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Mendoza-Maya E, Giles-Pérez GI, Vargas-Hernández JJ, Sáenz-Romero C, Martínez-Trujillo M, de Los Angeles Beltrán-Nambo M, Hernández-Díaz JC, Prieto-Ruíz JÁ, Jaramillo-Correa JP, Wehenkel C. Evolutionary drivers of reproductive fitness in two endangered forest trees. THE NEW PHYTOLOGIST 2024; 244:1086-1100. [PMID: 39187985 DOI: 10.1111/nph.20073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024]
Abstract
Population genetics theory predicts a relationship between fitness, genetic diversity (H0) and effective population size (Ne), which is often tested through heterozygosity-fitness correlations (HFCs). We tested whether population and individual fertility and heterozygosity are correlated in two endangered Mexican spruces (Picea martinezii and Picea mexicana) by combining genomic, demographic and reproductive data (seed development and germination traits). For both species, there was a positive correlation between population size and seed development traits, but not germination rate. Individual genome-wide heterozygosity and seed traits were only correlated in P. martinezii (general-effects HFC), and none of the candidate single nucleotide polymorphisms (SNPs) associated with individual fertility showed heterozygote advantage in any species (no local-effects HFC). We observed a single and recent (c. 30 thousand years ago (ka)) population decline for P. martinezii; the collapse of P. mexicana occurred in two phases separated by a long period of stability (c. 800 ka). Recruitment always contributed more to total population census than adult trees in P. mexicana, while this was only the case in the largest populations of P. martinezii. Equating fitness to either H0 or Ne, as traditionally proposed in conservation biology, might not always be adequate, as species-specific evolutionary factors can decouple the expected correlation between these parameters.
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Affiliation(s)
- Eduardo Mendoza-Maya
- Programa Institucional de Doctorado en Ciencias Agropecuarias y Forestales, Universidad Juárez del Estado de Durango, 34000, Durango, Mexico
| | - Gustavo Ibrahim Giles-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - J Jesús Vargas-Hernández
- Postgrado en Ciencias Forestales, Colegio de Postgraduados, Montecillo, Texcoco, 56264, Estado de México, Mexico
| | - Cuauhtémoc Sáenz-Romero
- Instituto de Investigaciones sobre los Recursos Naturales, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, 58330, Michoacán, Mexico
| | - Miguel Martínez-Trujillo
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, 58030, Michoacán, Mexico
| | | | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
| | - José Ángel Prieto-Ruíz
- Facultad de Ciencias Forestales y Ambientales, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, 34120, Durango, Mexico
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Cruz-Nicolás J, Jaramillo-Correa JP, Gernandt DS. Stochastic processes and changes in evolutionary rate are associated with diversification in a lineage of tropical hard pines (Pinus). Mol Phylogenet Evol 2024; 192:108011. [PMID: 38195010 DOI: 10.1016/j.ympev.2024.108011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/08/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
The study of the patterns of polymorphism and molecular evolution among closely related species is key to understanding the evolutionary forces involved in the diversification of lineages. This point is a big challenge in species with slow evolutionary rates, long life cycles, and ancient, shared polymorphisms such as conifers. Under the premise of divergence in a stepwise migration process, we expect clinal geographical patterns of purifying selection efficiency, and genetic structure related to latitude or longitude. If migration is accompanied by changes in the environment, we could further expect a role of positive selection in driving species divergence. Here, we infer patterns of polymorphism, efficiency of purifying selection, and molecular evolution using a dataset of 161 nuclear genes (∼71 Kb) in a lineage of hard pines from North America, the Caribbean, Mexico, and Central America presumed to have migrated from North America toward lower latitudes with tropical conditions. Under the premise of differences in selective pressures, we also look for possible signals of positive selection. To test our hypothesis, first we estimated different indices to infer patterns of polymorphism and efficiency of purifying selection (Ka, Ks, Ka/Ks, dN, dS, dN/dS, and dxy) and compared these metrics across five clades. Also, we investigated possible clinal patterns in these indices and morphological traits (needle length and cone length). Then we inferred genetic structure and environmental differences among species to test for possible signals of positive selection using phylogenetic methods in specific clades. We found differences among clades using Ka, Ks, and Ka/Ks with a relaxation of purifying selection, especially in the Elliotti and Patula clades. We also found environmental differences related to geographic distance, and among clades suggesting differences in selective pressures. The indices Ks, dxy, and needle length had relationships with geography but not ovulate cone length. Finally, we found that most analyzed genes are under purifying selection, but there was an exception of faster evolutionary rate in some pine species, suggesting the possible action of positive selection in divergence. Our study indicated that stochastic processes have played a key role in the diversification of the group, with a possible input of positive selection in pines from Mexico and Central America.
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Affiliation(s)
- Jorge Cruz-Nicolás
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico.
| | - Juan Pablo Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, Mexico.
