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Genetics in conservation biology

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					            Conservation Genetics (chapter 11)
Aims:
1. Molecular tools to assess factors affecting extinction risk.
2. Mitigation through management to preserve species as
   dynamic entities able to respond to environmental change

 Fisher's Fundamental Theorem of Natural Selection
  states that:

 1) the rate of evolutionary change in a population is
  proportional to its genetic diversity, thus preserving genetic
  diversity is of paramount importance to long term survival
  of species
 2) The level of heterozygosity within a population is
  sometimes related to fitness
Why is genetics important in conservation?
• Phenotypic traits influenced by genotypic variation
• Different forms of a gene = alleles - two in most sexually
  reproducing species
• Environment and allelic interactions during gene
  expression affect an individuals phenotype
• When an individual has the same alleles for a gene it is
  said to be Homozygous; When they are different =
  Heterozygous
Genetic diversity is measured at three levels:
1. Within Individual
2. Among individuals in a population (heterozygosity)
3. Among populations
HT = HP + DPT
where HT = total genetic diversity, HP is average within
population diversity, and DPT is average divergence among
populations
                              within pop'n   between pop'ns
Heterozygosity = Mean proportion of heterozygous loci in a
    population

Loss of genetic diversity may have both long and short-term
    effects

A.   Long-term: retards evolution

Much of the genetic variation in a species or among
populations has accumulated over long evolutionary time.

Low genetic diversity = loss of adaptive response capability
to changing environment compromised: Why?

Genes can influence phenotypic variation on which natural
selection acts
B. Short-term: reproductive fitness
• Loss of diversity can elevate the risk of inbreeding:
   i.e. matings in which parents are related due to common
   descent
• Leads to increased homozygosity i.e. a greater probability of
   identical alleles across loci
   Consequences include inbreeding depression: low survival and
   reproduction. In worst case scenario, we get an accumulation
   of deleterious mutations in the homozygous state resulting in
   mutational meltdown and a continuous (downward spiral) loss
   of fitness
• An individual’s inbreeding coefficient (F): Probability that
   alleles at a locus are identical by descent

• F ranges from 0 (i.e. parents unrelated) to 1 with complete
  inbreeding. In a two allele system: brother-sister matings, F =
  0.25, with self fertilization, F = 0.5

• Both short and long-term effects increase extinction probability
Are species naturally genetically diverse?




                                        Mean total
                                   heterozygosity varies
                                    across taxa. Vagile
                                    (mobile) taxa have
                                     lower differences
                                    among populations,
                                    presumably due to
                                   increased gene flow
               Is genetic diversity related to fitness?




# Heterozygote loci vs condition factor in trout      vs growth rate in clams




vs O2 consumption in Oysters                  vs No. asymmetric traits in trout
 By definition:
 Endangered species
 have poor survival &
 reproduction

 We would expect to
 see lower diversity in
 endangered species


Microsatellite loci


No Sampling effect
Is genetic diversity related to demography? YES




    Halocarpus: N.Z. conifer   Red cockaded woodpecker
    r = 0.94                   r = 0.48
For management purposes we need to know what causes
genetic diversity to change in populations

Allele distributions determines level of genetic diversity in a
population, i.e. through changes in their frequency from
generation to generation (= evolution)
 Causes

 1) Mutation: primary cause of all evolution. Heritable
    mutations provide the raw material. However, rates of m
    from one allele to another are low (10-4 to 10-6 per locus,
    per generation).

 2) Selection: will cause the frequency of a mutant allele to
    increase if the phenotypic effect is adaptive
3. Genetic drift: chance loss of alleles in a population

4. Gene flow: dispersal among populations (immigration,
    emigration)

5. Non-random mating: unequal contributions to
    reproduction, may result from assortative mating or
    female choice

6. Changes in population size, especially losses
Why is genetic diversity lower in small populations?
1.   Genetic drift: random loss of alleles is proportional to
     population size. Small populations have a greater
     probability of having less genetic variation due either to
     a) Founder effects: new populations founded by few inds.
     b) Bottlenecks: e.g. mass mortality
2.   Lower probability of new mutations in small pops.
3.   Greater isolation (sometimes) = less gene flow among
     populations e.g. habitat fragmentation: genetic
     homogenisation
 Should an estimated population size be a good indicator of
 genetic diversity? We would base our population size estimate
 (Nc) on a random census sample of our population

 Yet this may yield a poor estimator of the true diversity since
 not al individuals may reproduce (old, young, infirm, dominant,
 subordinate)
Effective population size (Ne): The population contributing to
heritable genetic variation

