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

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A species concept for bacteria based on adaptive divergence.

¹Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6666 GA Heteren, The Netherlands. michiel.vos@nioo.knaw.nl

Trends in Microbiology

|November 13, 2010

Summary

Bacterial species classification needs revision. This review proposes defining species by statistically significant adaptive divergence, aiding evolutionary understanding and identifying speciation processes.

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Area of Science:

Microbiology
Evolutionary Biology
Genomics

Background:

Current bacterial species classification relies on polyphasic taxonomy, which lacks evolutionary grounding and uses arbitrary boundaries.
Multilocus sequence typing (MLST) identifies phylogenetic clusters but struggles to define taxonomic levels for distinct evolutionary units.

Purpose of the Study:

To propose a revised species concept for bacteria based on evolutionary principles.
To introduce adaptive divergence as a criterion for species demarcation.
To explore the utility of adaptive divergence in reverse ecology.

Main Methods:

Review of current bacterial taxonomy and phylogenetic clustering methods.
Proposal of a new species definition based on statistically significant adaptive divergence.
Discussion of the application of adaptive divergence in identifying speciation events and adaptive genes.

Main Results:

Adaptive divergence offers a theoretically grounded method for bacterial species classification.
This concept addresses the arbitrary nature of current species boundaries.
It provides a framework for identifying lineages undergoing speciation.

Conclusions:

Classifying bacterial species should be based on statistically significant adaptive divergence.
The adaptive divergence concept enhances evolutionary understanding of bacterial diversity.
It facilitates a 'reverse ecology' approach to study bacterial evolution and speciation.