RPANDA-package {RPANDA}

RPANDA

Description

Implements macroevolutionary analyses on phylogenetic trees

Details

More information on the RPANDA package and worked examples can be found in Morlon et al. (2016)

Author(s)

Hélène Morlon <[e-mail]>

Julien Clavel <[e-mail]>

Fabien Condamine <[e-mail]>

Jonathan Drury <[e-mail]>

Eric Lewitus <[e-mail]>

Marc Manceau <[e-mail]>

Olivier Billaud <[e-mail]>

Odile Maliet <[e-mail]>

Leandro Aristide <[e-mail]>

Benoît Perez-Lamarque <[e-mail]>

References

Morlon, H., Potts, M.D., Plotkin, J.B. (2010) Inferring the dynamics of diversification: a coalescent approach, PLoS B 8(9): e1000493

Morlon, H., Parsons, T.L. and Plotkin, J.B. (2011) Reconciling molecular phylogenies with the fossil record, Proc Nat Acad Sci 108: 16327-16332

Morlon, H., Kemps, B., Plotkin, J.B., Brisson, D. (2012) Explosive radiation of a bacterial species group, Evolution 66: 2577-2586

Condamine, F.L., Rolland, J., and Morlon, H. (2013) Macroevolutionary perspectives to environmental change, Eco Lett 16: 72-85

Morlon, H. (2014) Phylogenetic approaches for studying diversification, Eco Lett 7: 508-525

Manceau, M., Lambert, A., Morlon, H. (2015) Phylogenies support out-of-equilibrium models of biodiversity, Eco Lett 18: 347-356

Lewitus, E., Morlon, H. (2016) Characterizing and comparing phylogenies from their Laplacian spectrum, Syst Biol 65: 495-507

Morlon, H., Lewitus, E., Condamine, F.L., Manceau, M., Clavel, J., Drury, J. (2016) RPANDA: an R package for macroevolutionary analyses on phylogenetic trees, MEE 7: 589-597

Drury, J., Clavel, J., Manceau, M., Morlon, H. (2016) Estimating the Effect of Competition on Trait Evolution Using Maximum Likelihood Inference, Syst Biol 65: 700-710

Manceau, M., Lambert, A., Morlon, H. (2017) A Unifying Comparative Phylogenetic Framework Including Traits Coevolving Across Interacting Lineages, Syst Biol 66: 551-568

Clavel, J., Morlon, H. (2017) Accelerated body size evolution during cold climatic periods in the Cenozoic, Proc Nat Acad Sci 114: 4183-4188

Drury, J., Tobias, J., Burns, K., Mason, N., Shultz, A., and Morlon, H. (2018) Contrasting impacts of competition on ecological and social trait evolution in songbirds. PLOS Biolog 16: e2003563

Clavel, J., Aristide, L., Morlon, H. (2019). A Penalized Likelihood framework for high-dimensional phylogenetic comparative methods and an application to new-world monkeys brain evolution. Syst Biol 68: 93-116

Maliet, O., Hartig, F., Morlon, H. (2019). A model with many small shifts for estimating species-specific diversification rates. Nature Ecol Evol 3: 1086-1092

Condamine, F.L., Rolland, J., Morlon, H. (2019) Assessing the causes of diversification slowdowns: temperature-dependent and diversity-dependent models receive equivalent support Ecology Letters 22: 1900-1912

Aristide, L., Morlon, H. (2019) Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification Ecology Letters 22: 2006-2017

Billaud, O., Moen, D. S., Parsons, T. L., Morlon, H. (2019) Estimating Diversity Through Time using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past Systematic Biology 69: 363–383

Lewitus, E., Aristide, L., Morlon, H. (2019) Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum Systematic Biology 69: 234–248

Maliet, O., Loeuille, N., Morlon, H. (2020) An individual-based model for the eco-evolutionary emergence of bipartite interaction networks Ecology Letters

Perez-Lamarque, B., Öpik, M., Maliet, O., Afonso Silva, A.C., Selosse, M-A., Martos, F., Morlon, H. (2022), Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont, Molecular Ecology, 31:3496–512.

Perez-Lamarque, B., Maliet, O., Pichon, B., Selosse, M-A., Martos, F., Morlon, H. (2022) Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks. bioRxiv, 2021.08.30.458192, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology.