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  • #1: CAM: An alignment-free method to recover phylogenies using codon aversion motifs

    • Submission

       

      Authors: Justin Miller, Lauren McKinnon, Michael Whiting, Perry Ridge

      Molecular Phylogenetics and Evolution

       

      Submitted: June 18, 2018

      Currently Under Review

    • Novelty of Approach

       

      -CAM uses codon aversion motifs to recover phylogenies without aligning genes.

       

       

       

       

       

    • Results

       

      -CAM is comparable to maximum likelihood in many instances.

      -Partial gene annotations do not significantly affect the recovered phylogeny.

      -We analyzed 229,742,339 genes from 23,428 species across all kingdoms of life.

       

    • Unique Tuples in Each Taxonomic Group

       

       

       

    • Comparison to Reference Phylogenies

      Comparison to Open Tree of Life

      Comparison to NCBI Taxonomy

    • CPU Runtime

      Taxonomic Group CAM Amino Acid Motifs FFP Maximum Likelihood
      All 17.279 20.2692 3.907 N/A
      Archaea 0.0667 0.1436 0.041 161.5
      Bacteria 14.699 17.4458 3.744 N/A
      Fungi 0.0783 0.2167 0.029 199.75
      Invertebrates 0.0763 0.2126 0.045 2.5
      Plants 0.0781 0.2211 0.038 6
      Protozoa 0.0287 0.0833 0.018 4
      Mammals 0.0718 0.2101 0.029 2.5
      Other vertebrates 0.0872 0.2356 0.032 6.75
      Viruses 0.1028 0.1161 0.102 N/A

  • #2: Codon Use and Aversion is Largely Phylogenetically Conserved Across the Tree of Life

    • Submission

       

      Authors: Justin Miller, Lauren McKinnon, Michael Whiting, Perry Ridge

      Molecular Phylogenetics and Evolution

       

      Submitted: July 23, 2018

      Currently With Editor

    • Novelty of Approach

       

      -Analyzes codon conservation in different taxonomic groups

      -Provides a statistical means to identify non-random parsimony informative characters

      -Describes the breadth of complete codon aversion throughout the Tree of Life

       

    • Results

       

       

      -Codon usages are 1,109x more likely than random to follow the Open Tree of Life.

      -We analyzed 890,814 codons from 12,337 species across all kingdoms of life.

      -We confirm turtles as sister taxa to archosaurs.

      -We provide a framework to analyze codon usages against any phylogeny.

       

       

    • Implications

       

      -Statistical approach can be used on any character

      -Shows that complete codon aversion is maintained through evolutionary time

      -Provides a method to test different tree hypotheses

       

    • Very Unlikely Character State Distributions

    • Statistical Evaluation of Taxonomic Groups