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Conservation Genetics and Phylogeny
Conservation Genetics and Phylogeny
Dr Christopher L. Parkinson
Parkinson Web Site
Dr Christopher L. Parkinson
Parkinson Web Site
• This short course will serve as an introduction to the This short course will serve as an introduction to the field of conservation genetics and phylogenetics. field of conservation genetics and phylogenetics.
• Conservation of genetic diversity. Conservation of genetic diversity.
• Genetic variation provides the raw material for Genetic variation provides the raw material for adaptation, and is therefore critical to continued adaptation, and is therefore critical to continued evolutionary change. evolutionary change.
• Many ongoing, human-associated changes to the Many ongoing, human-associated changes to the environment erode genetic diversity at the population environment erode genetic diversity at the population level.level.– founder effects, founder effects, – genetic drift in small populations, genetic drift in small populations, – inbreeding, inbreeding, – altered patterns of gene flow. altered patterns of gene flow.
• This short course will serve as an introduction to the This short course will serve as an introduction to the field of conservation genetics and phylogenetics. field of conservation genetics and phylogenetics.
• Conservation of genetic diversity. Conservation of genetic diversity.
• Genetic variation provides the raw material for Genetic variation provides the raw material for adaptation, and is therefore critical to continued adaptation, and is therefore critical to continued evolutionary change. evolutionary change.
• Many ongoing, human-associated changes to the Many ongoing, human-associated changes to the environment erode genetic diversity at the population environment erode genetic diversity at the population level.level.– founder effects, founder effects, – genetic drift in small populations, genetic drift in small populations, – inbreeding, inbreeding, – altered patterns of gene flow. altered patterns of gene flow.
• Modern tools of molecular geneticsModern tools of molecular genetics– population structurespopulation structures– breeding systemsbreeding systems– evolutionary relationships among evolutionary relationships among
taxa. taxa.
• Apply insights gained from modern Apply insights gained from modern genetic techniques to improve the genetic techniques to improve the effectiveness of traditional effectiveness of traditional approaches to conserve biological approaches to conserve biological diversity.diversity.
• Modern tools of molecular geneticsModern tools of molecular genetics– population structurespopulation structures– breeding systemsbreeding systems– evolutionary relationships among evolutionary relationships among
taxa. taxa.
• Apply insights gained from modern Apply insights gained from modern genetic techniques to improve the genetic techniques to improve the effectiveness of traditional effectiveness of traditional approaches to conserve biological approaches to conserve biological diversity.diversity.
• TIME AND PLACE:TIME AND PLACE:– Lecture:Lecture:
• Web Site: Web Site: http://biology.ucf.edu/~clp/Courses/colohttp://biology.ucf.edu/~clp/Courses/colombia/powerpoints.phpmbia/powerpoints.php
• Username: congenUsername: congen
• Password: evolvePassword: evolve
AssignmentsAssignments
READINGSREADINGS: Readings are very : Readings are very important; please have all papers/book important; please have all papers/book chapters read prior to lecture. chapters read prior to lecture.
READINGSREADINGS: Readings are very : Readings are very important; please have all papers/book important; please have all papers/book chapters read prior to lecture. chapters read prior to lecture.
