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1. Resilience of genetic diversity in forest trees over the Quaternary

Author

Milesi, Pascal, Kastally, Chedly, Dauphin, Benjamin, Cervantes, Sandra, Bagnoli, Francesca, Budde, Katharina B., Cavers, Stephen, Fady, Bruno, Faivre-Rampant, Patricia, González-Martínez, Santiago C., Grivet, Delphine, Gugerli, Felix, Jorge, Véronique, Lesur Kupin, Isabelle, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Pinosio, Sara, Plomion, Christophe, Rellstab, Christian, Rogier, Odile, Scalabrin, Simone, Scotti, Ivan, Vendramin, Giovanni G., Westergren, Marjana, Lascoux, Martin, and Pyhäjärvi, Tanja

Published
2024
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3. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource.

Author

Mosca, Elena, Cruz, Fernando, Gómez-Garrido, Jèssica, Bianco, Luca, Rellstab, Christian, Brodbeck, Sabine, Csilléry, Katalin, Fady, Bruno, Fladung, Matthias, Fussi, Barbara, Gömöry, Dušan, González-Martínez, Santiago C, Grivet, Delphine, Gut, Marta, Hansen, Ole Kim, Heer, Katrin, Kaya, Zeki, Krutovsky, Konstantin V, Kersten, Birgit, Liepelt, Sascha, Opgenoorth, Lars, Sperisen, Christoph, Ullrich, Kristian K, Vendramin, Giovanni G, Westergren, Marjana, Ziegenhagen, Birgit, Alioto, Tyler, Gugerli, Felix, Heinze, Berthold, Höhn, Maria, Troggio, Michela, and Neale, David B

Subjects
Abies, Computational Biology, Genomics, Genome, Plant, Databases, Genetic, Genome, Chloroplast, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing, Genome Size, Whole Genome Sequencing, Abies alba, annotation, chloroplast genome, conifer genome, genome assembly, Genome, Plant, Databases, Genetic, Chloroplast, Genetics
Abstract

Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.

Published
2019

5. Resilient forests for the future

Author

Perry, Annika, Aravanopoulos, Filippos A., Budde, Katharina Birgit, Hansen, Ole Kim, Rellstab, Christian, Schroeder, Hilke, Curtu, Alexandru Lucian, Perry, Annika, Aravanopoulos, Filippos A., Budde, Katharina Birgit, Hansen, Ole Kim, Rellstab, Christian, Schroeder, Hilke, and Curtu, Alexandru Lucian

Abstract

Forest ecosystems are of global importance, ecologically, economically and culturally. However, despite their fundamental role in mitigating the worst effects of climate change, to date there have been surprisingly few resources devoted to defining, conserving and planning resilient forests for the future. Progress in this field of research, which requires international and interdisciplinary cooperation, collaboration and communication, was presented and discussed at the second biannual conference of the European Research Group, Evoltree (https://www.evoltree.eu). Over four days more than 140 scientists met to share developments and to discuss forest ecology, genetics, genomics and evolution with a focus on realising “Resilient Forests for the Future”. From examining evolutionary dynamics and using the past to understand future responses, to evaluating breeding approaches and the sustainable use of forest genetic resources, the conference addressed critical themes with relevance to this topic. The role of genomics in conservation, investigation of biotic interactions and identifying climate resilient forests were also explored. Finally, innovative methods and approaches which promise to increase the scale and speed with which forest evolutionary research can progress were introduced and evaluated. The Evoltree network and conference series provides invaluable opportunities to share knowledge and increase collaboration on forest genetic research, the need for which has never been greater or more urgent.

Published
2024

7. Divergent selection in a Mediterranean pine on local spatial scales.

Author

Budde, Katharina B., Rellstab, Christian, Heuertz, Myriam, Gugerli, Felix, Hanika, Tom, Verdú, Miguel, Pausas, Juli G., and González‐Martínez, Santiago C.

Subjects
*CLUSTER pine, *GENETIC variation, *PINE, *GENE flow, *GENE frequency, *PLANT populations, *FLOWERING time
Abstract

The effects of selection on an organism's genome are hard to detect on small spatial scales, as gene flow can swamp signatures of local adaptation. Therefore, most genome scans to detect signatures of environmental selection are performed on large spatial scales; however, divergent selection on the local scale (e.g. between contrasting soil conditions) has also been demonstrated, in particular for herbaceous plants.Here, we hypothesised that in topographically complex landscapes, microenvironment variability is strong enough to leave a selective footprint in the genomes of long‐lived organisms. To test this, we investigated paired south‐ versus north‐facing Pinus pinaster stands on the local scale, with trees growing in close vicinity (≤820 m distance between paired south‐ and north‐facing stands), in a Mediterranean mountain area. While trees on north‐facing slopes experience less radiation, trees on south‐facing slopes suffer from especially harsh conditions, particularly during the dry summer season.Two outlier analyses consistently revealed five putatively adaptive loci (out of 4034), in candidate genes two of which encoded non‐synonymous substitutions. Additionally, one locus showed consistent allele frequency differences in all three stand pairs indicating divergent selection despite high gene flow on the local scale. Permutation tests demonstrated that our findings were robust.Functional annotation of these candidate genes revealed biological functions related to abiotic stress response, such as water availability, in other plant species.Synthesis. Our study highlights how divergent selection in heterogeneous microenvironments shapes and maintains the functional genetic variation within populations of long‐lived forest tree species, being the first to focus on adaptive genetic divergence between south‐ and north‐facing slopes within continuous forest stands. This is especially relevant in the current context of climate change, as this variation is at the base of plant population responses to future climate. [ABSTRACT FROM AUTHOR]

Published
2024
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8. 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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9. 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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10. 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, Alizoti, Paraskevi, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos A., von Arx, Georg, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Bajc, Marko, Ballesteros, Eduardo, Barbas, Evangelos, del Barrio, José M. García, Bastias, Cristina C., Bastien, Catherine, Beffa, Giorgia, Benavides, Raquel, Benoit, Vanina, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buret, Corinne, Buy, Melanie, Cabanillas-Saldaña, Ana M., Carvalho, Bárbara, Cavers, Stephen, Del Caño, Fernando, Cervantes, Sandra, Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Denou, Jean-Luc, Dokhelar, Bernard, Ducousso, Alexis, Fady, Bruno, Faivre-Rampant, Patricia, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, Gilg, Olivier, De Girardi, Nicolas, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issenhuth, Bernard, Jean, Florence, Jorge, Véronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo A., Kärkkäinen, Katri, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Le-Provost, Gregoire, Lejeune, Vincent, Lesur-Kupin, Isabelle, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meier, Benjamin, Meischner, Helge, Michotey, Célia, Morganti, Sandro, Myking, Tor, Nievergelt, Daniel, Eskild Nilsen, Anne, Notivol, Eduardo, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Ostreng, Geir, Pakull, Birte, Perry, Annika, Pinosio, Sara, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Raffin, Annie, Ramírez-Valiente, José A., Rellstab, Christian, Remi, Dourthe, Reutimann, Oliver, Richter, Sebastian, Robledo-Arnuncio, Juan J., Rogier, Odile, Sancho, Elisabet Martínez, Savolainen, Outi, Scalabrin, Simone, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Segundo, Sergio San, Semerikov, Vladimir, Slámová, Lenka, Spanu, Ilaria, Sønstebø, Jørn Henrik, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Valladares, Fernando, Vendramin, Giovanni G., Villar, Marc, Westergren, Marjana, Westin, Johan, Lascoux, Martin, James, Jennifer, Kastally, Chedly, Budde, Katharina B., González-Martínez, Santiago C., Milesi, Pascal, Pyhäjärvi, Tanja, Alizoti, Paraskevi, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos A., von Arx, Georg, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Bajc, Marko, Ballesteros, Eduardo, Barbas, Evangelos, del Barrio, José M. García, Bastias, Cristina C., Bastien, Catherine, Beffa, Giorgia, Benavides, Raquel, Benoit, Vanina, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buret, Corinne, Buy, Melanie, Cabanillas-Saldaña, Ana M., Carvalho, Bárbara, Cavers, Stephen, Del Caño, Fernando, Cervantes, Sandra, Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Denou, Jean-Luc, Dokhelar, Bernard, Ducousso, Alexis, Fady, Bruno, Faivre-Rampant, Patricia, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, Gilg, Olivier, De Girardi, Nicolas, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issenhuth, Bernard, Jean, Florence, Jorge, Véronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo A., Kärkkäinen, Katri, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Le-Provost, Gregoire, Lejeune, Vincent, Lesur-Kupin, Isabelle, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meier, Benjamin, Meischner, Helge, Michotey, Célia, Morganti, Sandro, Myking, Tor, Nievergelt, Daniel, Eskild Nilsen, Anne, Notivol, Eduardo, Ojeda, Dario I., Olsson, Sanna, Opgenoorth, Lars, Ostreng, Geir, Pakull, Birte, Perry, Annika, Pinosio, Sara, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Raffin, Annie, Ramírez-Valiente, José A., Rellstab, Christian, Remi, Dourthe, Reutimann, Oliver, Richter, Sebastian, Robledo-Arnuncio, Juan J., Rogier, Odile, Sancho, Elisabet Martínez, Savolainen, Outi, Scalabrin, Simone, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Segundo, Sergio San, Semerikov, Vladimir, Slámová, Lenka, Spanu, Ilaria, Sønstebø, Jørn Henrik, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Valladares, Fernando, Vendramin, Giovanni G., Villar, Marc, Westergren, Marjana, Westin, Johan, and Lascoux, Martin

