Transcript Endangered Species Have Lower Genetic Diversity than Non

Genetic Aspects of Rarity and
Endangerment
 Covered many aspects in discussion of
vortices and readings dealing with viable
populations
 I’ll fill in a few more details
– Genetic diversity
– Reduction in Ne
– Unique applications of genetics to conservation
Second Writing Assignment
 50pts. Due Week From WED
 Reconsider the species you assessed as a social problem in
the first assignment
– Is this species naturally rare? What biological aspects constrain it
to be rare?
– What factors have and continue to endanger the species?
– Considering all factors causing the species’ decline and their
feedbacks and interactions, describe the species’ place in an
extinction vortex.
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).
How to Measure Inbreeding?
Keller and Waller 2002
Endangered Species Have Lower Genetic
Diversity than Non-endangered Species
 Haig and Avise 1996
 DNA band sharing
inferred from
fingerprinting
 All data from birds
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!
Effects of Inbreeding in the Wild
 Deer Mice (Jimenez et al. 1994)
– captured in wild and inbred or not in lab
– n=367 inbred and n=419 noninbred released
– -inbred survived at rate only equal to 56% of
noninbred
– inbred lost weight after release, noninbred
maintained weight
Demonstrated effects of inbreeding
in wild populations (Caro 2000)
Species
History of Low
Heterozygosity
Current inbreeding?
Effects
European Adder
Recent
Yes
Small litters, deformed young
Song sparrow
Occasional
Some
Differential loss in cold weather
Sonoran Topminnow
Recent
Yes
High mortality, slow growth
Florida Panther
Recent
Yes
Testicular dysfunction
Ngorongoro lion
Very recent
Yes
Reduced yearling production
White-footed mouse
Recent
Some (experimental)
Lower survival, male weight
loss
Cheetah
Long
No
Sperm abnormalities
Glanville fritillary
butterfly
Recent
Yes
Low survival, reduce egg
hatching
Wide survey
of inbreeding
effects (Keller
and Waller
2002)
Genetic Rescue of Greater Prairie
Chickens (Westemeier et al. 1998)
 2000 chickens in 1962---only <50 in 1994
 Genetic diversity was low and fitness poor
 Translocated chickens from large, diverse
population (MN, KS, NE) in 1994
Fecundity
rises after
translocation
Inbreeding Effects in Cheetah??
 Low genetic variation (near clones) was
associated with poor reproduction in captivity
(O’Brien 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
Reasons for Cheetah declines
 Human population increase
 Direct killing by pastoralists
 Direct killing by farmers
 Overhunting of ungulate prey
(Caro 2000)
Black Robins Defy Genetic
Bottlenecks (Ardern and Lambert 1997)
Individuals (columns)
nearly identical!
 Current population of
200 birds was derived
from a SINGLE breeding
pair
– bottleneck down to n=5 in
1980, persistence as a small
population for 100 years
 Minisatellite DNA
Black Robin
Bush Robin
Recent bottleneck, but not
historical small population
variation non-existent
 But, reproduction and
survival is normal
Mauritius
Kestrel
 Population was reduced
to 2 pairs due to
pesticides
 Increasing now with
restoration efforts
Nichols et al. 2001
Low Genetic Heterogeneity
 Typically low for island species
 Subdivision of population may allow
heterogeneity to remain relatively high
despite very low population size
Nichols et al. 2001
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
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
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
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)
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 is proportional to the heritability of a
trait
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 phenotype=h2S
• h=heritability; S = selection differential
• evolution is determined by selection and
inheritance
Species Can have Low Heterozygosity
but High Evolutionary Potential
 heterozygosity (variation at molecular level, or average
heterozygotes per loci averaged across all loci) 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
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
• 2Ne is the number of gametes that were “chosen” from all gametes to
produce the genotype of current generation (assumes diploid adults).
1/2Ne is the probability of getting 2 alleles of same type in an individual
if gametes are selected at random
– mutation adds variation at 2m per generation
Relationship of Population Size
to Evolutionary Potential
 When Ne < few hundred, selection is unimportant
– 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 is determined by
equilibrium between drift and mutation, or
• V=2m-(1/(2Ne)) = 2Ne 2m-1, or 2Ne 2m according to Lynch
• Each incremental increase in population size is doubled with respect to
heritable variation thereby doubling the evolutionary potential of the
population
 When Ne > 1000, then drift is inconsequential
– balance between mutation and selection drives variation
(evolutionary potential)
– Extreme selection can wipe out genetic variation (lead to fixation of
“presently optimal” alleles
– variation is independent of population size
How Many Individuals do We
Need to Get Ne > 1000?
 5,000 to 10,000 (Lynch 1996)
– Ne usually is .1 to .3census N
Ne 
1
; N m  males, N f  females
 1

1



 4N

4
N
m
f


4N
2
Ne 
;

 variance in progeny
2
2 
1 1
1
1 
; N  population size per generation
N e  

 .... 
t  N1 N 2
Nt 
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 Ne<few dozen, extinction occurs in
10-few hundred generations without stochasticity
• extinction occurs an order of magnitude or more
faster with demographic or environmental
stochasticity
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
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
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.
References
 Haig, SM and JC Avise. 1996. Avian conservation genetics. PP160-189 In. JC
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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 50:2158-2164.
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. 25:45-69
Lynch, M. R. Burger, D. Butcher, and W. Gabriel. 1993. The mutational
meltdown in asexual populations. J. Heredity 84:339-344.
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 282:1695-1698.
More References
 Ardern, S. L. and D. M. Lambert. 1997. Is the black robin in genetic

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peril? Molecular Ecology 6:21-28
Caro, T. M. and M. K. Laurenson. 1994. Ecological and genetic factors in
conservation: a cautionary tale. Science 263:485-486.
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 266:271-273.
O’Brien, 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 227:14281434.
Roy, M. S., E. Geffen, D. Smith, and R. K. Wayne. 1996. Molecular
genetics of pre-1940 red wolves. Conservation Biology 10:1413-1424.
Vrijenhoek, R. C., M. E. Douglas, and G. K. Meffe. 1985. Conservation
genetics of endangered fish populations in Arizona. Science 229:400-402.
Still More Refs
 Hale, ML, Lurz, PWW, Shirley, MDF, Rushton, S., Fuller, RM, and K. Wolff. 2001.
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Impact of landscape management on the genetic structure of red squirrel populations.
Science 293:2246-2248.
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 17:230-241.
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
Nicholl, M.A.C. Jones, C.G., and K. Norris. 2003. Declining survival rates in a
reintroduced population of the Mauritius kestrel: evidence for non-linear density
dependence and environmental stochasticity. J. Anim. Ecol. 72:917-926.
Nichols, R. A., Bruford, M. W., and J. J. Groombridge. 2001. Sustaining genetic
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Mandel, J. T., Donlan,C. J., and J. Armstrong. 2010. A derivative approach to
endangered species conservation. Frontiers in Ecology and the Environment. 8:44-49.