Wildlife conservation genetics
ABG51806
Crash course provides videos on various topics with visuals that help clear up some theories and information.
https://www.youtube.com/watch?v=WhFKPaRnTdQ this links to one of their videos on population genetics.
Terminology
Explanation terminology
Main message
Examples or extra info
Lectures
Literature
I’ll put formulas and maths in black boxes like these
Lecture – Introduction
There is a lot of concern about the loss of biodiversity. Biodiversity can be split in evolutionary
ecology which focusses on ecosystems and population genetics which focusses on genetic
evolutionary processes. Evolution and ecology are tightly linked. The minor wildlife biodiversity
includes both these subjects.
Literature – Chapter 1 - Introduction
Reasons endangered species decline:
- Habitat loss
- Overexploitation
- Introduced species
- Pollution
Conservation genetics= the use of genetic theory and techniques to reduce the risk of extinction in
threatened species.
Biodiversity = the variety of ecosystems, species, populations within species, and genetic diversity
among and within these populations.
Extinction is a natural part of evolution. Species usually persist for 5-10 million years. Biodiversity is
maintained when extinction is balanced by speciation.
Conservation genetics focusses on reducing current extinction rates. Bioresources include: food,
pharmaceutical drugs, natural fibres, rubber, timber etc.
Ecosystem services = essential biological functions benefiting humankind, provided free of charge by
living organisms
Biodiversity also has aesthetic value and there are ethical reasons for conservation. The rate of
extinction has been increasing over time. The majority of threatened species are on islands.
18% of vertebrates, 29% of invertebrates and 49% of plant species are classified as threatened.
Extinction rates are predicted to greatly increase in the near future.
The IUCN classification of critically endangered, endangered, vulnerable and low risk reflect degrees
of extinction risk. They are defined by:
- Population decline
- Restriction habitat
- Current population size
Species endangerment is the basis for legal protection. Primary factors contribution to extinction are
direct or indirect human impacts.
,stochastic effects = naturally occurring fluctuations experienced by a small population with
environmental, catastrophic, demographic or genetic origins.
- Environmental stochasticity: random unpredictable variation in environmental factors
- Demographic stochasticity: random variation in birth and death rates and sex ratios due to
chance
- Catastrophes: extreme environmental events
- Inbreeding: reduces birth rates and increases death rates (inbreeding depression)
- Genetic diversity loss: reduces the ability of a population to adapt to changing environments
via natural selection
Extinction vortex = in small population genetic diversity decreases and due to decreased genetic
diversity population size further decreases creating a loop.
Major conservation management issues (pages 7-10 give examples for all of these):
- Inbreeding depression
- Loss of genetic diversity (loss of evolutionary potential)
- Fragmentation of populations and reduced gene flow
- Genetic drift overriding natural selection
- Accumulation and loss of deleterious mutations
- Genetic management of small captive populations and adverse effects of adaptations to the
captive environment
- Resolution of taxonomic uncertainties
- Definition of management units within species
- Use of molecular genetic analyses in forensics
Lecture – Chapter 1 - Introduction
Everywhere on earth biodiversity can be found. It is important to understand processes that
generate biodiversity to conserve it. 99,9% of the species that ever lived on earth are now extinct.
Bas haring states individual species are not important, they are interchangeable and he says the
value of biodiversity is debatable. He says if not ALL species die out, there is no serious problem.
Three reasons for conservation:
- Biodiversity is important as it defines nature
- Nature is our environment which we have to live in
- Bio-resources/ecosystem services/ethics/aesthetics
Ethics: humans do not have the right to drive other species to extinction. We have a moral obligation
to study life before its lost forever. The beauty should be preserved. Humans like to collect, order
and preserve.
Another reason for preserving biodiversity is for pharmaceutical reasons.
Ecosystems are essential for life for example due to their functions as oxygen producers, nutrient
cyclers and water purifiers.
Loss of biodiversity tends to make individual species more vulnerable. If there is variation it is unlikely
that one event can sweep complete ecosystems. However if you only have one or two species a
fungus can have a huge impact whilst it might not when there is more biodiversity.
Life on earth is characterized by speciation and extinction.
In a network some species are more important than others. These are key species. Conservation
genetics focusses on preserving biodiversity.
There have been 5 periods of mass extinction. When lots of species died out, opportunities for others
are created.
,The dynamics of extinction:
- Individuals struggle for existence
- Demographic stochasticity
- Populations go extinct which causes species to go extinct
Extinction is normal however the rate of extinction is increasing at an alarming rate.
Most extinctions that have occurred were on islands. This is because populations tend to be smaller
on islands and migration is lower.
The primary cause of the increasing extinction is due to the huge human population. The more
specific life history the more vulnerable the species is.
Human impacts:
- Large population size
- Habitat loss and fragmentation
- Introducing non-native species
- Overexploitation
- Pollution
There are three levels of stochasticity (randomness):
- Environmental – natural catastrophes
- Demographic – variation in birth/death rates or sex ratios
- Genetic – effects of inbreeding and loss of genetic variation in small populations
Extinction vortex:
The IUCN is a widely recognized system for risk of extinction assessment in a species.
, Literature – Chapter 2 – Genetic diversity
Genetic diversity is required for populations to adapt to change. Genetic diversity is usually
decreased in endangered species.
Environmental change is a continues process. Inbreeding leads to loss of genetic diversity and overall
fitness loss.
Gene = a sequence of nucleotide in a particular locus of a DNA molecule
Genetic diversity is a slight difference in these genes. The different sequence leads to different
proteins and this can lead to different phenotype, behaviour, reproductive rate etc. leading to
differences in fitness and survival.
Genetic diversity can be described with polymorphism, heterozygosity and allelic diversity.
Genetic diversity = the variety of alleles and genotypes present in the group under study
Molecular techniques can measure genetic diversity at individual loci.
Calculation genotype frequency = the proportion of a type in the whole population.
Usually allele frequencies are used. The letters p and q represent alleles. In this formula you fill in the
number of animals with the respective genotype. Total refers to the total number of animals
( 2∗PP ) + PQ
p=
2∗Total
Heterozygosity = the extent of genetic diversity at a locus
Observed heterozygosity (Ho) = the proportion of sampled individuals that are heterozygotes.
Genetic diversity is measured with allelic diversity. When talking about multiple loci the average
alleles per loci are used.
The hardy-Weinberg equilibrium shows the relationship between allele and genotype frequency. (If
you’re not familiar with this yet the video at the top of this summary explains the concept as well)
p and q are probabilities for alleles A1 and A2.
The probability for a homozygote is p x p = p2 or q x q = q2
The probability for a heterozygote is 2 x p x q = 2pq
And 1 = 2pq + q2 + p2
In the absence of outside influence and when mating is random p and q are at equilibrium. This is
expected for all loci except those on sex chromosomes.
Hardy-Weinberg illustrates two points:
- Heterozygotes cannot be greater than 0.5 for a locus with two alleles
- When an allele is rare most of its occurrence is in heterozygotes
Assumptions hardy-Weinberg:
- Large population size
- Closed population
- No mutation
- Normal mendelian segregation of alleles
- Equal fertility of parent genotypes
- Random union of gametes
- Equal fertilizing capacity of gametes
- Equal survival of all genotypes
Outbreeding = breeding of individuals that are relatively unrelated
ABG51806
Crash course provides videos on various topics with visuals that help clear up some theories and information.
https://www.youtube.com/watch?v=WhFKPaRnTdQ this links to one of their videos on population genetics.
Terminology
Explanation terminology
Main message
Examples or extra info
Lectures
Literature
I’ll put formulas and maths in black boxes like these
Lecture – Introduction
There is a lot of concern about the loss of biodiversity. Biodiversity can be split in evolutionary
ecology which focusses on ecosystems and population genetics which focusses on genetic
evolutionary processes. Evolution and ecology are tightly linked. The minor wildlife biodiversity
includes both these subjects.
Literature – Chapter 1 - Introduction
Reasons endangered species decline:
- Habitat loss
- Overexploitation
- Introduced species
- Pollution
Conservation genetics= the use of genetic theory and techniques to reduce the risk of extinction in
threatened species.
Biodiversity = the variety of ecosystems, species, populations within species, and genetic diversity
among and within these populations.
Extinction is a natural part of evolution. Species usually persist for 5-10 million years. Biodiversity is
maintained when extinction is balanced by speciation.
Conservation genetics focusses on reducing current extinction rates. Bioresources include: food,
pharmaceutical drugs, natural fibres, rubber, timber etc.
Ecosystem services = essential biological functions benefiting humankind, provided free of charge by
living organisms
Biodiversity also has aesthetic value and there are ethical reasons for conservation. The rate of
extinction has been increasing over time. The majority of threatened species are on islands.
18% of vertebrates, 29% of invertebrates and 49% of plant species are classified as threatened.
Extinction rates are predicted to greatly increase in the near future.
The IUCN classification of critically endangered, endangered, vulnerable and low risk reflect degrees
of extinction risk. They are defined by:
- Population decline
- Restriction habitat
- Current population size
Species endangerment is the basis for legal protection. Primary factors contribution to extinction are
direct or indirect human impacts.
,stochastic effects = naturally occurring fluctuations experienced by a small population with
environmental, catastrophic, demographic or genetic origins.
- Environmental stochasticity: random unpredictable variation in environmental factors
- Demographic stochasticity: random variation in birth and death rates and sex ratios due to
chance
- Catastrophes: extreme environmental events
- Inbreeding: reduces birth rates and increases death rates (inbreeding depression)
- Genetic diversity loss: reduces the ability of a population to adapt to changing environments
via natural selection
Extinction vortex = in small population genetic diversity decreases and due to decreased genetic
diversity population size further decreases creating a loop.
Major conservation management issues (pages 7-10 give examples for all of these):
- Inbreeding depression
- Loss of genetic diversity (loss of evolutionary potential)
- Fragmentation of populations and reduced gene flow
- Genetic drift overriding natural selection
- Accumulation and loss of deleterious mutations
- Genetic management of small captive populations and adverse effects of adaptations to the
captive environment
- Resolution of taxonomic uncertainties
- Definition of management units within species
- Use of molecular genetic analyses in forensics
Lecture – Chapter 1 - Introduction
Everywhere on earth biodiversity can be found. It is important to understand processes that
generate biodiversity to conserve it. 99,9% of the species that ever lived on earth are now extinct.
Bas haring states individual species are not important, they are interchangeable and he says the
value of biodiversity is debatable. He says if not ALL species die out, there is no serious problem.
Three reasons for conservation:
- Biodiversity is important as it defines nature
- Nature is our environment which we have to live in
- Bio-resources/ecosystem services/ethics/aesthetics
Ethics: humans do not have the right to drive other species to extinction. We have a moral obligation
to study life before its lost forever. The beauty should be preserved. Humans like to collect, order
and preserve.
Another reason for preserving biodiversity is for pharmaceutical reasons.
Ecosystems are essential for life for example due to their functions as oxygen producers, nutrient
cyclers and water purifiers.
Loss of biodiversity tends to make individual species more vulnerable. If there is variation it is unlikely
that one event can sweep complete ecosystems. However if you only have one or two species a
fungus can have a huge impact whilst it might not when there is more biodiversity.
Life on earth is characterized by speciation and extinction.
In a network some species are more important than others. These are key species. Conservation
genetics focusses on preserving biodiversity.
There have been 5 periods of mass extinction. When lots of species died out, opportunities for others
are created.
,The dynamics of extinction:
- Individuals struggle for existence
- Demographic stochasticity
- Populations go extinct which causes species to go extinct
Extinction is normal however the rate of extinction is increasing at an alarming rate.
Most extinctions that have occurred were on islands. This is because populations tend to be smaller
on islands and migration is lower.
The primary cause of the increasing extinction is due to the huge human population. The more
specific life history the more vulnerable the species is.
Human impacts:
- Large population size
- Habitat loss and fragmentation
- Introducing non-native species
- Overexploitation
- Pollution
There are three levels of stochasticity (randomness):
- Environmental – natural catastrophes
- Demographic – variation in birth/death rates or sex ratios
- Genetic – effects of inbreeding and loss of genetic variation in small populations
Extinction vortex:
The IUCN is a widely recognized system for risk of extinction assessment in a species.
, Literature – Chapter 2 – Genetic diversity
Genetic diversity is required for populations to adapt to change. Genetic diversity is usually
decreased in endangered species.
Environmental change is a continues process. Inbreeding leads to loss of genetic diversity and overall
fitness loss.
Gene = a sequence of nucleotide in a particular locus of a DNA molecule
Genetic diversity is a slight difference in these genes. The different sequence leads to different
proteins and this can lead to different phenotype, behaviour, reproductive rate etc. leading to
differences in fitness and survival.
Genetic diversity can be described with polymorphism, heterozygosity and allelic diversity.
Genetic diversity = the variety of alleles and genotypes present in the group under study
Molecular techniques can measure genetic diversity at individual loci.
Calculation genotype frequency = the proportion of a type in the whole population.
Usually allele frequencies are used. The letters p and q represent alleles. In this formula you fill in the
number of animals with the respective genotype. Total refers to the total number of animals
( 2∗PP ) + PQ
p=
2∗Total
Heterozygosity = the extent of genetic diversity at a locus
Observed heterozygosity (Ho) = the proportion of sampled individuals that are heterozygotes.
Genetic diversity is measured with allelic diversity. When talking about multiple loci the average
alleles per loci are used.
The hardy-Weinberg equilibrium shows the relationship between allele and genotype frequency. (If
you’re not familiar with this yet the video at the top of this summary explains the concept as well)
p and q are probabilities for alleles A1 and A2.
The probability for a homozygote is p x p = p2 or q x q = q2
The probability for a heterozygote is 2 x p x q = 2pq
And 1 = 2pq + q2 + p2
In the absence of outside influence and when mating is random p and q are at equilibrium. This is
expected for all loci except those on sex chromosomes.
Hardy-Weinberg illustrates two points:
- Heterozygotes cannot be greater than 0.5 for a locus with two alleles
- When an allele is rare most of its occurrence is in heterozygotes
Assumptions hardy-Weinberg:
- Large population size
- Closed population
- No mutation
- Normal mendelian segregation of alleles
- Equal fertility of parent genotypes
- Random union of gametes
- Equal fertilizing capacity of gametes
- Equal survival of all genotypes
Outbreeding = breeding of individuals that are relatively unrelated
