Genetic Aspects of Rarity and Endangerment

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Genetic Aspects of Rarity and Endangerment

• Covered many aspects in discussion of vortices
  and PVAs
• Reserve readings provide solid background on
  techniques and types of questions that are
  important
• Ill fill in a few more details
• Genetic diversity
• Reduction in Ne
• Unique applications of genetics to conservation

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Inbreeding Depression (Keller and Waller 2002)
Inbreeding is used to describe various related
phenomena that all refer to situations in which
matings occur among individuals that have
variously similar genotypes (relatives). As
conservation biologists we are concerned where
this reduces genetic variability or otherwise
reduces fitness (inbreeding depression).
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How to Measure Inbreeding?
Keller and Waller 2002
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Endangered Species Have Lower Genetic Diversity
than Non-endangered Species

• Haig and Avise 1996
• DNA band sharing inferred from fingerprinting
• All data from birds

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Inbreeding and Endangerment--Cause and Effect?

• Typical early studies suggested that endangered
  species are genetically impoverished
• Sonoran topminnow (Vrijenhoek et al. 1985)
• isolated populations in desert southwest are
  genetically much less diverse than widespread
  Mexican populations
• Recommend restocking from most diverse
  populations
• But no direct link to suggest genetic
  impoverishment caused endangerment--rather it
  likely resulted from it!

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Effects of Inbreeding in the Wild

• Deer Mice (Jimenez et al. 1994)
• captured in wild and inbred or not in lab
• n367 inbred and n419 noninbred released
• -inbred survived at rate only equal to 56 of
  noninbred
• inbred lost weight after release, noninbred
  maintained weight

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Demonstrated effects of inbreeding in wild
populations (Caro 2000)
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Wide survey of inbreeding effects (Keller and
Waller 2002)
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Genetic Rescue of Greater Prairie Chickens
(Westemeier et al. 1998)

• 2000 chickens in 1962---only
• Genetic diversity was low and fitness poor
• Translocated chickens from large, diverse
  population (MN, KS, NE) in 1994

Fecundity rises after translocation
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Inbreeding Effects in Cheetah??

• Low genetic variation (near clones) was
  associated with poor reproduction in captivity
  (OBrien et al. 1985)
• low sperm count, low fecundity, low conception,
  high infant mortality
• Classic signs of inbreeding
• seems not the case!
• Reproduction in wild is fine, but cubs are lost
  through predation to lions and hyenas (Caro and
  Laurenson 1994)
• poor husbandry was likely source of poor
  reproduction in captivity

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Reasons for Cheetah declines

• Human population increase
• Direct killing by pastoralists
• Direct killing by farmers
• Overhunting of ungulate prey

(Caro 2000)
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Black Robins Defy Genetic Bottlenecks (Ardern and
Lambert 1997)

• Current population of 200 birds was derived from
  a SINGLE breeding pair
• bottleneck down to n5 in 1980, persistence as a
  small population for 100 years
• Minisatellite DNA variation non-existent
• But, reproduction and survival is normal

Individuals (columns) nearly identical!
Black Robin Bush Robin
Recent bottleneck, but not historical small
population
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Does Genetic Variation Matter?

• For commonly measured variation (multilocus
  heterozygosity) it does not appear to matter
• DNA fingerprinting, mtDNA, etc.
• Britten (1996)
• meta-analysis of 22 correlations between
  heterozygosity and fitness surrogates (growth
  rate, developmental stability
• no significant relationship
• loci measured with molecular techniques are
  typically neutral in the eye of evolution
• only a small sample of actual loci are measured

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Could Inbreeding be Good?

• Purging (Keller and Waller 2002)
• Simple population genetics models predict that
  the increased homozygosity resulting from
  inbreeding will expose recessive deleterious
  alleles to natural selection, thereby purging the
  genetic load
• Further inbreeding would then cause little or no
  reduction in fitness.
• Studies of purging are inconclusive in
  demonstrating consistent, positive effects
• Purging may only work under limited conditions
• Strong deleterious effect, isolation precludes
  reintroduction of deleterious alleles by
  immigration, inbreeding is gradual

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Do Molecular Techniques Measure the Right Genes?

