Phylostems: A new graphical tool to investigate temporal signal of heterochronous sequences datasets

Doizy Anna, Prin Amaury, Cornu Guillaume, Chiroleu Frédéric, Rieux Adrien. 2023. Phylostems: A new graphical tool to investigate temporal signal of heterochronous sequences datasets. Bioinformatics Advances, 3 (1):vbad026, 5 p.

Url - autres données associées : https://gitlab.com/cirad-apps/phylostems / Url - autres données associées : https://pvbmt-apps.cirad.fr/apps/phylostems

Résumé : Motivation: Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Importantly, such inferences should only be performed on datasets displaying sufficient temporal signal, a feature important to test prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the 'root-to-tip regression' which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree scale (i.e. its root). Results: To overcome this limitation we introduce Phylostems, a new graphical user-friendly tool developed to investigate temporal signal within every clade of a phylogenetic tree. We provide a 'how to' guide by running Phylostems on an empirical dataset and supply guidance for results interpretation.

Mots-clés Agrovoc : phylogénie, évolution, séquence d'adn, méthode statistique, adn, tempête orageuse

Classification Agris : U10 - Informatique, mathématiques et statistiques
F40 - Écologie végétale

Champ stratégique Cirad : CTS 7 (2019-) - Hors champs stratégiques

Agences de financement européennes : European Regional Development Fund

Agences de financement hors UE : Agence Nationale de la Recherche, Région Réunion, Agropolis Fondation

Projets sur financement : (FRA) "Une nuit au musée": mieux reconstuire les emergences de bactéries pathogènes des cultures grâce à des échantillons historiques, (FRA) E-SPACE

Auteurs et affiliations

• Doizy Anna, DoAna (REU) ORCID: 0000-0002-2866-6918
• Prin Amaury
• Cornu Guillaume, CIRAD-ES-UPR Forêts et sociétés (FRA) ORCID: 0000-0002-7523-5176
• Chiroleu Frédéric, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0002-4874-5357
• Rieux Adrien, CIRAD-BIOS-UMR PVBMT (REU) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/607968/)

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