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Updated: Dec 15, 2025

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

The genomic view of diversification.

Julie Marin¹, Guillaume Achaz^1,2,3, Anton Crombach^1,4,5

¹Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.

Journal of Evolutionary Biology

|July 13, 2020

Summary

Conflicts in gene trees can reveal species diversification. New gene-based diversification models (GBD) account for gene flow, outperforming the traditional multispecies coalescent (MSC) model in analyzing complex evolutionary histories.

Keywords:

coalescent theory gene flow gene tree gene-based diversification model introgression multispecies coalescent phylogeny population genetics speciation species tree

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Last Updated: Dec 15, 2025

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

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Evolutionary Biology
Genomics
Phylogenetics

Background:

Species diversification is often simplified to a single species tree.
Reconstructing species trees from molecular data is challenging due to conflicting gene genealogies.
Gene flow between diverging lineages is a common cause of these conflicts.

Purpose of the Study:

To propose a new framework that models the joint evolution of gene and species lineages.
To challenge the traditional view of a strict hierarchy between species and gene trees.
To develop gene-based diversification (GBD) models that incorporate gene flow.

Main Methods:

Developed two gene-based diversification (GBD) models: GBD-forward and GBD-backward.
These models relax the hierarchy inherent in the multispecies coalescent (MSC) model.
Proposed an inference method utilizing differences between gene trees.

Main Results:

The GBD models feature parameters for colonization, gene flow, genetic drift, and genetic differentiation.
Applied to empirical data sets, the GBD-backward model showed better support than the MSC model.
Demonstrated that gene flow significantly impacts the accuracy of phylogenetic reconstruction.

Conclusions:

Gene conflicts should be viewed as informative signals of diversification processes, not just noise.
Gene-based diversification models offer a more comprehensive approach to understanding evolutionary history.
Highlight the importance of considering genomic histories beyond the traditional species tree.