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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Model-Based Inference of Punctuated Molecular Evolution.

Marc Manceau^1,2,3, Julie Marin¹, Hélène Morlon²

¹Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France.

Molecular Biology and Evolution

|June 11, 2020

Summary

This summary is machine-generated.

This study introduces a new "Relaxed Clock with Spikes" model for DNA sequence evolution. It identifies episodes of rapid divergence, or "spikes," occurring during speciation events, improving our understanding of molecular evolution and diversification.

Keywords:

diversification ecological speciation gene flow punctuated equilibrium theory relaxed molecular clock speciation genomics

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Area of Science:

Molecular Evolution
Genomics
Phylogenetics

Background:

Standard molecular evolution models assume constant or varying substitution rates (molecular clock, relaxed clock).
DNA sequences can exhibit episodes of rapid, synchronous divergence (spikes) at the macroevolutionary scale.
These spikes can complicate standard evolutionary rate estimations.

Purpose of the Study:

To develop a novel model, the Relaxed Clock with Spikes (RCS) model, for DNA sequence evolution.
To integrate clock-like substitutions with spike events occurring during speciation.
To detect and quantify spike events and their impact on molecular evolution.

Main Methods:

Developed the Relaxed Clock with Spikes (RCS) model.
Applied the model to a time-calibrated species phylogeny and multiple sequence alignment.
Estimated spike probability and amplitude at speciation events.
Identified conditions for distinguishing spikes from clock rate variations.

Main Results:

The RCS model successfully detects speciation events co-occurring with spike events.
Identified several gene-specific spikes in snake venom protein genes.
Determined conditions under which spikes are distinguishable from background molecular variation.
Demonstrated the model's ability to capture episodes of fast divergence.

Conclusions:

The RCS model provides a more nuanced understanding of molecular evolution by incorporating spike events.
This framework can reveal hidden speciation dynamics and gene-specific evolutionary patterns.
The method has potential applications in whole-genome analyses to inform species diversification.