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2. Opposing effects of plant traits on diversification

Author

Anderson, Bruce, Pannell, John, Billiard, Sylvain, Burgarella, Concetta, de Boer, Hugo, Dufay, Mathilde, Helmstetter, Andrew J., Méndez, Marcos, Otto, Sarah P., Roze, Denis, Sauquet, Hervé, Schoen, Daniel, Schönenberger, Jürg, Vallejo-Marin, Mario, Zenil-Ferguson, Rosana, Käfer, Jos, and Glémin, Sylvain

Published
2023
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5. David versus Goliath: Early career researchers in an unethical publishing system

Author

Receveur, Aurore, primary, Bonfanti, Jonathan, additional, D'Agata, Stephanie, additional, Helmstetter, Andrew J., additional, Moore, Nikki A., additional, Oliveira, Brunno F., additional, Petit‐Cailleux, Cathleen, additional, Rievrs Borges, Erica, additional, Schultz, Marieke, additional, Sexton, Aaron N., additional, and Veytia, Devi, additional

Published
2024
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6. Traits related to pollination and mating result in diverse reproductive strategies in angiosperms

Author

Helmstetter, Andrew J, primary, Mendez, Marcos, additional, Schonenberger, Jurg, additional, Burgarella, Concetta, additional, Anderson, Bruce, additional, Balthazar, Maria von, additional, Billiard, Sylvain, additional, Boer, Hugo de, additional, Cros, Johanne, additional, Delecroix, Pierre-Alexandre, additional, Dufay, Mathilde, additional, Pannell, John, additional, Savova Bianchi, Dessislava, additional, Schoen, Daniel, additional, Vallejo-Marin, Mario, additional, Zenil-Ferguson, Rosana, additional, Sauquet, Herve, additional, Glemin, Sylvain, additional, and Kafer, Jos, additional

Published
2024
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7. Trait‐dependent diversification in angiosperms : Patterns, models and data

Author

Helmstetter, Andrew J., Zenil‐Ferguson, Rosana, Sauquet, Hervé, Otto, Sarah P., Méndez, Marcos, Vallejo‐Marín, Mario, Schönenberger, Jürg, Burgarella, Concetta, Anderson, Bruce, de Boer, Hugo, Glemin, Sylvain, Käfer, Jos, Helmstetter, Andrew J., Zenil‐Ferguson, Rosana, Sauquet, Hervé, Otto, Sarah P., Méndez, Marcos, Vallejo‐Marín, Mario, Schönenberger, Jürg, Burgarella, Concetta, Anderson, Bruce, de Boer, Hugo, Glemin, Sylvain, and Käfer, Jos

Abstract

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.

Published
2023
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8. Trait‐dependent diversification in angiosperms: Patterns, models and data

Author

Helmstetter, Andrew J., primary, Zenil‐Ferguson, Rosana, additional, Sauquet, Hervé, additional, Otto, Sarah P., additional, Méndez, Marcos, additional, Vallejo‐Marin, Mario, additional, Schönenberger, Jürg, additional, Burgarella, Concetta, additional, Anderson, Bruce, additional, de Boer, Hugo, additional, Glémin, Sylvain, additional, and Käfer, Jos, additional

Published
2023
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10. Trait-dependent diversification in angiosperms: patterns, models and data

Author

Helmstetter, Andrew J., primary, Zenil-Ferguson, Rosana, additional, Sauquet, Hervé, additional, Otto, Sarah P., additional, Méndez, Marcos, additional, Vallejo-Marin, Mario, additional, Schönenberger, Jürg, additional, Burgarella, Concetta, additional, Anderson, Bruce, additional, de Boer, Hugo, additional, Glémin, Sylvain, additional, and Käfer, Jos, additional

Published
2022
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14. Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling

Author

Helmstetter, Andrew J, Glemin, Sylvain, Käfer, Jos, Zenil-Ferguson, Rosana, Sauquet, Hervé, de Boer, Hugo, Dagallier, Léo-Paul M J, Mazet, Nathan, Reboud, Eliette L, Couvreur, Thomas L P, Condamine, Fabien L, Helmstetter, Andrew J, Glemin, Sylvain, Käfer, Jos, Zenil-Ferguson, Rosana, Sauquet, Hervé, de Boer, Hugo, Dagallier, Léo-Paul M J, Mazet, Nathan, Reboud, Eliette L, Couvreur, Thomas L P, and Condamine, Fabien L

Published
2021
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15. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

Author

Papadopulos, Alexander S T, primary, Helmstetter, Andrew J, additional, Osborne, Owen G, additional, Comeault, Aaron A, additional, Wood, Daniel P, additional, Straw, Edward A, additional, Mason, Laurence, additional, Fay, Michael F, additional, Parker, Joe, additional, Dunning, Luke T, additional, Foote, Andrew D, additional, Smith, Rhian J, additional, and Lighten, Jackie, additional

