Transcript Conservation and extinction

Conservation
Genetics and
extinction
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Conservation Genetics
• 5 major extinction
events
• Rate of extinction
today is of concern
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Rate of Extinction
• Many species in the
past have gone
extinct eg. dinosaurs
• Concerns today is
the rate which
species are
disappearing eg.
Birds are at rate of
100X faster (Pimm et al.
2006 PNAS 103:10941-10946)
than in the past
• CO2 entering into the
oceans affecting
coral reefs (Zeebe et al
2008 Science 321:51-52)
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Extinction
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Extinction
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Yellow Penguin story:
mtDNA sequences
M. waitaha
Boessenkool et al 2009 (Pro R Soc B)
• Used morphological
(Ancient bones)
characters to identify
ancient species
• Megadyptes waitaha
sp.nov.
• Mt DNA aid with
species confirmation
M. antipodes
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Sample collections
and breeding range =
blue region
Yellow Penguin
story: mtDNA
sequences
Boessenkool et al
2009 (Mol Ecol)
Haplotype network using
control region (mt DNA)
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Boessenkool et al 2009
IUCN Categories
• Vulnerable
– 10% prob of extinction over 100 years
• Endangered
– 20% prob of extinction over 20 years or 5 generations
• Critically endangered
– 50% prob of extinction over 10 years or 3 generations
IUCN Scale:
Not Evaluated (NE)
Data Deficient (DD)
Least Concern (LC)
Near Threatened (NT) eg. yellow lady’s slipper
Vulnerable (VU)
Endangered (EN)
eg. great basin pocket mouse
Critically Endangered (CR)
Extinct in the wild (EW) eg. greater sage-grouse
Extinct (EX)
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International Union for
Conservation of Nature
(http://www.iucn.org/)
Species of the Day:
Plants
Animals
Insects
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Categories from IUCN
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Biodiversity
• IUCN—3 fundamental levels
– Ecosystem
– Species
– Genetic
• Why conserve it?
– Values
– “To keep every cog and wheel
is the first precaution of
intelligent tinkering”—A.
Leopold
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Ecosystem Services
• Essential biological services provided naturally
by healthy ecosystems
–
–
–
–
–
–
–
Oxygen production by plants
Clean water and air
Flood control
Carbon sequestration
Nutrient cycling
Pest control
Pollination of crops
• $33 trillion value
(global GNP = $18 trillion)
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Genetic Diversity
• Genetic markers are very useful and very
popular for assessing genetic diversity of
species
• Heterozgosity on average is 35% lower in
endangered species than non-threatened
species
• Be careful on the assumption that molecular
makers such as allozyme, microsatellites and
even AFLP are neutral (usually)
• Quantify adaptive variation wherever possible
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Conservation Genetics
Frankham et al. 2002. Introduction to Conservation
Genetics. Cambridge Univ. Press
• Conservation genetics is the application of genetics to
preserve species as dynamic entities capable of coping
with environmental change
– Genetic management of small populations
– Resolution of taxonomic uncertainties
– Identifying and defining units of conservation within
and between species
– Use of genetic information for wildlife forensics
• Address genetic factors that affect extinction risk and
genetic management to minimize or mitigate those risks
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11 major genetic issues in conservation biology
(Frankham et al.)
• Inbreeding and inbreeding
depression
• Loss of genetic diversity and
adaptive potential
• Population fragmentation and
loss of gene flow
• Genetic drift becomes more
important than natural
selection as main evolutionary
force
• Accumulation of deleterious
mutations (lethal equivalents)
• Adaptation to captivity and
consequences for captive
breeding and reintroductions
• Taxonomic uncertainties
masking true biodiversity or
creating false biodiversity
• Defining ESUs and
management units within
species
• Forensic analyses
• Understand species biology
• Outbreeding depression
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5 Broad categories of conservation genetics
publications
(Allendorf and Luikart)
• Management and reintroduction of captive populations,
and the restoration of biological communities
• Description and identification of individuals, genetic
population structure, kin relationships, and taxonomic
relationships
• Detection and prediction of the effects of habitat loss,
fragmentation and isolation
• Detection and prediction of the effects of hybridization
and introgression
• Understanding the relationships between adaptation or
fitness and the genetic characters of individuals or
populations
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Genetic effects of small population size
• Effective size (Ne) usually much smaller than
census size, compounding genetic effects
• Genetic drift—loss of alleles
– Fixation in extreme case
– Loss of adaptive potential?
