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Westergren M, Archambeau J, Bajc M, Damjanić R, Theraroz A, Kraigher H, Oddou-Muratorio S, González-Martínez SC. Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech. Mol Ecol 2023. [PMID: 37962106 DOI: 10.1111/mec.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.
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Affiliation(s)
| | | | - Marko Bajc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Rok Damjanić
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | | | | | - Sylvie Oddou-Muratorio
- INRAE, URFM, Avignon, France
- INRAE, Univ. de Pau et des Pays de l'Adour, E2S UPPA, ECOBIOP, Saint-Pée-sur-Nivelle, France
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2
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James J, Kastally C, Budde KB, González-Martínez SC, Milesi P, Pyhäjärvi T, Lascoux M. Between but Not Within-Species Variation in the Distribution of Fitness Effects. Mol Biol Evol 2023; 40:msad228. [PMID: 37832225 PMCID: PMC10630145 DOI: 10.1093/molbev/msad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/04/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.
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Affiliation(s)
- Jennifer James
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Swedish Collegium of Advanced Study, Uppsala University, Uppsala, Sweden
| | - Chedly Kastally
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Katharina B Budde
- Department of Forest Genetics and Forest Tree Breeding, Georg-August-University Goettingen, Goettingen, Germany
- Center of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Goettingen, Germany
| | - Santiago C González-Martínez
- National Research Institute for Agriculture, Food and the Environment (INRAE), University of Bordeaux, BIOGECO, Cestas, France
| | - Pascal Milesi
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, Uppsala, Sweden
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Martin Lascoux
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Archambeau J, Benito Garzón M, de Miguel M, Brachi B, Barraquand F, González-Martínez SC. Reduced within-population quantitative genetic variation is associated with climate harshness in maritime pine. Heredity (Edinb) 2023:10.1038/s41437-023-00622-9. [PMID: 37221230 DOI: 10.1038/s41437-023-00622-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023] Open
Abstract
How evolutionary forces interact to maintain genetic variation within populations has been a matter of extensive theoretical debates. While mutation and exogenous gene flow increase genetic variation, stabilizing selection and genetic drift are expected to deplete it. To date, levels of genetic variation observed in natural populations are hard to predict without accounting for other processes, such as balancing selection in heterogeneous environments. We aimed to empirically test three hypotheses: (i) admixed populations have higher quantitative genetic variation due to introgression from other gene pools, (ii) quantitative genetic variation is lower in populations from harsher environments (i.e., experiencing stronger selection), and (iii) quantitative genetic variation is higher in populations from heterogeneous environments. Using growth, phenological and functional trait data from three clonal common gardens and 33 populations (522 clones) of maritime pine (Pinus pinaster Aiton), we estimated the association between the population-specific total genetic variances (i.e., among-clone variances) for these traits and ten population-specific indices related to admixture levels (estimated based on 5165 SNPs), environmental temporal and spatial heterogeneity and climate harshness. Populations experiencing colder winters showed consistently lower genetic variation for early height growth (a fitness-related trait in forest trees) in the three common gardens. Within-population quantitative genetic variation was not associated with environmental heterogeneity or population admixture for any trait. Our results provide empirical support for the potential role of natural selection in reducing genetic variation for early height growth within populations, which indirectly gives insight into the adaptive potential of populations to changing environments.
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Affiliation(s)
- Juliette Archambeau
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, UK.
| | | | - Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Archambeau J, Garzón MB, Barraquand F, Miguel MD, Plomion C, González-Martínez SC. Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree. Am Nat 2022; 200:E141-E159. [DOI: 10.1086/720619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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de Pedro M, Mayol M, González-Martínez SC, Regalado I, Riba M. Environmental patterns of adaptation after range expansion in Leontodon longirostris: The effect of phenological events on fitness-related traits. Am J Bot 2022; 109:602-615. [PMID: 35067917 DOI: 10.1002/ajb2.1815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
PREMISE Because of expected range shifts associated with climate change, there is a renewed interest in the evolutionary factors constraining adaptation, among which are genetic bottlenecks, drift, and increased mutational load after range expansion. Here we study adaptation in the short-lived species Leontodon longirostris showing reduced genetic diversity and increased genetic load along an expansion route. METHODS We assessed the phenological patterns of variation, and their effect on fitness-related traits, on 42 L. longirostris populations and six populations of the sister taxa L. saxatilis in a common garden located within the current range of both species. The comparison among L. longirostris populations allowed us to test for genetic clines consistent with local adaptation, whereas the comparison between taxa provided evidence for common adaptive features at the species level. RESULTS We found significant within-species variability for most traits, as well as differences with its close relative L. saxatilis. In general, seeds from drier, warmer, and unpredictable habitats showed overall lower and more restricted conditions for germination, seedlings emerged later and plants flowered earlier. Consequently, genotypes from arid and unpredictable environments attained smaller reproductive sizes and allocated more biomass to reproduction. Flowering time had the strongest direct effect on total plant size, but seedling emergence also showed an important indirect effect. CONCLUSIONS Our results show the crucial role of phenological patterns in shaping adaptive clines for major life-history stage transitions. Furthermore, the genetic load observed in L. longirostris does not seem to preclude adaptation to the climatic variability encountered along the expansion route.
