Molecular Ecology

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Molecular Ecology

• Genetics Refresher
• Dynamics of large populations
• Dynamics of small populations
• How genetics is used in wildlife management
• Taxon identification
• Population Viability Analysis
• Captive management
• Forensics

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Dynamics of large populations

• Diploidy Two complete sets of chromosomes
• Gene vs allele
• Heterozygosity vs homozygosity
• Gene pool

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Dynamics of large populations

• One gene
• Each circle is an allele
• Each color is a different allele
• The collection of circles represents a gene pool

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Dynamics of large populations
homozygote
heterozygote
Each green rectangle is an individual
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Dynamics of large populations
Genetic variation is the diversity of alleles

• Three measures
• Allele frequency
• Proportion of all alleles that are red 8/34
  0.24
• Number of alleles 7
• Heterozygosity 14/17 0.82

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Dynamics of large populations

• Typically large populations have lots of genetic
  variation.
• Genetic variation is kept at equilibrium
• Hardy-Weinberg Equilibrium
• The simplest case of a population. One gene. Two
  alleles, A and Z

Z
A
Z
Z
A
Z
A
A
A
A
Z
A
A
Z
Z
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Z
A
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Sewall Wright
Gregor Mendel
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Dynamics of large populations

• Hardy-Weinberg Equilibrium
• Allele frequency of A p, Z q
• Predicted genotype frequency
• for AAp2
• for AZpq pq 2pq
• for ZZq2

Z
A
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Z
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Z
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Predicted vs. observed
A
Z
A
A
A
Z
Z
He 2pq 0.5 Ho 1.0
Z
Z
Z
A
A
A
Z
Z
A
A
Z
He 2pq 0.5 Ho 0.5
Z
He 2pq 0.5 Ho 0
Z
Z
A
Z
A
Z
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A
A
A
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Z
Z
A
A
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A
A
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A
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Assumptions of Hardy-Weinberg Equilibrium

• Random mating
• Normal Mendelian segregation of alleles
• No selection (equal fitness of all genotypes)
• Closed population (no migration)
• No mutation
• Large population size

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Opposing forces maintain equilibrium

• Addition of variation via mutation and migration
• Subtraction of variation via genetic drift or
  natural selection

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Dynamics of small populations

• The process of making a population small
• Population bottleneck
• Not in equilibrium
• Inbreeding
• Genetic drift

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Dynamics of small populations Population
bottleneck
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Dynamics of small populations Population
bottleneck Genetic drift

• a non-representative sample of the population
  that changes allele frequencies of the gene pool

• Initial frequency of red allele 7/30 0.23
• Final frequency of red allele 2/4 0.50
• Initial of alleles 7, Final of alleles 3

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• Dynamics of small populations
• Population bottleneck Genetic drift
• In large populations genetic drift is balanced
  by mutation
• In small populations genetic drift exceeds
  mutation
• Genetic diversity is lost
• In previous example 4 of 7 alleles were lost
• 57 of genetic diversity lost at that gene from
  the gene pool

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Dynamics of small populations Population
bottleneck - Inbreeding
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Dynamics of small populations Inbreeding
Several generations later

• Inbreeding is mating between relatives
• Inbreeding increases homozygosity in a population

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Dynamics of small populations Inbreeding
Several generations later

• 0 homozygous individuals in ancestral
  population, 2 heterozygous individuals
• 6 of 19 individuals are homozygous in the
  descendant population

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• Dynamics of small populations
• Inbreeding
• Mating between relatives which increases
  homozygosity in a population at the expense of
  heterozygosity
• When populations become small, the likelihood of
  mating with a relative increases, thus
  homozygosity increases

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Predicted vs. observed
A
Z
A
A
A
Z
Z
He 2pq 0.5 Ho 1.0
Z
Z
Z
A
A
A
Z
Z
A
A
Z
He 2pq 0.5 Ho 0.5
Z
He 2pq 0.5 Ho 0
Z
Z
A
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A
Z
A
A
A
A
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Z
Z
A
A
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A
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Z
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Z
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Z
A
A
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Z
Z
Z
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Z
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• Dynamics of small populations - Inbreeding
  depression
• Inbreeding can lead to inbreeding depression,
  the expression of recessive deleterious alleles
• Deleterious alleles are present in all
  populations, but the chance of expression is
  small in large populations