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, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised 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 there being 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 that evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

Published
2023

11. Can northern sessile oaks profit from southern genetic variants to face future climate change?

Author

Curtu, Alexandru Lucian, Ciocîrlan, Elena, Olofsson, Jill Katharina, Lobo, Albin, Hansen, Jon Kehlet, Nielsen, Lene, Budde, Katharina Birgit, Rellstab, Christian, Kjær, Erik Dahl, Curtu, Alexandru Lucian, Ciocîrlan, Elena, Olofsson, Jill Katharina, Lobo, Albin, Hansen, Jon Kehlet, Nielsen, Lene, Budde, Katharina Birgit, Rellstab, Christian, and Kjær, Erik Dahl

Abstract

In addition to valuable renewable wood resources, oak forests are essential ecosystems hosting a large amount of biodiversity. Although oaks are predicted to be less affected by a shift in climatic conditions, including more frequent and severe drought spells, compared to other forest tree species, they will have to adapt fast to future climatic changes. Here we use classical landscape genomics to locate genes with a potential adaptive role in drought-resistance among pan-European provenances of sessile oak (Quercus petraea). We ask if an enrichment with alleles beneficial for dry conditions from southern provenances often subjected to drought – be it by natural dispersal, gene flow or human plantings – can enhance the adaptive potential of the native Danish Q. petraea populations to a future drier climate. We find numerous genetic loci (single nucleotide polymorphisms; SNPs) associated with bioclimatic variables describing local precipitation. While many of the associated SNPs are found in inter-genic regions, some are indeed located in, or close to genes, known to be involved in drought stress responses. Thus, beneficial alleles have the potential to spread across the landscape. We will present detailed analyses of these beneficial alleles in order to determine whether they are absent in the local Danish gene pool, or if they are already present at low frequency, and thus enabling adaptation to a drier climate based on standing genetic variation. In conclusion, beneficial alleles found among southern populations of sessile oak is a valuable source for future enrichment of northern oak seed sources and natural populations to ensure their robustness under future climate.

Published
2023

12. Prospects and limitations of genomic offset in conservation management

Author

Rellstab, Christian, Dauphin, Benjamin, and Exposito‐Alonso, Moises

Subjects
Evolution, Perspective, predictive genomics, QH359-425, genomic vulnerability, assisted migration, genomic offset, local adaptation, conservation management
Abstract

In nature conservation, there is keen interest in predicting how populations will respond to environmental changes such as climate change. These predictions can help determine whether a population can be self‐sustaining under future alterations of its habitat or whether it may require human intervention such as protection, restoration, or assisted migration. An increasingly popular approach in this respect is the concept of genomic offset, which combines genomic and environmental data from different time points and/or locations to assess the degree of possible maladaptation to new environmental conditions. Here, we argue that the concept of genomic offset holds great potential, but an exploration of its risks and limitations is needed to use it for recommendations in conservation or assisted migration. After briefly describing the concept, we list important issues to consider (e.g., statistical frameworks, population genetic structure, migration, independent evidence) when using genomic offset or developing these methods further. We conclude that genomic offset is an area of development that still lacks some important features and should be used in combination with other approaches to inform conservation measures.

Published
2021

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

Author

Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, 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, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, Fonti, Patrick, Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, 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, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, and Fonti, Patrick

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

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

Author

European Commission, Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, 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, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, Fonti, Patrick, European Commission, Martínez-Sancho, Elisabet [0000-0003-4413-6818], Slámová, Lenka [0000-0001-8978-0688], Carvalho, Bárbara [0000-0002-4129-2746], Dauphin, Benjamin [0000-0003-0982-4252], Rellstab, Christian [0000-0002-0221-5975], Gugerli, Felix [0000-0003-3878-1845], Opgenoorth, Lars [0000-0003-0737-047X], Heer, Katrin [0000-0002-1036-599X], Knutzen, Florian [0000-0001-9172-4802], von Arx, Georg [0000-0002-8566-4599], Cavers, Stephen [0000-0003-2139-9236], Fady, Bruno [0000-0003-2379-7617], Alía Miranda, Ricardo [0000-0002-9426-0967], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Avanzi, Camilla [0000-0003-1632-5304], Bagnoli, Francesca [0000-0001-6909-0006], Barbas, Evangelos [0000-0002-5760-605X], Bastien, Catherine [0000-0002-9391-6637], Benavides, Raquel [0000-0003-2328-5371], Bernier, Frédéric [0000-0003-4945-7215], Bastias, Cristina C. [0000-0002-2479-2001], Charpentier, Jean-Paul [0000-0002-6029-0498], Climent Maldonado, José María [0000-0002-0815-2645], Danusevicius, Darius [0000-0002-1196-9293], Farsakoglou, Anna Maria [0000-0002-1906-2813], García Del Barrio, José Manuel [0000-0001-7267-6286], Gilg, Olivier [0000-0002-9083-4492], González-Martínez, S. C. [0000-0002-4534-3766], Hurel, Agathe [0000-0002-4853-9123], Kärkkäinen, Katri [0000-0002-3799-3013], Kujala, Sonja T. [0000-0003-0949-6156], Labriola, Mariaceleste [0000-0002-7622-1921], Lascoux, Martin [0000-0003-1699-9042], Lefebvre, Marlène [0000-0002-0929-5744], Le Provost, G. [0000-0003-1561-266X], Liesebach, M. [0000-0001-8840-5026], Malliarou, Ermioni [0000-0003-4478-9173], Matesanz, Silvia [0000-0003-0060-6136], Michotey, Célia [0000-0003-1877-1703], Myking, T. [0000-0002-8207-4542], Notivol, Eduardo [0000-0003-4272-4536], Pakull, Birte [0000-0003-0921-6732], Piotti, Andrea [0000-0002-3324-5325], Plomion, Christophe [0000-0002-3176-2767], Pyhäjärvi, Tanja [0000-0001-6958-5172], Raffin, Annie [0000-0003-2459-4264], Ramírez Valiente, José Alberto [0000-0002-5951-2938], Robledo-Arnuncio, Juan José [0000-0002-3909-8928], Schueler, S.[0000-0003-0155-5692], Semerikov, Vladimir [0000-0002-2942-8794], Spanu, Ilaria [0000-0002-5682-133X], Mette Tollefsrud, Mari [0000-0002-5939-7845], Vendramin, G. G. [0000-0001-9921-7872], Fonti, Patrick [0000-0002-7070-3292], Martínez-Sancho, Elisabet, Slámová, Lenka, Morganti, Sandro, Grefen, Claudio, Carvalho, Bárbara, Dauphin, Benjamin, Rellstab, Christian, Gugerli, Felix, Opgenoorth, Lars, Heer, Katrin, Knutzen, Florian, von Arx, Georg, Valladares Ros, Fernando, Cavers, Stephen, Fady, Bruno, Alía Miranda, Ricardo, Aravanopoulos, Filippos A., Avanzi, Camilla, Bagnoli, Francesca, Barbas, Evangelos, Bastien, Catherine, Benavides, Raquel, Bernier, Frédéric, Bodineau, Guillaume, Bastias, Cristina C., Charpentier, Jean-Paul, Climent Maldonado, José María, Corréard, Marianne, Courdier, Florence, Danusevicius, Darius, Farsakoglou, Anna Maria, García Del Barrio, José Manuel, 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, G., Liesebach, M., Malliarou, Ermioni, Mariotte, Nicolas, Matesanz, Silvia, Michotey, Célia, Milesi, Pascal, Myking, T., Notivol, Eduardo, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Pringarbe, Mehdi, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez Valiente, José Alberto, Ramskogler, Kurt, Robledo-Arnuncio, Juan José, Savolainen, Outi, Schueler, S., Semerikov, Vladimir, Spanu, Ilaria, Thévenet, Jean, Mette Tollefsrud, Mari, Turion, Norbert, Veisse, Dominique, Vendramin, G. G., Villar, Marc, Westin, Johan, and Fonti, Patrick

