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This course will cover statistical problems in population genetics and molecular evolution with an emphasis on coalescent theory.
Pauling and Zuckerkandl began their investigations of molecular evolution with the reasonable expectation that species with a relatively recent common ancestor should have relatively few differences when their amino acid sequences for a particular protein are compared.
Recent miRNA haplotypes were derived directly or indirectly from ancestral haplotypes, lost or potential original miRNA haplotypes by molecular evolution with random genetic drift.
Recently, molecular evolution with progression and to some degree heterogeneity between tumors in individual patients has been described [ 32].
ML analysis was carried out using PHYML v2.4.4 [ 35] under the HKY+Γ model of molecular evolution with four substitution rate classes with 500 bootstrap replicates.
The expected values for replacements were calculated on the basis of the computer simulation of cyclin molecular evolution with the package INDELible 1.03 [ 66].
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In addition to questions in speciation, we are broadly interested in molecular evolution within species, again with a particular focus on the effects of recombination.
A formal investigation of molecular evolution within these species (with a proper outgroup) would place selection pressure relative to species divergence.
To investigate whether rates of molecular evolution fit with a strict molecular clock model, the likelihood of the ML phylogeny was recalculated with the constraint of global molecular clock using the Rambaut parameterization for clock optimization implemented in PAUP4b10 [58].
To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection.
Molecular evolution associated with yeast display is a powerful strategy for antibody affinity maturation.
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