Download lecture_1 - Dr. Christopher L. Parkinson

Conservation Genetics and
Phylogeny
Dr Christopher L. Parkinson
Parkinson Web Site
[email protected]
• This short course will serve as an introduction to the
field of conservation genetics and phylogenetics.
• Conservation of genetic diversity.
• Genetic variation provides the raw material for
adaptation, and is therefore critical to continued
evolutionary change.
• Many ongoing, human-associated changes to the
environment erode genetic diversity at the population
level.
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founder effects,
genetic drift in small populations,
inbreeding,
altered patterns of gene flow.
• Modern tools of molecular genetics
– population structures
– breeding systems
– evolutionary relationships among
taxa.
• Apply insights gained from modern
genetic techniques to improve the
effectiveness of traditional
approaches to conserve biological
diversity.
• TIME AND PLACE:
– Lecture:
• Web Site:
http://biology.ucf.edu/~clp/Courses/colo
mbia/powerpoints.php
• Username: congen
• Password: evolve
Assignments
READINGS: Readings are very
important; please have all papers/book
chapters read prior to lecture.
Conservation Genetics
• The application of genetics to preserve
species as dynamic entities capable of
coping with environmental change.
• Encompasses:
• Genetic mgmt. of small populations
• Resolution of taxonomic uncertainties
• Defining mgmt. units w/in species
• Use of molecular genetic analyses in
forensics and understanding species
biology
Sixth Extinction
• Mass extinctions vs background extinction
– 5 mass extinctions based of paleontology
– KT boundary most recent 65 mya
• Dinosaurs
• humans
• Conservation genetics
motivated by
the need to reduce current rates of
extinction and preserve biodiversity
• Why conserve biodiversity?
– Bioresources
• Food, Pharmaceuticals, Raw materials
– Ecosystem services
• E.g., O2 production, nutrient cycling,
pollination
– Aesthetics
– Ethical reasons
• IUCN (World Conservation Union)
recognizes 3 levels of biodiversity:
– Genetic diversity
– Species diversity
– Ecosystem diversity
• IUCN (1996) classified over 50% of
vertebrate species and 12.5% of plant
species as threatened
Endangered Vertebrates
What is an endangered species?
Why list?
• Legal protection
• ESA and CITES
What causes extinctions?
• Primarily humans, via direct or indirect
impacts.
• Population growth 8.9 billion by 2050
• Stochastic
– Naturally occurring catastrophic events
• Hurricanes for beach mice
– Small 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
synonym for gene.
alleles.
An allele can be used as a
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
synonym for gene.
A
alleles.
An allele can be used as 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 mutations
transitions vs. transversions
Purine
Pyrimidine
Preliminary and background knowledge
C. How does genetic diversity arise?
1) Types of mutations
a. Point mutations
transitions vs. transversions
replacement vs. silent site
Preliminary and background knowledge
C. How does genetic diversity arise?
1) Types of mutations
a. Point mutations
transitions 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 mutations
transitions 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
AABB
AaBB
AABb
AaBb
aaBB
aaBb
Phenotype
A_B_
aaB_
Conservation genetics
11 major genetic issues
• Deleterious effects of inbreeding
• Loss of genetic diversity and ability to evolve
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in response to environmental change.
Fragmentation of populations and restriction
of gene flow
Random processes overriding natural
selection
Accumulation and loss of deleterious
mutations
11 major issues
• Genetic adaptation to captivity and its
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adverse effects of reintroduction success
Resolving taxonomic uncertainties
Defining management units within a species
Molecular issues in forensics
Molecular genetic aspects of species
biology
Deleterious effects on fitness as a result of
outbreeding (Outbreeding depression)
How is genetics used to
minimize extinction?
• Reducing extinction risk by minimizing
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inbreeding and loss of genetic diversity
Identifying populations of concern
Resolving population structure
Resolving taxonomic uncertainties
Defining management units within
species
Detecting hybridization
How is genetics used to
minimize extinction?
