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9. Modeling trait-dependent evolution on a random species tree

Author

Tahir, Daniah, Glémin, Sylvain, Lascoux, Martin, and Kaj, Ingemar

Subjects
Quantitative Biology - Populations and Evolution, Mathematics - Probability
Abstract

Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. A typical example is the evolution of mating systems in plant species. In this work, we present a probabilistic modeling framework for binary trait, random species trees, in which the number of species and their traits are represented by a two-type, continuous time Markov branching process. We develop our model by considering the impact of mating systems on dN/dS, the ratio of nonsynonymous to synonymous substitutions. A methodology is introduced which enables us to match model parameters with parameter estimates from phylogenetic tree data. The properties obtained from the model are applied to outcrossing and selfing species trees in the Geraniaceae and Solanaceae family. This allows us to investigate not only the branching tree rates, but also the mutation rates and the intensity of selection.

Published
2017

14. The Ornstein-Uhlenbeck process with migration: evolution with interactions

Author

Bartoszek, Krzysztof, Glémin, Sylvain, Kaj, Ingemar, and Lascoux, Martin

Subjects
Quantitative Biology - Populations and Evolution, Mathematics - Probability, Statistics - Applications
Abstract

The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes drift and stabilizing selection and assumes that species evolve independently. However, especially in plants, there is ample evidence of hybridization and introgression during evolution. In this work we present a statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Our model can also be useful for studying local adaptation among populations within the same species. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.

Published
2016
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18. Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Author

Zhou, Qiujie, primary, Karunarathne, Piyal, additional, Andersson-Li, Lili, additional, Chen, Chen, additional, Opgenoorth, Lars, additional, Heer, Katrin, additional, Vendramin, Giovanni Giuseppe, additional, Piotti, Andrea, additional, Nakvasina, Elena, additional, Lascoux, Martin, additional, and Milesi, Pascal, additional

Published
2023
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22. Between but Not Within-Species Variation in the Distribution of Fitness Effects.

Author

James, Jennifer, Kastally, Chedly, Budde, Katharina B, González-Martínez, Santiago C, Milesi, Pascal, Pyhäjärvi, Tanja, Lascoux, Martin, and Consortium, GenTree

Subjects
DEMOGRAPHIC change, RAW materials, BIOLOGICAL adaptation
Abstract

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact. [ABSTRACT FROM AUTHOR]

Published
2023
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26. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Barbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares, Fernando, Cavers, Stephen, Fady, Bruno, Alía, Ricardo, Aravanopoulos, Filippos, Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent, José M., Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna-Maria, del Barrio, José M. García, Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le-Provost, Grégoire, Liesebach, Mirko, Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, Tor, Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A., Ramskogler, Kurt, Robledo-Arnuncio, Juan J., Savolainen, Outi, Schueler, Silvio, Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, and Fonti, Patrick

Published
2020
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28. Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

Author

Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Barbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares, Fernando, Cavers, Stephen, Fady, Bruno, Alía, Ricardo, Aravanopoulos, Filippos, Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent, José M., Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna-Maria, García del Barrio, José M., Gilg, Olivier, González-Martínez, Santiago C., Gray, Alan, Hartleitner, Christoph, Hurel, Agathe, Jouineau, Arnaud, Kärkkäinen, Katri, Kujala, Sonja T., Labriola, Mariaceleste, Lascoux, Martin, Lefebvre, Marlène, Lejeune, Vincent, Le-Provost, Grégoire, Liesebach, Mirko, Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, Tor, Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A., Ramskogler, Kurt, Robledo-Arnuncio, Juan J., Savolainen, Outi, Schueler, Silvio, Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Veisse, Dominique, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, and Fonti, Patrick

Published
2020
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41. Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Author

