Host-symbiont-gene phylogenetic reconciliationuse asterix (*) to get italics

Hugo Menet, Alexia Nguyen Trung, Vincent Daubin, Eric TannierPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

2022

<p style="text-align: justify;"><strong>Motivation:</strong>&nbsp;Biological systems are made of entities organized at different scales e.g. macro-organisms, symbionts, genes...) which evolve in interaction.<br>These interactions range from independence or conflict to cooperation and coevolution, which results in them having a common history.<br>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.&nbsp;</p> <p style="text-align: justify;"><strong>Results:</strong> 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 host-symbiont 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.</p> <p style="text-align: justify;"><strong>Availability:</strong> Implementation is available on GitHub https://github.com/hmenet/TALE&nbsp; Data are available on Zenodo https://doi.org/10.5281/zenodo.7667342&nbsp;</p>

https://doi.org/10.5281/zenodo.7667342You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

https://github.com/hmenet/TALEYou should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Phylogenetic reconciliation, Symbiosis, Horizontal gene transfer, Coevolution

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Bioinformatics & Computational Biology, Phylogenetics / Phylogenomics

Christophe Dessimoz, christophe.dessimoz@unil.ch, Mukul S. Bansal, mukul.bansal@uconn.edu, Ran Libeskind-Hadas, hadas@cs.hmc.edu, Luay K. Nakhleh, nakhleh@rice.edu, Dannie Durand, durand@cmu.edu No need for them to be recommenders of PCIEvolBiol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

2022-08-21 18:34:27

Emmanuelle Jousselin