Published
2021
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17. Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling

Author

Helmstetter, Andrew J., primary, Glemin, Sylvain, additional, Käfer, Jos, additional, Zenil-Ferguson, Rosana, additional, Sauquet, Hervé, additional, de Boer, Hugo, additional, Dagallier, Léo-Paul M. J., additional, Mazet, Nathan, additional, Reboud, Eliette L., additional, Couvreur, Thomas L. P., additional, and Condamine, Fabien L., additional

Published
2021
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18. Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

Author

Schley, Rowan J., primary, Pennington, R. Toby, additional, Pérez‐Escobar, Oscar Alejandro, additional, Helmstetter, Andrew J., additional, Estrella, Manuel, additional, Larridon, Isabel, additional, Sabino Kikuchi, Izai Alberto Bruno, additional, Barraclough, Timothy G., additional, Forest, Félix, additional, and Klitgård, Bente, additional

Published
2020
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21. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution

Author

Papadopulos, Alexander S.T., primary, Helmstetter, Andrew J., additional, Osborne, Owen G., additional, Comeault, Aaron A., additional, Wood, Daniel P., additional, Straw, Edward A., additional, Mason, Laurence, additional, Fay, Michael F., additional, Parker, Joe, additional, Dunning, Luke T., additional, Foote, Andrew D., additional, Smith, Rhian J., additional, and Lighten, Jackie, additional

Published
2020
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24. Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)

Author

Helmstetter, Andrew J., primary, Kamga, Suzanne Mogue, additional, Bethune, Kevin, additional, Lautenschläger, Thea, additional, Zizka, Alexander, additional, Bacon, Christine D., additional, Wieringa, Jan J., additional, Stauffer, Fred, additional, Antonelli, Alexandre, additional, Sonké, Bonaventure, additional, and Couvreur, Thomas L. P., additional

Published
2020
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25. Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling.

Author

Helmstetter, Andrew J, Glemin, Sylvain, Käfer, Jos, Zenil-Ferguson, Rosana, Sauquet, Hervé, Boer, Hugo de, Dagallier, Léo-Paul M J, Mazet, Nathan, Reboud, Eliette L, Couvreur, Thomas L P, and Condamine, Fabien L

Subjects
*BIOLOGICAL extinction, *MACROEVOLUTION, *SCIENTIFIC community, *POPULATION viability analysis, *PHYLOGENY, *GENETIC speciation
Abstract

Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth–death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticized such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here, we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations, we illustrate the characteristics of newly proposed "pulled rates" and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modeling, but they in no way suggest we should abandon diversification modeling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community. [Birth–death models; extinction; phylogenetics; speciation.] [ABSTRACT FROM AUTHOR]

Published
2022
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26. Evolutionary reticulation makes an important contribution to Amazonian tree diversity

Author

Schley, Rowan J., Pennington, R. Toby, Pérez-Escobar, Oscar Alejandro, Helmstetter, Andrew J., de la Estrella, Manuel, Larridon, Isabel, Sabino Kikuchi, Izai Alberto Bruno, Barraclough, Timothy, Forest, Félix, and Klitgård, Bente

Abstract

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization has rarely been demonstrated among tree species in Amazonia, the world’s largest rainforest, and its role in diversification remains enigmatic. We show that within Brownea , a characteristic tree genus of Amazonia, there is extensive evidence of hybridization. Using both phylogenomic and population genomic approaches we find multiple historical hybridization events within Brownea , along with contemporary hybridization among co-occurring species. Finally, we infer homogeneous rates of gene flow among different genomic loci, indicating a lack of selection against hybrids, reflecting their persistence over time. These results demonstrate that gene flow between Amazonian tree species has occurred across temporal scales, which contrasts with previous work on Amazonian trees, and may have contributed to the evolution of the most diverse tree flora on Earth.

Published
2019
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29. Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

Author

Schley, Rowan J., primary, Pennington, R. Toby, additional, Pérez-Escobar, Oscar Alejandro, additional, Helmstetter, Andrew J., additional, de la Estrella, Manuel, additional, Larridon, Isabel, additional, Sabino Kikuchi, Izai Alberto Bruno, additional, Barraclough, Timothy, additional, Forest, Félix, additional, and Klitgård, Bente, additional

Published
2019
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33. Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

Author

Couvreur, Thomas L P, Helmstetter, Andrew J, Koenen, Erik J M; https://orcid.org/0000-0002-4825-4339, Bethune, Kevin, Brandão, Rita D, Little, Stefan A, Sauquet, Hervé, Erkens, Roy H J, Couvreur, Thomas L P, Helmstetter, Andrew J, Koenen, Erik J M; https://orcid.org/0000-0002-4825-4339, Bethune, Kevin, Brandão, Rita D, Little, Stefan A, Sauquet, Hervé, and Erkens, Roy H J

Abstract

Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown

Published
2019

37. Viviparity stimulates diversification in an order of fish

Author

Helmstetter, Andrew J., Papadopulos, Alexander S. T., Igea, Javier, Van Dooren, Tom J. M., Leroi, Armand M., Savolainen, Vincent, Imperial College London, Royal Botanical Gardens, University of Cambridge [UK] (CAM), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), CEREEP-Ecotron Ile de France (UMS 3194), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Naturalis Biodiversity Center [Leiden], UK Natural Environmental Research Council, Royal Society, European Research Council, Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut d'écologie et des sciences de l'environnement de Paris (IEES), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Naturalis Biodiversity Center, Universiteit Leiden [Leiden], Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
radiations, Time Factors, characters, extinction, biology, Science, fungi, Biodiversity, phylogeny, Models, Biological, cyprinodontiformes, Article, trait-dependent speciation, Quantitative Trait, Heritable, Viviparity, Nonmammalian, MD Multidisciplinary, evolution, origin, Animals, r package, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Species richness is distributed unevenly across the tree of life and this may be influenced by the evolution of novel phenotypes that promote diversification. Viviparity has originated ∼150 times in vertebrates and is considered to be an adaptation to highly variable environments. Likewise, possessing an annual life cycle is common in plants and insects, where it enables the colonization of seasonal environments, but rare in vertebrates. The extent to which these reproductive life-history traits have enhanced diversification and their relative importance in the process remains unknown. We show that convergent evolution of viviparity causes bursts of diversification in fish. We built a phylogenetic tree for Cyprinodontiformes, an order in which both annualism and viviparity have arisen, and reveal that while both traits have evolved multiple times, only viviparity played a major role in shaping the patterns of diversity. These results demonstrate that changes in reproductive life-history strategy can stimulate diversification., Live birth and an annual life cycle potentially enable access to new ecological niches and subsequent species diversification. Here, Helmstetter et al. build the phylogeny for fish in the order Cyprinodontiformes and find that, though live birth and annualism have each evolved multiple times, only live birth is associated with increased diversification.

Published
2016
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41. Toward a phylogenomic classification of magnoliids.

Author

Helmstetter AJ, Ezedin Z, de Lírio EJ, de Oliveira SM, Chatrou LW, Erkens RHJ, Larridon I, Leempoel K, Maurin O, Roy S, Zuntini AR, Baker WJ, Couvreur TLP, Forest F, and Sauquet H

Subjects
Genome, Plant, Phylogeny, Magnoliopsida genetics, Magnoliopsida classification
Abstract

Premise: Magnoliids are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families., Methods: For the first comprehensive phylogenomic analysis of magnoliids as a whole, we sampled 235 species from 199 (74%) genera and representing all families and most subfamilies and tribes. We analyzed newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies., Results: While our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we found support for the position of Hydnoraceae as sister to the remainder of Piperales, though evidence was conflicting, and resolved the backbone of relationships among most genera of Myristicaceae. Different analytical strategies tended to have rather small effects on branch support and topology., Conclusions: Although some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step toward reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for magnoliids, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae., (© 2025 The Author(s). American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Published
2025
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42. Viviparity stimulates diversification in an order of fish.

Author

Helmstetter AJ, Papadopulos AS, Igea J, Van Dooren TJ, Leroi AM, and Savolainen V

Subjects
Animals, Female, Models, Biological, Phylogeny, Quantitative Trait, Heritable, Time Factors, Biodiversity, Cyprinodontiformes physiology, Viviparity, Nonmammalian physiology
Abstract

Species richness is distributed unevenly across the tree of life and this may be influenced by the evolution of novel phenotypes that promote diversification. Viviparity has originated ∼150 times in vertebrates and is considered to be an adaptation to highly variable environments. Likewise, possessing an annual life cycle is common in plants and insects, where it enables the colonization of seasonal environments, but rare in vertebrates. The extent to which these reproductive life-history traits have enhanced diversification and their relative importance in the process remains unknown. We show that convergent evolution of viviparity causes bursts of diversification in fish. We built a phylogenetic tree for Cyprinodontiformes, an order in which both annualism and viviparity have arisen, and reveal that while both traits have evolved multiple times, only viviparity played a major role in shaping the patterns of diversity. These results demonstrate that changes in reproductive life-history strategy can stimulate diversification.

Published
2016
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