Download What is genetic variation?

What is genetic diversity ?
Thomas Geburek
Department of Genetics
Federal Research Centre for Forests, Natural Hazards,
and Landscape (BFW)
Austria
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Conditions for Forest Ecosystem Stability
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Species diversity
Temporal variation
Spatial variation
Patterns of interactions
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Conditions for Forest Ecosystem Stability
• Genetic diversity
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Species diversity
Temporal variation
Spatial variation
Patterns of interactions
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Ecosystem identity can be regarded as the totality
of
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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.
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Biodiversity – genetic, species, and landscape level
Noss (1990)
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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
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Forest trees are something special
• Longevity
• Spatial heterogeneity
Pinus aristata
Pinus sylvestris
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
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
Rehfeldt et al. (2002)
Response functions of 10 Pinus sylvestris populations
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The fundamental problems of plant conservation
genetics are loss of genetic diversity and harmful
irreversible changes in population structure
They are resulted from:
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reduction in population size
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loss, deterioration or fragmentation of habitats
• accelerated climate change
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population and species fragmentation
•
introduced pathogens
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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).
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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)
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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.
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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
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Individuals within a
species may vary strongly
phenotypically !
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Brassica wildtype
bushy
dwarf
wrinkly
Source: http://www.biochem.wisc.edu/brassicaclassroomgenetics/index.html
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Genetic Markers
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Nuclear genome in trees
• DNA content varies significantly in angiosperms
(1000-fold size variation) and gymnosperms (14fold 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 centiMorgan.
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
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.
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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.
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Gene: What is it?
5’ utr
DNA sequencer
gel image
3’ utr
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Levels of genetic organization
Gene
Chromosome
Text sequence
Chapter
Genome
Genepool
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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
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How much genotype is in phenotype?
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P = G + E + G×E
Phenotype = Genotype + Environment + Interaction
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.
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How to separate between genetic and
environmental effects?
Common Garden Experiment
Gene
Environment
Mixture of both
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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
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Genetic diversity
(1) 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
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• 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)
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How much genetic diversity is needed?
Darwin/MacArthur‘s Model
Ehrlich & Ehrlich‘s „rivet“ Model
Lawton‘s idiosyncratic Model
Walker‘s „driver and passenger“ Model
Peterson et al. (1998)
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How much genetic diversity is needed?
The so-called Allee effect
Oostermeijer et al. (2005)
Gentiana pneumonanthe
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By now you should know
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Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia