Transcript Conservation Genetics

Conservation Genetics
Currently (2004) the IUCN (International Union
for the Conservation of Nature) estimates there
have been 784 documented extinctions in 500
years.
Surprisingly 50% of documented extinctions in
last 20 years have occurred on continents.
One way to compare Contemporary vs. Historical
rates of extinction is to compare average species
lifespans:
In the fossil record the avgerage lifespan of a
species is 1-10 myrs.
In last century, bird and mammal extinctions
correspond to a lifespan of only 10,000 yrs i.e.
1/1000 of the average span in the fossil record.
If current trends continue, average lifespan can
be predicted to be as low as 200-400 yrs: 1/5000
– 1/25000 of the span in the fossil record.
In the IUCN Red List, 15,589 species face
extinction:
33% of amphibians of which 21% are critical
25% of mammals
12.5% of birds
These numbers are based on known species, or
about 3% of the 1.9 x 106 named.
There are many more in decline but not on the
IUCN red list: from McKinney and Lockwood
(1999)
We already know the main proximate causes:
1) Habitat loss / degradation; 2) Species
Introductions; 3) Exploitation; 4) Climate Change
The ultimate cause: to steal from an old comic
strip, Pogo, “We have met the enemy, and he is
us.” i.e. human population growth and total
population size.
To reduce the risk of extinctions we need to
identify species of conservation priority.
Often assessment is at an easily identifiable level,
based on basic population data…
presence/ absence
abundance
richness
Recruitment
Age structure
Diversity
The Shortcomings of Census data
1. Such metrics are useful but may identify a
threat much too late for recovery programmes to
be effective.
2. Census data cannot reveal possible threats to
the persistence of a species that are detectable
at the molecular level even before there is
numerical evidence of a threat.
Surveys of Genetic variation provide direct &
indirect indicators of the ‘health’ of a population
or species.
Some basic Genetic ideas:
• Both evolution and environment act on
phenotypes.
• Phenotypic traits are influenced by genotypic
variation.
• Both the environment and allelic interactions
during gene expression affect an individuals
phenotype.
Genetic diversity is usually measured at three
levels:
1. Within Individual (heterozygosity)
2. Among individuals in a population
3. Among populations
The basic theorem about evolutionary change
was developed by Sir Ronald Fisher. Fisher’s
theorem:
The rate of evolutionary change in a population is
proportional to the amount of available (additive)
genetic diversity within it.
The level of heterozygosity within a population is
(sometimes) related to fitness.
Heterozygosity = the mean proportion of loci
heterozygous in a population.
Loss of genetic diversity, as indicated by
heterozygosity, may thus have both long and
short-term effects.
In the long term lower genetic diversity retards
evolutionary adaptation. Much of the genetic
variation in a species or among populations has
accumulated over long evolutionary time. Not
only potential, but the actual adaptive traits may
be lost.
In the short term loss of genetic diversity leads to
increased homozygosity, i.e. a greater probability
of identical alleles across loci.
Loss of genetic diversity also elevates the risk of
inbreeding, i.e. matings in which parents are
related due to common descent.
The consequence is Inbreeding Depression:
reduced fitness through lower survival and
reproduction.
Both short-term & long-term effects will increase
extinction probability.
Some genetic measures and statistics you need
to know:
An Individual’s Inbreeding coefficient (F) is the
probability that alleles at a locus are identical by
descent.
F ranges from 0, i.e parents unrelated,
to 1 when inbreeding is complete
In a 2 allele system:
brother-sister matings have F = 0.25
With Self fertilization
F = 0.5
Effective population size Ne:
The effective population size is the population
contributing to heritable genetic variation. Usually
heritable variation is contributed effectively by
few individuals.
Thus an actual count or Nc may be a poor
indicator of population endangerment.
Ne is important because it determines the rate of
loss of H(eterozygosity) per generation.
Ne/Nc ratios average 1/10.
Why should Ne < N ?
Age structure: mature vs immature
Sex ratio: often uneven. Examples?
Unequal family size
Non-random mating
Let’s go through how each of these potential
reasons affects effective population size:
The effect of sex ratio on Ne
Ne 
4Nm N f
Nm  N f
An example: Assume a population has 500
mature adults. Within it the sex ratio is 50:50,
there is random mating, and there is equal
reproductive success. Then:
Ne = (4*250*250)/(250+250) = 500
However, this is unrealistic. Typically there is
dominance, social structure, and sex-related
mortality.
Now consider a population of essentially similar
size – an elephant seal population where there
are 5 breeding males and 500 breeding females.
Each male mates with a harem of 100 females.
Ne = (4*500*5)/(505) = 19.80
Any deviation from 1:1 sex ratio decreases ratio
of Ne:N
The effect of variation in family size on Ne
If we know all family sizes, we can use the
variance in family size in a simple formula:
N e  4 N c / ( s  2)
2
or
k ( Nk  1)
Ne  2
s  k ( k  1)
Where s2 = variance in family size,
k = mean number of progeny
An example:
Assume a stable population with a mean family
size = 2 and an average of 1 Male & 1 Female to
replace each parent.
Assume s2 = 2: some Females have 0 offspring;
some 4.
If Nc = 10, Ne = (4*10)/(2+2) = 10 (using the
simple formula), or
= 2(20 – 1)/[2 + 2(2-1)] = 9.5
This is again unrealistic.
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:
In the lynx/ snowshoe
hare predator-prey
cycle the population
size of the hare has
shown an 80 fold
change in abundance
in the cycle.
In small populations drift has a large influence on
genetic loss.
Greater genetic diversity is lost through drift after
population crashes. Even if numbers recover
rapidly, effects of low population size inbreeding
may still be apparent.
Ne is estimated using the harmonic mean and
time over which fluctuation occurs:
1 / N e  1 / t[1 / N 1  1 / N 2  ... 1 / N t ]
t = no. generations
Ni = population size at each time or generation
An example:
Northern Elephant seals were hunted to near
extinction. Assume that at the low the population
had decreased to 20-30 individuals, but now has
recovered to 100,000.
For the sample calculation assume an initial
population of 100,000, then a crash to 20 then
back to 100,000.
What is the effect of this crash and recovery on
N e?
If decline and recovery each took 1 generation –
1/Ne = 1/3[1/100000 + 1/20 + 1/100000]
Ne = 59.98
If decline and recovery occurred over 6
generations in total, and growth was essentially
linear over those generations –
1/Ne = 1/6[1/100000 + 1/20 + 1/100 + 1/1000 +
1/10000 + 1/100000]
Ne = 98.17
When Ne is low genetic diversity loss
exacerbated by:
drift
low gene flow
non-random mating
uneven sex ratio
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.
Most of the genetic variation will remain in next
generation.
Here’s a plot of genetic variation remaining as a
function of Ne and generations:
Note from the figure that the level of diversity
remaining is also affected by the number of
generations Ne remains at a low level. The
formula for the remaining diversity after t
generations is:
t

