Conservation Genetics and extinction

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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 10310941-10946) than in
  the past
• CO2 entering into the oceans affecting coral
  reefs (Zeebe et al 2008 Science 32151-52)

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Extinction
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Extinction
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Yellow Penguin story mtDNA sequencesBoessenkool
et al 2009 (Pro R Soc B)
M. waitaha

• 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 sequencesBoessenkool
et al 2009 (Mol Ecol)
Haplotype network using control region (mt DNA)
Boessenkool et al 2009
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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 ladys 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

• IUCN3 fundamental levels
• Ecosystem
• Species
• Genetic
• Why conserve it?
• Values
• To keep every cog and wheel is the first
  precaution of intelligent tinkeringA. 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 GeneticsFrankham 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 driftloss 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 OBrien et al. 1983) 47 enzymes
  and all monomorphic ( 2 pop n55)
• 14 reciprocal skin grafts from unrelated
  individuals were not rejected (OBrien 1985)
• In 2008, using n89 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/wildflowers/regions/pacificno
rthwest/IronMountain/index.shtml
http//www.scientificamerican.com/article.cfm?ide
arth-talks-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?