Conservation GeneticsConservation Genetics
• The application of genetics to preserve The application of genetics to preserve species as species as dynamic entitiesdynamic entities capable of capable of coping with environmental change.coping with environmental change.• Encompasses:Encompasses:
• Genetic mgmt. of small populationsGenetic mgmt. of small populations• Resolution of taxonomic uncertaintiesResolution of taxonomic uncertainties• Defining mgmt. units w/in speciesDefining mgmt. units w/in species• Use of molecular genetic analyses in Use of molecular genetic analyses in
forensics and understanding species forensics and understanding species biologybiology
• The application of genetics to preserve The application of genetics to preserve species as species as dynamic entitiesdynamic entities capable of capable of coping with environmental change.coping with environmental change.• Encompasses:Encompasses:
• Genetic mgmt. of small populationsGenetic mgmt. of small populations• Resolution of taxonomic uncertaintiesResolution of taxonomic uncertainties• Defining mgmt. units w/in speciesDefining mgmt. units w/in species• Use of molecular genetic analyses in Use of molecular genetic analyses in
forensics and understanding species forensics and understanding species biologybiology
Sixth ExtinctionSixth Extinction
• Mass extinctions Mass extinctions vsvs background extinction background extinction– 5 mass extinctions based of paleontology5 mass extinctions based of paleontology– KT boundary most recent 65 myaKT boundary most recent 65 mya• DinosaursDinosaurs
• humanshumans
• Mass extinctions Mass extinctions vsvs background extinction background extinction– 5 mass extinctions based of paleontology5 mass extinctions based of paleontology– KT boundary most recent 65 myaKT boundary most recent 65 mya• DinosaursDinosaurs
• humanshumans
• Conservation genetics motivated by Conservation genetics motivated by the need to the need to reduce current rates of reduce current rates of extinctionextinction and and preserve biodiversitypreserve biodiversity
• Why conserve biodiversity?Why conserve biodiversity?– BioresourcesBioresources• Food, Pharmaceuticals, Raw materialsFood, Pharmaceuticals, Raw materials
– Ecosystem servicesEcosystem services
• E.g., OE.g., O2 2 production, nutrient cycling, production, nutrient cycling,
pollinationpollination
– AestheticsAesthetics– Ethical reasonsEthical reasons
• Conservation genetics motivated by Conservation genetics motivated by the need to the need to reduce current rates of reduce current rates of extinctionextinction and and preserve biodiversitypreserve biodiversity
• Why conserve biodiversity?Why conserve biodiversity?– BioresourcesBioresources• Food, Pharmaceuticals, Raw materialsFood, Pharmaceuticals, Raw materials
– Ecosystem servicesEcosystem services
• E.g., OE.g., O2 2 production, nutrient cycling, production, nutrient cycling,
pollinationpollination
– AestheticsAesthetics– Ethical reasonsEthical reasons
• IUCN (World Conservation Union) IUCN (World Conservation Union) recognizes 3 levels of biodiversity:recognizes 3 levels of biodiversity:– Genetic diversityGenetic diversity– Species diversitySpecies diversity– Ecosystem diversityEcosystem diversity
• IUCN (1996) classified over 50% of IUCN (1996) classified over 50% of vertebrate species and 12.5% of plant vertebrate species and 12.5% of plant species as threatenedspecies as threatened
• IUCN (World Conservation Union) IUCN (World Conservation Union) recognizes 3 levels of biodiversity:recognizes 3 levels of biodiversity:– Genetic diversityGenetic diversity– Species diversitySpecies diversity– Ecosystem diversityEcosystem diversity
• IUCN (1996) classified over 50% of IUCN (1996) classified over 50% of vertebrate species and 12.5% of plant vertebrate species and 12.5% of plant species as threatenedspecies as threatened
Endangered VertebratesEndangered Vertebrates
What is an endangered species?What is an endangered species?
Why list?Why list?
• Legal protectionLegal protection
• ESA and CITESESA and CITES
• Legal protectionLegal protection
• ESA and CITESESA and CITES
What causes extinctions?What causes extinctions?
• Primarily humans, via direct or indirect Primarily humans, via direct or indirect impacts.impacts.
• Population growth 8.9 billion by 2050Population growth 8.9 billion by 2050
• StochasticStochastic– Naturally occurring catastrophic eventsNaturally occurring catastrophic events• Hurricanes for beach miceHurricanes for beach mice
– Small population pressuresSmall population pressures
• Primarily humans, via direct or indirect Primarily humans, via direct or indirect impacts.impacts.