Abstract

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

Published
2020

16. Genetics to the rescue: managing forests sustainably in a changing world

Author

European Commission, Fady, Bruno [0000-0003-2379-7617], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Benavides, Raquel [0000-0003-2328-5371], González-Martínez, S. C. [0000-0001-6604-889X], Grivet, Delphine [0000-0001-8168-4456], Lascoux, Martin [0000-0003-1699-9042], Lindner, Marcus [0000-0002-0770-003X], Rellstab, Christian [0000-0002-0221-5975], Valladares Ros, Fernando [0000-0002-5374-4682], Vinceti, B. [0000-0001-8908-2994], Fady, Bruno, Aravanopoulos, Filippos A., Benavides, Raquel, González-Martínez, Santiago C., Grivet, Delphine, Lascoux, Martin, Lindner, Marcus, Rellstab, Christian, Valladares Ros, Fernando, Vinceti, B., European Commission, Fady, Bruno [0000-0003-2379-7617], Aravanopoulos, Filippos A. [0000-0001-7194-2642], Benavides, Raquel [0000-0003-2328-5371], González-Martínez, S. C. [0000-0001-6604-889X], Grivet, Delphine [0000-0001-8168-4456], Lascoux, Martin [0000-0003-1699-9042], Lindner, Marcus [0000-0002-0770-003X], Rellstab, Christian [0000-0002-0221-5975], Valladares Ros, Fernando [0000-0002-5374-4682], Vinceti, B. [0000-0001-8908-2994], Fady, Bruno, Aravanopoulos, Filippos A., Benavides, Raquel, González-Martínez, Santiago C., Grivet, Delphine, Lascoux, Martin, Lindner, Marcus, Rellstab, Christian, Valladares Ros, Fernando, and Vinceti, B.

Abstract

There is growing concern that the implementation of political agreements on climate change and biodiversity will not be enough to protect forests in the short run and up to the end of the 21st century. As mitigation efforts are lagging behind self-imposed, reasonable targets, genetic diversity will have a large and significant part to play in the process of adapting forests to climate change. Genetic diversity, the raw material of evolution, can be used for adaptation by natural selection and artificial breeding, in naturally regenerated and plantation forests alike. The 2-day scientific conference: “#rescueforests: Genetics to the rescue - Managing forests sustainably in a changing world,” addressed the genetic diversity of forests. More specifically, the conference was about natural as well as assisted adaptive processes, their spatial scale, from fine grain to landscape and ecoregions, and how much of the genome it involves. It also dealt with phenotypes and how much of their variation is determined by underlying genetic diversity. And finally, and perhaps most importantly, the conference emphasized the importance of conservation and sustainable use of this genetic diversity as a nature-based solution to adapt under the fast pace of climate change. The conference demonstrated how improved knowledge on genomic diversity and evolutionary mechanisms can help to rescue forests, either naturally or by means of management.

Published
2020

17. Genomics and adaptation in forest ecosystems

Author

Neophytou, Charalambos, Heer, Katrin, Milesi, Pascal, Peter, Martina, Pyhäjärvi, Tanja, Westergren, Marjana, Rellstab, Christian, Gugerli, Felix, Neophytou, Charalambos, Heer, Katrin, Milesi, Pascal, Peter, Martina, Pyhäjärvi, Tanja, Westergren, Marjana, Rellstab, Christian, and Gugerli, Felix

Abstract

Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of "Genomics and Adaptation in Forest Ecosystems" brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations.

Published
2022
Full Text
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22. The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Author

Opgenoorth, Lars, Dauphin, Benjamin, Benavides, Raquel, Heer, Katrin, Alizoti, Paraskevi, Martínez-Sancho, Elisabet, Alía, Ricardo, Ambrosio, Olivier, Audrey, Albet, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia, Bagnoli, Francesca, Barbas, Evangelos, Bastias, Cristina C, Bastien, Catherine, Ballesteros, Eduardo, Beffa, Giorgia, Bernier, Frédéric, Bignalet, Henri, Bodineau, Guillaume, Bouic, Damien, Brodbeck, Sabine, Brunetto, William, Buchovska, Jurata, Buy, Melanie, Cabanillas-Saldaña, Ana M, Carvalho, Bárbara, Cheval, Nicolas, Climent, José M, Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Del Caño, Fernando, Denou, Jean-Luc, Di Gerardi, Nicolas, Dokhelar, Bernard, Ducousso, Alexis, Nilsen, Anne Eskild, Farsakoglou, Anna-Maria, Fonti, Patrick, Ganopoulos, Ioannis, García Del Barrio, José M, Gilg, Olivier, González-Martínez, Santiago C, Graf, René, Gray, Alan, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Hollenbach, Enja, Hurel, Agathe, Issehut, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan-Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T, Kumpula, Timo A, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Lejeune, Vincent, Le-Provost, Gregoire, Levillain, Joseph, Liesebach, Mirko, López-Quiroga, David, Meier, Benjamin, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Mas, Antonio, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Nievergelt, Daniel, Notivol, Eduardo, Østreng, Geir, Pakull, Birte, Perry, Annika, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez-Valiente, José A, Rellstab, Christian, Remi, Dourthe, Richter, Sebastian, Robledo-Arnuncio, Juan J, San Segundo, Sergio, Savolainen, Outi, Schueler, Silvio, Schneck, Volker, Scotti, Ivan, Semerikov, Vladimir, Slámová, Lenka, Sønstebø, Jørn Henrik, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, von Arx, Georg, Westin, Johan, Fady, Bruno, Myking, Tor, Valladares, Fernando, Aravanopoulos, Filippos A, Cavers, Stephen, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Philipps Universität Marburg = Philipps University of Marburg, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Aristotle University of Thessaloniki, Department of Forest Ecology and Genetics, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale Forêt Pierroton (UEFP), Istituto di Bioscienze e BioRisorse [Palermo] (IBBR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Biomasse Forestières ORléans (GBFOR), Vytautas Magnus University - Vytauto Didziojo Universitetas (VDU), Unité de Recherche Génomique Info (URGI), Gobierno de Aragon, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unité Expérimentale Entomologie et Forêt Méditerranéenne (UEFM), Bavarian Office for Forest Seeding and Planting, Partenaires INRAE, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), LIECO GmbH & Co KG, Natural Resources Institute Finland (LUKE), University of Oulu, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Thunen Institute of Forest Ecosystems, Thünen Institute, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Universidad Rey Juan Carlos [Madrid] (URJC), Austrian Research Centre for Forests (BFW), Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences (UB RAS), Skogforsk - Swedish Forestry Research Institute, Swiss Secretariat for Education, Research and Innovation (SERI) 6.0032, European Project: 676876,H2020,H2020-SFS-2015-2,GenTree(2016), Philipps Universität Marburg, Museo Nacional de Ciencias Naturales (CSIC), Consiglio Nazionale delle Ricerche (CNR), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centro de Investigacion Y Tecnologia Agroalimentaria de Aragon, Norwegian Institute of Bioeconomy Research (NIBIO), and Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA)

Subjects
crown size, fruit number, Skogsvetenskap, bark thickness, AcademicSubjects/SCI02254, DBH, Forest Science, soil depth, forking index, Botany, Pinus sylvestris, Botanik, Forests, Data Note, stem straightness, Ecology and Environment, Trees, regeneration, branch angle, Fagus, AcademicSubjects/SCI00960, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Picea, height
Abstract

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.

