Transcript Genetics in conservation biology

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 O2 consumption in Oysters
vs growth rate in clams
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
r = 0.94
Red cockaded woodpecker
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.
3.
Lower probability of new mutations in small pops.
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
B
A
B
a
b F1
A
B
a
b
a
b
A
B
a
b
1. Loss of local adaptation
Genotypes adapted to
neither environment
Recombination
F2
a
B
A
b
2. Loss of Co-adapted gene complexes
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
D
High gene flow
C
A
B
No gene flow
E
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 reintroduction 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
Species
Population Growth Rate (%
year-1)
Annual per capita
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
elephant
102
98
700
6600
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/