Transcript Genetic Diversity

Genetic diversity is the backbone
of evolution !
Why do we need diversity?
The large picture
• Political demand for diversity
• Man’s activities may lead to
extinction of populations and species
• Man’s influence seems to grow
• Man became most important
ecological factor 50000 years ago
• Diversity is the basis for evolution
and thus life
Man destroys biodiversity
Not long ago, giant wingless birds like this moa paced New
Zealand's open country and brushy woodlands. Without large
native predators to threaten them, moas evolved to be the
biggest land predators on their island home.
But moas couldn't stand up
to human hunting
Humans first reached New Zealand by
canoe about 1000 years ago. These
settlers quickly learned to hunt the
defenceless moas. In fact, they learned
too well--in only about 700 years, every
last moa was gone.
“Biodiversity” is appealing
Evolution
• Diversity lost by selection and chance
• Diversity created by mutation
• Balance, population size 500 probably enough for
sustainable diversity
• Forests much larger than that
• Forest tree breeding often operates with numbers
larger than that (>500)
Numeric example
‘The more A, the better'
Ranking for A
AA**AA**AA 6A
**AA*A***A 4A
**AAAA**** 4A
A*****A*** 2A
*A*****A** 2A
A***A***** 2A
*A**A***** 2A
********A* 1A
The three top ranking has
together only 8 A
If
all
are
selected
the
potential for 10 A remains
Selecting best may mean missing something!
Variance in sample
Variance in sample
1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
1
11
21
31
41
Sample Size
A sample need not be large to preserve the variance of the original population!
Rare alleles
What alleles are rare?
 Almost all rare alleles are rather recent mutations and of no
value;
 Little recent advantage;
 Most rare alleles in our forest trees will die away naturally.
Even if they are of potential value, it is not easy
to utilise rare alleles
 many generations to get effect;
 in few initial genomes  inbreeding problems if utilised,
 expensive screening to identify.
Mechanisms for important rare alleles:
balanced polymorphism?
sometimes a little bad, sometimes very good?
better if in low frequency.
A gene with a frequency of 10% is likely
to be conserved but a gene with frequency
of 2% is likely to be lost in a random
mating population of size 20.
Limited impact of breeding
•
•
•
•
Areas never regenerated on purpose,
”Natural” regeneration 25%,
Natural ”volunteers in plantations,
Pollen contamination (50% of pollen) in
seed orchards.
Unimproved
Improved
Diversity in a stand
Genetic diversity in a stand is likely to favour
biological production:
• A single genotype demands the same things at the same
time, bad site use!
• In a mix another genotype may take over the ecological
space left by a failed genotype.
• A disease spreads faster in a uniform crop.
This expectation has generally been confirmed by a number
of experiments with different agricultural crops
Too much diversity in
plantations?!
Most crop- and many forest managers do not like diversity,
•
•
•
•
Uniform trees = better economy, simpler management - even if
biological production is lost,
Genetic superiority of the best clones is much larger than the
loss in biomass production by uniformity,
The current demand for diversity in intensively managed
forests is – in my opinion - unreasonable expensive in lost
future gain,
Most of the benefits with diversity is obtained by five genotypes
instead of an infinite number.
Seed orchard crops are diverse!
•Phenotypic selection of plus trees are uncertain,
preserves diversity,
•Marker gene measurements indicate that seed orchard
crops can be more diverse than stand seeds!
•Seed orchard clones are recruited from a large area,
which favours diversity compared to stands,
•Pollen sources outside the seed orchard favours diversity,
•Variances depends little on clonal number,
•In a small piece of a natural forest, trees are as related as
trees from a seed orchard plantation.
Measured with marker genes, most of the diversity is within
stands and little between stands, table from (El-Kassaby 1991).
GST gives the share of the genetic diversity that falls between stands.
Species
P sylvestris
P abies
GST (%)
3.0
Reference
Rudin et al 1974
16.0
Mejnartowitz 1979
2.0
Gullberg et al 1985
4.0
Bergman 1974
5.0
Tigerstedt 1974
2.0
Lundkvist och Rudin 1977
3.0
Lundkvist 1979
Reasons to consider gene diversity
in breeding
• To boost breeding value when breeding population is creamed for
production population,
• To obtain a production population with little inbreeding,
• To offer desirable gene diversity for production population (acceptability
and production),
• To allow more aggressive breeding in the first cycles,
• To consume while accumulating additive effects,
• To keep inbreeding manageable in the breeding stock,
• To be prepared for changed emphasises,
• To combine breeding and gene conservation,
• Some intuitive feeling that diversity could be good to have,
• To demonstrate that breeders care for sustainability, breeding is not mining,
• A sense of respect,
• Genetic diversity is the basis for the professions forest geneticist and tree
breeder.
Too much diversity in breeding
population?!
• Expensive
• In conflict with gain
Extremest value increases slowly with number
The most extreme value of a population is raising extremely slow as
a function of population size, thus to increase numbers is rather
unefficient!
Artificial selection is not a major
short time threat to diversity
• Low heritability = conserved variance also after
intensive phenotypic selection (gets worse when
selection is on genotype instead of phenotype),
• 35000+ genes interact to produce a phenotype. The
influence of selection on the frequency of each gene
must be small …,
• Selection for quantitative traits are likely to be
selection for different genes at different selection
occasions.
Need of genetic diversity measure
• Demonstration that we care,
• For chiefs and "politicians" to demonstrate that they care,
• To monitor operations,
• To control operations,
• Review and compare different options for operations,
• Classify old and new forests, multiplication units, programs,
development by time, diversity on stand, landscape, region and
national level,
• Trade off with other quantifiable variables in the breeding
system, like genetic gain, cost and time,
• Use for gene conservation purposes.
Coancestry
Coancestry is the probability that genes
taken at random from each of a pair of
individuals origin from the same gene in
a common ancestor.
Group coancestry is the probability that
two genes taken at random from a
population origin from the same gene in
a common ancestor (genomsnittligt
släktskap)
Group coancestry
• Average coancestry including self-coancestry
(“genomsnittligt släktskap”)
• Loss of gene diversity = group coancestry
• Group coancestry is a measure of gene diversity!
mother
aunt
uncle
sister
cousin
What is the group coancestry of this
”family”?
Group coancestry and status number are
useful as diversity measures!
We need measures to control accumulation of relatedness
Interaction: conservation and
breeding
Gene conservation can be said to keep group
coancestry low
Breeding should combine a high gain and a
reasonable group coancestry
or
Breeding is much the art of balancing gain and
group coancestry
Diversity changes at generation
shifts because:
1) Drift (unavoidable),
2) Balance of founder genes (can be optimised).