Download 8. Conservation genetics

8. Conservation genetics
8.1. Extinctions
8.2. Molecular biology in conservation
8.3. Inbreeding
8.3.1. Genetic load
8.3.2. Genetic consequences of inbreeding
8.3.3. Genotype frequencies and breeding system
8.3.4. Estimation of F
8.3.5. Pedigrees and F
8.3.6. Inbreeding depression
8.3.7. Genetic basis of ID
8.4. Genetic diversity as a conservation issue
8.4.1. Genetic restoration
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8.1. Extinctions
• Commonplace
–
–
–
–
3-30 million species are thought to exist on earth today
5-50 billion species has existed at one time or another
truly lousy survival record: 99.9% failure (Raup 1999)
extinction rate not constant
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Mass extinctions
• Five
–
–
–
–
–
Ordovician
Devonian
Permian
Triassic
Cretacous (65 mya)
• 38% marine animals
went extinct; among
land animals the
percentage higher
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Sixth mass extinction today?
• World Conservation Union (IUCN)
• founded 1948, assesses conservation status of
species
• Red List of Threatened Species
http://www.iucnredlist.org/
– 20 219 species threatened by 2012
•
•
•
•
•
•
•
EX = Extinct (hävinnyt)
EW = Extinct in the wild (hävinnyt luonnosta)
CR = Critically endangered (äärimmäisen uhanalainen)
EN = Endangered (erittäin uhanalainen)
VU = Vulnerable (vaaraantunut)
NT = Near threatened (silmälläpidettävä)
LC = Least consern (elinvoimainen)
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5 501 mammals; 1 138 (25%)threatened
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10 064 birds; 1 303 (13%) threatened
EX
EW
CR
EN
VU
NR
LC
bad data
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Sixth mass extinction today?
•
•
Many with small population sizes, for
example island endemics
Many with large populations has been
progressively reduced to the point of
endangerment
– Last passenger pigeon (Ectopistes
migratorious) died in Cincinnati zoo in
1914
– Less than 50 years earlier billions of
individuals:
– ’ John James Audubon watched a flock
pass overhead for three days and
estimated that at times more than 300
million pigeons flew by him each hour’
– Hunted for meat
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8.2. Molecular biology in
conservation
• In early days destructive sampling
• PCR-technology
– non-destructive sampling
– non-invasive sampling
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• Conservation Genetics
– understand the relationship between genetic variability and
population viability
• monitoring genetic diversity using both neutral and adaptive
genetic markers
• low level of genetic diversity may interact with other factors,
such as demographic and environmental variation, to
generate an "extinction vortex"
– much of conservation genetics involves the estimation of
effective population size, structure and gene flow among
populations
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• Example: Effective population size in
Finnish wolf population
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Jannson et al 2014 BMC Evolutionary Biology
• Estimation using the temporal method
§ Is based on changes in allele frequencies that occur
between two or more temporal samples taken from a small
population
§ Larger changes in allele frequencies in smaller populations
because of genetic drift
§ Effective population size could be estimated on the basis
of the amount of change
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• Estimates of Ne in Finnish wolf population using
several temporal methods (Jansson et al. 2012 Mol Ecol)
–
–
–
–
Number of breeding individuals in 2004 = 34
Migration and inbreeding avoidance increase Ne
Ne/Nc = 0.16 – 1.17
Ne large enough for self sustaining population?
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8.3. Inbreeding
8.3.1. Genetic load
•
•
When parents of an individual share one or more
common ancestors, the individual is inbred
Inbreeding depression
= Reduction of fitness due to breeding between close
relatives
•
genetic load
= The reduction in the mean fitness for a population
compared to the theoretical maximum fitness
– The magnitude depends on how many and how
harmful recessive alleles are found in the population
•
Example: Great tit (van Nordwijk & Scharloo 1981)
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Example: Swedish captive wolfs
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Laikre & Ryman. 1991. Conservation Biology 5
8.3.2. Genetic consequences of
inbreeding
Genotype frequencies in self-fertilization: e.g. p = q = 0.5
Genotype
Frequency
AA
0.25
Aa
0.5
aa
0.25
Let’s assume individuals of each genotype has an offspring
Parent
genotypes
Offspring genotypes
Frequency
AA
Aa
aa
AA
0.5 Aa + 0.25 AA +0.25 aa
aa
0.25x1 + 0.5x0.25 = 0.375
0.5x0.5 = 0.25
0.25x1 + 0.5x0.25 = 0.37515
• the frequency of heterozygotes is halved
• no changes in allele frequencies
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Inbreeding reveals diseases caused by rare resessive alleles;
examples from human population:
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8.3.3. Genotype frequencies
and breeding system
Genotypes
Population
F
A/A
A/a
a/a
Random mating
0
p2
2pq
q2
Fully inbred
1
p
0
q
Partially inbred
F
p2(1-F)+Fp
=p2 + Fpq
2pq(1-F)+Fx0
=2pq(1-F)
q2 (1-F)+Fq
=q2 +Fpq
•
The ratio of heterozygosity in an inbred population relative to
that in an outbred population is :
HI/H0 = 2pq(1-F)/2pq = 1- F
F = 1 – (HI/H0) (F is the inbreeding coefficient)
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8.3.4. Estimation of F
•
Deficiency of heterozygotes at a locus controlling black vs.