Ne: usually contributed effectively by few individuals, thus
using actual or Nc may be a poor indicator of population
endangerment

Ne is important because it determines the rate of loss of H per
generation
Why should Ne < NC ?
1. Age structure: mature vs immature
2. Sex ratio: often uneven
3. Unequal family size
4. Non-random mating
5. Fluctuations in population size over time:
   environment and/or human induced
              The effect of sex ratio on Ne

Ne = (4*NM * NF)/(NM + NF)
   where NM and NF are the number of breeding males
   and breeding females, respectively
1) Assume 500 mature adults: 50:50 sex ratio, random mating,
equal reproductive success:
       Ne = (4*250*250)/(250+250) = 500

But this may be unrealistic owing to dominance, social
structures, sex-related mortality etc. So, consider an elephant
seal harem as a population:

2) 1 male and 100 mature females, he mates with all of them

Ne = (4*100*1)/(101) = 3.96
The effect of variation in family size on Ne

Ne = 4Nc/(s+2) where s = variance in female reproduction

Assume a stable population of mean family size = 2
with average of 1 M and 1 F to replace each parent. Assume
s = 2, with some females producing 0 offspring, others 4

If Nc = 10, then Ne = (4*10)/(2+2) = 10

Again, this is unrealistic.


             variance
         The effect of variation in population size on Ne
Variation in the environment can cause major fluctuations in
population size over time, e.g. predator-prey cycles

 •lynx/snowshoe hare: 80 fold change
  in abundance in last 100 yrs.
 •Recall, in small populations drift has
  a large influence on loss
 •Greater genetic diversity is lost
  through drift after population crashes
 •If numbers recover rapidly, the
  adverse effect of low population size
  and inbreeding may be mitigated
The effect of population size fluctuation on Ne

Estimated using the Harmonic mean and time over which fluctuation
occurs:

1/Ne = 1/t * (1/N1+ 1/N2 + 1/N3 …1/Nt) where t = number of
 generations, and N = population size at each time or
 generation

Northern Elephant seals: hunted to 20-30 individuals, now
 recovered to 100,000
•Assume initial population 100,000 to 20 then 100,000, with
 5 generations of loss and 5 generations of recovery

•What is the effect of this crash and recovery on Ne? We
 need to know the Ne for each generation, then plug it into
 the equation
Loss of genetically effective
population over each generation
depending on initial population
size

The influence of Ne on the level
of diversity remaining in the next
generation is estimated as:

1 - (1/(2Ne))

If Ne is large, terms subtracted
from 1 will be low: and most of
genetic variation will remain in
next generation

 Populations with Ne > 100 lose less genetic diversity.
 General recommendation not to let population fall below 500
The level of diversity remaining is also dependent on
the number of generations Ne remains at a low level

Diversity Remaining = (1-(1/2Ne))t

Assume t = 10, Ne = 10

Then: (1-(1/2*10)) = 0.9510 = 0.6

after 10 years, only 60% of the original genetic diversity
remains
  High population growth rate allows populations to
 escape deleterious effect of low population size (after
                    disasters etc)


r = intrinsic growth rate
      Effect of drift on the loss of rare alleles

• By definition, rare alleles occur
  at low frequencies since they
  may not be adaptive.
• But, this could be adaptive if
  selective pressure changes
• Decreasing Ne elevates the
  rate of loss of rare alleles
  through drift
• This may compromise
  response to environmental
  variation.
                      loss of rare alleles in an
                    endangered daisy in Australia
The flightless Galapagos Island Cormorant:
                    Endemic and a species of high
                    conservation priority.
                     •N = 1000, distributed in 10
                      subpopulations
                     •Long life-span, stable
                      numbers, sex ratio, age
                      structure.
                     •Gene flow considerable
                     •But reproductive success low
                      and variable
                     •Estimated Ne = 648 < Nc
                     •Low Ne & Nc suggest a high
                      risk of inbreeding depression
With estimates of Ne and the amount of genetic diversity
lost per generation we can predict levels of inbreeding

• Valle (1995) estimated that a level of homozygosity of
  0.997 would be achieved in 189,000 years.

• 95% of expected heterozygosity lost in ~54,000 years.

