Genetic Diversity by maclaren1


									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
• 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*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     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
 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.
             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
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        GST (%)          Reference

    P sylvestris    3.0             Rudin et al 1974

                   16.0             Mejnartowitz 1979

                    2.0             Gullberg et al 1985

    P abies         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
• A sense of respect,
• Genetic diversity is the basis for the professions forest geneticist and tree
 Too much diversity in breeding
• 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
    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
 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 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
                 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

                                   What is the group coancestry of this
        sister                     ”family”?

Group coancestry and status number are
useful as diversity measures!

 We need measures to control accumulation of relatedness
     Interaction: conservation and
Gene conservation can be said to keep group
coancestry low
Breeding should combine a high gain and a
reasonable group coancestry
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).

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