#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