Published
2021

23. The GenTree Leaf Collection: inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Benavides, Raquel, Carvalho, Bárbara, Bastias, Cristina C., López‐Quiroga, David, Mas, Antonio, Cavers, Stephen, Gray, Alan, Albet, Audrey, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia V., Bagnoli, Francesca, Ballesteros, Eduardo, Barbas, Evangelos, Bastien, Catherine, Bernier, Frédéric, Bignalet, Henry, Bouic, Damien, Brunetto, William, Buchovska, Jurata, Cabanillas‐Saldaña, Ana M., Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Del Caño, Fernando, Denou, Jean‐Luc, Dokhelar, Bernard, Dourthe, Rémi, Farsakoglou, Anna‐Maria, Fera, Andreas, Fonti, Patrick, Ganopoulos, Ioannis, García del Barrio, José M., Gilg, Olivier, González‐Martínez, Santiago C., Graf, René, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issehuth, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan‐Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Le Provost, Gregoire, Liesebach, Mirko, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Martínez‐Sancho, Elisabet, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Myking, Tor, Nilsen, Anne E., Notivol, Eduardo, Opgenoorth, Lars, Østreng, Geir, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez‐Valiente, José A., Rellstab, Christian, Richter, Sebastian, Robledo‐Arnuncio, Juan J., San Segundo, Sergio, Savolainen, Outi, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Semerikov, Vladimir, Henrik Sønstebø, Jørn, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, Fady, Bruno, Valladares, Fernando, Benavides, Raquel, Carvalho, Bárbara, Bastias, Cristina C., López‐Quiroga, David, Mas, Antonio, Cavers, Stephen, Gray, Alan, Albet, Audrey, Alía, Ricardo, Ambrosio, Olivier, Aravanopoulos, Filippos, Auñón, Francisco, Avanzi, Camilla, Avramidou, Evangelia V., Bagnoli, Francesca, Ballesteros, Eduardo, Barbas, Evangelos, Bastien, Catherine, Bernier, Frédéric, Bignalet, Henry, Bouic, Damien, Brunetto, William, Buchovska, Jurata, Cabanillas‐Saldaña, Ana M., Cheval, Nicolas, Climent, José M., Correard, Marianne, Cremer, Eva, Danusevičius, Darius, Dauphin, Benjamin, Del Caño, Fernando, Denou, Jean‐Luc, Dokhelar, Bernard, Dourthe, Rémi, Farsakoglou, Anna‐Maria, Fera, Andreas, Fonti, Patrick, Ganopoulos, Ioannis, García del Barrio, José M., Gilg, Olivier, González‐Martínez, Santiago C., Graf, René, Grivet, Delphine, Gugerli, Felix, Hartleitner, Christoph, Heer, Katrin, Hollenbach, Enja, Hurel, Agathe, Issehuth, Bernard, Jean, Florence, Jorge, Veronique, Jouineau, Arnaud, Kappner, Jan‐Philipp, Kärkkäinen, Katri, Kesälahti, Robert, Knutzen, Florian, Kujala, Sonja T., Kumpula, Timo, Labriola, Mariaceleste, Lalanne, Celine, Lambertz, Johannes, Lascoux, Martin, Le Provost, Gregoire, Liesebach, Mirko, Malliarou, Ermioni, Marchon, Jérémy, Mariotte, Nicolas, Martínez‐Sancho, Elisabet, Matesanz, Silvia, Meischner, Helge, Michotey, Célia, Milesi, Pascal, Morganti, Sandro, Myking, Tor, Nilsen, Anne E., Notivol, Eduardo, Opgenoorth, Lars, Østreng, Geir, Pakull, Birte, Piotti, Andrea, Plomion, Christophe, Poinot, Nicolas, Pringarbe, Mehdi, Puzos, Luc, Pyhäjärvi, Tanja, Raffin, Annie, Ramírez‐Valiente, José A., Rellstab, Christian, Richter, Sebastian, Robledo‐Arnuncio, Juan J., San Segundo, Sergio, Savolainen, Outi, Schneck, Volker, Schueler, Silvio, Scotti, Ivan, Semerikov, Vladimir, Henrik Sønstebø, Jørn, Spanu, Ilaria, Thevenet, Jean, Tollefsrud, Mari Mette, Turion, Norbert, Vendramin, Giovanni Giuseppe, Villar, Marc, Westin, Johan, Fady, Bruno, and Valladares, Fernando

Abstract

Motivation: Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU‐Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra‐ and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes. Main types of variable contained: We chose morphological and chemical characters linked to trade‐offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope 13C and 15N in leaves. Spatial location and grain: We surveyed between 18 and 22 populations per species, 141 in total, across Europe. Time period: Leaf sampling took place between 2016 and 2017. Major taxa and level of measurement: We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea. Software format: The data files are in ASCII text, tab delimited, not compressed.

Published
2021

25. Genetics to the rescue : managing forests sustainably in a changing world

Author

Fady, Bruno, Aravanopoulos, Filippos, Benavides, Raquel, Gonzalez-Martinez, Santiago, Grivet, Delphine, Lascoux, Martin, Lindner, Marcus, Rellstab, Christian, Valladares, Fernando, Vinceti, Barbara, Fady, Bruno, Aravanopoulos, Filippos, Benavides, Raquel, Gonzalez-Martinez, Santiago, Grivet, Delphine, Lascoux, Martin, Lindner, Marcus, Rellstab, Christian, Valladares, Fernando, and Vinceti, Barbara

Abstract

There is growing concern that the implementation of political agreements on climate change and biodiversity will not be enough to protect forests in the short run and up to the end of the 21st century. As mitigation efforts are lagging behind self-imposed, reasonable targets, genetic diversity will have a large and significant part to play in the process of adapting forests to climate change. Genetic diversity, the raw material of evolution, can be used for adaptation by natural selection and artificial breeding, in naturally regenerated and plantation forests alike. The 2-day scientific conference: "#rescueforests: Genetics to the rescue - Managing forests sustainably in a changing world," addressed the genetic diversity of forests. More specifically, the conference was about natural as well as assisted adaptive processes, their spatial scale, from fine grain to landscape and ecoregions, and how much of the genome it involves. It also dealt with phenotypes and how much of their variation is determined by underlying genetic diversity. And finally, and perhaps most importantly, the conference emphasized the importance of conservation and sustainable use of this genetic diversity as a nature-based solution to adapt under the fast pace of climate change. The conference demonstrated how improved knowledge on genomic diversity and evolutionary mechanisms can help to rescue forests, either naturally or by means of management.

Published
2020
Full Text
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26. Evolutionary genomics can improve prediction of species’ responses to climate change

Author

Waldvogel, Ann-Marie, Feldmeyer, Barbara, Rolshausen, Gregor, Exposito-Alonso, Moises, Rellstab, Christian, Kofler, Robert, Mock, Thomas, Schmid, Karl, Schmitt, Imke, Bataillon, Thomas, Savolainen, Outi, Bergland, Alan, Flatt, Thomas, Guillaume, Frederic, Pfenninger, Markus, Waldvogel, Ann-Marie, Feldmeyer, Barbara, Rolshausen, Gregor, Exposito-Alonso, Moises, Rellstab, Christian, Kofler, Robert, Mock, Thomas, Schmid, Karl, Schmitt, Imke, Bataillon, Thomas, Savolainen, Outi, Bergland, Alan, Flatt, Thomas, Guillaume, Frederic, and Pfenninger, Markus

Abstract

Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco‐evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large‐scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco‐ evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available re

Published
2020

27. Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species

Author

Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, Zoller, Stefan, Sailer, Christian; https://orcid.org/0000-0003-0070-0317, Tedder, Andrew; https://orcid.org/0000-0002-7378-4673, Gugerli, Felix; https://orcid.org/0000-0003-3878-1845, Shimizu, Kentaro K; https://orcid.org/0000-0002-6483-1781, Holderegger, Rolf; https://orcid.org/0000-0001-7062-1759, Widmer, Alex; https://orcid.org/0000-0001-8253-5137, Fischer, Martin C; https://orcid.org/0000-0002-1888-1809, Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, Zoller, Stefan, Sailer, Christian; https://orcid.org/0000-0003-0070-0317, Tedder, Andrew; https://orcid.org/0000-0002-7378-4673, Gugerli, Felix; https://orcid.org/0000-0003-3878-1845, Shimizu, Kentaro K; https://orcid.org/0000-0002-6483-1781, Holderegger, Rolf; https://orcid.org/0000-0001-7062-1759, Widmer, Alex; https://orcid.org/0000-0001-8253-5137, and Fischer, Martin C; https://orcid.org/0000-0002-1888-1809

