Conservation Genetics

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Conservation Genetics

• Lecture Outline
• Basic Population Genetics
• How is genetic variation measured?
• How are evolutionary processes inferred from
  patterns of genetic variation?
• Scope of Conservation Genetics
• Conservation Genetics of Populations
• Is genetic variation important for evolutionary
  potential?
• Does genetic variation influence extinction risk?
• What are the consequences of genetic drift and
  inbreeding depression in wildlife populations?
• Does increasing gene flow help mitigate the
  negative genetic effects of fragmentation?
• Are demographic and genetic factors equally
  important for understanding extinction?

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Words Well Use A Lot Today!

• Locus / Loci
• position on a chromosome
• Gene
• segment of DNA whose sequence codes for protein,
  or regulates other genes
• Diploid
• cell/individual has two copies of each
  (homologous) chromosome
• Allele
• alternative form of a gene or locus
• Homozygous
• individual with two copies of the same allele
• Heterozygous
• organism with different alleles
• Genotype
• an organisms genetic composition

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Genetic Variation

• Types
• Neutral
• Adaptive
• Detrimental
• Measures of Genetic Variation
• Polymorphism proportion of loci that are
  polymorphic in a population
• Heterozygosity (H) proportion of individuals in
  a population that are heterozygotes at a
  particular locus
• Allelic Diversity number of alleles at a locus

Hawaiian Happy-face Spiders, Theridion grallator
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Data Collection

• Tissue samples
• Genetic markers
• Loci useful for distinguishing individuals and
  populations
• Basic methods
• PCR
• Amplify DNA
• Gel Electrophoresis
• Visualize alleles for a locus

Negative Charge
Fragments migrate
Positive Charge
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Measuring Genetic Variation
6 individuals

• Is locus A polymorphic? Locus B?
• If the locus is polymorphic, how many individuals
  are heterozygotes?
• Calculate H for the polymorphic loci

locus A
locus B
Kemps Ridley Sea Turtle, Lepidochelys kempii
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Measuring Genetic Variation
6 individuals

• Is locus A polymorphic? Locus B?
• Locus B only
• If the locus is polymorphic, how many individuals
  are heterozygotes?
• 4 individuals
• Calculate H for the polymorphic loci
• H 4/6 0.667

locus A
locus B
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Measuring Genetic Variation
6 individuals

• Allele Frequencies
• Genotype Frequencies
• Locus B
• Close allele B1
• Far allele B2
• F(B1) 6/12 0.5
• F(B2) 6/12 0.5
• F(B1B1) 1/6 0.167
• F(B1B2) 4/6 0.67
• F(B2B2) 1/6 0.167

locus A
locus B
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Evolution

• Change in allele frequencies across generations
• Hardy-Weinberg Principle
• Allele frequencies in a population will not
  change over time unless an evolutionary process
  is acting on the population
• Genotype frequencies remain constant after 1
  generation of random mating

Weinberg
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Hardy-Weinberg Equilibrium

• Can calculate genotype frequencies for a given
  set of allele frequencies when the following
  assumptions are met
• Hardy-Weinberg model as an animated question
  mark

Departure from HW equilibrium suggests that
important evolutionary processes are acting on
the population of interest.
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Hardy-Weinberg

• Consider a single locus with 2 alleles A1 and A2
• Allele Frequencies p freq. of A1
• q
  freq. of A2
• p q 1
• Genotype Frequencies p2 freq. of A1A1
• 2pq freq. of A1A2
• q2 freq. of A2A2
• p2 2pq q2 1

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Rana pipiens Example

• 2000 Individuals
• Observed Genotype Frequencies
• BB 600/2000 0.3
• Bb 400/2000 0.2
• bb 1000/2000 0.5
• Observed Allele Frequencies
• B 1600/4000 0.4 p
• b 2400/4000 0.6 q
• Expected Genotype Frequencies
• BB p2 0.16 320 ind.
• Bb 2pq 0.48 960 ind.
• bb q2 0.36 720 ind.

b allele
Wild Type
B allele
Burnsi
Observed N Expected N BB 600
320 Bb 400 960 Bb 1000 720
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Daphnia obtusa

• Spitze (1993)
• PGI Locus
• Genotyped 127 individuals from Nothing Pond in
  Morton, IL
• RR 11
• Rr 55
• rr 61
• Calculate the observed genotype and allele
  frequencies.
• Calculate the expected genotype frequencies under
  HWE.
• Is this population in HWE?

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Daphnia obtusa

• Observed Genotype Frequencies
• RR 11 11/127 0.087
• Rr 55 55/127 0.43
• rr 61 61/127 0.48
• Observed Allele Frequencies
• R 77 77/254 0.30
• r 177 177/254 0.70
• Expected Genotype Frequencies
• F N
• RR p2 0.302 0.09 ? 11.43
• Rr 2pq 20.30.7 0.42 ? 53.34
• rr q2 0.702 0.49 ? 62.23
• Is this population in HWE? Yes

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Conservation Genetics

• Otto Frankel 1974 Genetic conservation our
  evolutionary responsibility.
• Key contribution to conservation biology focus
  on long-term evolutionary potential in species

First we should get to know much more about
the structure and dynamics of natural populations
and communities Second, even now the geneticist
can play a part in injecting genetic
considerations into the planning of reserves of
any kind Finally, reinforcing the grounds for
nature conservation with an evolutionary
perspective may help to give conservation a
permanence which a utilitarian, and even an
ecological grounding, fail to provide in mens
minds.
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Topics in Conservation Genetics

