Phylogentic Trees

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12 Terms

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Estimating phylogenetic trees

Ways

  • DNA replication: undergoes mutation

  • Substitution: mutation that is fixed in the population

Ex. Simplest measure of sequence divergence: proportion of nucleotide sites in which 2 sequences are different


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Comparing phylogenetic data

  1. sample DNA/RNA locus (specific physical location) of a homologous gene from organisms of interest

  2. Recall that a homologous gene is a gene inherited by a common ancestor

  3. Construct an “alignment” of the sequences (list each vertical column as a homologous nucleotide site)

  4. After alignment, we can calculate the number of nucleotide differences between pairs of sequences


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No

Are the number of nucleotide differences the same as the actual number of nucleotides that have changed during evolution?

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Nucleotide

Many instances where the number of actual substitutions does NOT equal the number of ______ differences between taxa

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Single substitution

1 change, 1 difference

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Multiple substitution

2 changes, 1 difference

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Coincidental substitution

2 change, 1 difference

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Parallel substitution & back substitution

2 changes, no difference

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Convergent substitution

3 changes, no difference

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Models of molecular evolution

  • mathematical models of nucleotide substitution are necessary to model evolution and estimate phylogenies from sequence data


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Bootstrapping methodology

Original dataset → replicates (rearranged data many different times)

  • each time a tree is created , some parts of tree are reproduced (no matter rearrangements, we still get “this” relationship)

  1. Create pseudo-replicates (datasets) usually 1000 times

  2. For each pseudo-dataset, a tree is created

  3. The trees are tabulated, calculate how often parts of that tree show up

  4. From tabulated results (percentages), a consensus tree is built

“Proportional of differences”


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Bayesian statistics

  • Bayesian methods also increase estimations of confidence measures

  • Many trees are generated

  • Posterior (Bayesian) probabilities: from 0 to 1 (measures the confidence level that a particular clade is monophyletic)

    • 1 is most confident

  • Bootstrap proportions: range from 0 to 100