Salojärvi, Jarkko, Smolander, Olli-Pekka, Nieminen, Kaisa, Rajaraman, Sitaram, Safronov, Omid, Safdari, Pezhman, Lamminmäki, Airi, Immanen, Juha, Lan, Tianying, Tanskanen, Jaakko, Rastas, Pasi, Amiryousefi, Ali, Jayaprakash, Balamuralikrishna, Kammonen, Juhana I, Hagqvist, Risto, Eswaran, Gugan, Ahonen, Viivi Helena, Serra, Juan Alonso, Asiegbu, Fred O, de Dios Barajas-Lopez, Juan, Blande, Daniel, Blokhina, Olga, Blomster, Tiina, Broholm, Suvi, Brosché, Mikael, Cui, Fuqiang, Dardick, Chris, Ehonen, Sanna E, Elomaa, Paula, Escamez, Sacha, Fagerstedt, Kurt V, Fujii, Hiroaki, Gauthier, Adrien, Gollan, Peter J, Halimaa, Pauliina, Heino, Pekka I, Himanen, Kristiina, Hollender, Courtney, Kangasjärvi, Saijaliisa, Kauppinen, Leila, Kelleher, Colin T, Kontunen-Soppela, Sari, Koskinen, J Patrik, Kovalchuk, Andriy, Kärenlampi, Sirpa O, Kärkönen, Anna K, Lim, Kean-Jin, Leppälä, Johanna, Macpherson, Lee, Mikola, Juha, Mouhu, Katriina, Mähönen, Ari Pekka, Niinemets, Ülo, Oksanen, Elina, Overmyer, Kirk, Palva, E Tapio, Pazouki, Leila, Pennanen, Ville, Puhakainen, Tuula, Poczai, Péter, Possen, Boy J H M, Punkkinen, Matleena, Rahikainen, Moona M, Rousi, Matti, Ruonala, Raili, van der Schoot, Christiaan, Shapiguzov, Alexey, Sierla, Maija, Sipilä, Timo P, Sutela, Suvi, Teeri, Teemu H, Tervahauta, Arja I, Vaattovaara, Aleksia, Vahala, Jorma, Vetchinnikova, Lidia, Welling, Annikki, Wrzaczek, Michael, Xu, Enjun, Paulin, Lars G, Schulman, Alan H, Lascoux, Martin, Albert, Victor A, Auvinen, Petri, Helariutta, Ykä, and Kangasjärvi, Jaakko

Published
2019
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42. Oak genome reveals facets of long lifespan

Author

Plomion, Christophe, Aury, Jean-Marc, Amselem, Joëlle, Leroy, Thibault, Murat, Florent, Duplessis, Sébastien, Faye, Sébastien, Francillonne, Nicolas, Labadie, Karine, Le Provost, Grégoire, Lesur, Isabelle, Bartholomé, Jérôme, Faivre-Rampant, Patricia, Kohler, Annegret, Leplé, Jean-Charles, Chantret, Nathalie, Chen, Jun, Diévart, Anne, Alaeitabar, Tina, Barbe, Valérie, Belser, Caroline, Bergès, Hélène, Bodénès, Catherine, Bogeat-Triboulot, Marie-Béatrice, Bouffaud, Marie-Lara, Brachi, Benjamin, Chancerel, Emilie, Cohen, David, Couloux, Arnaud, Da Silva, Corinne, Dossat, Carole, Ehrenmann, François, Gaspin, Christine, Grima-Pettenati, Jacqueline, Guichoux, Erwan, Hecker, Arnaud, Herrmann, Sylvie, Hugueney, Philippe, Hummel, Irène, Klopp, Christophe, Lalanne, Céline, Lascoux, Martin, Lasserre, Eric, Lemainque, Arnaud, Desprez-Loustau, Marie-Laure, Luyten, Isabelle, Madoui, Mohammed-Amin, Mangenot, Sophie, Marchal, Clémence, Maumus, Florian, Mercier, Jonathan, Michotey, Célia, Panaud, Olivier, Picault, Nathalie, Rouhier, Nicolas, Rué, Olivier, Rustenholz, Camille, Salin, Franck, Soler, Marçal, Tarkka, Mika, Velt, Amandine, Zanne, Amy E., Martin, Francis, Wincker, Patrick, Quesneville, Hadi, Kremer, Antoine, and Salse, Jérôme

Published
2018
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47. Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication

Author

Duan, Tianlin, Sicard, Adrien, Glemin, Sylvain, and Lascoux, Martin

Subjects
Agricultural Science
Abstract

Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.

Published
2023

49. Teasing apart the joint effect of demography and natural selection in the birth of a contact zone

Author

Li, Lili, primary, Milesi, Pascal, additional, Tiret, Mathieu, additional, Chen, Jun, additional, Sendrowski, Janek, additional, Baison, John, additional, Chen, Zhi‐qiang, additional, Zhou, Linghua, additional, Karlsson, Bo, additional, Berlin, Mats, additional, Westin, Johan, additional, Garcia‐Gil, Maria Rosario, additional, Wu, Harry X., additional, and Lascoux, Martin, additional

Published
2022
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