• Management and Reintroduction of Captive Species
• Individual and Species Identification
• Species ID, population of origin, sex,
  mark-recapture
• Genealogies and Kin Relationships
• Parentage, reproductive success
• Taxonomic and Phylogenetic Relationships
• USFWS Priority taxonomic distinctiveness
• ESA Evolutionary Significant Units
• Genetic Population Structure
• Effects of habitat loss, fragmentation, and
  isolation on distribution of genetic variation
• Historical effects, effective population size,
  movement rates and connectivity
• Hybridization and Introgression
• ESA policy
• Genetics of Adaptation
• Relationships between adaptation, fitness, and
  the genetic basis of traits influencing fitness

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Genetic Variation and Adaptation

• Of all forces that influence population genetic
  structure, natural selection is the only force
  producing adaptive change
• Acts on heritable, phenotypic variation

Genetic variation is the raw material for
adaptive evolution. Maintaining evolutionary
potential is achieved by maintaining genetic
variation.
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Genetic Variation and Extinction Risk

• Extinction is a demographic process, caused by
  two main types of threats
• Deterministic ? e.g., habitat destruction
• Stochastic ? random changes in genetic,
  demographic, or environmental factors
• Two types of genetic stochasticity
• Drift ? random change in allele frequencies
• Inbreeding ? mating with relatives
• Genetic stochasticity erodes genetic variation
• Qualitative effect loss of alleles
• Quantitative effect decline in heterozygosity

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Genetic Drift

• Allele frequencies change from generation to
  generation due random sampling error
• Some alleles get passed on, some dont

Drift erodes genetic variation within
populations, and increases variation between
populations
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Effect of N on Genetic Drift
N 15
N 500
Strength of genetic drift is inversely related to
population size.
s selective disadvantage of a detrimental
allele ( reduction in fitness) Ne
effective population size
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Selection and Drift
Miller and Lambert 2004
Chatham Island black robin

• Two consequences of drift overwhelming selection
  in small populations
• Deleterious alleles not weeded out by selection
• Local adaptation is compromised

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Genetic Drift and Fragmentation

• Habitat Loss
• Crash in population size
• population bottleneck
• Isolation
• Metapopulation structure
• Extinction-colonization dynamics
• Colonization of resource patch
• founder event

Regal Fritillary Butterfly
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Genetic Drift and Fragmentation
Allelic Differentiation MW gt GP Genetic
Differentiation (FST) MW gt GP Greatest
between MW/GP E Allelic Diversity E
9.00 MW 16.15 GP 22.65
GP unfragmented MW recently fragmented E
historically isolated
HT heterozygosity in metapopulation HS
heterozygosity in subpopulation
Williams et al. 2003
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Fitness Effects of Genetic Drift

• Large changes in allele frequency
• Deleterious alleles occur at low frequency, and
  most rare alleles are lost following bottlenecks
• BUT, every individual carries harmful alleles,
  and these alleles increase in frequency following
  bottlenecks
• Recovery time is critical
• Loss of allelic diversity
• Greater effect than on heterozygosity
• E.g., loss of MHC alleles more susceptible to
  disease

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Inbreeding

• Inbreeding ? mating between individuals that are
  more closely related than expected by chance

Inbreeding increases homozygosity at all loci.
The most extreme form of inbreeding is selfing
Generation Heterozygotes 0 100
1 50 2 25 3 12.5
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Inbreeding Depression

• Reduction in fitness of progeny from matings
  between related individuals relative to progeny
  of unrelated individuals
• Can contribute to population extinction
• Causes
• Increased homozygosity
• Reduces fitness due to expression of deleterious
  recessive alleles
• Decreased heterozygosity
• Reduces fitness in cases when heterozygotes have
  selective advantage

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Inbreeding Depression and Extinction

• Inbreeding depression must affect traits
  influencing population viability
• Saccheri et al. 1998
• Glanville fritillary butterfly, 42 populations,
  Finland

Factors Influencing Extinction Model Parameters
Variation Population size
24 Regional trend in N 20 Flower
abundance 12 Heterozygosity
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low N
Extinction Probability
high N
Fitness Traits Affected Larval survival Adult
longevity Egg hatching rate
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Drift, Inbreeding, and Fragmentation

• Habitat loss and decreased connectivity lead to
  loss of genetic variation due to drift and
  inbreeding
• Inbreeding depression
• Reduced heterozygosity due to drift
• Increased homozygosity due to inbreeding
• Loss of rare alleles
• Inefficiency of selection
• Mutational meltdown
• Decreased evolutionary potential

Mills
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Conservation Measures

• Facilitate an increase in population size
• Translocation
• Gene flow via increased connectivity
• Improve matrix, construct corridors
• Gene flow effective dispersal
• Disadvantages of increasing movement
• Demographic
• Disease, social structure
• Genetic
• Outbreeding depression ? reduction in fitness of
  hybrids
• Parents from different populations are locally
  adapted
• Disruption of coadapted gene complexes
• One-Migrant-Per-Generation Rule (Mills and
  Allendorf 1993)

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Greater Prairie Chicken in Illinois
Mean Alleles Per Locus Illinois
3.67 Kansas 5.83 Minn.
5.33 Nebraska 5.83 Illiinos
5.12 before bottleneck
Inbreeding depression due to Drift Inbreedin
g Counteracted by translocations in 1992.
Westemeier et al. 1998
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Genetics and Demography

• Lande (1988) argues that basic demography has
  been neglected, and the effect of genetic
  structure on extinction has been over-emphasized
• Consider why demography may be of more immediate
  importance than genetics in small populations.
• What demographic factors influence extinction?
• Are there interactions between demographic and
  genetic effects of habitat loss and isolation
  that can increase extinction probability?

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