• Population growth 8.9 billion by 2050Population growth 8.9 billion by 2050
• StochasticStochastic– Naturally occurring catastrophic eventsNaturally occurring catastrophic events• Hurricanes for beach miceHurricanes for beach mice
– Small population pressuresSmall population pressures
Preliminary and background knowledge
A. What is a gene?
- A general term- The physical entity transmitted from parent to offspring in reproduction that influences hereditary traits.
e.g. Genes influence human characteristics such as hair color and height, but also various aspects of behavior. However, a gene need not code for a protein.
Preliminary and background knowledge
A. What is a gene?
- A general term- The physical entity transmitted from parent to offspring in reproduction that influences hereditary traits.
e.g. Genes influence human characteristics such as hair color and height, but also various aspects of behavior. However, a gene need not code for a protein.
Various forms of a gene are called alleles. An allele can be used as a synonym for gene.
Preliminary and background knowledge
A. What is a gene?
- A general term- The physical entity transmitted from parent to offspring in reproduction that influences hereditary traits.
e.g. Genes influence human characteristics such as hair color and height, but also various aspects of behavior. However, a gene need not code for a protein.
Various forms of a gene are called alleles. An allele can be used as a synonym for gene.
A locus (plural is loci) is a physical location of a gene on a chromosome and is also a synonym for a gene.
Preliminary and background knowledge
B. What is genetic diversity?
Yellow-pine chipmunk
Preliminary and background knowledge
B. What is genetic diversity?
Think of genetic diversity as occurring at four levels:
a) Among species – differences among species of various organisms
b) Among populations – Differentiation among populations may reflect historical impediments to movement and thus to relatively ancient population subdivisions. Differences among populations can also reflect natural, contemporary patterns of gene flow, provide insights into how natural populations maintain genetic variation and indicate the impact of anthropogenic fragmentation events on the movement of individuals.
a) Within populations – Loss of genetic diversity is believed to have implications for population persistence over various temporal scales.
b) Within individuals – In diploid organisms, within-individual genetic diversity is an important component of variability where any particular locus may be heterozygous (with two alleles distinct in DNA sequence) or homozygous (identical alleles on both homologous chromosomes).
Preliminary and background knowledge
C. How does genetic diversity arise?
MUTATIONS!
Preliminary and background knowledge
C. How does genetic diversity arise? 1) Types of mutations
a. Point mutationstransitions vs. transversions
Purine Pyrimidine
Preliminary and background knowledge
C. How does genetic diversity arise? 1) Types of mutations
a. Point mutationstransitions vs. transversions
replacement vs. silent site
Preliminary and background knowledge
C. How does genetic diversity arise? 1) Types of mutations
a. Point mutationstransitions vs. transversions
replacement vs. silent site
b. Frameshift mutations – “In-del’s”
Preliminary and background knowledge
C. How does genetic diversity arise? 1) Types of mutations
a. Point mutationstransitions vs. transversions
replacement vs. silent site
b. Frameshift mutations – “In-del’s”
2) Mutations only matter in genetics if they are germ-line mutations (as opposed to somatic mutations).
Preliminary and background knowledge
D. Segregation, independent assortment and recombination
1) Segregation and Independent Assortment
P1: AABB x aabb
F1: AaBb => F1 cross = AaBb x AaBb
F2: Genotype PhenotypeAABBAaBB A_B_AABbAaBbaaBBaaBb aaB_
Conservation geneticsConservation genetics
11 major genetic issues11 major genetic issues
• Deleterious effects of inbreedingDeleterious effects of inbreeding
• Loss of genetic diversity and ability to evolve Loss of genetic diversity and ability to evolve in response to environmental change.in response to environmental change.
• Fragmentation of populations and restriction Fragmentation of populations and restriction of gene flowof gene flow
• Random processes overriding natural Random processes overriding natural selectionselection
• Accumulation and loss of deleterious Accumulation and loss of deleterious mutationsmutations
• Deleterious effects of inbreedingDeleterious effects of inbreeding
• Loss of genetic diversity and ability to evolve Loss of genetic diversity and ability to evolve in response to environmental change.in response to environmental change.