Abstract

It has long been discussed to what extent related species develop similar genetic mechanisms to adapt to similar environments. Most studies documenting such convergence have either used different lineages within species or surveyed only a limited portion of the genome. Here, we investigated whether similar or different sets of orthologous genes were involved in genetic adaptation of natural populations of three related plant species to similar environmental gradients in the Alps. We used whole‐genome pooled population sequencing to study genome‐wide SNP variation in 18 natural populations of three Brassicaceae (Arabis alpina, Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We first de novo assembled draft reference genomes for all three species. We then ran population and landscape genomic analyses with ~3 million SNPs per species to look for shared genomic signatures of selection and adaptation in response to similar environmental gradients acting on these species. Genes with a signature of convergent adaptation were found at significantly higher numbers than expected by chance. The most closely related species pair showed the highest relative over‐representation of shared adaptation signatures. Moreover, the identified genes of convergent adaptation were enriched for nonsynonymous mutations, suggesting functional relevance of these genes, even though many of the identified candidate genes have hitherto unknown or poorly described functions based on comparison with Arabidopsis thaliana. We conclude that adaptation to heterogeneous Alpine environments in related species is partly driven by convergent evolution, but that most of the genomic signatures of adaptation remain species‐specific.

Published
2020

28. Ready-to-use workflows for the implementation of genetic tools in conservation management

Author

Holderegger, Rolf; https://orcid.org/0000-0001-7062-1759, Schmidt, Benedikt R; https://orcid.org/0000-0002-4023-1001, Grünig, Christoph, Meier, Robert, Csencsics, Daniela, Gassner, Martin, Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, Stapfer, André, Holderegger, Rolf; https://orcid.org/0000-0001-7062-1759, Schmidt, Benedikt R; https://orcid.org/0000-0002-4023-1001, Grünig, Christoph, Meier, Robert, Csencsics, Daniela, Gassner, Martin, Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, and Stapfer, André

Abstract

We present a conservation genetics tool kit, which offers two ready-to-use workflows for the routine application of genetic methods in conservation management. The workflows were optimized for work load and costs and are accompanied by an easy-to-read and richly illustrated manual with guidelines regarding sampling design, sampling of genetic material, necessary permits, laboratory methods, statistical analyses and documentation of results in a practice-oriented way. The manual also provides a detailed interpretation help for the implementation of the results in conservation management. One workflow deals with the identification of pond-breeding amphibians based on metabarcoding and environmental DNA (eDNA) from water samples. This workflow also discriminates the morphologically similar water frogs (Pelophylax sp.) and other closely related species (e.g. Triturus cristatus and T. carnifex). The second workflow studies connectivity among populations using microsatellite markers. Its statistical analyses encompass the detection of genetic groups and historical, recent and current dispersal and gene flow. Using the two workflows does not involve academic research institutes; they can be applied by environmental consultancies, laboratories from the private sector, governmental agencies or non-governmental organisations. These and additional conservation genetic workflows will hopefully foster the routine use of genetic methods in conservation management.

Published
2020

29. Evolutionary genomics can improve prediction of species’ responses to climate change

Author

Waldvogel, Ann-Marie; https://orcid.org/0000-0003-2637-0766, Feldmeyer, Barbara; https://orcid.org/0000-0002-0413-7245, Rolshausen, Gregor, Exposito-Alonso, Moises; https://orcid.org/0000-0001-5711-0700, Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, Kofler, Robert; https://orcid.org/0000-0001-9960-7248, Mock, Thomas; https://orcid.org/0000-0001-9604-0362, Schmid, Karl, Schmitt, Imke, Bataillon, Thomas; https://orcid.org/0000-0002-4730-2538, Savolainen, Outi, Bergland, Alan, Flatt, Thomas; https://orcid.org/0000-0002-5990-1503, Guillaume, Frederic; https://orcid.org/0000-0003-0874-0081, Pfenninger, Markus; https://orcid.org/0000-0002-1547-7245, Waldvogel, Ann-Marie; https://orcid.org/0000-0003-2637-0766, Feldmeyer, Barbara; https://orcid.org/0000-0002-0413-7245, Rolshausen, Gregor, Exposito-Alonso, Moises; https://orcid.org/0000-0001-5711-0700, Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, Kofler, Robert; https://orcid.org/0000-0001-9960-7248, Mock, Thomas; https://orcid.org/0000-0001-9604-0362, Schmid, Karl, Schmitt, Imke, Bataillon, Thomas; https://orcid.org/0000-0002-4730-2538, Savolainen, Outi, Bergland, Alan, Flatt, Thomas; https://orcid.org/0000-0002-5990-1503, Guillaume, Frederic; https://orcid.org/0000-0003-0874-0081, and Pfenninger, Markus; https://orcid.org/0000-0002-1547-7245

Abstract

Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco-evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large-scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco-evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available res

Published
2020

30. The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe

Author

Benavides, Raquel, primary, Carvalho, Bárbara, additional, Bastias, Cristina C., additional, López‐Quiroga, David, additional, Mas, Antonio, additional, Cavers, Stephen, additional, Gray, Alan, additional, Albet, Audrey, additional, Alía, Ricardo, additional, Ambrosio, Olivier, additional, Aravanopoulos, Filippos, additional, Auñón, Francisco, additional, Avanzi, Camilla, additional, Avramidou, Evangelia V., additional, Bagnoli, Francesca, additional, Ballesteros, Eduardo, additional, Barbas, Evangelos, additional, Bastien, Catherine, additional, Bernier, Frédéric, additional, Bignalet, Henry, additional, Bouic, Damien, additional, Brunetto, William, additional, Buchovska, Jurata, additional, Cabanillas‐Saldaña, Ana M., additional, Cheval, Nicolas, additional, Climent, José M., additional, Correard, Marianne, additional, Cremer, Eva, additional, Danusevičius, Darius, additional, Dauphin, Benjamin, additional, Del Caño, Fernando, additional, Denou, Jean‐Luc, additional, Dokhelar, Bernard, additional, Dourthe, Rémi, additional, Farsakoglou, Anna‐Maria, additional, Fera, Andreas, additional, Fonti, Patrick, additional, Ganopoulos, Ioannis, additional, García del Barrio, José M., additional, Gilg, Olivier, additional, González‐Martínez, Santiago C., additional, Graf, René, additional, Grivet, Delphine, additional, Gugerli, Felix, additional, Hartleitner, Christoph, additional, Heer, Katrin, additional, Hollenbach, Enja, additional, Hurel, Agathe, additional, Issehuth, Bernard, additional, Jean, Florence, additional, Jorge, Veronique, additional, Jouineau, Arnaud, additional, Kappner, Jan‐Philipp, additional, Kärkkäinen, Katri, additional, Kesälahti, Robert, additional, Knutzen, Florian, additional, Kujala, Sonja T., additional, Kumpula, Timo, additional, Labriola, Mariaceleste, additional, Lalanne, Celine, additional, Lambertz, Johannes, additional, Lascoux, Martin, additional, Le Provost, Gregoire, additional, Liesebach, Mirko, additional, Malliarou, Ermioni, additional, Marchon, Jérémy, additional, Mariotte, Nicolas, additional, Martínez‐Sancho, Elisabet, additional, Matesanz, Silvia, additional, Meischner, Helge, additional, Michotey, Célia, additional, Milesi, Pascal, additional, Morganti, Sandro, additional, Myking, Tor, additional, Nilsen, Anne E., additional, Notivol, Eduardo, additional, Opgenoorth, Lars, additional, Østreng, Geir, additional, Pakull, Birte, additional, Piotti, Andrea, additional, Plomion, Christophe, additional, Poinot, Nicolas, additional, Pringarbe, Mehdi, additional, Puzos, Luc, additional, Pyhäjärvi, Tanja, additional, Raffin, Annie, additional, Ramírez‐Valiente, José A., additional, Rellstab, Christian, additional, Richter, Sebastian, additional, Robledo‐Arnuncio, Juan J., additional, San Segundo, Sergio, additional, Savolainen, Outi, additional, Schneck, Volker, additional, Schueler, Silvio, additional, Scotti, Ivan, additional, Semerikov, Vladimir, additional, Henrik Sønstebø, Jørn, additional, Spanu, Ilaria, additional, Thevenet, Jean, additional, Tollefsrud, Mari Mette, additional, Turion, Norbert, additional, Vendramin, Giovanni Giuseppe, additional, Villar, Marc, additional, Westin, Johan, additional, Fady, Bruno, additional, and Valladares, Fernando, additional

