Jan 4, 2016

Statistical Evidence for Common Ancestry: Testing for Signal in Silent Sites

BioRxiv : the Preprint Server for Biology
Martin BontragerDavid Baum

Abstract

1. The common ancestry of life is supported by an enormous body of evidence and is universally accepted within the scientific community. However, some potential sources of data that can be used to test the thesis of common ancestry have not yet been formally analyzed. 2. We developed a new test of common ancestry based on nucleotide sequences at amino acid invariant sites in aligned homologous protein coding genes. We reasoned that since nucleotide variation at amino acid invariant sites is selectively neutral and, thus, unlikely to be due to convergent evolution, the observation that an amino acid is consistently encoded by the same codon sequence in different species could provide strong evidence of their common ancestry. Our method uses the observed variation in codon sequences at amino acid invariant sites as a test statistic, and compares such variation to that which is expected under three different models of codon frequency under the alternative hypothesis of separate ancestry. We also examine hierarchical structure in the nucleotide sequences at amino acid invariant sites and quantified agreement between trees generated from amino acid sequence and those inferred from the nucleotide sequences at amino acid invariant sit...Continue Reading

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Mentioned in this Paper

Trees (plant)
Phylogenetic Analysis
Site
Codon Genus
Codon (Nucleotide Sequence)
Primates
Nucleotides
Structure
Base Sequence
Species

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