• Fragmentation of populations and restriction Fragmentation of populations and restriction of gene flowof gene flow
• Random processes overriding natural Random processes overriding natural selectionselection
• Accumulation and loss of deleterious Accumulation and loss of deleterious mutationsmutations
11 major issues11 major issues
• Genetic adaptation to captivity and its Genetic adaptation to captivity and its adverse effects of reintroduction successadverse effects of reintroduction success• Resolving taxonomic uncertaintiesResolving taxonomic uncertainties• Defining management units within a speciesDefining management units within a species• Molecular issues in forensicsMolecular issues in forensics• Molecular genetic aspects of species Molecular genetic aspects of species
biologybiology• Deleterious effects on fitness as a result of Deleterious effects on fitness as a result of
outbreeding (Outbreeding depression)outbreeding (Outbreeding depression)
• Genetic adaptation to captivity and its Genetic adaptation to captivity and its adverse effects of reintroduction successadverse effects of reintroduction success• Resolving taxonomic uncertaintiesResolving taxonomic uncertainties• Defining management units within a speciesDefining management units within a species• Molecular issues in forensicsMolecular issues in forensics• Molecular genetic aspects of species Molecular genetic aspects of species
biologybiology• Deleterious effects on fitness as a result of Deleterious effects on fitness as a result of
outbreeding (Outbreeding depression)outbreeding (Outbreeding depression)
How is genetics used to minimize extinction?
How is genetics used to minimize extinction?
• Reducing extinction risk by minimizing Reducing extinction risk by minimizing inbreeding and loss of genetic diversityinbreeding and loss of genetic diversity
• Identifying populations of concernIdentifying populations of concern
• Resolving population structureResolving population structure
• Resolving taxonomic uncertaintiesResolving taxonomic uncertainties
• Defining management units within Defining management units within speciesspecies
• Detecting hybridizationDetecting hybridization
• Reducing extinction risk by minimizing Reducing extinction risk by minimizing inbreeding and loss of genetic diversityinbreeding and loss of genetic diversity
• Identifying populations of concernIdentifying populations of concern
• Resolving population structureResolving population structure
• Resolving taxonomic uncertaintiesResolving taxonomic uncertainties
• Defining management units within Defining management units within speciesspecies
• Detecting hybridizationDetecting hybridization
How is genetics used to minimize extinction?
How is genetics used to minimize extinction?
• Non-intrusive samplingNon-intrusive sampling
• Defining sites for reintroductionDefining sites for reintroduction
• Choosing the best populations for Choosing the best populations for introductionintroduction
• ForensicsForensics
• Understanding species biologyUnderstanding species biology
• Non-intrusive samplingNon-intrusive sampling
• Defining sites for reintroductionDefining sites for reintroduction
• Choosing the best populations for Choosing the best populations for introductionintroduction
• ForensicsForensics
• Understanding species biologyUnderstanding species biology
Island themesIsland themes
• Many parallels between island Many parallels between island populations and fragmented habitatspopulations and fragmented habitats
• Many parallels between island Many parallels between island populations and fragmented habitatspopulations and fragmented habitats
Genetics and ExtinctionGenetics and Extinction
• Inbreeding and loss of genetic diversity Inbreeding and loss of genetic diversity are inevitable in small populationsare inevitable in small populations
• Short Term Consequences:Short Term Consequences:– reduced reproduction and survivalreduced reproduction and survival
• Long Term Consequences: Long Term Consequences: – diminished capacity of a population to diminished capacity of a population to
evolve in response to environmental evolve in response to environmental changechange
• Inbreeding and loss of genetic diversity Inbreeding and loss of genetic diversity are inevitable in small populationsare inevitable in small populations
• Short Term Consequences:Short Term Consequences:– reduced reproduction and survivalreduced reproduction and survival
• Long Term Consequences: Long Term Consequences: – diminished capacity of a population to diminished capacity of a population to
evolve in response to environmental evolve in response to environmental changechange