• Non-intrusive sampling
• Defining sites for reintroduction
• Choosing the best populations for
introduction
• Forensics
• Understanding species biology
Island themes
• Many parallels between island
populations and fragmented habitats
Genetics and Extinction
• Inbreeding and loss of genetic diversity
are inevitable in small populations
• Short Term Consequences:
– reduced reproduction and survival
• Long Term Consequences:
– diminished capacity of a population to
evolve in response to environmental
change
Genetics were previously
considered inconsequential to
the fate of endangered species
• E.g., Lande (1988)
‘demographic and environmental
catastrophes will cause extinction
before genetic deterioration becomes
a serious threat to wild populations’
• Though still debated, now compelling
theoretical and empirical evidence
supporting the effects of genetic
changes on the fate of small
populations
– Many surviving pops show reduced
genetic diversity and evidence of
inbreeding
– Inbreeding causes extinctions in
deliberately inbred captive populations
– Computer projections indicate that
inbreeding will cause elevated extinction
risks in realistic situations faced by natural
populations
Inbreeding
• Inbreeding:
– The production of offspring by individuals
related by descent (e.g., self-fertilization,
brother-sister, parent-offspring matings)
• Inbreeding Depression:
– Reduced reproduction and survival
(reproductive fitness) due to inbreeding
Evidence of inbreeding depression
• Ralls and Ballou (1983)
– In 41 of 44 captive mammal pops, inbred ind.
showed higher juvenile mortality than outbred
ind.
– Brother-sister mating resulted in a 33% reduction
in juvenile survival
• Crnokrak & Roff (1999)
– Reviewed 157 data sets including 34 species for
inbreeding depression in natural situations
– In 141 cases (90%), inbred individuals had poorer
attributes than comparable outbred individuals
Documented cases of inbreeding
depression
• Mammals:
– Golden lion tamarins, lions, native mice,
shrews,
– Birds:
– Greater prairie chicken, Mexican jay, song
sparrow, American kestrel, reed warbler
• Fish:
– Atlantic salmon, desert topminnow,
rainbow trout
• Many others (reptiles, inverts, plants, etc.)
How do we measure the extent of
inbreeding?
• The inbreeding coefficient (F)
– For an individual, F refers to how closely related
its parents are
– When parents are unrelated, offspring F = 0
– When inbreeding is complete, F = 1
Inbreeding
• Inbreeding accumulates in closed
populations (those without immigration)
• Complete inbreeding can be reached
with repeated inbred matings
• An F of 0.999 is reached after 10
generations of self-fertilization
• An F of 0.986 is reached after 20
generations of brother-sister mating
Nigerian Giraffe
• Giraffe X was born
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in Paris Zoo in
1992
Highly inbred calf
had an inbreeding
coefficient of 0.52
Calf died 3 weeks
after birth
Average Inbreeding
• The AVERAGE inbreeding coefficient of
ALL individuals in a population
• Small, closed populations:
– Average F will rise as mates become
increasingly related
– Average F increases at a rate of 1/(2N) per
generation in a randomly breeding
population of size N
Average inbreeding coefficient
• Increase in average inbreeding coefficient in
populations of 10 and 20 randomly breeding
individuals
Inbreeding Relative to Random
Breeding
• Comparison of the average relatedness
of mates (parents) to what one would
expect if the population is mating at
random
Genetic Diversity
• The extent of heritable variation in a
population, or species, or across a
group of species, e.g. heterozygosity,
or number of alleles, or heritability.
Inbreeding and Extinction
• Frankel & Soule‘ (1981)
– 80-95% of deliberately inbred populations
of laboratory and domestic plants and
animals die out after eight generations of
brother-sister mating or three generations
of self-fertilization
• E.g., Japanese quail
– 383 populations inbred by continued
brother-sister mating, all populations went
extinct after four generations
Relationship between inbreeding
and extinction
Inbreeding cont.
• Even slow rates of inbreeding increase the
•
risk of extinction
Taxonomic groups such as mammals, birds,
and invertebrates show similar levels of
susceptibility to inbreeding depression
– In plants, inbreeding depression higher in
gymnosperms than angiosperms
• polyploidy
• Growing evidence shows that inbreeding
elevates extinction risks in wild populations
Computer simulations
Butterfly extinction
Interactions Create
Island populations
• Majority of extinctions have been on
islands
• Human factors drive population size
down.
• Island pops typically have less
diversity and are more inbreed than
mainland congeners
Genetic diversity and extinction
• To evolve species require genetic
diversity
• Genetic variations allows pops to
tolerate a wide range of environmental
extremes.
• Low diversity on islands, less
evolution?
Motivations for considering the
genetic consequences of
inbreeding
• Management of captive populations of rare or
endangered species
– Breeding programs usually designed to minimize
inbreeding and maximize outbreeding
• In situ management of rare species (small population
sizes)
– Lack of unrelated mates
• Random genetic drift
– In small, finite populations, genetic drift can occur even if
the population is randomly mating
• More generally, these issues apply to any species
with artificially or naturally fragmented or naturally
patchy spatial distributions