Published
2021
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31. Evolutionary genomics can improve prediction of species’ responses to climate change

Author

Waldvogel, Ann‐Marie, primary, Feldmeyer, Barbara, additional, Rolshausen, Gregor, additional, Exposito‐Alonso, Moises, additional, Rellstab, Christian, additional, Kofler, Robert, additional, Mock, Thomas, additional, Schmid, Karl, additional, Schmitt, Imke, additional, Bataillon, Thomas, additional, Savolainen, Outi, additional, Bergland, Alan, additional, Flatt, Thomas, additional, Guillaume, Frederic, additional, and Pfenninger, Markus, additional

Published
2020
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34. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.):A Community-Generated Genomic Resource

Author

Mosca, Elena, Cruz, Fernando, Gomez-Garrido, Jessica, Bianco, Luca, Rellstab, Christian, Brodbeck, Sabine, Csillery, Katalin, Fady, Bruno, Fladung, Matthias, Fussi, Barbara, Gomory, Dusan, Gonzalez-Martinez, Santiago C., Grivet, Delphine, Gut, Marta, Hansen, Ole Kim, Heer, Katrin, Kaya, Zeki, Krutovsky, Konstantin V., Kersten, Birgit, Liepelt, Sascha, Opgenoorth, Lars, Sperisen, Christoph, Ullrich, Kristian K., Vendramin, Giovanni G., Westergren, Marjana, Ziegenhagen, Birgit, Alioto, Tyler, Gugerli, Felix, Heinze, Berthold, Hoehn, Maria, Troggio, Michela, Neale, David B., Mosca, Elena, Cruz, Fernando, Gomez-Garrido, Jessica, Bianco, Luca, Rellstab, Christian, Brodbeck, Sabine, Csillery, Katalin, Fady, Bruno, Fladung, Matthias, Fussi, Barbara, Gomory, Dusan, Gonzalez-Martinez, Santiago C., Grivet, Delphine, Gut, Marta, Hansen, Ole Kim, Heer, Katrin, Kaya, Zeki, Krutovsky, Konstantin V., Kersten, Birgit, Liepelt, Sascha, Opgenoorth, Lars, Sperisen, Christoph, Ullrich, Kristian K., Vendramin, Giovanni G., Westergren, Marjana, Ziegenhagen, Birgit, Alioto, Tyler, Gugerli, Felix, Heinze, Berthold, Hoehn, Maria, Troggio, Michela, and Neale, David B.

Published
2019

35. A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource

Author

Mosca, Elena, primary, Cruz, Fernando, additional, Gómez-Garrido, Jèssica, additional, Bianco, Luca, additional, Rellstab, Christian, additional, Brodbeck, Sabine, additional, Csilléry, Katalin, additional, Fady, Bruno, additional, Fladung, Matthias, additional, Fussi, Barbara, additional, Gömöry, Dušan, additional, González-Martínez, Santiago C, additional, Grivet, Delphine, additional, Gut, Marta, additional, Hansen, Ole Kim, additional, Heer, Katrin, additional, Kaya, Zeki, additional, Krutovsky, Konstantin V, additional, Kersten, Birgit, additional, Liepelt, Sascha, additional, Opgenoorth, Lars, additional, Sperisen, Christoph, additional, Ullrich, Kristian K, additional, Vendramin, Giovanni G, additional, Westergren, Marjana, additional, Ziegenhagen, Birgit, additional, Alioto, Tyler, additional, Gugerli, Felix, additional, Heinze, Berthold, additional, Höhn, Maria, additional, Troggio, Michela, additional, and Neale, David B, additional

Published
2019
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36. Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution

Author

Csilléry, Katalin; https://orcid.org/0000-0003-0039-9296, Rodríguez-Verdugo, Alejandra; https://orcid.org/0000-0002-2048-129X, Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, Guillaume, Frédéric; https://orcid.org/0000-0003-0874-0081, Csilléry, Katalin; https://orcid.org/0000-0003-0039-9296, Rodríguez-Verdugo, Alejandra; https://orcid.org/0000-0002-2048-129X, Rellstab, Christian; https://orcid.org/0000-0002-0221-5975, and Guillaume, Frédéric; https://orcid.org/0000-0003-0874-0081

Abstract

Over the last decade, the genomic revolution has offered the possibility to generate tremendous amounts of data that contain valuable information on the genetic basis of phenotypic traits, such as those linked to human diseases or those that allow for species to adapt to a changing environment. Most ecologically relevant traits are controlled by a large number of genes with small individual effects on trait variation, but that are connected with one another through complex developmental, metabolic, and biochemical networks. As a result, it has recently been suggested that most adaptation events in natural populations are reached via correlated changes at multiple genes at a time, for which the name polygenic adaptation has been coined. The current challenge is to develop methods to extract the relevant information from genomic data to detect the signature of polygenic evolutionary change. The symposium entitled “Detecting the Genomic Signal of Polygenic Adaptation and the Role of Epistasis in Evolution” held in 2017 at the University of Zürich aimed at reviewing our current state of knowledge. In this review, we use the talks of the invited speakers to summarize some of the most recent developments in this field.

Published
2018

37. Bottom-up control of whitefish populations in ultra-oligotrophic Lake Brienz

Author

Müller, Rudolf, Breitenstein, Martina, Bia, Mampasi, Rellstab, Christian, Kirchhofer, Arthur, Müller, Rudolf, Breitenstein, Martina, Bia, Mampasi, Rellstab, Christian, and Kirchhofer, Arthur

Abstract

Lake Brienz, an oligotrophic pre-alpine Swiss lake, went through a mesotrophic period between around 1960 and 1990. The lake is moderately turbid caused by fine suspended solids from glaciers. In 1999, yield of the economically important whitefish collapsed to about 10% of preceding years. Age and growth analysis of the two whitefish types examined - small and large type - revealed an almost complete halt of growth from 1999 until June 2000, paralleled by poor condition. Zooplankton data showed that cladocerans, the preferred food of whitefish, were rare from January 1999 until June 2000. In order to elucidate the trophic relationships between zooplankton and fish, the <> was applied. The analysis showed that poor growth and condition of whitefish in 1999 and 2000 were caused by the scarcity of primary food organisms. The relatively small and slender fish could not be caught by legal gillnets, which resulted in poor fishing yield. Evidence is presented that cladoceran biomass governs food consumption by the fish (<>), while the effect of fish predation on cladocerans was found to be negligible, most likely also during the period of poor growth. Turbidity did not appear to significantly interfere with the feeding of whitefish. Growth, condition and commercial yield of whitefish partly increased again after 2000, but due to the very low productivity of Lake Brienz, fishing yield will remain low. Food chains in such oligotrophic systems are fragile. It is likely that a future collapse of the cladoceran population and, thus, the whitefish fishery will happen again

Published
2018

38. Starving with a full gut? Effect of suspended particles on the fitness of Daphnia hyalina

Author

Rellstab, Christian, Spaak, Piet, Rellstab, Christian, and Spaak, Piet

Abstract

Suspended particles are abiotic factors that can affect the abundance of cladocerans such as daphnids. Ultra-oligotrophic Lake Brienz, situated in the front ranges of the Swiss Alps, is dominated by two major inflows that annually transport over 300,000 tons of suspended glacial material into the lake. A laboratory flow-through experiment was performed to test whether these suspended particles have an influence on the fitness of Daphnia hyalina from Lake Brienz, measured as body size, fecundity and juvenile growth rate, especially when they are simultaneously exposed to low food concentrations. Our results show that the concentration of suspended particles present in Lake Brienz does not reduce the fitness of daphnids, even at very low food concentration. In fact, a low concentration of suspended particles increased the fitness. Reduction of fitness could only be observed at a suspended particle concentration of over 25mgl−1, a level that has never been recorded in Lake Brienz

