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Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation.

Blerina Sinaimeri1, Laura Urbini2,3,4, Marie-France Sagot2,3,4

  • 1Libera Università Internazionale degli Studi Sociali Guido Carli, Rome, Department of Business and Management, Viale Romania, 32 - 00197, Rome, Italy.

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|September 13, 2023
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Summary
This summary is machine-generated.

AmoCoala models symbiont invasions (spread events) in host-symbiont coevolution, improving phylogenetic tree reconciliation accuracy. This method enhances understanding of multiple symbiont-host associations, crucial for evolutionary biology.

Keywords:
Approximate Bayesian computation methodcophylogenyreconciliationspread

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Phylogenetic tree reconciliation is vital for studying host-symbiont coevolution.
  • Existing methods struggle with modeling symbiont invasions (spread events) leading to multiple host associations.
  • Accurate cost values are essential for parsimonious reconciliation.

Purpose of the Study:

  • To introduce AmoCoala, a novel method for realistic cophylogeny event probability estimation.
  • To incorporate spread events (vertical and horizontal) into coevolutionary models.
  • To improve the accuracy of host-symbiont phylogenetic tree reconciliation.

Main Methods:

  • Expanded the classical 4-event coevolutionary model to include vertical and horizontal spread events.
  • Estimated spread event probabilities using heuristic frequencies.
  • Employed approximate Bayesian computation to infer probabilities of classical events (cospeciation, duplication, host switch, loss).

Main Results:

  • AmoCoala accurately estimates cophylogeny event probabilities, even with spread events.
  • The model enables more precise consideration of multiple symbiont-host associations.
  • Validated through synthetic datasets and real-world examples, showing biologically plausible reconciliations.

Conclusions:

  • AmoCoala provides a more realistic and accurate approach to host-symbiont phylogenetic reconciliation.
  • The inclusion of spread events significantly enhances the reliability of evolutionary analyses.
  • Improved cost sets lead to more dependable reconciliation of host and symbiont evolutionary histories.