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A Practical Guide to Phylogenetics for Nonexperts

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Multi-model approaches to phylogenetics: Implications for idealization.

¹Boston University Department of Philosophy, 745 Commonwealth Ave, Boston 02215, Massachusetts, USA. Electronic address: http://www.ajawatkins.org.

Studies in History and Philosophy of Science

|November 12, 2021

Summary

This summary is machine-generated.

Phylogenetic models are evolving beyond simple trees to include reticulate structures, reflecting complex evolutionary events like gene transfer. This study proposes reconciling genealogical discordance to better understand life

Keywords:

Genealogical discordance Hybridization Idealization Lateral gene transfer Phylogenetics

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Area of Science:

Evolutionary Biology
Phylogenetics
Philosophy of Science

Background:

Traditional phylogenetic models assume a strictly-branching tree structure for life's history.
Increasing evidence shows that evolutionary events like lateral gene transfer, endosymbiosis, and hybridization create reticulate (non-tree-like) patterns.
This necessitates the development of phylogenetic models that can accommodate reticulate structures.

Purpose of the Study:

To propose and explore methods for incorporating reticulate structures into phylogenetic models.
To utilize the reconciliation of genealogical discordance as a tool for understanding evolutionary history.
To argue for specific philosophical implications regarding scientific idealization in the context of complex evolutionary models.

Main Methods:

Employing the reconciliation of genealogical discordance, which analyzes disagreements between gene trees.
Using patterns of discordance to infer lateral branching events in phylogenetic trees.
Applying these methods to inform philosophical discussions on scientific modeling and idealization.

Main Results:

Demonstrated the utility of genealogical discordance reconciliation for identifying reticulate evolutionary events.
Provided a framework for updating phylogenetic models to include non-tree-like evolutionary histories.
Identified key areas for philosophical consideration regarding scientific idealization in evolutionary studies.

Conclusions:

Reticulate phylogenetic models are essential for accurately representing the history of life.
The reconciliation of genealogical discordance offers a powerful method for inferring these complex evolutionary events.
This work highlights the need for refined philosophical accounts of scientific idealization to accommodate the complexities of modern biological modeling.