grey lemma colour in oats (kaleen väri kauralla)
Genotype
BB
Bb
bb
Observed
0.548
0.071
0.281
Expected
(HW)
0.340
0.486
0.173
F = 1 – (HI/H0) = 1-(0.071/0.486) = 0.85
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• Loss of heterozygosity and F
– Estimate of inbreeding coefficient for a population can be
obtained from the loss of genetic diversity over time:
Ht /H0 = (1- ½ Ne)t (1-F0)= 1 – F
F = 1-(1- ½ Ne)t (1-F0)
Where t = number of generations and F0 = initial inbreeding
Or simplified, when heterozygosity of the original population
is compared to inbred:
F = 1 – (Ht/H0)
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• Example: Grey wolf, Isle Royale
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• Grey wolves
– in the endangered Isle Royal
population allozyme
heterozygosity was 3.9%
– In a nearby mainland
population heterozygosity
was 8.7%
F = (1- Ht /H0 ) = (1- 0.039/0.087) = 0.55
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8.3.5. Pedigrees and F
• Calculation of F-coefficient
A1A2
Probability that A1 is passed from A
to D is ½ and D to X is ½
A
D
E
Probability that A1 is passed from A
to E is ½ and E to X = = ½
Probability that A2 is passed from A
to D is ½ and D to X is ½
X
?
Probability that A2 is passed from A
to E is ½ and E to X = = ½
F = (½)4 + (½)4 = 1/8= 0.125
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• More complicated pedigrees:
– Chain counting method
• Find all possible chains through different ancestors
• Count number of individuals (n) in chains (except
individual I, for which you are calculating F).
• In each chain inbreeding coefficient is F = (1/2)n
• Add the contributions of different counts:
• F = Σ(½)n(1 + Fca),
Where n is # of individuals in path to common ancestor and
back and Fca is inbreeding coefficient of common ancestor
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Example:
The common ancestors, their chains,
inbreeding coefficents and contribution to
inbreeding coefficient of Z
All other CAs have an inbreeding coefficient of 0
except H:
FH (CAD) = 1+(1/2)3=1.125
CA
Path
n
Effect to F
A
XKGCADHLY
9
(½)9
0.00195
B
XKHDBEJMY
8
(½)8
0.00391
B
XKHDBEALY
8
(½)8
0.00391
C
XKGCHLY
7
(½)7
0.00781
H
XKHLY
5
(½)5 (1.125)
0.03516
Fx =
0.05273
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8.3.6. Inbreeding depression
•
Production of calves in muskox (Laikre, Ryman & Lundh 1997;
Cons. Biol. 79: 197-204
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•
Production of cubs in Swedish wolves
(Liberg et al. 2006; Biol Letters)
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• Quantitative characters closely related to fitness
show more inbreeding depression than those that
are less closely related to fitness
• DeRose & Roff 1999. Evolution:
– At inbreeding coefficient of 0.25 (=full-sib mating):
– In morphological traits inbreeding depression reduced
fitness by 2.2 %
– In life-history traits fitness reduced by 11.8%
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Measuring inbreeding depression
•
•
ID = inbreeding depression = 1(compare with F = 1 −
)
Lethal equivalents
- group of detrimental alleles that would cause on average
one death if homozygous
- Probability of survival (S) can be expressed as
- S = e –(A+BF) => ln S = -A-BF
• where e-A is the fitness in outbred population (A is a measure
of death due largely to environmental factors but also to other
factors not included in B)
• B is a measure of the hidden genetic damage that would be
expressed fully in a complete homozygote (F = l)
• F is the coefficient of inbreeding
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• Lethal equivalents in Okapi (de Bois et
al. 1990)
– slope of the regression line is –1.8
suggesting that population contains 1.8
haploid and 3.6 diploid lethal equivalents
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•
The number of lethal equivalents may be also estimated as
Morton et al. (1956) and Sorensen (1969)
2B = - 4 ln R
where R is the relative survivorship of offspring from selfpollination in relation to offspring from cross-pollination (=F)
and 2B is the average number of lethal equivalents per
zygote
•
In bilberry (Vacinium myrtillus) in the
experimental field (Nuortila, Tuomi, Aspi
& Laine, 2006):
– mean inbreeding depression at the
embryonic stage R = 0.8 (± 0.04)
– Lead to a mean of 2B = 7.8 (± 0.8; N = 18)
lethal equivalents per zygote
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8.3.7. Genetic basis of ID
•
Dominance hypothesis
Alleles
Fitness
A1A1
1
A1A2
1 – hs
A2A2
1 –s
h=degree of dominance of A2
s=selection coefficient against A2A2
Þ maladaptive and lethal, caused by partially or mostly recessive
alleles
– mutation brings new, selection against (mutation- selection model)
•
Overdominance hypothesis
Alleles
Fitness
A1A1
1-t
A1A2
1
A2A2
1 –s
t=selection coefficient against A1A1
s=selection coefficient against A2A2
Þheterozygosity itself ‘good’
– allele frequencies higher than in the mutation-selection model
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• How to study?
