Black Rhino

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Black Rhino
Conservation Genetics
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Exam Next Tuesday (in class)
1 - Help Sessions Monday afternoon 630 to
9 101 Morrison 2 - Old examines on the web
(answers) 3 - Crib Sheet and calculator (graphing
is fine) 4 Try to be here early 5 Do not
need to know particular traits
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Molecular Conservation Genetics Mary V.
Ashley American Scientist January - February 1999
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• Black Rhino Study
• lt5000 individuals left (3 lines)
• Priority for protection in 1980s

• Problems
• Small and isolated groups
• Increased levels of inbreeding
• Consolidation? Subspecies?

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• Mitochondria DNA Study
• DNA that exists in cytoplasm.
• Study involves looking at diversity in the mtDNA
  among animals in the different lines.

• Alleles present in different lines and their
  allele frequencies.

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Mitochondria DNA (mtDNA) Advantages
Maternally Inherited (female lineage)
Mutations usually single base pair
Rapid rate of evolution, mutation rates 5 to 10
time nuclear DNA
No recombination
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Mitochondria DNA (mtDNA) Disadvantages
No record of male gene flow
Does not measure loss of nuclear genetic
diversity.
mtDNA will show greater effect of founder events
and bottlenecks than nuclear DNA.

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Analysis

• Looked at variation in mutations

• Found the three distinct lines
  differing by only 0.4 base pair mutations. gt
  Consolidation of breeding programs.

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Lecture 9
Population Genetics
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Population Genetics

• The study of populations over time with
  particular attention paid to gene and genotypic
  frequencies.

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Population Genetics

• The study of populations over time with
  particular attention paid to gene and genotypic
  frequencies.
• The individual is mortal. Date of birth and
  death can be documented. The population,
  practically speaking, is immortal. (JAY L. LUSH)

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Gene and Genotypic Frequencies

• Blood type (M N)

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Gene and Genotypic Frequencies

• Blood type (M N)
• Codominant (M N)

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Gene and Genotypic Frequencies

• Blood type (M N)
• Codominant (M N)

Genotype Phenotype MM M MN
MN NN N
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Gene and Genotypic Frequencies

• Blood type (M N)
• Codominant (M N)

Genotype Phenotype observed MM
M 130,000 MN MN 265,000 NN
N 105,000
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Gene and Genotypic Frequencies

• Blood type (M N)
• Codominant (M N)

Genotype Phenotype observed MM
M 130,000 MN MN 265,000
NNN N 105,000 500,000 people 1,000,00
0 genes
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Genotypic frequencies
f(MM) MM 130,000 .26 TOTAL
500,000
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Genotypic frequencies
f(MM) MM 130,000 .26 TOTAL
500,000 f(MN) .53 f(NN)
.21 1.00
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Genotypic frequencies
f(MM) MM 130,000 .26 TOTAL
500,000 f(MN) .53 f(NN)
.21 1.00
With codominance it is easy to calculate
frequencies.
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Gene frequencies
f(M allele) of M total genes
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Gene frequencies
f(M allele) of M 2(MM) (MN)
total genes 2 ( of people)
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Gene frequencies
f(M allele) of M 2(MM) (MN)
total genes 2 ( of people) f(N
allele) 1 - f(M)
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Gene frequencies
Note Computing gene frequencies from
genotypic frequencies f(M allele) 2(MM)
(MN) 2 ( of people) 2(MM)
(MN) 2 ( of people) 2 (
of people) f(MM) 1/2 f(MN)

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Gene frequencies
f(M) f(MM) 1/2 f(MN) .26 1/2
(.53) .525

f(N) f(NN) 1/2 f(MN) .475
Special cases f(allele) 1.0 allele is
fixed f(allele) 0 allele is lost
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Gene frequencies can differ by breed
Demonstrated by molecular identification of
alleles at the loci for Growth
Hormone Prolactin Parathyroid Hormone
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Gene frequencies can differ by breed
Angus Brahman GH alleles Chromosome
19 A B C D
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Gene frequencies can differ by breed
Angus Brahman GH alleles Chromosome
19 A 1.0 .33 B C D
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Gene frequencies can differ by breed
Angus Brahman GH alleles Chromosome
19 A 1.0 .33 B 0 .17 C
0 .30 D 0 .20
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Gene frequencies can differ by breed
Angus Brahman Prolactin Chromosome
23 A .89 .86 B .11 .14
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Gene frequencies can differ by breed
Angus Brahman Parathyroid Chromosome
15 A .81 .17 B .05 .58 C
.02 .21 D .12 .04
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Gene Frequency Dominance
With codominance there is a one to one
relationship between the phenotypes and genotypes
leading to easy calculations of gene and
genotypic frequencies.
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Gene Frequency Dominance
With codominance there is a one to one
relationship between the phenotypes and genotypes
leading to easy calculations of gene and
genotypic frequencies. With dominance there is
not a one to one relationship so calculations of
gene and genotypic frequencies is not
straightforward.
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Dominance
Example -- Coloring in deer
D_ natural color of deer D gt d dd piebald
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natural 9,900 (DD and Dd) piebald 100 (dd)
10,000