Why so high?
• No regional populations
• Relatively small Ne, and low rate of new mutations
• Lack of future evolutionary potential = high extinction
  probability


Immediate threats:
• Predator introduction and habitat disturbance
 Inbreeding depression
• Recall, inbreeding increases the probability of two identical
  alleles at a locus in the homozygous state
• If they are recessive lethal or sub-lethal, they will may cause
  death or lower fitness
• Fitness reductions appear dependent on the number of these
  ‘lethal equivalents' in a population
Inbreeding causes a
reduction in fitness
(solid line) from the
outbred case (dotted
line). Slope of solid
line is equivalent to
the inbreeding load.
Individual B is more
inbred than individual
A.
Evidence that inbreeding compromises fitness
in captive animals




Juvenile mortality in inbred captive mammal populations far
exceeds the same species in outbred situations
Survival of Inbred and Ourbred white-footed mice


                   Non-inbred F = 0              Jimenez et al.
                                                (1994) Science




                Inbred F = 0.25




• Inbred mice: weekly survival rate 56% of non-inbred lines
• Inbred males: lost significantly more body mass
• Non-inbred: no significant loss
How can we rescue wild species in which low Ne and
high inbreeding predict extinction?
Appropriate Management:
1. Providing benign environments such as managed
   reserves with low predator prevalence, minimize
   disease through vaccinations, minimize natural and
   human disturbance, reduce habitat loss
2. Supplement genetic diversity through reintroductions
3. Transplant species to novel habitat: very controversial
Genetic Rescue
Inbreeding Depression: Reduction in fitness as a result of
   increased homozygosity.

Solution: Outbreeding

Outbreeding: reverse deleterious effects of inbreeding by
  mating with “rescue” populations

BUT, if introduced populations are highly divergent, concern
  for outbreeding depression
 Outbreeding Depression
Populations with different combinations of loci specially adapted
  to different environments

  Cold environment           Hot environment

  A        A                 a          a
  B        B                 b          b


      A         a                   a          1. Loss of local adaptation
                        A
      B         b F1                b            Genotypes adapted to
                        B
                                                   neither environment
                Recombination

                a        A         2. Loss of Co-adapted gene complexes
           F2   B        b       Loci not paired with alleles of same source
                                 pop. = loss of co-adapted gene complexes
Identifying ESU (Evolutionary Significant Unit)
 • ESU= Distinct population segment of a species

 Criteria:
 • Must be substantially reproductively isolated from other
   population units of the same species
 • Must represent an important component in the
   evolutionary legacy of the species
 • Crandall et al. (2000) suggested that Ecological
   Exchangeability also be considered:
   - In populations where there has been historical or recent
   gene flow, there may be little genetic divergence,
   suggesting management as single ESU.
   - However, if populations differ phenotypically, in habitat
   use, or have particular gene loci under selection, then
   they should also be managed as distinct populations
Effective conservation relies on identifying appropriate
managements units
 •Species are clearly separate ESUs
 •However, species exists as loosely connected populations with
 some dispersal and gene flow to others
 •Degree of isolation, coupled with environmental variation, may
 also lead to adaptive differences
 •Knowledge of how genetic variation is partitioned at different
 spatial scales can guide management



  High gene flow                                 D

 A                          C                              E
                                  No gene flow
                  B                                  High gene flow
Most of the variation is partitioned between regional groups with a
lesser variation among populations within regions (2 possible ESUs)
 Failure to identify ESUs may result in poor management
 decisions with profound consequences
Out-breeding depression: Tatra mountain Ibex
• Following extirpation in Czech., a population
   was successfully re-established by
   translocation of Austrian animals
• Additional supplementation of desert adapted
   animals (unknown to be a different subspecies)
   introduced from Turkey & Sinai desert
Adapted to different environmental conditions
 •Mountain species bred late in year, desert
  species earlier; hybridization disrupted the
  breeding cycle
 •Hybrids rutted too early: young born in Feb.
  and all died
 •Loss of local adaptive differences
  Genetic rescue of the Florida Panther
• Putatively, 29 sub-species of panther
  (cougar, puma, mountain lion) in the
  Americas
• Formerly widespread throughout SE USA,
  now restricted to Mid-west and west

• In S. Florida only 60-70 individuals
  remained, due to road kills, hunting

• Genetic analyses: some individuals
  introgressed from S. American puma
  genes after release by private breeders
• Hybrids occurred in areas distant from
  ‘true’ population

1967: listed as federally endangered
‘True’ populations: low allozyme, mtDNA and microsatellite
diversity compared to hybrids or puma populations in west

Evidence of severe inbreeding depression
1. Kinked tails,
2. Cardiac defects
3. Poor semen quality
4. Cryptorchidism in all pure males: At least
    one undescended testis
5. High disease prevalence
                                                Mid-piece constricted




