the genome
  6. Detect evolutionary homologous changes (similar due to descent from a common ancestor)
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12
Q

What are codominant markers?

A

The differences that give rise to polymorphic markers are carried on individual chromosomes and can be visualised as alleles. (Mendelian inheritance applies)
- We can see whether an organism is a homozygote or a heterozygote

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13
Q

What are dominant markers?

A

Markers that allow for analysis of many loci at the time, without any previous knowledge of the polymorphic sites
- Presence or absence of bands (1 or 0)

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14
Q

What is neutral variation?

A

Mutations gives no selective advantage

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15
Q

What are some examples of neutral variation?

A
  • When an amino acid replaces another of similar chemistry so that the secondary structure is unchanged)
  • When a DNA change occurs that doesn’t change the amino acid (aka synonymous change)
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16
Q

What can we use neutral variation for?

A
  1. It gives us a “null” hypothesis to test observed alleles or gene frequencies against (We can detect deviations from HWE)
  2. It is a “Molecular clock”: For any one gene, evolution occurs at a constant rate which allows dating for evolutionary events
  3. We can infer common ancestry for genotypes that are the same (homologous)
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17
Q

Hardy Weinberg Equilibrium, HWE

A

States that: Allele and genotype frequencies in a population will remain constant from generation to generation in the absence of evolutionary influences (Mate choice, mutation, selection, genetic drift, gene flow, meiotic drive=

Completely unrealistic situation.

Random mating, no migration, genetic drift or natural selection.
Allele frequencies do not change = No evolution.

Null state/ Null model in population genetics where none of the microevolutionary processes are operating. Population size is infinitely large, no genetic drift, no mutation, no selection, no geneflow in or out.

We can figure out which of the processes is driving the population away from the HWE.

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18
Q

What is adaptive variation?

A

The mutations give the organism either a selective advantage or disadvantage.

Non-synonymous change resulting in aminoacid change.

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19
Q

What is homoplasy?

A

When genomes are in a similar state due to convergence

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20
Q

What is an allozyme and how can it work as a marker?

A

A protein used as a genetic marker.
Allozymes /isozymes -> proteins -> tells us about function.

Popular method from mid 60’s to 80’s but not used any more

We use Non-denatured proteins with different net charges migrate at different rates through gels.

We can get alleles from it because it has co-dominant variation

Charge feautures stem mainly from 3 AAs with positive side chains (lysine, arginine and histidine) and 2 AAs with negative sidechains (aspartic acid and glutamic acid)

The polymorphisms went from low to high.

Obviously, this method is influenced by selection and the environment, because we are looking at the protein that has been expressed

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21
Q

What are Fragment length polymorphisms?

A

A mix of co-dominant and dominant markers.

Technical details differ, but common principle:
Banding profiles obtained (binary presence or absence data)

RFLP: Restriction Fragment Length Polymorphism

AFLP: Amplified Fragment Length Polymorphism

ISSR: Interspersed Simple Sequence Repeats

RAPD: Randomly Amplified Polymorphic DNA

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22
Q

What are Microsatellites?

A

Repeated DNA, commonly caused by misalignment during replication in meiosis. We count repeat number.

aka STRs (Short Tandem Repeats) or SSRs (Simple Sequence Repeats)

Poly A/T are most common.
1-10 bp tandemly repeated -> “Micro-satellite”
> 10 bp -> “Mini-satellite”

Are found in the nuclear DNA and are co-dominant

Drawbacks: We can get extra repeats or lose repeats as time goes on, so the number of repeats gives us a false sense of time and might underestimate the divergence.

Expensive and requires a lot of lab work-

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23
Q

What are SNPs?

A

Single Nucleotide Polymorphisms.

Point mutations that only change a single base-pair.

Are the most common polymorphisms (1 in 350 bp)

Most occur in non-coding regions (non-coding SNPs)
yet these can still cause phenotypic changes if they are in a promoter or other regulatory region.

Coding SNPs can cause non-synonymous mutations (AA change -> different protein)
OR Synonymous (silent) mutation with no change to the protein.

THE GOOD THING ABOUT SNPs is that we can do simultaneous genotyping of 100-1000s of SNPs through microarrays and NGS

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24
Q

What are the differences between mtDNA and nDNA?

