Phylostems: A new graphical tool to investigate temporal signal of heterochronous sequences datasets
2023
Doizy, Anna | Prin, Amaury | Cornu, Guillaume | Chiroleu, Frédéric | Rieux, Adrien | DoAna | Forêts et Sociétés (UPR Forêts et Sociétés) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) | Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | European Regional Development Fund;ERDF;UE;http://dx.doi.org/10.13039/501100008530 | Agence Nationale de la Recherche;ANR;FRA;http://dx.doi.org/10.13039/501100001665 | Région Réunion;;REU; | Agropolis Fondation;AF;FRA;http://dx.doi.org/10.13039/100007599 | ANR-17-CE35-0009,MUSEOBACT,“Une nuit au musée”: mieux reconstuire les emergences de bactéries pathogènes des cultures grâce à des échantillons historiques(2017)
Source Agritrop Cirad (https://agritrop.cirad.fr/607968/) * Autres projets (id;sigle;titre): 1504-004;;(FRA) E-SPACE//
اظهر المزيد [+] اقل [-]International audience
اظهر المزيد [+] اقل [-]إنجليزي. 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.
اظهر المزيد [+] اقل [-]الكلمات المفتاحية الخاصة بالمكنز الزراعي (أجروفوك)
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تم تزويد هذا السجل من قبل Institut national de la recherche agronomique