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Section: Evolutionary Biology
Topic: Evolution, Genetics/Genomics

Host-symbiont-gene phylogenetic reconciliation

Menet, Hugo1 ; Trung, Alexia Nguyen1; Daubin, Vincent1  ; Tannier, Eric1, 2  
1 Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
2 Inria, Centre de recherche de Lyon, 69622 Villeurbanne, France

10.24072/pcjournal.273 - Peer Community Journal, Volume 3 (2023), article no. e47.

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Motivation Biological systems are made of entities organized at different scales (e.g. macro-organisms, symbionts, genes…) which evolve in interaction. These interactions range from independence or conflict to cooperation and coevolution, which results in them having a common history. The evolution of such systems is approached by phylogenetic reconciliation, which describes the common patterns of diversification between two different levels, e.g. genes and species, or hosts and symbionts for example. The limit to two levels hides the multi-level inter-dependencies that characterize complex systems. Results We present a probabilistic model of evolution of three nested levels of organization which can account for the codivergence of hosts, symbionts and their genes. This model allows gene transfer as well as host switch, gene duplication as well as symbiont diversification inside a host, gene or symbiont loss. It handles the possibility of ghost lineages as well as temporary free-living symbionts. Given three phylogenetic trees, we devise a Monte Carlo algorithm which samples evolutionary scenarios of symbionts and genes according to an approximation of their likelihood in the model. We evaluate the capacity of our method on simulated data, notably its capacity to infer horizontal gene transfers, and its ability to detect hostsymbiont co-evolution by comparing host/symbiont/gene and symbiont/gene models based on their estimated likelihoods. Then we show in a aphid enterobacter system that some reliable transfers detected by our method, are invisible to classic 2-level reconciliation. We finally evaluate different hypotheses on human population histories in the light of their coevolving Helicobacter pylori symbionts, reconciled together with their genes. Availability Implementation is available on GitHub https://github.com/hmenet/TALE. Data are available on Zenodo https://doi.org/10.5281/zenodo.7667342.

Published online:
DOI: 10.24072/pcjournal.273
Type: Research article
Keywords: symbiont ; holobiont ; phylogeny; evolution ; co-evolution ; horizontal transfer ; host switch ; Helicobacter pylori ; human migrations ; phylogenetic reconciliation
Menet, Hugo 1; Trung, Alexia Nguyen 1; Daubin, Vincent 1; Tannier, Eric 1, 2

1 Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
2 Inria, Centre de recherche de Lyon, 69622 Villeurbanne, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Menet, Hugo; Trung, Alexia Nguyen; Daubin, Vincent; Tannier, Eric. Host-symbiont-gene phylogenetic reconciliation. Peer Community Journal, Volume 3 (2023), article  no. e47. doi : 10.24072/pcjournal.273. https://peercommunityjournal.org/articles/10.24072/pcjournal.273/

Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100593

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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