Molecular Evolution

A. The structure and function of molecules can change over time.

B. Hypothesis of neutral evolution

1. most changes in molecular structure that persist in lineages do not affect molecular function
2. neutral substitutes accumulate at a rate that is approximately equal to the mutation rate (natural selection does not affect this rate)
3. amino acid sequence of insulin
a. very similar (but not identical) among mammal species
b. certain regions vary; others usually don't
c. in some cases, insulin from one species can function in another
4. amino acid sequence of cytochrome c

C. Exons and introns

1. exons only - most prokaryotes
2. exons and introns - eukaryotes

D. Gene duplication and gene families

1. Gene families are sets of genes that share a common origin
2. Genes in gene families are very similar to one another
3. Gene duplication lens to the existence of gene families
a. accidents during crossing over
b. transposable elements
4. Gene families may include pseudogenes that do not function
5. When a gene is duplicated, the new copy is free to evolve a new function, because the old copy is already carrying out the required function.
6. globin gene families in humans
a. my globin family
- one gene
- on chromosome 22
- codes for myoglobin, which binds to O2 in muscle
b. alpha globin family
- 3 genes, 2 pseudogenes
- on chromosome 16
- code for components of hemoglobin, which binds O2 in blood
c. beta globin family
- 5 genes, 1 pseudogene
- on chromosome 11
- code for components of hemoglobin
d. hemoglobin consists of 2 alpha polypeptides and 2 beta polypeptides
e. different alpha and beta genes are expressed at different times in development

E. Interspecific variation in genome size

1. There is a general trend for larger, more complex organisms to have larger genomes (e.g., prokaryotes vs. eukaryotes)
2. But there are many exceptions to his observation.
3. examples
a. most prokaryotes have one circular chromosome and sometimes a tiny additional bit of DNA
b. diploid number (2n) in eukaryotes varies between 2 and >1200
- Penicillium (2n = 2)
- fruit fly (2n = 8)
- human (2n = 46)
- chimpanzee (2n = 48)
- dog (2n = 78)
- adder's tounge fern (2n = 1262)
4. Ife we just consider the coding DNA, disparity in genome size makes more sense (i.e., in general more complex organisms have more coding DNA).

F. molecular clocks

1. can use DNA, proteins
2. mutation rate must be estimated
a. compare the same molecule in two species - how many differences?
b. use fossil record or geologic history to estimate when the two species diverged
c. provides relationship between number of differences in molecule time
3. Once the rate at which a given molecule's clock ticks is estimated, any two species can be compared and their divergence time estimated.
4. Why does it work? Most mutations are neutral. (see above)
5. problem - selection changes the clock's rate; solutions - look at more than one molecule; interpret results with caution
6. problem - different molecules "tick" at different rates; solution - each molecule's rate must be determined independently
7. When making inferences about the past, the more information the better.

G. phylogenetic reconstruction

1. different molecules are suitable for different problems
a. e.g., relationships within a genus - use a relatively fast, evolving gene or protein
b. e.g., relationships among classes - use a relatively slow-evolving gene or protein
2. it is sometimes possible to extract DNA from fossils (Table 23.1 in text)
a. small fragments, not the entire genome
b. we can't reproduce extinct organisms by using this DNA (sorry, no Jurassic Park)

H. Mapping and sequencing genes

1. Human Genome Project
2. Caenorhabditis elegans (a nematode)
a. model organism (development, population genetics, etc.)
b. ca. 1 mm long
c. consists of 959 somatic cells
d. all genes have been mapped and sequenced