– If heterozygosity itself is good, then individual
heterozygosity and fitness should correlate
• However, this phenomenon could be caused for
example by population structure or partial inbreeding
• Enzyme gene heterozygosity: only rarely
heterozygosity-fitness correlation, which could not be
explained by the population structure
• However several cases of correlations with DNAstudies
– Biometrical evidence: only a little evidence of
overdominance
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• If continuous and fragmented populations of a
same species are considered then (Whitlock 2003;
Genetics):
– According to the dominance theory: small fragmented
population should have less inbreeding depression:
deleterious alleles are purged in small inbred populations
A1A1
A1A2
A2A2
1
1 – hs
1–s
– According to the overdominance theory: there should not
be large differences between fragmented and continuous
populations
A1A1
A1A2
A2A2
1–t
1
1–s
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• Example: Inbreeding depression in Glanville fritillary
in Finland and France (Haikola et al. 2001,
Conservation Genetics 2: 325-335)
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• Finland (Åland): fragmented small populations
• France: continuous large populations
Less inbreeding depression in Finnish populations - dominance
model – purging
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8.4. Genetic diversity as a
conservation issue
• ”Small populations are generally likely to go extinct
because of demographical and environmental
stochasticity and genetics is unlikely to make a
substantial difference” (Lande 1989)
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• Models in which non-genetic (environmental
stochasticity and population demography) and
genetic processes are included have shown that
many populations will loose most or all of their
neutral genetic diversity before non-genetic random
events lead to extinction
(Vuketich, J. A. & Waite. T. A. 1998. Erosion of
heterozygosity in fluctuating populations. Conservation
Biology 13: 860-868)
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•
Genetic diversity is important: island populations
more prone to extinctions (Frankham 1998)
–
–
Of animal extinctions since 1600, 75% have been of
island species
90% of species driven to extinction in historic times
have been island dwellers
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• In island populations inbreeding coefficients are high
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• Example: Black robin (Petroica traversi,
Chathaminsieppo)
– In 1980 the entire black robin
species comprised only of 5
birds, and the current population
of 287 mature individuals (2013)
is known to be derived from a
single breeding pair
(S. L. Ardern & D. M. Lambert.
1997. Is the black robin in
genetic peril? Mol Ecol 6 : 21–
28)
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• Levels of minisatellite DNA variation in the black
robin are among the lowest reported for any avian
species in the wild.
• Surprisingly, similarly bottlenecked control
populations of a closely related species (P. australis
australis) exhibit significantly higher levels of
genetic variation.
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•
The observed pattern suggests that the black
robin's persistence in a single small population
for the last 100 years, rather than the recent
bottleneck itself, accounts for the low genetic
variation observed.
•
Despite genetic impoverishment, survival and
reproductive performance indicate that the black
robin is viable under existing conditions.
•
This illustrates that significant levels of genetic
variation are not a necessary prerequisite for
endangered species' survival.
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• Example: Glanville fritillary (Saccheri et al. 1998)
–
Genetic diversity important: extinction risk and inbreeding
• Seven loci studied (5 allozymes, 2 microsatellites) in
populations with different numbers of individuals
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•
•
•
Level of heterozygosity made a significant contribution to the
model explaining the observed extinctions
Inbreeding affects several fitness components in Glanville fritillary
populations
Single generation of brother-sister inbreeding decreased egg
hatching rate by ca 30%
Black = extinct
White = surviving
sample model:
isoclines for the
extinction risk
predicted by the
model, including
ecological factors
and heterozygosity
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• Adder population in Sweden (Madsen et al. 1999;
Nature 102: 34-35)
– adding a single new male increased significantly the
number of adults and recruits
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