Published
2018

39. Temporary collapse of the Daphnia population in turbid and ultra-oligotrophic Lake Brienz

Author

Rellstab, Christian, Maurer, Vinzenz, Zeh, Markus, Bürgi, Hans, Spaak, Piet, Rellstab, Christian, Maurer, Vinzenz, Zeh, Markus, Bürgi, Hans, and Spaak, Piet

Abstract

The cyclical parthenogen Daphnia is a key species in aquatic food webs. Its abundance is influenced by environmental factors like food quantity and quality, predation, diseases, temperature and washout by discharge. In ultra-oligotrophic Lake Brienz (Switzerland), which is turbid from suspended glacial material, Daphnia density has continuously decreased since the 1990 s. In spring and summer 1999, during and after a severe flood, Daphnia density was below detection level, but the population recovered the following year. Simultaneously, a drastic two-year decline occurred in the yield of whitefish (Coregonus sp.), which mainly feed on Daphnia. Several hypotheses were tested to explain the collapse of the Daphnia population: a negative effect of the suspended particles, a covering of the diapausing eggs by sediment, and a combined washout/temperature effect. A direct negative effect of the particles and covering of diapausing eggs could be excluded. According to model calculations, the spring growth of the Daphnia population could not compensate the washout losses, as it was limited by poor food conditions due to re-oligotrophication and reduced by extraordinarily low water temperatures. Moreover, ephippia abundance analysed from sediment cores was consistent with the process of eutrophication and re-oligotrophication and indicated that daphnids did not persist in the lake in the period before eutrophication (until 1955). Like most peri-alpine lakes in Europe, Lake Brienz has returned to its natural ultra-oligotrophic state and is now unable to support a large Daphnia population and fishing yield

Published
2018

40. Additional file 2: Table S2. of Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

Author

Fischer, Martin, Rellstab, Christian, Leuzinger, Marianne, Roumet, Marie, Gugerli, Felix, Shimizu, Kentaro, Holderegger, Rolf, and Widmer, Alex

Abstract

Characteristics of 20 microsatellite markers used for Arabidopsis halleri. Source refers to the species for which a microsatellite marker was originally developed. Sequences of forward and reverse primers are shown in 5′ - 3′ direction. The fluorescent dyes used in multiplex PCRs and allele size ranges in base pairs are given for each locus. (PDF 60 kb)

Published
2017
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41. Additional file 10: Figure S6. of Estimating genomic diversity and population differentiation â an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

Author

Fischer, Martin, Rellstab, Christian, Leuzinger, Marianne, Roumet, Marie, Gugerli, Felix, Shimizu, Kentaro, Holderegger, Rolf, and Widmer, Alex

Abstract

Comparison of pairwise population genetic differentiation (F ST) among nine populations of Arabidopsis halleri based on 12 cross-species microsatellite markers and seven species-specific microsatellite markers. r MT represents the correlation coefficient of the Mantel test and p the significance of the correlation. (PDF 181Â kb)

Published
2017
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42. Additional file 9: Figure S5. of Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

Author

Fischer, Martin, Rellstab, Christian, Leuzinger, Marianne, Roumet, Marie, Gugerli, Felix, Shimizu, Kentaro, Holderegger, Rolf, and Widmer, Alex

Abstract

Pearson’s correlation (dashed line) between exome-wide θ Watterson and θ Watterson calculated from introns and intergenic regions in Arabidopsis halleri. (PDF 191 kb)

Published
2017
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43. Additional file 5: Figure S1. of Estimating genomic diversity and population differentiation â an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

Author

Fischer, Martin, Rellstab, Christian, Leuzinger, Marianne, Roumet, Marie, Gugerli, Felix, Shimizu, Kentaro, Holderegger, Rolf, and Widmer, Alex

Abstract

(A) Population specific allele frequency distributions in nine populations of A. halleri for 19 microsatellite markers (blue). (B) Minor allele frequency distributions in the same nine populations across 2,064,681 SNPs (green). Histograms are labelled with population codes (Additional file 1: Table S1). (PDF 1421Â kb)

Published
2017
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44. Additional file 8: Figure S4. of Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

Author

Fischer, Martin, Rellstab, Christian, Leuzinger, Marianne, Roumet, Marie, Gugerli, Felix, Shimizu, Kentaro, Holderegger, Rolf, and Widmer, Alex

Abstract

Relationships between expected SNP heterozygosity (SNP-H e) and expected microsatellite heterozygosity (SSR-H e) of Arabidopsis halleri estimated on the basis of 19 microsatellites and 41,294 genetically unlinked genome-wide single nucleotide polymorphisms (SNPs). For this analysis only every 50th SNP of the more than 2 million SNPs was used. The median distance among two neighbouring SNPs is 1600 bp on the A. thaliana reference genome. (PDF 198 kb)

Published
2017
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45. Additional file 7: Figure S3. of Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

Author

Fischer, Martin, Rellstab, Christian, Leuzinger, Marianne, Roumet, Marie, Gugerli, Felix, Shimizu, Kentaro, Holderegger, Rolf, and Widmer, Alex

Abstract

Observed (solid red lines) versus expected (dotted black lines) distributions of Tajima’s D for nine populations of Arabidopsis halleri. The expected normal distribution consists of 22,210 values with an average of zero and the same standard deviation as the real dataset. p-values indicate whether there was a significant deviation of the average from zero using a t-test. (PDF 370 kb)

Published
2017
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47. Lake origin determines Daphnia population growth under winter conditions

Author

Rellstab, Christian, Spaak, Piet, Rellstab, Christian, and Spaak, Piet

Abstract

In large oligotrophic lakes, growth rates of zooplankton populations decline to low or negative values in winter as a result of low food concentration and water temperature. Daphnia, a key species in the aquatic food web, has two strategies to overwinter: either by sexual reproduction resulting in diapause or as asexual clones in the open water. We investigated how asexually overwintering Daphnia clones, originating from different taxa and lakes with different trophic state, survive under winter conditions. We performed a laboratory experiment exposing D. hyalina and D. hyalina×galeata clones to low water temperature (5°C) and either no or low food (<0.1 mg C L−1) conditions. We used clones from three pre-alpine lakes in Switzerland with contrasting trophic state: ultra-oligotrophic Lake Brienz, mesotrophic Lake Constance and eutrophic Greifensee. Our results show that Daphnia clones can withstand starvation for an average of 6 weeks under low food concentration and for almost 2 weeks under complete absence of food. Besides strong clonal variation, we found a significant effect of food concentration and its interaction with lake origin on population growth rate. Our study indicates that adaptation to local winter conditions is a key factor in defining the clonal, but not necessarily the taxonomic composition of a Daphnia population in unproductive lakes

Published
2017

48. QuercAdapt: Zusammenhang zwischen ökologischen Gradienten und adaptiver genetischer Variation bei Eichen (Quercus robur, Q. petraea und Q. pubescens): Sind Herkunftsregionen heute und in Zukunft ökologisch berechtigt?: Schlussbericht im Forschungsprogramm Wald und Klimawandel

Author

Gugerli, Felix, Walthert, Lorenz, Sperisen, Christoph, and Rellstab, Christian

Subjects
Genetische Variation, Klimawandel, KLIMATISCHE FAKTOREN (PFLANZENÖKOLOGIE), Adaptation
Abstract

