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31 results on '"Morlon, Hèléne"'

1. Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks

Author

Perez-Lamarque, Benoît, Maliet, Odile, Pichon, Benoît, Selosse, Marc-André, Martos, Florent, and Morlon, Hélène

Subjects
Archaeology, CC1-960, Science
Abstract

Whether interactions between species are conserved on evolutionary time-scales has spurred the development of both correlative and process-based approaches for testing phylogenetic signal in interspecific interactions: do closely related species interact with similar partners? Here we use simulations to test the statistical performances of the two approaches that are the most widely used in the field: Mantel tests and the Phylogenetic Bipartite Linear Model (PBLM). Mantel tests investigate the correlation between phylogenetic distances and dissimilarities in sets of interacting partners, while PBLM is a process-based approach that relies on strong assumptions about how interactions evolve. We find that PBLM often detects a phylogenetic signal when it should not. Simple Mantel tests instead have infrequent false positives and moderate statistical power; however, they often artifactually detect that closely related species interact with dissimilar partners. Partial Mantel tests, which are used to partial out the phylogenetic signal in the number of partners, actually fail at correcting for this confounding effect, and we instead recommend evaluating the significance of Mantel tests with network permutations constraining the number of partners. We also explore the ability of simple Mantel tests to analyze clade- specific phylogenetic signals. We provide general guidelines and an application on an interaction network between orchids and mycorrhizal fungi.

Published
2022
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6. The reconstructed tree in the lineage-based model of protracted speciation

Author

Lambert, Amaury, Morlon, Hélène, and Etienne, Rampal S.

Subjects
Quantitative Biology - Populations and Evolution, Mathematics - Probability, 60J80 (Primary) 92D15, 60J85, 92D25, 92D40, 60G51, 60G55 (Secondary)
Abstract

A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne & Rosindell (2012) proposed a lineage-based model of diversification, called protracted speciation, where species remain incipient during a random duration before turning good species, and showed that this can explain the slowdown in lineage accumulation observed in real phylogenies. However, they were unable to provide a general likelihood formula. Here, we present a likelihood formula for protracted speciation models, where rates at which species turn good or become extinct can depend both on their age and on time. Our only restrictive assumption is that speciation rate does not depend on species status. Our likelihood formula utilizes a new technique, based on the contour of the phylogenetic tree and first developed in Lambert (2010). We consider the reconstructed trees spanned by all extant species, by all good extant species, or by all representative species, which are either good extant species or incipient species representative of some good extinct species. Specifically, we prove that each of these trees is a coalescent point process, that is, a planar, ultrametric tree where the coalescence times between two consecutive tips are independent, identically distributed random variables. We characterize the common distribution of these coalescence times in some, biologically meaningful, special cases for which the likelihood reduces to an elegant analytical formula or becomes numerically tractable., Comment: 27 pages, 5 figures

Published
2013

17. Towards a genetic theory of island biogeography: Inferring processes from multidimensional community-scale data

Author

Overcast, Isaac, Achaz, Guillaume, Aguilée, Robin, Andújar, Carmelo, Arribas, Paula, Creedy, Thomas J., Economo, Evan P., Etienne, Rampal S., Gillespie, Rosemary, Jacquet, Claire, Jay, Flora, Kennedy, Susan, Krehenwinkel, Henrik, Lambert, Amaury, Meramveliotakis, Emmanouil, Noguerales, Victor, Perez-Lamarque, Benoit, Roderick, George, Rogers, Haldre, Ruffley, Megan, Sanmartín, Isabel, Vogler, Alfried P., Papadopoulou, Anna, Emerson, Brent C., Morlon, Hèléne, Overcast, Isaac, Achaz, Guillaume, Aguilée, Robin, Andújar, Carmelo, Arribas, Paula, Creedy, Thomas J., Economo, Evan P., Etienne, Rampal S., Gillespie, Rosemary, Jacquet, Claire, Jay, Flora, Kennedy, Susan, Krehenwinkel, Henrik, Lambert, Amaury, Meramveliotakis, Emmanouil, Noguerales, Victor, Perez-Lamarque, Benoit, Roderick, George, Rogers, Haldre, Ruffley, Megan, Sanmartín, Isabel, Vogler, Alfried P., Papadopoulou, Anna, Emerson, Brent C., and Morlon, Hèléne

Abstract

Background: MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography. Motivation/goal: We aim to promote the development of process-based biodiversity models that predict community genetic diversity patterns together with other community-scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community-scale data including a genetic component. Main conclusions: Our review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top-down or a bottom-up approach. Finally, we highlight key ecological and evolutionary questions t

Published
2023

19. Understanding How Biodiversity Is Distributed in Space and Time

Author

Morlon, Hélène, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Fages, François, editor, and Piazza, Carla, editor

Published
2014
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20. Predictive ecology in a changing world

Author

Mouquet, Nicolas, Lagadeuc, Yvan, Devictor, Vincent, Doyen, Luc, Duputié, Anne, Eveillard, Damien, Faure, Denis, Garnier, Eric, Gimenez, Olivier, Huneman, Philippe, Jabot, Franck, Jarne, Philippe, Joly, Dominique, Julliard, Romain, Kéfi, Sonia, Kergoat, Gael J., Lavorel, Sandra, Le Gall, Line, Meslin, Laurence, Morand, Serge, Morin, Xavier, Morlon, Hélène, Pinay, Gilles, Pradel, Roger, Schurr, Frank M., Thuiller, Wilfried, and Loreau, Michel

Published
2015

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