• E.g., Lande (1988) E.g., Lande (1988) ‘‘demographic and environmental demographic and environmental
catastrophes will cause extinction catastrophes will cause extinction before genetic deterioration becomes before genetic deterioration becomes a serious threat to wild populations’a serious threat to wild populations’
• E.g., Lande (1988) E.g., Lande (1988) ‘‘demographic and environmental demographic and environmental
catastrophes will cause extinction catastrophes will cause extinction before genetic deterioration becomes before genetic deterioration becomes a serious threat to wild populations’a serious threat to wild populations’
Genetics were previously considered inconsequential to the fate of endangered species
Genetics were previously considered inconsequential to the fate of endangered species
• Though still debated, now compelling Though still debated, now compelling theoretical and empirical theoretical and empirical evidenceevidence supporting the effects of genetic supporting the effects of genetic changes on the fate of small changes on the fate of small populationspopulations– Many Many surviving popssurviving pops show reduced show reduced
genetic diversity and evidence of genetic diversity and evidence of inbreedinginbreeding
– Inbreeding causes extinctionsInbreeding causes extinctions in in deliberately inbred deliberately inbred captive populationscaptive populations
– Computer projectionsComputer projections indicate that indicate that inbreeding will cause elevated extinction inbreeding will cause elevated extinction risks in realistic situations faced by natural risks in realistic situations faced by natural populationspopulations
• Though still debated, now compelling Though still debated, now compelling theoretical and empirical theoretical and empirical evidenceevidence supporting the effects of genetic supporting the effects of genetic changes on the fate of small changes on the fate of small populationspopulations– Many Many surviving popssurviving pops show reduced show reduced
genetic diversity and evidence of genetic diversity and evidence of inbreedinginbreeding
– Inbreeding causes extinctionsInbreeding causes extinctions in in deliberately inbred deliberately inbred captive populationscaptive populations
– Computer projectionsComputer projections indicate that indicate that inbreeding will cause elevated extinction inbreeding will cause elevated extinction risks in realistic situations faced by natural risks in realistic situations faced by natural populationspopulations
InbreedingInbreeding
• Inbreeding:Inbreeding:– The production of offspring by individuals The production of offspring by individuals
related by descent (e.g., self-fertilization, related by descent (e.g., self-fertilization, brother-sister, parent-offspring matings)brother-sister, parent-offspring matings)
• Inbreeding Depression:Inbreeding Depression:– Reduced reproduction and survival Reduced reproduction and survival
(reproductive fitness) due to inbreeding(reproductive fitness) due to inbreeding
• Inbreeding:Inbreeding:– The production of offspring by individuals The production of offspring by individuals
related by descent (e.g., self-fertilization, related by descent (e.g., self-fertilization, brother-sister, parent-offspring matings)brother-sister, parent-offspring matings)
• Inbreeding Depression:Inbreeding Depression:– Reduced reproduction and survival Reduced reproduction and survival
(reproductive fitness) due to inbreeding(reproductive fitness) due to inbreeding
Evidence of inbreeding depressionEvidence of inbreeding depression
• Ralls and Ballou (1983)Ralls and Ballou (1983)– In 41 of 44 captive mammal pops, inbred ind. In 41 of 44 captive mammal pops, inbred ind.
showed higher juvenile mortality than outbred showed higher juvenile mortality than outbred ind.ind.
– Brother-sister mating resulted in a 33% reduction Brother-sister mating resulted in a 33% reduction in juvenile survivalin juvenile survival
• Crnokrak & Roff (1999)Crnokrak & Roff (1999)– Reviewed 157 data sets including 34 species for Reviewed 157 data sets including 34 species for
inbreeding depression in natural situationsinbreeding depression in natural situations– In 141 cases (90%), inbred individuals had poorer In 141 cases (90%), inbred individuals had poorer
attributes than comparable outbred individualsattributes than comparable outbred individuals
• Ralls and Ballou (1983)Ralls and Ballou (1983)– In 41 of 44 captive mammal pops, inbred ind. In 41 of 44 captive mammal pops, inbred ind.
showed higher juvenile mortality than outbred showed higher juvenile mortality than outbred ind.ind.