• Inbreeding
– Decreases heterozygosity
– Expression of deleterious recessive mutations
• Chance of extinction of locally adapted forms
– Reintroduction of other forms may not be successful
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Locally adapted forms
• Phenotype – product of genotype and environment
• VP = VG + VE
• Types of phenotypic variation:
– Morphology
• Peppered moths in UK
• Gazelles in Saudi Arabia
• Bighorn sheep in Alberta
– Behavior
• Migration in birds and salmon
• Feeding behavior of garter snakes
– Adaptation to local conditions
• Yarrow in Sierra Nevada
– Countergradient variation
• Genetic effects counteract environmental effects; thus, genetic
differences are opposite to observed phenotypic differences
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Lacking genetic
diversity
• Cheetahs have not fair well (multiple bottlenecks)
• Genetic diversity greatly reduced
• Isozyme (Stephen O’Brien et al. 1983) 47
enzymes and all = monomorphic ( 2 pop – n=55)
• 14 reciprocal skin grafts from unrelated individuals
were not rejected (O’Brien 1985)
• In 2008, using n=89 cheetahs and 19 polymorphic
microsatellite loci, show low variation
• Yet they are surviving well for now
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Small population - specific
problems
• Island population are much more vulnerable to
extinction
• Claustrophobic events eg. hurricanes, human
disturbances, poaching and selling of “prized
organisms”
• Lucas Keller and Peter Arcese have been
studying island populations of song sparrows
and have found large reductions in population
size
• Small immigration (1-2) recover diversity in 1-2
generations (Keller et al 1994, Keller, 1998)
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Inbreeding
• Extreme
example
in
humans
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Inbreeding
• Loss of heterozygosity and accumulate
deleterious alleles
• Fitness reduction in the offspring =
inbreeding depression
• Most severe in large populations since
rare alleles can persist as “het” individuals
• Damaging to the offspring but not so much
for a population
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Outbreeding depression
• Decrease in fitness resulting from outcrosses of
individuals from differentiated populations
• Possibly due to additive effects of alleles
conferring advantages under different
environments or breaking up of co-adaptive
gene complexes
• Particularly important when we are doing genetic
“rescue”
• Genetic and environmental backgrounds needs
to match if at all possible
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Genetic restoration
• Documentation and discovery of genetic decline
of a population(s) are the first steps
• Why the reduction of genetic diversity eg.
predation, habitat destruction, human hunting
and possible inbreeding as a second step
• Restoration of genetics diversity is a possible
next step
• Introduction from captive stock or other wild
population
• Local adaptation might be lost and possible out
breeding depression
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Possible genetic consequences
of immigrants: genetic rescue
http://www.fs.fed.us/wild
flowers/regions/pacificno
rthwest/IronMountain/in
dex.shtml
http://www.scientificamerican.com/article.cfm?id=earthtalks-florida-panthe
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Genetic restoration
• Genetic resource banks
• For plants there are 1,300 genebanks throughout the
world eg. Svalbard Global Seed Vault, Millennium Seed
Bank project – Kews Garden (UK)
• For animals there are many DNA banks (for
sperm/eggs/embryos) eg. Centre for Reproduction of
Endangered Species – San Diego Zoo, Calif.
• Issues to think about:
– May not work eg. technical failures, in viable specimens
– Preservation problems
– Specimens are “frozen in time” may not adapt to new
environment
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Extreme genetic restoration
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Propagation for plants
Cloning in animals
Ethically are these the right things to do?
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