Dark blue is the allele for misshapen hemoglobin
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Dynamics of small populations - Inbreeding
depression

• Chance of inbreeding depression greater in small
  populations
• If the force of genetic drift exceeds the force
  of natural selection, a deleterious trait can
  become fixed in a population

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Outbreeding
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Outbreeding
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Predicted vs. observed
A
Z
A
A
A
Z
Z
He 2pq 0.5 Ho 1.0
Z
Z
Z
A
A
A
Z
Z
A
A
Z
He 2pq 0.5 Ho 0.5
Z
He 2pq 0.5 Ho 0
Z
Z
A
Z
A
Z
A
A
A
A
Z
Z
Z
A
A
Z
A
A
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Z
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Z
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Z
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Z
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Outbreeding depression

• Decrease in fitness of progeny

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Molecular Ecology

• How genetics is used in wildlife management
• Taxon identification
• Population Viability Analysis
• Captive management
• Forensics

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Molecular tools

• Pedigree
• Molecular Data
• Sequence data
• Microsatellite data

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• Pedigree - calculation

?
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• Sequence data

AAGCCTCTAGATTCGAAACTGGTGAC
A
T
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Phylogenetic tree
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(No Transcript)
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• Microsatellite data

ATTCGAAATGTGTGTGTGTCTGGTGAC
TAAGCTTTACACACACACAGACCACTG
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220 bp
Offspring of Annie
Offspring of Scarface
150 bp
100 bp
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How genetics is used in wildlife management

• Resolution of taxonomic uncertainties
• Defining evolutionary significant units
• Typically defines subspecies
• Defining management units
• Ecologically distinct populations
• Hybridization may decrease viability of species
  and resources wasted on their protection

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Phylogenetic tree
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Ensatina spp.
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• Puma concolor
• Eight recognized subspecies
• Based on morphology
• Phylogenetic reconstruction revealed all one
  subspecies
• Implications
• Number of separate subspecies requiring
  management is reduced
• Endangered Florida panther management

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Genetics in Wildlife Management

• Population Viability Analysis - models the
  effects of different life history, environmental
  and genetic factors on the population size and
  extinction risk of a species

Inbreeding
Harvest
Population size
Habitat fragmentation
Population
Predation
Habitat loss
Life History
Disease
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Genetics in Wildlife Management

• Population Viability Analysis - models the
  effects of different life history, environmental
  and genetic factors on the population size and
  extinction risk of a species

Inbreeding
Harvest
Population size
Habitat fragmentation
Population
Predation
Habitat loss
Life History
Disease
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Genetics in Wildlife - Population Viability
Analysis

• Habitat fragmentation
• Creates small populations with limited gene flow
  between populations
• Increases genetic drift, inbreeding
• How much migration occurs between populations can
  be estimated with genetics
• Nm the effective number of migrants per
  generation
• In general, Nm 1 to maintain gene flow and
  genetic variation

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Martes pennanti

• Large home range size (79 km2)
• Ability to disperse long distances ( 100km)
• Genetic data indicate that ability to disperse
  does not predict gene flow.
• Populations separated by migrants only once every 50 generations
• Populations have greater chance of extinction
  than once thought

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Genetics in Wildlife - Population Viability
Analysis

• Life history traits
• Who breeds?
• How many breed?
• Important for determining harvest limits,
  vulnerability to extinction.
• Genetic paternity, maternity, and relatedness
  tests reveal who and how many.

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Monogamous mating
Lek mating
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Genetics in Wildlife - Population Viability
Analysis

• Population size
• The most basic yet most difficult thing to
  measure for a population is its size.
• Wildlife management devotes much time to
  monitoring population size
• Genetic techniques can sometimes estimate
  population size more economically and more
  accurately

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Mark and recapture using feces
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Genetics in Wildlife Management

• Captive Management
• For display, breeding for conservation, breeding
  for management.
• Maximize retention of genetic variation through
  time
• Must know relatedness of putative parents
• By pedigree or by molecular techniques

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Identification of genetically valuable animals
for breeding
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Wisely et al. 2002
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Genetics in Wildlife Management

• Wildlife forensics
• To detect and prosecute poachers
• To detect illegal import/export of wildlife
  products
• To reinstate live animals to population of origin

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Poaching
Importation Repatriation