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3
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Simões ASB, Borges MM, Grazina L, Nunes J. Stone Pine ( Pinus pinea L.) High-Added-Value Genetics: An Overview. Genes (Basel) 2024; 15:84. [PMID: 38254973 PMCID: PMC10815827 DOI: 10.3390/genes15010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Stone pine (Pinus pinea L.) has received limited attention in terms of genetic research. However, genomic techniques hold promise for decoding the stone pine genome and contributing to developing a more resilient bioeconomy. Retrotransposon and specific genetic markers are effective tools for determining population-specific genomic diversity. Studies on the transcriptome and proteome have identified differentially expressed genes PAS1, CLV1, ATAF1, and ACBF involved in shoot bud formation. The stone pine proteome shows variation among populations and shows the industrial potential of the enzyme pinosylvin. Microsatellite studies have revealed low levels of polymorphism and a unique genetic diversity in stone pine, which may contribute to its environmental adaptation. Transcriptomic and proteomic analyses uncover the genetic and molecular responses of stone pine to fungal infections and nematode infestations, elucidating the defense activation, gene regulation, and the potential role of terpenes in pathogen resistance. Transcriptomics associated with carbohydrate metabolism, dehydrins, and transcription factors show promise as targets for improving stone pine's drought stress response and water retention capabilities. Stone pine presents itself as an important model tree for studying climate change adaptation due to its characteristics. While knowledge gaps exist, stone pine's genetic resources hold significant potential, and ongoing advancements in techniques offer prospects for future exploration.
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Affiliation(s)
- Ana Sofia B. Simões
- Association BLC3–Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição 2, Lagares da Beira, 3405-155 Oliveira do Hospital, Portugal; (M.M.B.); (L.G.); (J.N.)
| | - Margarida Machado Borges
- Association BLC3–Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição 2, Lagares da Beira, 3405-155 Oliveira do Hospital, Portugal; (M.M.B.); (L.G.); (J.N.)
| | - Liliana Grazina
- Association BLC3–Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição 2, Lagares da Beira, 3405-155 Oliveira do Hospital, Portugal; (M.M.B.); (L.G.); (J.N.)
| | - João Nunes
- Association BLC3–Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição 2, Lagares da Beira, 3405-155 Oliveira do Hospital, Portugal; (M.M.B.); (L.G.); (J.N.)
- BLC3 Evolution Lda, 3405-155 Oliveira do Hospital, Portugal
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Zhu X, Zou R, Tang J, Deng L, Wei X. Genetic diversity variation during the natural regeneration of Vatica guangxiensis, an endangered tree species with extremely small populations. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
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Scotti I, Lalagüe H, Oddou-Muratorio S, Scotti-Saintagne C, Ruiz Daniels R, Grivet D, Lefevre F, Cubry P, Fady B, González-Martínez SC, Roig A, Lesur-Kupin I, Bagnoli F, Guerin V, Plomion C, Rozenberg P, Vendramin GG. Common microgeographical selection patterns revealed in four European conifers. Mol Ecol 2023; 32:393-411. [PMID: 36301304 DOI: 10.1111/mec.16750] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/06/2022] [Accepted: 10/11/2022] [Indexed: 01/11/2023]
Abstract
Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.
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Affiliation(s)
| | - Hadrien Lalagüe
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, Campus Agronomique, Kourou, France
| | | | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | | | | | - Philippe Cubry
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
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Giles‐Pérez GI, Aguirre‐Planter E, Eguiarte LE, Jaramillo‐Correa JP. Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico. Mol Ecol 2022; 31:5074-5088. [PMID: 35951172 PMCID: PMC9804182 DOI: 10.1111/mec.16646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 01/05/2023]
Abstract
Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they may also evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify factors that may have led to putative reproductive isolation. We explored various competing demographypotheses to account for the rapid divergence of a fir species complex (Abies flinckii-A. religiosa) distributed in "sky-islands" across central Mexico (i.e., along the Trans-Mexican Volcanic Belt; TMVB). Despite co-occurring in two independent sympatric regions (west and centre), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1147 single nucleotide polymorphisms, generated by GBS (genotyping by sequencing), across 23 populations, and compared multiple scenarios based on the geological history of the TMVB. The best-fitting model revealed one of the most rapid and complete speciation cases for a conifer species-pair, dating back to ~1.2 million years ago. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly evolving species complexes as they may account for the large tropical and subtropical diversity.
