1. Evolution of Genes and Traits
Chapter 20
Evolution of Genes and Traits
Darwinian evolution, mutations and molecular evolution, a case study in natural selection, morphological evolution; the origin of new genes and protein functions

2. Major principles of Darwinian evolution
Principle of variation—among individuals in a population, variation exists
Principle of heredity—offspring resemble parents more than unrelated individuals
Principle of selection—some forms more successful at survival and reproduction in a given environment (natural selection)
heritable variationheritable differences between populations over time

3. Diversification – the origin of new species over time
Phyletic evolution – continuous change over time in a single line of descent
Diversification – the origin of new species over time
Two patterns of evolution may occur concurrently. Phenotypes of organisms in populations may gradually change over time (phyletic evolution). Alternately, populations may fragment into new species (diversification).

4. Darwin’s Finches and Adaptive Radiation
A phylogenetic tree is a visual representation in tree form of how we think evolution has occurred, often based on fossils.
Famous example:
Galapagos finches, with numerous feeding adaptations
Finches of the Galapagos Islands are famous because of Darwin’s observations and conclusions concerning their evolution. Darwin recorded the many forms and adaptations of these finches and speculated on their relationship to mainland species. These observations comprise some of the data that Darwin used to formulate his concepts of species origins. In recent times, Darwin’s finches have been observed over a 30 year period and now, studied genetically. in this slide we see the genetic relationships of the finches as a tree. Data suggests that a single (or few) finch arrived on the Galapagos Islands and over time multiplied, colonized other islands, and radiated into new species and forms that were adapted to specific ecological niches (predominantly the kind of food that was available.) The strongest evidence of adaptation and change associated with selection pressure came relatively recently while Rosemarie and Peter Grant were studying finches on the islands. Severe food depletion resulted in death of finches with specific beak types and survival of others. This led to a change in beak configuration of the survivors within a very short period of time. The abstract of their paper is given below.
Science 14 July 2006: vol no. 5784, pp Evolution of Character Displacement in Darwin's Finches
PETER R. GRANT* and B. Rosemary GRANT
Competitor species can have evolutionary effects on each other that result in ecological character displacement; that is, divergence in resource-exploiting traits such as jaws and beaks. Nevertheless, the process of character displacement occurring in nature, from the initial encounter of competitors to the evolutionary change in one or more of them, has not previously been investigated. Here we report that a Darwin's finch species (Geospiza fortis) on an undisturbed Galápagos island diverged in beak size from a competitor species (G. magnirostris) 22 years after the competitor's arrival, when they jointly and severely depleted the food supply. The observed evolutionary response to natural selection was the strongest recorded in 33 years of study, and close to the value predicted from the high heritability of beak size. These findings support the role of competition in models of community assembly, speciation, and adaptive radiations.

5. Neo-Darwinian evolution—Darwin’s principles w/genetics, population biology

6. Different models of selection
Directional selection- pushes population toward homozygosity and phenotypes toward one extreme
Balancing selection- favors heterozygotes but maintains all phenotypes
Disruptive selection- favors both homozygotes, eliminates heterozygotes and increases extremes of phenotypes

7. Mutations and Molecular Evolution
3 different effects on fitness by mutations:
deleterious
increase efficiency or performance
no effect (“neutral”)
can be a little more specific:
effectively neutral mutationsselection intensity so low that mutation is retained
effectively selected mutationsselection high enough that mutation is weeded out

8. Mutation rate of synonymous sites higher than nonsynonymous
Synonymous changes refer to a mutation which substitutes the same amino acid
Deleterious mutations removed by purifying selection-shown by lower rate of nonsynonymous mutations
In order to estimate times of divergence using data from protein coding sequences, we need to be aware of the difference between mutations which do not cause a change in a amino acid (synonymous mutations) and mutations which do cause an amino acid substitution (nonsynonymous mutations). Mutations which cause an amino acid change, are more likely to lead to changes in protein function. Some of these changes which will be inviable and selected against leading to an apparent lower rate of nonsynonymous mutations. In the genetic code, mutations in the third base in the codon tend to be synonymous because mutations at this site often code for the same amino acid. This can easily be seen by looking at a codon chart. Mutations in bases one and two of a codon are more likely to be non-synonymous because a mutation is likely to result in a amino acid substitution. Mathematical models of evolution often consider the difference in apparent mutation rate at different codon positions.

