What is genetic diversity

1
What is genetic diversity ?
Thomas Geburek Department of Genetics Federal
Research Centre for Forests, Natural Hazards,
and Landscape (BFW) Austria
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
2
Conditions for Forest Ecosystem Stability

• Species diversity
• Temporal variation
• Spatial variation
• Patterns of interactions

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
3
Conditions for Forest Ecosystem Stability

• Genetic diversity

• Species diversity
• Temporal variation
• Spatial variation
• Patterns of interactions

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
4
Ecosystem identity can be regarded as the
totality of

• material balance
• energy balance
• information balance

Certain degree of constancy of the information
needed must be of a biological nature, and has
its material basis in the hereditary substance
DNA.
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
5
Biodiversity genetic, species, and landscape
level
Noss (1990)
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
6
Significance of genetic diversity
Adjustment to changing environmental conditions
may be based on
physiological adaptation internal self-regulating
mechanisms, the more (allelic) genes the better
the physiological buffer
epigenetic adaptation triggered by environmental
signals, not based on Mendelian inheritance, may
regulate gene expression over generations
collective adaptation population adjusts its
genetic composition through evolutionary factors
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
7
Forest trees are something special

• Longevity
• Spatial heterogeneity

Pinus aristata
Pinus sylvestris
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
8
Mother Nature has equipped tree species with a
high amount of genetic diversity necessary to
cope with environmental changes in evolutionary
time scales. A long-term sustainable management
of forest ecosystems requires the maintenance of
genetic diversity in probably all tree
populations.
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
9
Rehfeldt et al. (2002)
Response functions of 10 Pinus sylvestris
populations
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
10
The fundamental problems of plant conservation
genetics are loss of genetic diversity and
harmful irreversible changes in population
structure

• They are resulted from
• reduction in population size
• loss, deterioration or fragmentation of habitats
• accelerated climate change
• population and species fragmentation
• introduced pathogens
• hybridization with nonnative species, and other
  detrimental factors

Most (if not all) of these are due to human
activity (such as habitat alteration, pollution,
overexploitation, etc).
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
11
The major objective of conservation genetics is
to preserve the existing genetic diversity as
potential for adaptation and evolution, and,
therefore, to ensure that the adaptation and
evolutionary potential of important regional tree
species are maintained. Wild species must
have available a pool of genetic diversity if
they are to survive environmental pressures ..
If this is not the case, extinction would appear
inevitable. (Otto Frankel 1983)
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
12
Key terms definition

• Genetic diversity (sensu lato) is the variety of
  alleles and genotypes present in a population,
  species or group of species.
• Genotype is the combination of alleles and genes
  in an organism.
• Phenotypic variation is the difference in
  morphology, physiology, or behavior among
  individuals of a species caused by genetic and
  environmental factors.
• Phenotype is the observed trait (physical,
  biochemical, behavioral, etc.) of an organism
  controlled by the interaction of its genes with
  the environment.

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
13
Where do we find genetic information ?
The vast majority of genetic information is
maintained in the nucleus and is reshuffled from
generation to generation. Biparental
inheritance
Genetic information is transmitted without chance
to the next tree generation. Uniparental
inheritance
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
14
Individuals within a species may vary strongly
phenotypically !
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
15
Brassica wildtype
dwarf
bushy
wrinkly
Source http//www.biochem.wisc.edu/brassicaclassr
oomgenetics/index.html
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
16
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
17
Nuclear genome in trees

• DNA content varies significantly in angiosperms
  (1000-fold size variation) and gymnosperms
  (14-fold size variation).

• Hypothetical explanation different amount of
  junk DNA (higher content of repeated DNA or
  single-copy, non-transcribed DNA).

• Number of genes presumably varies between 30.000
  und 50.000 covering 1.000 4.000 centi-Morgan.

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
18
Mitochondrial Genome

• Size varies between 200 kb and 2.500 kb, most
  often between 300 kb and 600 kb.

• characteristic large, highly variable repeats

• 40 - 50 genes (mainly for respiration)

• Recombination between repeats may form a complex
  genome (in it simpliest form a master and a
  slaves genome.

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
19
Chloroplast Genome

• Size varies between 120 (gymnosperms) and 150 kb
  (angiosperms).

• Approx. 100 to 120 genes (mainly for
  photosynthesis)

• Genes are tightly packed, large non-coding
  regions are missing.

• Order of genes is nearly identical
• among all plant species.

• Mutation rate is two up to
• threefold lesser than in the
• nuclear DNA and up to four
• times larger than in mt-DNA.

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
20
Gene What is it?
DNA sequencer
gel image
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
21
Levels of genetic organization
Gene
Text sequence
Training Workshop on Forest Biodiversity, Kualar
Lumpur, Malaysia 5-16 June 2006
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
22
Sum of genetic information 30.000 50.000 genes
(genotype)
Sum of environmental factors variation of the
site in time and space, light, water, nutrients,
etc
Phenotype
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
23
How much genotype is in phenotype?
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
24

• Organisms are different because of the
• genetic differences among individuals,
• different environments where individuals are
  growing, and
• interactions between genotypes and environments
  in which they exist.

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
25
How to separate between genetic and environmental
effects?
Common Garden Experiment
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
26
Common garden experiments

• provided insights into the adaptive variation of
  complex traits
• often geographical patterns, such as steep
  latitudinal or altitudinal clines
• time consuming and relatively expensive solely
  based on the phenotypes
• can estimate genetic parameters on measurable
  traits
• can neither provide information on what
  particular genes and how many of them are
  involved in adaptation nor how much of phenotypic
  variation can be explained by genetic variation
  in these genes

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
27
Genetic diversity

• Quantitative genetic variation (genetic
  variances)

• additive variance ( variances of the breeding
  values),
• non-additive genetic variance

• (2) Qualitative genetic diversity
• information at single gene(s) must be available

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
28

• Variation within genes
• alleles haplotypes
• Variation within individuals
• individual heterozygosity
• Variation within populations
• allele frequencies, average heterozygosity,
  average number of polymorphic alleles and loci
  and other summary statistics, effective number of
  alleles, pairwise individual genetic similarity
  or distance, etc
• Variation among populations
• differentiation and genetic distance (pairwise
  and average)

Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
29
How much genetic diversity is needed?
Darwin/MacArthurs Model
Ehrlich Ehrlichs rivet Model
Walkers driver and passenger Model
Lawtons idiosyncratic Model
Peterson et al. (1998)
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
30
How much genetic diversity is needed?
The so-called Allee effect
Oostermeijer et al. (2005)
Gentiana pneumonanthe
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia
31
By now you should know ...........
Training Workshop on Forest Biodiversity, Kuala
Lumpur, Malaysia