A

Advantages of mtDNA:

  • Maternally inherited (usually)
  • Good for tracin female migration
  • Easily isolated, but that’s not so important now due to PCR
  • We can use universal primers
  • Quuick fixation in a population because of small Ne (effective population size)
  • Good for phylogenies

Advantages of nDNA

  • Biparentally inherited (Both male and female migration)
  • Slower fixation (Greater influence of mutation and migration compared to drift)
  • Some have very high mutation rates
  • Greater number of independent markers
  • > mtDNA all genes are physically bound to each other so you can’t use them as independent markers
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25
Q

What are the 3 metrics for distribution of genetic variation in populations?

A

Diversity, Distance and Differentiation

The most difficult one to estimate is genetic differentiation

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26
Q

Give a simple definition of evolution

A

Change in allele frequency over time

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27
Q

What is genetic drift?

A

Changes in the genetic composition of a population due to random sampling in a finite population.

Imperfect sampling from one generation to the next causes some alleles to be underrepresented relative to others. Potential loss of alleles from a population.

(Small sample sizes make it more likely that we lose alleles)

Drift is one of the main drivers of evolution in small populations

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28
Q

What is natural selection?

A

If we start out with equal allele frequencies, but environment is unfavorable for one allele, that allele will become less common in the population

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29
Q

Why is it problematic if a species has low genetic variation?

A

Because genetic variation is the raw material that selection acts upon. If there is no variation there is no adaptive capacity and the species is fucked in the face of environmental changes.

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30
Q

What is adaptive capacity?

A

A genetically based trait that can evolve in response to an environmental challenge.

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31
Q

The success of a population or species over time is proportional to what?

A

its genetic variation aka genetic diversity

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32
Q

Genetic diversity is closely tied to

A

Population size.

This is why genetic diversity is of such importance in populations of conservation concern

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33
Q

What is net population genetic diversity a funcion of?

A

The forces that create new variation and those that erode diversity

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34
Q

What is introgression

A

Introgression is when gametes are succesfully integrated into a population (= gene flow)

It is slightly different from migration, although similar

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35
Q

Which three things maintain and increase genetic variation in a population?

A
  1. Disruptive/diversifying selection
  2. Frequency dependent selection
  3. Heterozygote advantage
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36
Q

What erodes genetic variation within a population?

A
  1. Genetic drift (Random/chance loss of alleles, Founder effects, genetic bottlenecks)
  2. Inbreeding
  3. Some types of selection (Directional and stabilising selection)
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37
Q

What is genetic diversity?

A

Amount of genetic variation within a biological entity.

Can be measured within individuals, populations, species

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38
Q

What is genetic distance?

A

Amount of genetic variation between pairs of biological entities.

Can be measured between pairs of individuals, populations, species

39
Q

What is genetic differentiation?

A

Distribution of genetic variation among individuals or populations

40
Q

What are rare alleles?

A

Rare alleles are often deleterious alleles hidden in the heterozygote. Since they are “hidden” behind less rare, more beneficial alleles they are not a problem, unless there is inbreeding in the population, the increase of homozygosity will expose the deleterious alleles and cause the fitness to drop.

41
Q

How can we use genomics for species management?

A
  • Clarification of taxonomic status
  • Identification of inbreeding and outbreeding depression
  • Defining ESUs and MUs
  • Identification of populations of concern or interest
  • Genetic rescue
  • Planning for translocation and repopulation
  • Identifying local adaptation
  • Minimising further loss of genetic diversity

(From Shannons pre-lab presentation)

42
Q

Why does genetic diversity decline in small populations?

A
  • Genetic drift (Loss of genetic diversity and fixation of alleles -> Reduced ability to evolve)
  • Population bottlenecks
  • Inbreeding and inbreeding depression.
43
Q

What drives change in genetic composition in large populations?

A

Mutation, selection and migration

44
Q

What drives change in genetic composition in small populations?

A

Role of chance (= genetic drift) is predominant

Effects of selection are reduced or absent

Some alleles, especially rare ones, may be lost by chance, which means that allelic composition will differ greatly from the parental generation.

45
Q

What are the 3 consequences of genetic drift?

A
  1. Loss of diversity and fixation of alleles
  2. Diversification of allele frequencies among replicate populations from the same source (e.g. fragmented populations)
  3. Genetic drift will overpower the effect of selection and beneficial alleles may be lost by chance
46
Q

What is a population bottleneck?

A

A type of genetic drift.
A sharp reduction in population size, that reduces the genetic variation in populations.
The consequences depend on the magnitude, length/duration and frequency of bottlenecks

Founders of a population will affect the genetic composition of the populations = Founder event.

47
Q

What determines the consequences of a population bottleneck?

