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Molecular Phylogenetics Continued.docx

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Boston College
BIOL 3150

• Construction of any phylogenetic tree requires use of an outgroup (a homologous character that is less likely related to the group being compared) to establish root of tree • External node represents a character being compared and internal node represents the corresponding ancestral character o Length of branches show degree of differences • Agene tree may look different form a species tree due to different assumptions regarind their internal nodes • Molecular clocks: using a known time (ex. Fossil record) to calibrate the mutation rate so as to assign time to branch points in a gene tree o Molecular clock has to run at a constant rate in both species being compared • Sequence alignment done with BLAST or Clustal • Dot matrix technique provides an intuitive visual output for sequence alignment: a correct alignment forms a continuous dotted line w/ broken points corresponding to point mutations and shifting lines to indels • Simple approach before gene tree building was to convert differences in nt between pairs of gene sequences for a given gene into evolutionary distances using a distance matrix o Distance: number of nt differences between two sequences over total length • Extant ancestral sequences or sequences that are products of recombination could complicate standard tree reconstruction approach • Differ
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