– Brother-sister mating resulted in a 33% reduction Brother-sister mating resulted in a 33% reduction in juvenile survivalin juvenile survival
• Crnokrak & Roff (1999)Crnokrak & Roff (1999)– Reviewed 157 data sets including 34 species for Reviewed 157 data sets including 34 species for
inbreeding depression in natural situationsinbreeding depression in natural situations– In 141 cases (90%), inbred individuals had poorer In 141 cases (90%), inbred individuals had poorer
attributes than comparable outbred individualsattributes than comparable outbred individuals
Documented cases of inbreeding depression
Documented cases of inbreeding depression
• Mammals:Mammals:– Golden lion tamarins, lions, native mice, Golden lion tamarins, lions, native mice,
shrews, shrews, – Birds:Birds:– Greater prairie chicken, Mexican jay, song Greater prairie chicken, Mexican jay, song
sparrow, American kestrel, reed warblersparrow, American kestrel, reed warbler
• Fish:Fish:– Atlantic salmon, desert topminnow, Atlantic salmon, desert topminnow,
rainbow troutrainbow trout
• Many others Many others (reptiles, inverts, plants, etc.)(reptiles, inverts, plants, etc.)
• Mammals:Mammals:– Golden lion tamarins, lions, native mice, Golden lion tamarins, lions, native mice,
shrews, shrews, – Birds:Birds:– Greater prairie chicken, Mexican jay, song Greater prairie chicken, Mexican jay, song
sparrow, American kestrel, reed warblersparrow, American kestrel, reed warbler
• Fish:Fish:– Atlantic salmon, desert topminnow, Atlantic salmon, desert topminnow,
rainbow troutrainbow trout
• Many others Many others (reptiles, inverts, plants, etc.)(reptiles, inverts, plants, etc.)
How do we measure the extent of inbreeding?
How do we measure the extent of inbreeding?
• The inbreeding coefficient (F)The inbreeding coefficient (F)– For anFor an individual individual, F refers to how closely related , F refers to how closely related
its parents areits parents are– When parents are unrelated, offspring F = 0When parents are unrelated, offspring F = 0– When inbreeding is complete, F = 1When inbreeding is complete, F = 1
• The inbreeding coefficient (F)The inbreeding coefficient (F)– For anFor an individual individual, F refers to how closely related , F refers to how closely related
its parents areits parents are– When parents are unrelated, offspring F = 0When parents are unrelated, offspring F = 0– When inbreeding is complete, F = 1When inbreeding is complete, F = 1
• Inbreeding accumulates in closed Inbreeding accumulates in closed populations (those without immigration)populations (those without immigration)
• Complete inbreeding can be reached Complete inbreeding can be reached with repeated inbred matingswith repeated inbred matings
• An An FF of 0.999 is reached after 10 of 0.999 is reached after 10 generations of self-fertilizationgenerations of self-fertilization
• An An FF of 0.986 is reached after 20 of 0.986 is reached after 20 generations of brother-sister matinggenerations of brother-sister mating
• Inbreeding accumulates in closed Inbreeding accumulates in closed populations (those without immigration)populations (those without immigration)
• Complete inbreeding can be reached Complete inbreeding can be reached with repeated inbred matingswith repeated inbred matings
• An An FF of 0.999 is reached after 10 of 0.999 is reached after 10 generations of self-fertilizationgenerations of self-fertilization
• An An FF of 0.986 is reached after 20 of 0.986 is reached after 20 generations of brother-sister matinggenerations of brother-sister mating
InbreedingInbreeding
Nigerian GiraffeNigerian Giraffe
• Giraffe X was born Giraffe X was born in Paris Zoo in in Paris Zoo in 19921992
• Highly inbred calf Highly inbred calf had an inbreeding had an inbreeding coefficient of 0.52coefficient of 0.52
• Calf died 3 weeks Calf died 3 weeks after birthafter birth
• Giraffe X was born Giraffe X was born in Paris Zoo in in Paris Zoo in 19921992
• Highly inbred calf Highly inbred calf had an inbreeding had an inbreeding coefficient of 0.52coefficient of 0.52
• Calf died 3 weeks Calf died 3 weeks after birthafter birth
Average InbreedingAverage Inbreeding
• The The AVERAGEAVERAGE inbreeding coefficient of inbreeding coefficient of ALLALL individuals in a population individuals in a population
• Small, closed populations:Small, closed populations:– Average Average FF will rise as mates become will rise as mates become
increasingly relatedincreasingly related– Average Average FF increases at a rate of 1/(2 increases at a rate of 1/(2NN) per ) per
generation in a randomly breeding generation in a randomly breeding population of size population of size NN
• The The AVERAGEAVERAGE inbreeding coefficient of inbreeding coefficient of ALLALL individuals in a population individuals in a population
• Small, closed populations:Small, closed populations:– Average Average FF will rise as mates become will rise as mates become
increasingly relatedincreasingly related– Average Average FF increases at a rate of 1/(2 increases at a rate of 1/(2NN) per ) per
generation in a randomly breeding generation in a randomly breeding population of size population of size NN
Average inbreeding coefficientAverage inbreeding coefficient
• Increase in average inbreeding coefficient in Increase in average inbreeding coefficient in populations of 10 and 20 randomly breeding populations of 10 and 20 randomly breeding individualsindividuals
• Increase in average inbreeding coefficient in Increase in average inbreeding coefficient in populations of 10 and 20 randomly breeding populations of 10 and 20 randomly breeding individualsindividuals
Inbreeding Relative to Random Breeding
Inbreeding Relative to Random Breeding
• Comparison of the average relatedness Comparison of the average relatedness of mates (parents) to what one would of mates (parents) to what one would expect if the population is mating at expect if the population is mating at randomrandom
• Comparison of the average relatedness Comparison of the average relatedness of mates (parents) to what one would of mates (parents) to what one would expect if the population is mating at expect if the population is mating at randomrandom
Genetic DiversityGenetic Diversity
• The extent of heritable variation in a The extent of heritable variation in a population, or species, or across a population, or species, or across a group of species, e.g. heterozygosity, group of species, e.g. heterozygosity, or number of alleles, or heritability.or number of alleles, or heritability.
• The extent of heritable variation in a The extent of heritable variation in a population, or species, or across a population, or species, or across a group of species, e.g. heterozygosity, group of species, e.g. heterozygosity, or number of alleles, or heritability.or number of alleles, or heritability.
Inbreeding and ExtinctionInbreeding and Extinction
• Frankel & SouleFrankel & Soule‘ (1981)‘ (1981)– 80-95% of deliberately inbred populations 80-95% of deliberately inbred populations
of laboratory and domestic plants and of laboratory and domestic plants and animals die out after eight generations of animals die out after eight generations of brother-sister mating or three generations brother-sister mating or three generations of self-fertilizationof self-fertilization• E.g., Japanese quailE.g., Japanese quail
– 383 populations inbred by continued 383 populations inbred by continued brother-sister mating, all populations went brother-sister mating, all populations went extinct after four generationsextinct after four generations
• Frankel & SouleFrankel & Soule‘ (1981)‘ (1981)– 80-95% of deliberately inbred populations 80-95% of deliberately inbred populations
of laboratory and domestic plants and of laboratory and domestic plants and animals die out after eight generations of animals die out after eight generations of brother-sister mating or three generations brother-sister mating or three generations of self-fertilizationof self-fertilization• E.g., Japanese quailE.g., Japanese quail
– 383 populations inbred by continued 383 populations inbred by continued brother-sister mating, all populations went brother-sister mating, all populations went extinct after four generationsextinct after four generations
Relationship between inbreeding and extinction
Relationship between inbreeding and extinction
Inbreeding cont.Inbreeding cont.
