Introduction to Evolution (Biological!) and Evolvability General - PowerPoint PPT Presentation

Introduction to Evolution (Biological!) and Evolvability General Principles of Evolution Adaptive vs Non-adaptive selection Conservation, Constraints and Convergence Examples Mutation/Selection/Evolution in Bacterial Systems Mutation/Repair Horizontal Transfer Induced Mutagenesis Eukaryotic Evolution in Real time Darwin’s Finches HSP90- Development and Evolution DNA Shuffling / In Vitro Evolution

Evolution: a process in which the gene pool of a population gradually changes in response to environmental pressures, natural selection, and genetic mutations. Evolvabilty: the capacity of an organism to evolve Niche: the ecological ‘environment occuppied by a species Evolution is generally thought as the progression from simple to complex but this is not necessarily true. e.g. Host- parasite interactions / symbiotic relationships

Speciation: the process giving arise to new species, usally through splitting of lineages (geographic/ temporal isolation, reproductive isolation). The ‘key element of evolution’. Adaptive evolution: Selection for a modification of a species that makes it more fit for reproduction and/or existence under the conditions of its environment . Natural Selection e.g Darwin’s finches Non-adaptive evolution: Selection for a modification of a species that is selected but is not immediately tied to fitness. e.g. Cichlid fishes of Lake Victoria

Darwin’s Finches A group of finches that are found on the Galapogas Islands that have evolved from a single species of finch that colonized the islands approximately 0.5-1 million years ago. That have evolved into 14 present day species that occupy a vaiety of niches on the islands. They are not the best example of adaptive radiation but they are of historical interest because * Darwin was the first to descibe their behavior in detail and collect samples. Also from the work of Peter and Rosemary Grant over the past few decades have described the evolution of a vertebrate species within this group * woodpecker finch evolve tool use in order to take advantage of the niche usually occupied by woodpeckers.

Cichlid Fish of Lake Victoria • over 200 species have evolved in the past 750,000 years • many by adaptive evloution based on food sources (e.g. fish, zooplankton, mollucs,algae, fish scales) • some clusters have evolved based on mate selection, differing only in the color of the male fish (non-adaptive)

Morphological diversification in metazoans is not reflected in the underlying cellular/molecular mechanism for generating diversification. Morphological diversity arises from cellular diversity but the underlying language and devices are the same. i.e - there is conservation at the molecular level. - signal transduction (sensing / repsonding to the environment including other cells - cytoskeletal scaffolds that can generate diversity at the cell level - haploid genomes (single copy of genes) limits mutational space that can sample - Cambrian “explosion” -

The Cambrian Explosion / The Burgess Shale An explosion in the diversity in metazoan body plans exemplified by the bizarre world of the Burgess Shale (Yoho National Park).

The evolution of the Roman arch requires many elements of the door to be individually modified- specialization. Roman arch The evolution of the Mayan arch requires only the rearrangement of the existing parts - temporal and spatial modifications. Mayan arch The St. Louis arch is constructed from entirely new technologies. St. Louis arch from Gerhart and Kirscher 1997

Evolution at the cellular levels ustilizes all three types of mechanisms however the “Mayan arch” strategy is used predominantly. Conserved building blocks used to build novel structures- modularity in design There are constraints imposed by using conserved blocks - i.e. they are embedded in other processes (gene duplication)

Morphological convergence - similar structure have evolved independently. This can be only at the functional level or at both a functional and morphological level. from Gerhart and Kirscher 1997

GeneralProblems when thinking about evolution: • defining niche (ecological) • defining fitness / fitness landscapes • defining species reproductive vs geographic isolation bacteria • time scales make experimentation difficult/impossible with vertebrates Evolution is a balance between stability and variability.