9. MOLECULAR CLOCKS: mutations/amino acid differences can be used to estimate evolutionary divergence times
This is a graph of time since divergence of major groups. Plants and animals separated approximately 1,200 myo. Vertebrates and insects separated approximately 600 myo. Mammals radiated relatively recently. Percent change in amino acids is given on the vertical axis. The lines represent three relatively conserved genes. Cytochrome C is very conserved with a maximum of 40 changes per 100 residues in 1,200 million years. This suggests that most mutations occurring in this protein are deleterious and that selection removes them. Fibrinopeptides are much less critical and mutations in this protein are higher, suggesting that mutations are not so deleterious to the organisms and are not removed by selection. Molecular clocks must be calibrated for each gene studied.

10. Natural Selection in Action: An exemplary case
Genotypes could be measured
The genetic and molecular basis of variation was identified
The physiological role of the gene/protein was well understood
The environmental (natural) selection process was understood
We are talking about the connection between sickle cell anemia and malaria

11. Malaria Life Cycle

12. Red blood cells in someone with sickle-cell trait

13. Malarial parasites live within red blood cells

14. Electrophoresis of hemoglobin variants

15. The hemoglobin molecule

16. The first seven N-terminal amino acids in normal and sickle cell hemoglobin  polypeptides
GAG
GUG
GLU = Glutamic acid is acidic
VAL = Valine is neutral non-polar

17. Gene frequency for HbS allele high in malaria (mosquitoes-rich) zones
HbAS heterozygous are more resistant to malaria

18. Survival analysis of sickle-cell genotypes

19. Morphological evolution-melanism in rock pocket mouse (adaptive changes)

20. Morphological evolution—melanism in rock pocket mouse
Pinacate region of SE Arizona has blackish lava rock areas interspersed with pale brown rock areas
rock pocket mouse (Chaetodipus intermedius) has 2 melanic forms growing in 2 different substrates
dark form inhabits blackish areas
pale ancestral form lives in sand-colored areas
Nachman et al. found 4 mutations in melanocortin 1 receptor (MC1R) gene of dark mice, causing protein to be constitutively active and lay down pigment constantly

21. Morphological evolution—melanism in MC1R protein of organisms

22. Peppered Moths in Great Britain
The well-known example of the peppered moth in Great Britain following the industrial revolution shows how gene frequencies in populations can change under selective pressure. Before the industrial revolution, trees in Great Britain were light-colored and covered with lichens. In this habitat, the peppered moth light form is hidden visually from predators ( bottom panel) and was the dominant form within the population. The Industrial Revolution produced severe air pollution that killed lichens and turned trees black. In this environment, the dark form of the peppered moth had a selective advantage and appeared in the moth population at higher and higher frequencies until virtually all moths were black. When air pollution controls were instituted, trees again became lighter in color and once again the light form of the peppered moth had a selective advantage in terms of predation and became the dominant form within the population. These observations show that selective pressures acting on populations can change allele frequencies within that population.

23. Morphological evolution-evolution of albinism in blind cave fishes (gene inactivation)

24. Morphological evolution—albinism in blind cave fishes
albinism common in cave organisms (incl. fishes, crustaceans), often accompanied by eye loss
genetic studies of Mexican blind cave fish (Astyonax mexicanus) in 2 different populations, Pachón and Molino, revealed different mutations in Oca2 gene—gene inactivation
Pachón fishes are homozygous for deletion of intron and most of exon in Oca2 gene

25. Morphological evolution-wing spots on fruit flies (regulatory sequence evolution)
Drosophila melanogaster
Drosophila biarmipes

26. Origin of New Genes
New genes and proteins necessary for wholly new functions and processes
Sources of new genes/DNA:
Polyploidy-duplicate genomes can diverge
Gene duplications-duplicated genes can diverge
Transposition (transposable elements)
Retrotransposition (retrotransposons)
Imported DNA from organelles or horizontal gene transfer

27. The alternative fates of duplicated genes

29. Final Thoughts
The one process now going on that will take millions of years to correct is the loss of genetic and species diversity by the destruction of natural habitats. This is the folly our descendants are least likely to forgive us. --E. O. Wilson
It's an important point to realize that the genetic programming of our lives is not fully deterministic. It is statistical - it is in any animal merely statistical - not deterministic. --Richard Dawkins
If you liked genetics (PBIO 3300/5300), consider taking biotechnology and genetic engineering (PBIO 4500/5500) in the fall. –Allan Showalter