What is genetic diversity ? Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia Thomas...
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Transcript of What is genetic diversity ? Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia Thomas...
What is genetic diversity ?
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Thomas Geburek
Department of GeneticsFederal Research Centre for Forests, Natural Hazards,
and Landscape (BFW)
Austria
Conditions for Forest Ecosystem Stability
• Species diversity• Temporal variation• Spatial variation• Patterns of interactions
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Conditions for Forest Ecosystem Stability
• Species diversity• Temporal variation• Spatial variation• Patterns of interactions
• Genetic diversity
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
• material balance
• energy balance
• information balance
Ecosystem identity can be regarded as the totality of
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
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Noss (1990)
Biodiversity – genetic, species, and landscape level
Significance of genetic diversity
Adjustment to changing environmental conditions may be based on:
physiological adaptationinternal self-regulating mechanisms, the more
(allelic) genes the better the physiological buffer
epigenetic adaptationtriggered by environmental signals, not based on Mendelian inheritance, may regulate gene expression over generations
collective adaptationpopulation adjusts its genetic composition through evolutionary factors
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Forest trees are something special
• Longevity
• Spatial heterogeneity
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Pinus aristata
Pinus sylvestris
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
Response functions of 10 Pinus sylvestris populations
Rehfeldt et al. (2002)
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
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
The fundamental problems of plant conservation genetics are loss of genetic diversity and harmful irreversible changes in population structure
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
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
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
Genetic information is transmitted without chance to the next tree generation.
Uniparental inheritance
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
The vast majority of genetic information is maintained in the nucleus and is reshuffled from generation to generation.
Biparental inheritance
Where do we find genetic information ?
Individuals within a species may vary strongly phenotypically !
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Source: http://www.biochem.wisc.edu/brassicaclassroomgenetics/index.html
Brassica wildtype
bushy dwarf
wrinkly
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Nuclear genome in trees
• DNA content varies significantly in angiosperms (1000-fold size variation) and gymnosperms (14-fold size variation).
• Number of genes presumably varies between 30.000 und 50.000 covering 1.000 – 4.000 centi-Morgan.
• Hypothetical explanation: different amount of junk DNA (higher content of repeated DNA or single-copy, non-transcribed DNA).
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
• Recombination between repeats may form a complex genome (in it simpliest form a master and a slaves genome.
• 40 - 50 genes (mainly for respiration)
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
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
Gene: What is it?
5’ utr
3’ utr
DNA sequencer
gel image
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Levels of genetic organization
Gene Text sequence
Chromosome Chapter
Genome
Genepool
Training Workshop on Forest Biodiversity, Kualar Lumpur, Malaysia 5-16 June 2006 Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Sum of environmental factors:variation of the site in time and space,light, water, nutrients, etc
Phenotype
Sum of genetic information:30.000 – 50.000 genes (genotype)
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
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.
P = G + E + G×E
Phenotype = Genotype + Environment + Interaction
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
How to separate between genetic and environmental effects?
Common Garden Experiment
Environment
Gene
Mixture of both
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
• 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
Common garden experiments
Genetic diversity
(1) Quantitative genetic variation (genetic variances)
(2) Qualitative genetic diversity
information at single gene(s) must be available
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
additive variance ( = variances of the breeding values), non-additive genetic variance
• Variation within genes alleles & haplotypes
• Variation within individualsindividual heterozygosity
• Variation within populationsallele 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 populationsdifferentiation and genetic distance (pairwise and average)
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
How much genetic diversity is needed?
Peterson et al. (1998)
Darwin/MacArthur‘s Model Ehrlich & Ehrlich‘s „rivet“ Model
Walker‘s „driver and passenger“ ModelLawton‘s idiosyncratic Model
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia
Oostermeijer et al. (2005)
Gentiana pneumonanthe
How much genetic diversity is needed?
The so-called Allee effect
Training Workshop on Forest Biodiversity, Kuala Lumpur, Malaysia