A

The consequences depend on the magnitude, length and frequency of bottlenecks

If the reduction in Ne is short-lived and small, there will be transient effects. (e.g. a reduction to an Ne of 20 for 1 generation results in a predicted 2.5 % decrease in heterozygosity)

If the reduction is long-lived it will have a large effect (e.g. reduction to Ne of 100 for 57 generations results in actual decrease of heterozygosity of 25 %)

NOTE that a reduction in N has a greater effect in molecular markers with smaller Ne’s e.g. mitochondria and chloroplasts have much higher loss of genetic diversity

48
Q

What is a founder event?

A

Founders of a population (e.g. after a population bottleneck) will affect the genetic composition of the populations = Founder event.

49
Q

What is inbreeding?

A

Matings among closely related individuals.
Unavoidable in small populations, as they will all become related by descent over time.

Inbreeding alone does not change allele frequencies!! Therefore, inbreeding acting alone does not cause evolution.
What is does, is that it reorganises alleles into genotypes: heterozygotes -> homozygotes.

I.e. when inbreeding goes up, homozygosity goes up and heterozygosity goes down.

Remember that Fis (0 to 1) is the inbreeding coefficient. This will go up.

50
Q

What is inbreeding depression?

A

The reduction of fitness incurred because of level of inbreeding.

Inbreeding increases homozygosity which exposes rare alleles that are often deleterious and recessive.
Humans carry 4-6 alleles that would be fatal if we were homozygous for that allele. “Genetic load”.

This acts as an intrinsic biological factor that can interact with other factors and increase a populations extinction threat.

Interestingly, the impact differs between populations, so that populations which are used to outbreeding are far more affected by inbreeding depression compared to populations that are naturally inbreeding, most likely because their genetic load might have been purged over a long time.

51
Q

What is a genetic load?

A

The proportion of a genome that contains deleterious mutations that may give rise to a reduction in fitness.

Naturally outbreeding populations contain deleterious recessive alleles that are hidden in the heterozygote.

52
Q

What are the two reasons that increased homozygosity is a problem?

A
  1. Most research shows that inbreeding depression is caused by exposure of deleterious recessive alleles via increased homozygosity
  2. To a lesser extent, inbreeding depression is also caused by a reduction in probability of being heterozygous for alleles that give heterozygous advantage. (e.g. immune systems relying on diversity of major histocompatibility complex (MAC). The more diverse it is the better immune system you have. Homozygosity will give you a worse immune response)
53
Q

Give a summary of the genetic consequences of small populations

A

Small populations suffer loss of genetic diversity due to genetic drift, population bottlenecks, inbreeding and inbreeding depression.

This leads to reduced reproductive fitness (mostly via inbreeding depression) and reduced ability to evolve in response to environmental change (due to loss of genetic diversity)

54
Q

How big is Ne often compared to N?

A

Ne is often only 11 % of N

55
Q

What does the term Genetically Viable Population mean?

A

It describes how large a population needs to be to maintain genetic health

56
Q

What are the revised recommendations for genetically viable population sizes?

A

Ne > 100 to avoid inbreeding depression

Ne > 1000 to maintain evolutionary potential

Since Ne is usually around 11 % of N we have to multiply the recommended number for Ne by ~10 to get the recommended Census population size

57
Q

What does Minimal Viable Population (MVP) mean?

A

A viable population is a population that has a high probability of surviving for a long time.
Minimum viable population is a census population size that would be viable in the long term

58
Q

What is Frankham’s definition of a population?

A

A group of individuals living in sufficiently close proximity that any member of the group can potentially reproduce with any other member

59
Q

What is population fragmentation?

A

The separation of a population into partially or completely isolated fragments

60
Q

Why is fragmentation so bad?

A

Genetic problems due to inadequate gene flow are widespread.

Deleterious effects of reduced population size take effect: Loss of genetic diversity, Inbreeding depression AND it’s usually worse than in a non-fragmented population of the same size because of the isolation.
Gene flow is reduced.

61
Q

What are the two parts of genetic diversification?

A
  1. Initial genetic subdivision - The alleles in the original population is distributed by chance in the new fragmented population, and there will be different allele frequencies in the populations (Genetic drift due to Founder events)
    OBS there are more differentiation among the smaller fragments compared to among the larger fragments because the large ones sample more of the original population.
  2. Cumulative diversification, multigeneration effects - Inbreeding and genetic drift will create greater differentiation of allele frequencies over time. Variance in allele frequencies increase with time and faster in smaller populations.
62
Q

Which factors does the level of genetic fragmentation depend on?

A

Dispersal ability and distance.
(Also time, as in how long has it been since the population was fragmented)
Interestingly, adaptive differences will hinder geneflow as well.

Observed examples from the literature:
Taxa that can fly generally have lower Fst than those that walk.
Taxa that swim generally have lower Fst than those who can fly or walk.

Low Fst = less genetic differentiation

63
Q

Isolation by distance (Wright 1969)

A

Genetic differentiation is often related to geographical distance.

Distant populations can exhibit reduced gene flow and isolation by distance.

64
Q

What are the genetic effects of fragmentation?

A

“A critical but little appreciated expectation in conservation genetics is that population fragments simultaneously become genetically differentiated, lose genetic diversity and become inbred due to drift” Frankham 2019

65
Q

What is the Wahlund effect?

A

The Wahlund effect is when the Heterozygosity Ho for the entire population declines compared to HWE expectations as population fragments drift apart

66
Q

How do we diagnose genetically fragmented populations?

A

We use HWE, so if the heterozygosities are lower than HWE expectations populations are genetically fragmented (Fst > 0.15-0.2)

67
Q

How much faster does inbreeding occur in small fragments (several small) compared to one population of the accumulated Ne (single large)?

A

Ne of 100.
Split into 5 populations of Ne=20 and one population of Ne=100.

Inbreeding (Fis) increases at a rate of 2.5 % per generation in the small
while it increases at a rate of 0.5 % in the large.

After 10 generations the Fis is 40 % in the small fragments and
4.9 % in the large.

68
Q

Compared to a single large population of the same size, fragments that are completely isolated suffer:

A
  • Greater loss of genetic diversity
  • Increased inbreeding
  • Elevated extinction risk
69
Q

What can a single migrant per generation help prevent and what can’t it prevent?

A

It can help prevent complete genetic differentiation between population fragments, irrespective of population size.

It can’t prevent the harmful effects of inbreeding.

70
Q

Frankham 2010 recognises 7 different population structures

A
  1. Totally isolated fragments (no gene flow)
  2. Effectively Single Large (Gene flow is sufficient to result effectively in a single large population)
  3. Mainland to island / Source to sink (One-way from mainland to islands) a)
  4. Island structure (Migration is equal among equal sized islands) b)
  5. Linear stepping-stone (Only neighbours exchange migrants) c)
  6. 2D stepping stone (Only surrounding neighbours exchange migrants) d)
  7. Metapopulation (Regular extinction and recolonisation events) e)
71
Q

What is a metapopulation?

A

A group of partially isolated populations that undergo local extinctions and recolonisations

72
Q

How do we measure historical and contemporary gene flow?

A

Historical: Fst is a good estimate.

Contemporary: Fst is bad.
Mark and recapture
Genetic markers that identify source populations of migrant individuals or gametes.

73
Q

What is outbreeding depression?

A

A decrease in reproductive fitness caused by hybridising evolutionary distinct taxa due to selection against hybrids.

“A reduction in reproductive fitness due to crossing of two populations or sub-species or species”

Most real life cases have happened due to incorrect taxonomy.

74
Q

Why is it difficult to determine taxonomy?

A
  • Incipient species (In the process of diverging)
  • Inadequate data (e.g. cryptic species)
  • Use of different species definitions (~22 definitions)
75
Q

What characterises the most suitable species definitions for conservation purposes?

A

They are based on evolutionary units and gene flow.

76
Q

What is the most accepted species definition?

A

Ernst Mayrs Biological Species Concept, 1963

“A group of actually or potentially interbreeding individuals and natural populations that cannot interbreed with individuals from all other such groups”

Frankham 2010 uses a modern version:
“Individuals within a species have linked evolutionary fates as they are capable of gene exchange, while different species have independent evolutionary trajectories”

77
Q

How do we resolve taxonomic status?

A

We use multiple lines of evidence e.g.

  • Morphology
  • Breeding behaviour
  • Chromosomes
  • Neutral nuclear and organelle genetic markers (Phylogenies)
78
Q

What is an ESU?

A

Evolutionary Significant Unit (Ryder 1986)

A population that has a high priority for separate conservation based on adaptive distinctiveness and reproductive and historical isolation.

Not necessarily the same as a species, but it might be the same as a species

79
Q

What is an MU?

A

Management unit (Crandall et al. 2000)

Ecological and genetic exhangeability (Are the populations replaceable?)

We also look at whether the differentiation is recent (human induced) or historical
and
we then do a pairwise comparison of all of this (genetic, ecological exchangeability vs. recent or historical timeframes) to determine the MU.

Ecological exchangeability is rejected if there is evidence for population differentiation due to natural selection or genetic drift. (e.g. life history traits, morphology, habitat, loci under selection)

Genetic exchangeability is rejected if there is evidence of restricted gene flow (e.g. multiple nuclear loci such as microsatellites or SNPs)

80
Q

What is the general goal of conservation efforts?

A

To increase population size to a point where the population is relatively immune to demographic, environmental, catastrophic and genetic threats.

81
Q

What actions can we take to achieve the general goal of conservation?

A

Identify and remove the causes of decline.

  • Control hunting and harvesting
  • Designation of reserves
  • Reduction of pollutants
  • Improvement of habitat quality
  • Eradication of unnatural (introduced) predators and competitors
82
Q

What are the specific genetic goals of management of wild populations?

A
  1. Maintain reproductive fitness
    - Minimise inbreeding
    - Avoid outbreeding depression caused by hybridising evolutionary distinct taxa.
  2. Conserve genetic diversity
    - To allow adaptive evolution to environmental change
83
Q

Genetic management of fragmented populations?

A

Options to minimise inbreeding and maximise genetic diversity:

  • Increase habitat area and quality
  • Create habitat corridors
  • Artificially increase the rate of gene flow (e.g. by translocation) to match historical levels
  • Reestablish populations in suitable habitat where they have become extinct
84
Q

What is genetic rescue and why is it controversial?

A

Essentially moving individuals from one place to another.

A management action intended to improve reproductive fitness and restore genetic diversity in small inbred populations by outcrossing to a closely related population.

Concerns about the risk of outbreeding depression and losing adaptive distinctiveness of populations makes genetic rescue controversial

Source individuals can be

  • Outbred from a genetically healthy population
  • Inbred but genetically distinct from the population they are rescuing
  • NOT from another species, even if closely related
85
Q

What is the cause of outbreeding depression?

A
  • Parental populations adapted to different environments (wet vs. dry) and the hybrids are not well suited to the place they live.
  • Disruption of co-adapted gene complexes when hybridised as interacting alleles, deleterious when recombined (e.g. jaw bone length and tooth position mixed between a large jawed and small jawed population)
86
Q

What is the value of captive breeding as a conservation tool?

A
  1. Education of the public into conservation, making people care about the animals
    1. Improving understanding of species biology, we can observe them closer and understand especially breeding biology better.
    2. Establishing captive, breeding populations ex situ
    3. Provides individuals for reintroduction to the wild (as long as they are kept in captivity short-term)
87
Q

Why do we say that a captive population should be founded from at least 20-30 individuals (preferably more)

A

Because an Ne = 30 retains appr. 98 % heterozygosity

However, we need far more than 20-30 to retain allelic diversity

88
Q

What does the retainment of allelic diversity in a captive population depend on?

A

Number of alleles at each locus (A)

Rarity of alleles

89
Q

In captive breeding programmes, what is the definition of the Target Population SIze that we hope to achieve?

A

Target Population Size = the population size that retains 90 % of genetic diversity for 100 years.

This depends on the founder event (the captive breeding programme), Ne/N ratio, generation time, rate of population increase after founder event.

For species with shorter generation times you need a larger population size compared to a species with longer generation times

90
Q

Why is it important that we perform genetic management during the maintenance phase of captive breeding?

A

Captive populations go through genetic deterioration in captivity

  • Inbreeding depression
  • Loss of genetic diversity
  • Mutational accumulation (new mutations become fixed in small populations)
  • Adaptation to captivity which makes it less likely that they will survive in the wild.
91
Q

If kinship is minimised (in breeding)…

A

… Heterozygosity is maximised

This also maintains allelic diversity

92
Q

How can fragmentation of populations be used to avoid loss of genetic diversity and adaptation to captivity?

A

If populations are fragmented, maintained and then pooled (interbred that is) prior to release, the fitness and genetic diversity is higher than for a single large population with the same number of individuals.

SLOSS: As long as no fragmented populations go extinct fragmented populations retain more overall genetic diversity than a single large population.

93
Q

What factors increase the success rate of reintroductions?

A
  • Having a wild source population (compared to a captive one)
  • Releasing a large number of animals at once
  • Removing the cause of the original decline

Ecological and Conservation Genetics (3 decks)

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