Damit eine Population an einem Standort erfolgreich bestehen kann, muss sie an die lokal herrschenden Umweltbedingungen angepasst sein. Demzufolge müssen Populationen ihre genetische Zusammensetzung verändern, um mit den Umweltveränderungen, wie sie insbesondere als Folge des globalen Klimawandels auftreten, Schritt halten zu können. Wenn diese genetischen Änderungen nicht schnell genug stattfinden, reduziert sich die Fitness einer Population und damit ihre Überlebenswahrscheinlichkeit. Kenntnisse über das Ausmass genetischer Variation und über Zusammenhänge dieser Variation mit Umweltfaktoren bilden eine wichtige Grundlage für die Beurteilung der Angepasstheit von Populationen an heutige Umweltbedingungen. Diese Grundlage erlaubt die Einschätzung des Anpassungspotenzials einer Population oder Art an zukünftige Umweltbedingungen. Im Forschungsprojekt QUERCADAPT untersuchten wir am Beispiel der drei häufigsten in der Schweiz vorkommenden Eichenarten, der Traubeneiche (Quercus petraea), Flaumeiche (Q. pubescens) und Stieleiche (Q. robur), ob sich Zusammenhänge zwischen genetischer Variation und Gradienten in Umweltfaktoren aufzeigen lassen, inwieweit diese Zusammenhänge artspezifisch sind und welche Bedeutung diese Erkenntnisse in Bezug auf die forstlichen Herkunftsregionen haben. In 71 Eichenbeständen, verteilt auf die drei Eichenarten und sechs (teils zusammengefasste) Herkunftsregionen, wurden folgende Datensätze erhoben: • interpolierte und modellierte Klimadaten jedes Probenahmestandorts für die Zeiträume 1931-1960 ("heutig", d.h. während der Etablierung der gegenwärtig vorhandenen Bestände) und 2071-2100 (zukünftig); • physikalisch/chemische Bodenfaktoren und Modellierung von Wasserhaushalt sowie von Trockenheitsindices; • Variation an einem molekularen Marker der Chloroplasten-DNA zur Identifizierung möglicher allochthoner Bestände (Abweichung vom Muster aufgrund postglazialer Rückwanderung); • Blattmorphologie und neutrale molekulare Marker (nukleäre Mikrosatelliten) zur Zuteilung der beprobten Bestände zu den drei Eichenarten; • Variation der DNA-Sequenz, erfasst mit Hilfe moderner Sequenziertechnologie, in 95 Genregionen, die aufgrund der Literatur als Kandidaten für lokale Anpassung sind. Die vier in der Einleitung formulierten Fragen und zugehörigen Hypothesen des Projekts QUERCADAPT können wir folgendermassen beantworten: 1) In den 95 Genregionen der drei untersuchten Eichenarten wurden sowohl artspezifisch als auch artübergreifend Genorte identifiziert, die sich durch extreme genetische Differenzierung und/oder eine statistische Beziehung zu Umweltgradienten auszeichnen. Diese Resultate deuten darauf hin, dass die entsprechenden Gene unter starker umweltbedingter Selektion stehen. 2) Die neutrale genetische Differenzierung von Eichenvorkommen innerhalb bzw. zwischen Herkunftsregionen unterscheidet sich nur schwach, was durch weiträumigen Genfluss vornehmlich durch Pollen zu erklären ist. Somit messen wir in Bezug auf die Angepasstheit der untersuchten Populationen den lokalen Standortbedingungen mehr Gewicht bei als den Herkunftsregionen. Bei der Herkunftswahl bei Saatguttransfer sollten somit in erster Linie standörtliche Aspekte (innerhalb wie auch zwischen Herkunftsregionen) berücksichtigt werden. 3) Aufgrund des obigen Resultats erachten wir die Bedeutung der Herkunftsregionen bei der Auswahl von forstlichem Vermehrungsgut als weniger wichtig als die lokalen Standortbedingungen und die genetische Zusammensetzung. Gleiches gilt auch für die Eignung spezifischer Samenerntebestände. Die Herkunft von Saatgut für Anpflanzungen sollte also vorab aufgrund ökologischer und genetischer und nicht grossräumiger geographischer Kriterien erfolgen. 4) Wir haben ein einfaches Konzept entwickelt, anhand dessen die Unangepasstheit einer Herkunft an zukünftige Umweltbedingungen abgeschätzt werden kann. Darauf basierend lässt sich ein diagnostischer molekular-genetischer Test entwickeln, der die Eignung einer Herkunft oder eines Saatguterntebestands in Bezug auf eine spezifische Allel–Umweltbeziehung abschätzen lässt. Diese Entwicklung ist zurzeit in Bearbeitung. Die drei untersuchten Eichenarten zeigten deutliche Unterschiede in ihren Assoziationen von genetischer Variation mit Umweltfaktoren. Ausserdem gab es eine grosse Anzahl artspezifischer genetisch variabler Stellen in den DNA-Sequenzen. Diese Resultate deuten auf eine grosse genetische Vielfalt in den untersuchten Beständen hin, eine wichtige Voraussetzung für lokale Anpassung durch natürliche Selektion. Der Vergleich zwischen "heutigen" und zukünftigen (modellierten) Klimabedingungen an den Probenahmestandorten weist darauf hin, dass alle drei Arten grossen Umweltveränderungen ausgesetzt werden, die entsprechende Anpassungen auf genetischer Ebene erfordern (Änderungen der Allelfrequenzen). Dabei erwies sich die Stieleiche gegenüber der zukünftigen mittleren Jahrestemperatur von den drei Eichenarten am wenigsten gefährdet, während sie in Bezug auf die modellierte Standortwasserbilanz von den drei Eichenarten am schlechtesten angepasst zu sein scheint. Nebst der Anpassung aufgrund von Allelfrequenzänderungen im Bestand selbst dürfte auch der weitreichende Genfluss, vorab durch den windausgebreiteten Pollen, bei Naturverjüngung zu angepassten zukünftigen Eichenbeständen führen. Aufgrund der vorliegenden Resultate empfehlen wir, natürliche Ausbreitung und Naturverjüngung durch entsprechende waldbauliche Massnahmen zu begünstigen und dadurch eine grosse genetische Vielfalt als breite Basis für die natürliche Selektion zu fördern. Dabei wird mit Areal- und Artenverschiebungen zu rechnen sein. Bei Pflanzungen sollte darauf geachtet werden, Vermehrungsgut aus Herkünften zu verwenden, die ähnliche Standortbedingungen aufweisen wie sie am Standort des zu bepflanzenden Bestands herrschen oder in Zukunft zu erwarten sind. Die Muster genetischer Differenzierung an adaptiven Loci sollten dabei berücksichtigt werden, idealerweise durch deren Charakterisierung in Samenerntebestände. In zweiter Priorität sollte wenn möglich auch das genetische Muster der nacheiszeitlichen Rückwanderung und somit die natürlich erfolgte Ausbreitung der Eichenarten in Betracht gezogen und damit erhalten werden. Wir gehen davon aus, dass die natürliche Dynamik, unterstützt durch forstliche Eingriffe zur Förderung der Eichenetablierung, als auch die individuelle Plastizität wesentlich dazu beitragen werden, dass die drei Eichenarten auch in Zukunft ihre Nische im Schweizer Wald finden und behaupten können.

Published
2016
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50. Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

Author

Rellstab, Christian, Zoller, Stefan, Tedder, Andrew, Gugerli, Felix, Fischer, Martin C, and University of Zurich

Subjects
1000 Multidisciplinary, Genotype, lcsh:R, lcsh:Medicine, Genetic Variation, High-Throughput Nucleotide Sequencing, 1100 General Agricultural and Biological Sciences, Polymorphism, Single Nucleotide, 10127 Institute of Evolutionary Biology and Environmental Studies, Gene Frequency, 1300 General Biochemistry, Genetics and Molecular Biology, Brassicaceae, 570 Life sciences, biology, 590 Animals (Zoology), lcsh:Q, lcsh:Science, Research Article
Abstract

Sequencing of pooled samples (Pool-Seq) using next-generation sequencing technologies has become increasingly popular, because it represents a rapid and cost-effective method to determine allele frequencies for single nucleotide polymorphisms (SNPs) in population pools. Validation of allele frequencies determined by Pool-Seq has been attempted using an individual genotyping approach, but these studies tend to use samples from existing model organism databases or DNA stores, and do not validate a realistic setup for sampling natural populations. Here we used pyrosequencing to validate allele frequencies determined by Pool-Seq in three natural populations of Arabidopsis halleri (Brassicaceae). The allele frequency estimates of the pooled population samples (consisting of 20 individual plant DNA samples) were determined after mapping Illumina reads to (i) the publicly available, high-quality reference genome of a closely related species (Arabidopsis thaliana) and (ii) our own de novo draft genome assembly of A. halleri. We then pyrosequenced nine selected SNPs using the same individuals from each population, resulting in a total of 540 samples. Our results show a highly significant and accurate relationship between pooled and individually determined allele frequencies, irrespective of the reference genome used. Allele frequencies differed on average by less than 4%. There was no tendency that either the Pool-Seq or the individual-based approach resulted in higher or lower estimates of allele frequencies. Moreover, the rather high coverage in the mapping to the two reference genomes, ranging from 55 to 284x, had no significant effect on the accuracy of the Pool-Seq. A resampling analysis showed that only very low coverage values (below 10-20x) would substantially reduce the precision of the method. We therefore conclude that a pooled re-sequencing approach is well suited for analyses of genetic variation in natural populations. ISSN:1932-6203

Published
2013

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