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natural 9,900 (DD and Dd) piebald 100 (dd)
10,000
f(dd) .01 f(D_) .99
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natural 9,900 (DD and Dd) piebald 100 (dd)
10,000
f(dd) .01 f(D_) .99 f(DD) f(Dd) (cant
separate unless we evoke some assumptions)
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Hardy-Weinberg Law 1908

• In a large random mating population, in the
  absence of forces which change gene frequencies,
  both genes and genotypic frequencies remain
  constant from one generation to the next.

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Hardy-Weinberg Law 1908

• In a large random mating population, in the
  absence of forces which change gene frequencies,
  both genes and genotypic frequencies remain
  constant from one generation to the next.
• Population is said to be in the Hardy-Weinberg
  equilibrium.

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Hardy-Weinberg Law 1908
Assumptions for this to be true.
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Hardy-Weinberg Law 1908
Assumptions for this to be true. A) Large
population
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Hardy-Weinberg Law 1908
Assumptions for this to be true. A) Large
population -- ensures limited change by chance
alone (genetic drift).
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Hardy-Weinberg Law 1908
Assumptions for this to be true. A) Large
population -- ensures limited change by chance
alone (genetic drift). B) Random mating
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Hardy-Weinberg Law 1908
Assumptions for this to be true. A) Large
population -- ensures limited change by chance
alone (genetic drift). B) Random mating -- every
individual has an equal opportunity of mating
with another individual of the opposite sex.
Defined by trait, not species.
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Hardy-Weinberg Law 1908
Assumptions for this to be true. A) Large
population -- ensures limited change by chance
alone (genetic drift). B) Random mating -- every
individual has an equal opportunity of mating
with another individual of the opposite sex.
Defined by trait, not species. C) No forces to
change gene frequency (mutation, migration, and
selection).
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Hardy-Weinberg Law 1908
1) Mutation -- sudden heritable change in
genetic material.
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Hardy-Weinberg Law 1908
1) Mutation -- sudden heritable change in
genetic material. 2) Migration -- movement of
breeding animals from one population to another.

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Hardy-Weinberg Law 1908
1) Mutation -- sudden heritable change in
genetic material. 2) Migration -- movement of
breeding animals from one population to another.
3) Selection (artificial or natural) -- relative
success in becoming a parent based on genotypes
or phenotypes.
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Nomenclature
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Nomenclature

• p f(D)

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Nomenclature

• p f(D)
• q f(d)

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Nomenclature

• p f(D)
• q f(d)
• p q 1

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Nomenclature

• p f(D)
• q f(d)
• p q 1
• (p q)2 p2 2pq q2

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IF equilibrium Genotype Frequency
DD p2 Dd 2pq dd q2
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natural 9,900 (DD and Dd) piebald 100 (dd)
10,000
f(dd) .01 f(D_) .99 f(DD) f(Dd)
(assuming H-W equilibrium we can now press on)
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If true f(D_) p2 2pq .99 f(dd) q2
.01
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If true f(D_) p2 2pq .99 f(dd) q2
.01 q f(dd) .1 p 1-q .9
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If true f(D_) p2 2pq .99 f(dd) q2
.01 q f(dd) .1 p 1-q .9 f(DD)
p2 .81 f(Dd) 2pq .18
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Small Populations
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Small Populations

• Subject to random drift (genetic)

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Small Populations

• Random drift the fluctuations in gene
  frequencies observed from one generation to the
  next due to chance alone.

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Small Populations

• Subject to random drift (genetic)
• population f(d) .1 and f(D) .9 P(DD)
  p2 .81

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Small Populations

• Subject to random drift (genetic)
• population f(d) .1 and f(D) .9 P(DD)
  p2 .81
• 10 progeny (probability all are DD) (.81)10
  .12
• gt Prob(losing d) .12

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Small Populations

• Subject to random drift (genetic)
• population f(d) .1 and f(D) .9 P(DD)
  p2 .81
• 10 progeny (probability all are DD) (.81)10
  .12
• gt Prob(losing d) .12
• 20 progeny (probability all are DD) (
  .81)20 .015 gt P(losing d) .015

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Large populations Drift is less of an issue and
with very large populations it is virtually
nonexistent.