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Stochastic mutations that do not cause disease phenotype are neutral. Polymorphisms help map when species separated.
Genetic drift, founder's effect, and bottleneck effect can have dramatic affect on small populations.
Usage of molecular gene sequences to learn about prokaryotic diversity. Use environmental rRNA gene libraries to determine the number of different types of genes in the specific environment.
Use fluorescent phylogenetic probes that are complementary to signature sequences in the rRNA. Collect microbial cells from the environment and try to hybridize the probe.
Bacteria and archaea - compact genomes, large genetic diversity, lateral gene transfer; eukarya - larger genomes, exons, "repeated sequences".
Compare genomes of various species to reveal functionally essential genes, exons, promoters, and other regulatory elements.
Use of mitochondrial DNA and Y chromosome to establish relatedness and evolutionary tree.