Mutation, Selection and Evolution in Bacterial Systems The balance between variability and stability

Mutagenesis at the sequence level Spontaneous error rate of replication Mutagens (environmental, metabolic byproducts) Inducible ‘mutations’ - mutational hotspots - error prone replication DNA rearrangements Recombination (minimal in most bacteria because of single copy chromosome)

Phase Variation: reversible changes in expression patterns that are due to ‘reversible’ geneotypic changes Switching frequencies can differ in each direction

DNA Acquisition: - conjugation - plasmids - transposons (jumping genes) - integrating bacteriophage - ‘other’ mechanisms In contrast to sequence mutations, DNA acquisition mechanisms involve intact genes and functional units. e.g. antibiotic resistance, toxin production , pesticide degradation

Mutation Rates – set the rate of variability For E. coli 5 x 10 -10 mutations per bp per replication 0.0025 mutations per genome per replication In 1 ml of culture 10 9 cells 2.5 x10 6 mutations 500 mutations per gene These rates of spontaneous mutation differ between organisms (even between bacteria)- this is a ‘selected’ phenotype.

Mutation Rates – set the rate of variability The basal rate of mutation in the absence of environmental mutagens is set by the fidelity of replication, rate of chemical mutation of DNA and the ability or efficiency of DNA repair systems in the bacteria. Many bacteria can alter their mutation rates – I.e. they have some genetic control of their ‘Evolvability’. Bacteria can control the fidelity of replication and the ability or efficiency of DNA repair systems * in the bacteria – in stressful conditions, the mutagenesis rate increases: they accelerate their own evolution. * - decrease in repair efficiency also facilitates ‘horizontal gene transfer’

Eukaryotic Evolution in Real time Darwin’s Finches - within approximately 10 years of extreme drought, a population of finches evolved that was morphologically distinct from the ‘founding population’ -small populations/bottlenecks - what does this say about the plasticity/evlovability of Darwin’s finches? - can this be generalized? ( The Beak of the Finch : A Story of Evolution in Our Time. Jonathan Weiner (1995)) HSP90- Development and Evolution in Drosophila

Hsp90 as a capacitor for morphological evolution Suzanne L. Rutherford*† and Susan Lindquist* Nature 396, 336 - 342 (1998) ‘heat shock proteins’ - assist in protein folding and degradtion of denatured proteins in the cell (coping with stresses) Hsp90 - an unusual ‘heat shock protein’ that seems to be dedicated to signal transduction proteins that are involved in the cell cycle and development

Observation: In strains with mutant Hsp90 alleles morphological abnormalities arise with high frequency (1-2% of the progeny). This can be mimicked by adding Hsp90 inhibitors to the food supply.

The spontaneous appearance of these developmental abnormalities result from abnormal Hsp90 function. Why? 1) Mutants may be more sensitive to environment and subtle variability in microenvironments of the developing embryos maylead to the observed phenotypes. 2) Hsp90 may be involved in DNA repair and these Hsp90 alleles may have higher mutation rates 3) ‘cryptic’ genetic variability might be expressed to a greater extent i.e. Hsp90 may normal act to suppress genetic variation in several developmental pathways.

Normal Conditions instability Unfolded ‘Folded’ active Inactive protein Protein Refolding by Hsp90 The cell-cell and developmental signal transduction proteins are naturally unstable and the role of Hsp90 is to keep them in their active conformation.

Stress Conditions instability Unfolded Inactive ‘Folded’ active Protein protein Refolding by Hsp90 Denaturation Refolding by Hsp90 Under stress conditions, Hsp90 is recruited in the folding of other proteins and can not maintain sufficient quantities of its normal substrates and development is compromised

Silent polymorphisms exist in the population that become ‘expressed’ under conditions of stress . Natural populations of fruit flies have a ‘reserve’ of diversity that can be explored under conditions of stress. Under conditions of stress, Hsp90 becomes overwhelmed with stress- damaged proteins and consequently there is insufficient ‘Hsp90 activity’ to maintain its normal substrates in a functional mode. (Threshold) similar situation in Neiserria?

Robustness and Evolvability Robustness . Stability of a phenotypic property to changes in parameters giving rise to that phenotype. Evolvability . The ability to evolve new functions. 1. Robustness seems to be a feature of many biochemical/genetic networks They are stable with respect to perturbations (genetic, environmental) 2. Robustness and evolvability appear to be contradictory. stability is the opposite of evolution 3. How can one select for “Evolvability”? i.e. selecting for a phenotype that will appear in the future.