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Standard Candles for Dating Microbial Lineages.

Gregory P Fournier1, Chris W Parsons2, Elise M Cutts2

  • 1Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. g4nier@mit.edu.

Methods in Molecular Biology (Clifton, N.J.)
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Molecular clock dating for microbes is difficult. New "substrate standard candles" use eukaryote-derived substrates to estimate microbial evolution times, improving phylogenetic analyses.

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Area of Science:

  • Microbial Phylogenetics
  • Evolutionary Biology
  • Molecular Evolution

Background:

  • Molecular clock analyses for microbial phylogenies are hindered by a lack of reliable fossil calibrations for absolute time constraints.
  • Horizontal gene transfer of proteins for eukaryote-derived substrate utilization offers an alternative dating approach.

Purpose of the Study:

  • To formally develop and describe the concept of "substrate standard candles" for microbial molecular clock dating.
  • To demonstrate how these standard candles can be applied to microbial species trees and gene family phylogenies.

Main Methods:

  • Utilizing the inheritance of proteins specific for animal, algal, and plant-derived substrates as temporal anchors.
  • Applying these "standard candles" to estimate divergence times in microbial groups across the Tree of Life.
  • Evaluating the suitability of candidate standard candles considering their evolutionary and metabolic histories.

Main Results:

  • The study formally develops the "substrate standard candle" concept for microbial dating.
  • Methods for propagating and applying these candles to microbial phylogenies are described.
  • Evaluations of candidate standard candles highlight their potential and complexities.

Conclusions:

  • Substrate standard candles provide a novel and powerful approach to overcome limitations in microbial molecular clock dating.
  • This method expands the scope of informative molecular clock investigations for microbial evolution.
  • Careful consideration of evolutionary and metabolic histories is crucial for accurate application.