1 
1 

 2Ne 
Again by example, assume the Ne = 10 and loss
occurs over 10 generations:
Remaining fraction of diversity =
(1-[1/(2*10)])10 = 0.9510 = 0.6
Effect of drift on the loss of rare alleles
By definition rare alleles occur at low frequencies
since they may not be adaptive.
However, those rare alleles could become
adaptive if selective pressure changes.
Decreasing Ne elevates the rate of loss of rare
alleles through drift, and may compromise
response to environmental variation.
Now let’s consider the evidence of genetic
diversity and the fitness consequences of low
genetic diversity…The mean proportion of loci
heterozygous averages ~10%, with a range of 0
 40%.
There is lots of evidence that genetic diversity is
correlated with fitness…
# Heterozygote loci vs condition factor in trout
vs growth rate in clam
vs O2 consumption in Oysters
vs # assymetric traits in trout
By definition
endangered
species have
poor survival and
reproduction. We
would expect to
see lower
diversity in
endangered
species. Do we?
Even in species that are not obviously
threatened, we would expect to find genetic
diversity related to population size…
Halocarpus, a New Zealand
conifer, r = 0.94
red-cockaded woodpecker
r = 0.48
Why is genetic diversity lower in small
populations?
1.
Genetic drift: random loss of alleles is
proportional to population size. The causes:
a) Founder effects: young populations are
frequently founded by few individuals
b) Bottlenecks: populations may be exposed
to mass mortality, and decline at least
temporarily to small numbers.
2.
There is a lower probability of new
mutations appearing in small populations.
3.
Greater isolation (sometimes): One obvious
reason for small population size is isolation
due to some form of habitat fragmentation.
There is less gene flow among such
populations, and as a result genetic
homogenisation within fragments.
Small population size, low gene flow, and
isolation all point to islands as a good place to
explore genetic diversity, fitness, and extinction.
Genetic factors associated with elevated
extinction risk in Island populations
Endemic island species have shown high risk of
extinction. 75% of extinctions since 1600 and
90% of bird extinctions have occurred in island
endemics. Why? The main reasons:
• Introduced species
• Habitat destruction
• Exploitation
Is inbreeding a major factor?
Frankham (1998): reported high levels of
inbreeding in island populations, but found
that endemic island populations were more
inbred than non-endemic island populations.
A survey of deliberately inbred lab and domestic
populations found a negative correlation between
survival and inbreeding:
The point at which domestic
populations suffered elevated
extinction was within the
range of F ( inbreeding
coefficients) in island
populations.
There is also clear evidence that inbreeding
compromises fitness in captive animals from
juvenile mortality in inbred vs. outbred captive
mammal populations:
Let’s finish with an example of a species of
conservation interest and prority, the flightless
Galapagos Island Cormorant:
Whole pop. = 1000
Long lifespan, stable #s, sex
ratio, age structure.
Distributed in 10 subpopulations with considerable
gene flow among them.
However reproductive
success is low & variable.
Estimates of overall Ne =
648. This is < Nc
Low Ne & Nc suggest high
risk of inbreeding depression
With estimates of Ne and the amount of genetic
diversity lost per generation we can predict levels of
inbreeding.
Loss per generation:
1/(2*648) = 0.0008 (0.08%) lost per generation
Valle (1995) estimated that a level of homozygosity
of 0.997 would be achieved in 189,000 years, but
that 95% of expected heterozygosity would be lost in
only ~54,000 years.
Why so high?
• No regional populations
• Small Ne, thus a low rate of new mutations
• Lack of future evolutionary potential = high
extinction probability
How can we rescue wild species in which low Ne
and high inbreeding predict extinction?
Appropriate Management:
1. Providing benign environments:
managed reserves
low predator prevalence
minimize disease
limit disturbance
reduce habitat loss
2.
Supplement genetic diversity through
reintroductions