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Affiliation(s)
- Gustavo I. Giles‐Pérez
- Programa de Doctorado en Ciencias BiomédicasUniversidad Nacional Autónoma de MéxicoCDMXMexico,Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
| | - Erika Aguirre‐Planter
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
| | - Luis E. Eguiarte
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
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7
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Figueroa‐Corona L, Moreno‐Letelier A, Ortega‐Del Vecchyo D, Peláez P, Gernandt DS, Eguiarte LE, Wegrzyn J, Piñero D. Changes in demography and geographic distribution in the weeping pinyon pine ( Pinus pinceana) during the Pleistocene. Ecol Evol 2022; 12:e9369. [PMID: 36225821 PMCID: PMC9534753 DOI: 10.1002/ece3.9369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/12/2022] Open
Abstract
Climate changes, together with geographical barriers imposed by the Sierra Madre Oriental and the Chihuahuan Desert, have shaped the genetic diversity and spatial distribution of different species in northern Mexico. Pinus pinceana Gordon & Glend. tolerates extremely arid conditions. Northern Mexico became more arid during the Quaternary, modifying ecological communities. Here, we try to identify the processes underlying the demographic history of P. pinceana and characterize its genetic diversity using 3100 SNPs from genotyping by sequencing 90 adult individuals from 10 natural populations covering the species' entire geographic distribution. We inferred its population history and contrasted possible demographic scenarios of divergence that modeled the genetic diversity present in this restricted pinyon pine; in support, the past distribution was reconstructed using climate from the Last Glacial Maximum (LGM, 22 kya). We inferred that P. pinceana diverged into two lineages ~2.49 Ma (95% CI 3.28-1.62), colonizing two regions: the Sierra Madre Oriental (SMO) and the Chihuahuan Desert (ChD). Our results of population genomic analyses reveal the presence of heterozygous SNPs in all populations. In addition, low migration rates across regions are probably related to glacial-interglacial cycles, followed by the gradual aridification of the Chihuahuan Desert during the Holocene.
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Affiliation(s)
- Laura Figueroa‐Corona
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | | | - Diego Ortega‐Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de MéxicoJuriquillaMexico
| | - Pablo Peláez
- Centro de Ciencias GenómicasUniversidad Nacional Autónoma de MéxicoCuernavacaMorelosMexico
| | - David S. Gernandt
- Departamento de BotánicaInstituto de Biología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Luis E. Eguiarte
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Daniel Piñero
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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Chen J, Bataillon T, Glémin S, Lascoux M. What does the distribution of fitness effects of new mutations reflect? Insights from plants. THE NEW PHYTOLOGIST 2022; 233:1613-1619. [PMID: 34704271 DOI: 10.1111/nph.17826] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
The distribution of fitness effects (DFE) of new mutations plays a central role in molecular evolution. It is therefore crucial to be able to estimate it accurately from genomic data and to understand the factors that shape it. After a rapid overview of available methods to characterize the fitness effects of mutations, we review what is known on the factors affecting them in plants. Available data indicate that life history traits (e.g. mating system and longevity) have a major effect on the DFE. By contrast, the impact of demography within species appears to be more limited. These results remain to be confirmed, and methods to estimate the joint evolution of demography, life history traits, and the DFE need to be developed.
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Affiliation(s)
- Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, C.F. Möllers Allé 8, Aarhus C, DK-8000, Denmark
| | - Sylvain Glémin
- Centre National de la Recherche Scientifique (CNRS), ECOBIO (Ecosystèmes, Biodiversité, Evolution) - Unité Mixte de Recherche (UMR) 6553, Université de Rennes, Rennes, F-35000, France
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 75236, Sweden
| | - Martin Lascoux
- Program in Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, 75236, Sweden
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Olsson S, Lorenzo Z, Zabal-Aguirre M, Piotti A, Vendramin GG, González-Martínez SC, Grivet D. Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches. PLANT MOLECULAR BIOLOGY 2021; 106:367-380. [PMID: 33934278 DOI: 10.1007/s11103-021-01155-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Complementary gene-resequencing and transcriptomic approaches reveal contrasted evolutionary histories in a species complex. Pinus halepensis and Pinus brutia are closely related species that can intercross, but occupy different geographical ranges and bioclimates. To study the evolution of this species complex and to provide genomic resources for further research, we produce and analyze two new complementary sets of genetic resources: (i) a set of 172 re-sequenced genomic target loci analyzed in 45 individuals, and (ii) a set of 11 transcriptome assemblies. These two datasets provide insights congruent with previous studies: P. brutia displays high level of genetic diversity and no genetic sub-structure, while P. halepensis shows three main genetic clusters, the western Mediterranean and North African clusters displaying much lower genetic diversity than the eastern Mediterranean cluster, the latter cluster having similar genetic diversity to P. brutia. In addition, these datasets provide new insights on the timing of the species-complex history: the two species would have split at the end of the tertiary, and the changing climatic conditions of the Mediterranean region at the end of the Tertiary-beginning of the Quaternary, together with the distinct species tolerance to harsh climatic conditions would have resulted in different geographic distributions, demographic histories and genetic patterns of the two pines. The multiple glacial-interglacial cycles during the Quaternary would have led to the expansion of P. brutia in the Middle East, while P. halepensis would have been through bottlenecks. The last glaciations, from 0.6 Mya on, would have affected further the Western genetic pool of P. halepensis.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
| | - Zaida Lorenzo
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Mario Zabal-Aguirre
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Santiago C González-Martínez
- UMR BIOGECO, INRAE, University of Bordeaux, 33610, Cestas, France
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain
| | - Delphine Grivet
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain.
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