Introduction to Evolution (Biological!) and Evolvability

General Principles of Evolution Adaptive vs Non-adaptive selectionConservation, Constraints and ConvergenceExamples

Mutation/Selection/Evolution in Bacterial SystemsMutation/RepairHorizontal TransferInduced Mutagenesis

Eukaryotic Evolution in Real timeDarwin’s FinchesHSP90- Development and Evolution

DNA Shuffling / In Vitro Evolution

Evolution: a process in which the gene pool of a populationgradually changes in response to environmental pressures, naturalselection, and genetic mutations.

Evolvabilty: the capacity of an organism to evolve

Evolution is generally thought as the progression from simple tocomplex but this is not necessarily true.

e.g. Host- parasite interactions / symbiotic relationships

Niche: the ecological ‘environment occuppied by a species

Speciation: the process giving arise to new species, usallythrough splitting of lineages (geographic/ temporal isolation,reproductive isolation). The ‘key element of evolution’.

Adaptive evolution: Selection for a modification of a speciesthat makes it more fit for reproduction and/or existence under theconditions of its environment. Natural Selectione.g Darwin’s finches

Non-adaptive evolution: Selection for a modification of aspecies that is selected but is not immediately tied to fitness.e.g. Cichlid fishes of Lake Victoria

Darwin’s Finches

* woodpecker finch

*

evolve tool use in order to take advantage ofthe niche usually occupied by woodpeckers.

A group of finches that are found on theGalapogas Islands that have evolved from a singlespecies of finch that colonized the islandsapproximately 0.5-1 million years ago.

That have evolved into 14 present dayspecies that occupy a vaiety of niches on theislands. They are not the best example of adaptiveradiation but they are of historical interest becauseDarwin was the first to descibe their behavior indetail and collect samples. Also from the work ofPeter and Rosemary Grant over the past fewdecades have described the evolution of avertebrate species within this group

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, differingonly in the color of the male fish (non-adaptive)

Morphological diversification in metazoans is not reflected in the underlyingcellular/molecular mechanism for generating diversification.

Morphological diversity arises from cellular diversity but the underlyinglanguage and devices are the same. i.e - there is conservation at the molecularlevel.

- 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 inmetazoan body plans exemplified by thebizarre world of the Burgess Shale(Yoho National Park).

Roman arch

Mayan arch

St. Louis archfrom Gerhart and Kirscher 1997

The evolution of the Roman arch requiresmany elements of the door to be individuallymodified- specialization.

The evolution of the Mayan arch requiresonly the rearrangement of the existing parts -temporal and spatial modifications.

The St. Louis arch is constructed from entirelynew technologies.

Evolution at the cellular levels ustilizes all three types ofmechanisms however the “Mayan arch” strategy is usedpredominantly.

Conserved building blocks used to build novelstructures- modularity in design

There are constraints imposed by using conservedblocks - i.e. they are embedded in other processes (geneduplication)

Morphological convergence - similar structure have evolvedindependently. This can be only at the functional level or at both afunctional 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 isolationbacteria

• 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 mechanismsinvolve 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 replication0.0025 mutations per genome per replication

In 1 ml of culture 109 cells2.5 x106 mutations500 mutations per gene

These rates of spontaneous mutation differ between organisms (evenbetween 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 setby the fidelity of replication, rate of chemical mutation of DNA and theability or efficiency of DNA repair systems in the bacteria.

Many bacteria can alter their mutation rates – I.e. they have some geneticcontrol of their ‘Evolvability’.

Bacteria can control the fidelity of replication and the ability or efficiency ofDNA repair systems* in the bacteria – in stressful conditions, themutagenesis 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 fromthe ‘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 evolutionSuzanne L. Rutherford*† and Susan Lindquist*

Nature 396, 336 - 342 (1998)

‘heat shock proteins’ - assist in protein folding and degradtion ofdenatured proteins in the cell (coping with stresses)

Hsp90 - an unusual ‘heat shock protein’ that seems to be dedicated tosignal transduction proteins that are involved in the cell cycle anddevelopment

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

The spontaneous appearance of these developmental abnormalitiesresult from abnormal Hsp90 function.

Why?

1) Mutants may be more sensitive to environment and subtlevariability in microenvironments of the developing embryos mayleadto the observed phenotypes.

2) Hsp90 may be involved in DNA repair and these Hsp90 allelesmay have higher mutation rates

3) ‘cryptic’ genetic variability might be expressed to a greater extenti.e. Hsp90 may normal act to suppress genetic variation in severaldevelopmental pathways.

‘Folded’ activeprotein

instability

Refolding by Hsp90

UnfoldedInactiveProtein

Normal Conditions

The cell-cell and developmental signal transduction proteins arenaturally unstable and the role of Hsp90 is to keep them in theiractive conformation.

‘Folded’ activeprotein

instability

Refolding by Hsp90

UnfoldedInactiveProtein

Refolding by Hsp90

Stress Conditions

Denaturation

Under stress conditions, Hsp90 is recruited in the folding of other proteinsand can not maintain sufficient quantities of its normal substrates anddevelopment 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 beexplored 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. Stability of a phenotypic property to changes in parameters givingrise to that phenotype.

Evolvability. The ability to evolve new functions.

1. Robustness seems to be a feature of many biochemical/genetic networksThey 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.

Robustness and Evolvability

The example of chemotaxis:

Tumble frequencySteady-State Tumble Frequency

Adaptation TimeAdaptation precision

Adaptation precision (i.e. exact adaptation) is Robust

Adaptation time is very sensitive to parameters

Adaptation Time

TumbleFrequency

“normal’parameters

Robustness in chemotaxis

Adaptation Time

TumbleFrequency

Robustness in chemotaxis

“normal’parameters

Parameter spacewhere precise

adaptation works

Parameter spacewhere precise

adaptation fails(non-chemotactic)

Adaptation Time

TumbleFrequency

Robustness in chemotaxis

“normal’parameters

Parameter spacewhere precise

adaptation works

Parameter spacewhere precise

adaptation fails(non-chemotactic)

Robustness facilitates evolution within the network- i.e. lets thenetwork explore behavioral space

DNA Shuffling: a single gene or multiple genes are cleaved into fragmentsand recombined creating a population of novel gene sequences. The novel genescreated by DNA Shuffling are then selected for one or more desiredcharacteristics. This selection process yields a population of genes whichbecomes the starting point for the next cycle of recombination.

In Vitro Evolution In Silico Evolution DNA Shuffling Genetic Algorthims

Generate mutants or natural variants

Fragment randomly into smaller peices

Reassemble

repeat

selectionNote that assemblyis ordered.

Some applications of DNA shuffling

Target enzyme Target Change ApproachFunction effected

Kanamycin thermostability >200X mutator strain resistance

subtilisin E activity in organic ~ 170-fold error-prone PCRsolvents

b-lactamase enzyme activity >32,000X DNA shuffling

b-galactosidase enzyme activity >1000X specificity DNA shuffling > 66X activity

arsenate pathway arsenic resistance 12X increase DNA shuffling(detoxification)

References:

Cells, Embryos and Evolution. J. Gerhart and M. Kirschner. BackwellScience Press. (1997)

What Evolution Is? Ernst Mayr Basic Books (2001)

Ecology and Evolution of darwin’s Finches. P.R. Grant. Princeton University Press(1986).

The Beak of the Finch : A Story of Evolution in Our Time. Jonathan Weiner (1995)