                                     Bent acrosome

                 good
Management intervention:
Increase genetic variability via introductions from other
populations

In 1995, 8 females introduced from Texas (the nearest source)
Controversial decision: Would it lead to outbreeding
depression?
Test (Culver et al. 2000): Estimated genetic population
structure in panther populations used mtDNA, microsatellites
Results
1. mtDNA: 6 groupings = 6 subspecies, but all North
American animals were similar: of 194 individuals, 190 had
identical haplotypes and the remaining 4 individuals differed by
a Single Nucleotide Polymorphism (SNP)
 2. Microsatellite loci: Evolve quicker and provide finer
 population resolution:
• 6 major sub-groups as inferred in
  mtDNA (not 29 subspecies)
• Based on genetic divergence and
  estimated mutation rate: all groups
  diverged from a common ancestor
  ~400,000ya.
• All North American populations
  occurred as a single ESU-evolved
  within 12,000yrs
• Florida museum specimens were
  more diverse than extant Florida
  individuals but not differentiated from
  Texas

Conclusion

 Out-breeding depression predicted to be low after re-
 introduction program
Rescue had Immediate Measurable Fitness Benefits

Pimm et al. (2006):

• 5 of the released females produced
  20 kittens lacking kinked tails

• ‘Hybrids’ had 3 fold greater survival
  to adulthood than purebred

• Adult Hybrid females have higher
  natural survivorship

• ‘Hybrids’ are expanding their range
  to areas previously considered
  unsuitable
Captive Breeding

Captive breeding can be done to maximise genetic diversity:
• select for fitness
• maximise allozyme diversity
• equalise family size
• minimise kinship: i.e. maximise matings between distantly
  related individuals
                  Guam Rail

• Flightless: endemic to Pacific Island of Guam

• Brown tree snake: Introduced WW II
• Novel predator


• Rail population
   • 1960s- 80,000 individuals
   • 1980s- very few individuals
   • 21 individuals taken into captivity
   • Wild population extinct by 1986
To reduce Inbreeding:
• DNA fingerprint profiles facilitate selection of unrelated
  individuals:
• 6 chosen and placed into 2 different groups

Offspring reared:
   – Contingency releases on nearby Rota island that lacked
     tree snakes
   – Until 2000, 384 Rails released on Rota
   – 1999: First successful reproduction from 3 pairs of
     previously captive-reared birds

Problem:
• In Guam, Brown tree snake is still present
• In 1998: Snakes eliminated in a 60 acre site over 26 weeks
• Predator fences erected to create enclosure: 16 Birds
  released
• 9 rails produced 40 hatchlings
        Are Captive Breeding Programs the way forward?
Balmford et al. (1995) est. value of in situ vs ex situ conservation programs
                    Population Growth Rate (%        Annual per capita
     Species
                      year-1)                          Cost $
                        In Situ         Ex Situ        In Situ     Ex Situ
     lion tamarin        111             129            500         1900
     gorilla             103             102           1700         2000
     Asiatic lion        102             103            800         2000
     tiger               110              115          1100         5000
     Asian
                         102              98            700         6600
        elephant
     white rhino         110              99            800         2100
     black rhino         111             101            700         2600
     Indian rhino        105             105            200        10000
     Eld's deer          111             108            400         900

  Field-based programs cheaper, and as effective as captive breeding
 Forensics
 • Illegal hunting of protected species is difficult to police
 • Difficult to prosecute from sale of Illegal meat or body parts
 • Molecular genetics can resolve origins of biological material
Whales
•Used mtDNA to monitor trade in
 dolphin/whale products by purchasing
 from retail markets in Korea & Japan
•Some samples grouped with Minke
•Many others grouped with protected
 species
•Some were from dolphins and
 porpoises!
•In response, Japan argued that the
 meat was from freezer stock piles
 collected before 1985 ban
•No evidence for this and low supply of
 Minke on the market suggests when
 they come on the market they sell
 quickly
 Cloning of Extinct Species?
• Until recently, it looked like cloning of endangered species
  was only science fiction.
 • However, early in 2009 a press report described
   successful cloning of the Pyrenean (Spanish) ibex Capra
   pyrenaica, from tissue skin cells in 2000 when the last
   living specimen died
• DNA taken from these skin
  samples was put in place of
  the genetic material in eggs
  from domestic goats, to clone a
  female Pyrenean ibex
• The animal died shortly after
  birth from lung problems, but it
  raises a promising method of
  preventing formal extinction               www.telegraph.co.uk/

				
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