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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Eradicating typological thinking in prokaryotic systematics and evolution.

W F Doolittle¹

¹Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada B3H 1X5. ford@dal.ca

Cold Spring Harbor Symposia on Quantitative Biology

|August 12, 2009

Summary

This summary is machine-generated.

Prokaryotic evolution still relies on outdated typological thinking. Embracing population thinking and acknowledging widespread genetic transfer is key to a modern evolutionary synthesis for microbiology.

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Area of Science:

Evolutionary biology
Microbiology
Genomics

Background:

John Maynard Smith called for a "New Synthesis" for prokaryotic evolution in 1982.
Typological thinking, antithetical to population thinking, still dominates microbiology.
Debates persist regarding prokaryotic species, the term "prokaryote," and the "tree of life" (TOL).

Purpose of the Study:

To argue for the adoption of population thinking in microbiology.
To demonstrate how interlineage genetic transfer necessitates a re-evaluation of core evolutionary concepts for prokaryotes.
To advocate for discarding reified concepts like "species," "domains," and the "TOL" in light of genomic data.

Main Methods:

Analysis of evidence from phylogenomics.
Examination of ongoing debates in prokaryotic taxonomy and evolutionary history.

Main Results:

The prevalence of interlineage genetic transfer challenges traditional taxonomic and phylogenetic frameworks.
Concepts such as "species," "domains," and the "tree of life" are identified as reifications.
Genomics and metagenomics provide data that dissolves these traditional constructs.

Conclusions:

The field of microbiology requires a "Darwinization" through the adoption of population thinking.
The concepts of "species," "domains," and the "TOL" are unnecessary and hinder evolutionary understanding.
A modern synthesis for prokaryotic evolution must account for pervasive horizontal gene transfer.