• Mitton (1994) points out that variation detected
  by molecular techniques (DNA) does not correlate
  with fitness like variation measured at
  polymorphic protein loci (protein
  electrophoresis)
• metabolism, growth rate, and viability are
  correlated with protein variation
• Fleischer (1998) points out that quantitative
  genetics measures variability in traits under
  multilocus control by measuring heritability
• measure variability in potentially important
  traits like body size or clutch size
• Lynch (1996) details the potential importance of
  quantitative genetics to conservation biology

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Quantitative Genetics

• Measures and develops theory about heritability
  (in addition to other concepts)
• how genotype influences phenotype and how
  genotypes change through time (evolution)
• Molecular genetics measures variation in loci,
  most of which are neutral with respect to
  evolution (do not affect fitness or even
  phenotype)

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What is Heritability?

• Heritability (Lynch 1996)
• fraction of phenotypic variance that has an
  additive genetic basis
• how much you can expect a trait to change in the
  next generation when selection acts on it in the
  present generation
• the ability to respond to novel selective
  challenges if proportional to the heritability of
  a trait

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Do Heritable Traits Correlate with Fitness?

• Perhaps not in a simple way
• body size in Pinyon Jays is heritable (parent and
  offspring mass is correlated), but not directly
  related to survival or reproduction (Marzluff and
  Balda 1988)
• But it is a fundamental LAW that heritability
  determines the ability of a population to evolve
• change in mean phenotypeh2S
• hheritability S selection differential
• evolution is determined by selection and
  inheritance

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Species Can have Low Heterozygosity but High
Evolutionary Potential

• heterozygosity (variation at molecular level) is
  produced by mutation (rate of 10-8 - 10-5 per
  year)
• heritability (variation in quantitative traits)
  is introduced at rate of 10-3-10-2 per generation
• If population goes through a bottleneck and
  looses both sources of variation, heritability
  recovers more quickly.
• Species can have low molecular variation, but
  high heritability (hence high ability to evolve)
• Cheetahs are an example of this.
• Lack of heterozygosity does not mean lack of
  evolutionary potential

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General Principles Relevant to Conservation
(Lynch 1996)

• Genetic variance is determined by interplay of
  selection, drift, and mutation
• when population size is constant and selection is
  constant then mutation balances drift which sets
  up an equilibrium level of variation
• drift reduces variation at rate of 1/(2Ne) per
  generation as discussed earlier
• mutation adds variation at ?2m per generation

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Relationship of Population Size to Evolutionary
Potential

• When Ne
• selection effects are spread over many loci that
  control a single character so effect on any 1
  locus is swamped by drift
• genetic variation in heritable characters equals
  2Ne ?2m
• doubling population size leads to doubling in
  heritable variation or doubling the evolutionary
  potential of the population
• When Ne 1000, then drift is inconsequential
• balance between mutation and selection drives
  variation (evolutionary potential)
• variation is independent of population size

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How Many Individuals do We Need to Get Ne 1000?

• 5,000 to 10,000 (Lynch 1996)
• Ne usually is .1 to .3census N

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Mutational Meltdown (Lynch et al. 1993)

• Same as f-vortex
• drift becomes more important as population
  declines to very small size
• drift begins to act synergistically with
  accumulation of deleterious mutations
• for flies when Ne10-few hundred generations without stochasticity
• extinction occurs an order of magnitude or more
  faster with demographic or environmental
  stochasticity

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Is Adding Individuals from Captive Propagation
Beneficial?

• Increase in numbers, but also may upset genetic
  adaptation to local conditions
• esp. likely if use non-native stock
• hatchery fish, yellowstone wolves
• accentuated by long periods of selection in
  captivity
• develop deleterious behavior with genetic
  component
• Also relevant when considering inducing migration
  between isolates
• human activity fragments habitat and sets up
  unique selective regime in different fragments

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Unique Genetic Applications

• Fleischers (1998) look to the future
• may be able to completely type the genotype of
  many organisms quickly
• Genetic engineering
• add genes for disease resistance
• add genes for parasitic egg recognition
• clone old individuals to keep them in breeding
  population

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Bessie and Noah (Seattle Times Oct. 9, 2000)

• DNA from a cow egg (Bessie) was fused with skin
  cell from a living Asian Guar to create an embryo
  (Noah) that was implanted back into Bessie for
  gestation
• Cloned Guar that does not produce immunologic
  rejection in cow
• This is no longer science fiction. Its very
  real (Lanza, author of this study published in
  Cloning)

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Using Genetics to Guide Recovery

• Red Wolves in SE United States (Roy et al. 1996)
• Are they a basal canid or a recent hybrid?
• Listed because they were believed to be a native
  species from Pleistocene that was ancestral to
  coyotes and gray wolves
• Mitochondrial and nuclear DNA suggest red wolves
  are result of hybridization between gray wolves
  and coyotes--timing of this is uncertain
• Reintroduction sites should be selected that are
  in areas with few coyotes to reduce future
  hybridizing

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Effects of Forest Loss on Squirrel Genetics
(Hale et al. 2001)
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Thoughts from Lande (1999)

• Evaluates Extinction Risk from stochastic,
  deterministic, and genetic factors
• Deterministic declines in population due to human
  factors (habitat loss, invasive species, climate
  change, etc.) are more important than stochastic
  factors in causing species declines
• Very large populations (5000) may be needed to
  maintain rare alleles such as those needed to
  resist new diseases
• Once populations are small
• Inbreeding depression is most severe when
  population declines have been rapid (little
  purging occurred), but it is easily reversed with
  minimal migration (1 unrelated individual joins
  each population every 1 or 2 generations)
• Small populations with low fitness may go extinct
  from fixation of new deleterious mutations. But
  even very small populations with high fitness
  rarely suffer from fixation of deleterious
  mutations.

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References

• Haig, SM and JC Avise. 1996. Avian conservation
  genetics. PP160-189 In. JC Avise and JL Hamrick
  (ed.) Conservation genetics. Chapman Hall. New
  York.
• Lynch, M. 1996. A quantitative-genetic
  perspective on conservation issues. PP 471-501
  In. JC Avise and JL Hamrick (ed.) Conservation
  genetics. Chapman Hall. New York.
• Britten, HB. Meta-analyses of the association
  between multilocus heterozygosity and fitness.
  Evolution 502158-2164.
• Fleischer, RC. 1998. Genetics and avian
  conservation. PP 29-47 In. JM Marzluff and R
  Sallabanks (eds.) Avian Conservation. Island
  Press. Covelo, CA.
• Mitton, JB. 1994. Molecular approaches to
  population biology. Ann. Rev. Ecol. Syst.
  2545-69
• Lynch, M. R. Burger, D. Butcher, and W. Gabriel.
  1993. The mutational meltdown in asexual
  populations. J. Heredity 84339-344.
• Westemeier, R. L., Brawn, J. D., Simpson, S. A.,
  Esker, T. L., Jansen, R. W., Walk, J. W.,
  Kershner, E. L., Bouzat, J. L., and K. N. Paige.
  1998. Tracking the long-term decline and recovery
  of an isolated population. Science 2821695-1698.

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More References

• Ardern, S. L. and D. M. Lambert. 1997. Is the
  black robin in genetic peril? Molecular Ecology
  621-28
• Caro, T. M. and M. K. Laurenson. 1994. Ecological
  and genetic factors in conservation a cautionary
  tale. Science 263485-486.
• Jimenez, J. A., K. A. Hughes, G. Alaks, L.
  Graham, and R. C. Lacy. 1994. An experimental
  study of inbreeding depression in a natural
  habitat. Science 266271-273.
• OBrien, S.J., Roelke, M. E., Marker, L., Newman,
  A., Winkler, C. A., Meltzer, D., Colly, L.,
  Evermann, J. F., Bush, M., and D. E. Wildt. 1985.
  Genetic basis for species vulnerability in the
  Cheetah. Science 2271428-1434.
• Roy, M. S., E. Geffen, D. Smith, and R. K. Wayne.
  1996. Molecular genetics of pre-1940 red wolves.
  Conservation Biology 101413-1424.
• Vrijenhoek, R. C., M. E. Douglas, and G. K.
  Meffe. 1985. Conservation genetics of endangered
  fish populations in Arizona. Science 229400-402.

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Still More Refs

• Hale, ML, Lurz, PWW, Shirley, MDF, Rushton, S.,
  Fuller, RM, and K. Wolff. 2001. Impact of
  landscape management on the genetic structure of
  red squirrel populations. Science 2932246-2248.
• Caro, T. 2000. Controversy over behavior and
  genetics in Cheetah conservation. In. LM Gosling
  and WJ Sutherland, eds. Behavior and
  Conservation.
• Keller, LF and DM Waller. 2002. Inbreeding
  effects in wild populations. Trends in Ecology
  and Evolution 17230-241.
• Lande, R. 1999. Extinction risks from
  anthropogenic, ecological, and genetic factors.
  Pp 1-22. In Genetics and the Extinction of
  Species (Landweber, LF and AP Dobson, eds.).
  Princeton University Press