• Even slow rates of inbreeding increase the Even slow rates of inbreeding increase the risk of extinctionrisk of extinction
• Taxonomic groups such as mammals, birds, Taxonomic groups such as mammals, birds, and invertebrates show similar levels of and invertebrates show similar levels of susceptibility to inbreeding depressionsusceptibility to inbreeding depression– In plants, inbreeding depression higher in In plants, inbreeding depression higher in
gymnosperms than angiospermsgymnosperms than angiosperms• polyploidypolyploidy
• Growing evidence shows that inbreeding Growing evidence shows that inbreeding elevates extinction risks in wild populationselevates extinction risks in wild populations
• Even slow rates of inbreeding increase the Even slow rates of inbreeding increase the risk of extinctionrisk of extinction
• Taxonomic groups such as mammals, birds, Taxonomic groups such as mammals, birds, and invertebrates show similar levels of and invertebrates show similar levels of susceptibility to inbreeding depressionsusceptibility to inbreeding depression– In plants, inbreeding depression higher in In plants, inbreeding depression higher in
gymnosperms than angiospermsgymnosperms than angiosperms• polyploidypolyploidy
• Growing evidence shows that inbreeding Growing evidence shows that inbreeding elevates extinction risks in wild populationselevates extinction risks in wild populations
Computer simulationsComputer simulations
Butterfly extinctionButterfly extinction
Interactions CreateInteractions Create
Island populationsIsland populations
• Majority of extinctions have been on Majority of extinctions have been on islandsislands
• Human factors drive population size Human factors drive population size down.down.
• Island pops typically have less Island pops typically have less diversity and are more inbreed than diversity and are more inbreed than mainland congenersmainland congeners
• Majority of extinctions have been on Majority of extinctions have been on islandsislands
• Human factors drive population size Human factors drive population size down.down.
• Island pops typically have less Island pops typically have less diversity and are more inbreed than diversity and are more inbreed than mainland congenersmainland congeners
Genetic diversity and extinctionGenetic diversity and extinction
• To evolve species require genetic To evolve species require genetic diversitydiversity
• Genetic variations allows pops to Genetic variations allows pops to tolerate a wide range of environmental tolerate a wide range of environmental extremes.extremes.
• Low diversity on islands, less Low diversity on islands, less evolution?evolution?
• To evolve species require genetic To evolve species require genetic diversitydiversity
• Genetic variations allows pops to Genetic variations allows pops to tolerate a wide range of environmental tolerate a wide range of environmental extremes.extremes.
• Low diversity on islands, less Low diversity on islands, less evolution?evolution?
Motivations for considering the genetic consequences of
inbreeding
Motivations for considering the genetic consequences of
inbreeding• Management of captive populations of rare or Management of captive populations of rare or
endangered speciesendangered species– Breeding programs usually designed to minimize Breeding programs usually designed to minimize
inbreeding and maximize outbreedinginbreeding and maximize outbreeding
• In situIn situ management of rare species (small management of rare species (small population sizes)population sizes)– Lack of unrelated matesLack of unrelated mates
• Random genetic driftRandom genetic drift– In small, finite populations, genetic drift can occur even if In small, finite populations, genetic drift can occur even if
the population is randomly matingthe population is randomly mating
• More generally, these issues apply to any species More generally, these issues apply to any species with artificially or naturally fragmented or naturally with artificially or naturally fragmented or naturally patchy spatial distributionspatchy spatial distributions
• Management of captive populations of rare or Management of captive populations of rare or endangered speciesendangered species– Breeding programs usually designed to minimize Breeding programs usually designed to minimize
inbreeding and maximize outbreedinginbreeding and maximize outbreeding
• In situIn situ management of rare species (small management of rare species (small population sizes)population sizes)– Lack of unrelated matesLack of unrelated mates
• Random genetic driftRandom genetic drift– In small, finite populations, genetic drift can occur even if In small, finite populations, genetic drift can occur even if
the population is randomly matingthe population is randomly mating
• More generally, these issues apply to any species More generally, these issues apply to any species with artificially or naturally fragmented or naturally with artificially or naturally fragmented or naturally patchy spatial distributionspatchy spatial distributions
