Download Conservation Genetics BIOL/WLF 493/693

Conservation
Genetics
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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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Other topics
• Phylogeography
– Distribution of gene lineages in space and
time
• Landscape genetics
– Combination of landscape ecology and
population genetics
– Dispersion of alleles across a landscape
• Island populations
– More later
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Evolutionary genetics
Taxonomic uncertainties
Understanding
species biology
Introgression
Conservation Genetics
Forensics
Small populations
Inbreeding
Loss of genetic diversity
Population structure
& fragmentation
Outbreeding
Mutational accumulation
Reproductive fitness
Genetic management
Extinction
Identify mgmt units
Adaptation to captivity
Wild
Captive
Reintroduction
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Genetic affects 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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Inbreeding
• In small populations, major deleterious
effects are removed (purging) and hence
individuals might still have reduce fitness
but not be greatly affected by inbreeding
depression and yet “fixation” of mildly
deleterious alleles
• Deleterious recessives seems to be the
major cause of inbreeding depression
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Inbreeding avoidance
• Effective with large populations however
inbreeding is unavoidable when
populations are reduced in size eg. captive
programs
• Examples in dogs (pure breeds ie types),
due to human selection and highly inbreed
practices, these dogs now have lower
genetic diversity than most mammals even
compared with Pandas
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Inbreeding coefficients
• Inbreeding coefficient (F) range from 0 to 1 where 0=fully
outbred and 1=completely inbred
• F=0 eg. if two fully outbred heterozygous parents
• F=0.25 eg. if siblings mated
• F=0.5 eg. selfing heterozygote
• Inbreeding can be estimated over time by:
Ft= 1-(1-1/2Ne)t where t = # of generation and Ne is the
harmonic mean of Ne in each generation
• By estimating the changes in heterozygosity using
neutral markers, you can estimate the amount of
inbreeding in a population
• Note FIS, stats can also give you an estimate of
inbreeding within a single generation
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Inbreeding depression and cost
• Cost of inbreeding depression (genetic load) can be in
the form of phenotypic disadvantage, mistiming of critical
events eg. flowering time or time of metamorphosis
leading to possible death of a population especially when
immigration has stopped
• Purging of deleterious alleles might be possible without
the lost of fertility or viability, this theory is better for
animals (if they survive) than for plants
• Once loci are fixed, only mutations can restore genetic
diversity in the absence of immigration
• Lab populations used for inbreeding studies fair better
than wild populations due to less selective pressures
• Amos and Balmford (2001) Heredity 87:257-265 * have a
different take on inbreeding depression
• Inbreeding could be a positive affect on populations
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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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Island population – specific
issues
• Wilson et al (2009) Conservation Genetics 10:419-430
• Island populations = lower genetic variation (lower allelic
richness) vs mainland populations
• However a lot depend on the size and remoteness of
the island
• Private alleles resulting from drift or mutation or
perhaps natural selection could provide genetic richness
on islands verses mainland populations
• History of the island (possible refugia events) could also
help with preservation of genetic richness of a species
• Pattern of neutral genetic variation may not reflect the
variation at adaptive loci
• Study of island populations verses mainland populations
are a necessity when considering conservation issues 30
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
•
•
•
Propagation for plants
Cloning in animals
Ethically are these the right things to do?
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Use of genetics in conservation
biology
• Systematics
– Clarification of species eg. defining the
species in the field
– Identification of lineages in need of
conserving
– Priorities for conservation
– Hybridization effect and conservation of rare
species
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Genetics in conservation
biology
• Genetics data does not always =
conservation of species
• Pocket gophers (Geomys colonus)
• List as endangered in Georgia (<100 = n)
• Allozymes and RFLP of mtDNA no
differences with much commoner pocket
gopher (G. pinetis)
• Hence the population in Georgia was no
longer red listed
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Genetics in conservation
biology
• Species at their edge of the ecological
range could certainly have problems
• Morphologically they could look different
due to diet, environment etc.
• Genetically they could be very similar
• Think domestic dogs eg. mountain
beaver
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Genetic diversity as ESU
• DNA sequencing has been more and more
affordable and abundant
• Moritz had invoked “evolutionarily significant
units (ESU) for conservation
• Molecular ecologist would use haplotypes as
possible distinctive units to identify management
units
• Construction of phylogeny and comparative
phylogeography are used for the identification or
sinking subspecies or populations
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Molecular markers in
Conservation genetics
• PCR based markers to reduce tissue need
• Big caution with contamination and misamplifying of heterozygotes (excessive
homozygotes)
• Allozymes, microsatellites, mitochondrial
sequencing and MHC sequencing are all very
useful molecular markers
• Genome sequences can help with SNP
identification and use for creating other
molecular markers for conservation studies
• Sampling size is a big problem for analysis ie
lack statistic confidence
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