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Affiliation(s)
| | - Maria Mayol
- CREAF, Cerdanyola del Vallès 08193, Spain
- Univ. Autònoma Barcelona, Cerdanyola del Vallès 08193, Spain
| | | | | | - Miquel Riba
- CREAF, Cerdanyola del Vallès 08193, Spain
- Univ. Autònoma Barcelona, Cerdanyola del Vallès 08193, Spain
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de Miguel M, Rodríguez-Quilón I, Heuertz M, Hurel A, Grivet D, Jaramillo-Correa JP, Vendramin GG, Plomion C, Majada J, Alía R, Eckert AJ, González-Martínez SC. Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae). Mol Ecol 2022; 31:2089-2105. [PMID: 35075727 DOI: 10.1111/mec.16367] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic, i.e., they have a genetic architecture determined by numerous loci each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyze this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response traits) in a clonal common-garden network, planted in contrasted environments (over 12,500 trees). Most of the analyzed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change.
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Affiliation(s)
- Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.,EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Agathe Hurel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Juan-Pablo Jaramillo-Correa
- Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México City, CDMX 04510, Mexico
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino (FI), Italy
| | | | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental ''La Mata'', 33820, Grado, Principado de Asturias, Spain
| | - Ricardo Alía
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Koot E, Arnst E, Taane M, Goldsmith K, Thrimawithana A, Reihana K, González-Martínez SC, Goldsmith V, Houliston G, Chagné D. Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) growing on indigenous Māori land. Hortic Res 2022; 9:uhab012. [PMID: 35039864 PMCID: PMC8771449 DOI: 10.1093/hr/uhab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 06/14/2023]
Abstract
Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9-12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.
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Affiliation(s)
- Emily Koot
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | - Elise Arnst
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - Melissa Taane
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | | | | | - Kiri Reihana
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | | | | | - Gary Houliston
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
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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 Mol Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Opgenoorth L, Dauphin B, Benavides R, Heer K, Alizoti P, Martínez-Sancho E, Alía R, Ambrosio O, Audrey A, Auñón F, Avanzi C, Avramidou E, Bagnoli F, Barbas E, Bastias CC, Bastien C, Ballesteros E, Beffa G, Bernier F, Bignalet H, Bodineau G, Bouic D, Brodbeck S, Brunetto W, Buchovska J, Buy M, Cabanillas-Saldaña AM, Carvalho B, Cheval N, Climent JM, Correard M, Cremer E, Danusevičius D, Del Caño F, Denou JL, di Gerardi N, Dokhelar B, Ducousso A, Eskild Nilsen A, Farsakoglou AM, Fonti P, Ganopoulos I, García Del Barrio JM, Gilg O, González-Martínez SC, Graf R, Gray A, Grivet D, Gugerli F, Hartleitner C, Hollenbach E, Hurel A, Issehut B, Jean F, Jorge V, Jouineau A, Kappner JP, Kärkkäinen K, Kesälahti R, Knutzen F, Kujala ST, Kumpula TA, Labriola M, Lalanne C, Lambertz J, Lascoux M, Lejeune V, Le-Provost G, Levillain J, Liesebach M, López-Quiroga D, Meier B, Malliarou E, Marchon J, Mariotte N, Mas A, Matesanz S, Meischner H, Michotey C, Milesi P, Morganti S, Nievergelt D, Notivol E, Ostreng G, Pakull B, Perry A, Piotti A, Plomion C, Poinot N, Pringarbe M, Puzos L, Pyhäjärvi T, Raffin A, Ramírez-Valiente JA, Rellstab C, Remi D, Richter S, Robledo-Arnuncio JJ, San Segundo S, Savolainen O, Schueler S, Schneck V, Scotti I, Semerikov V, Slámová L, Sønstebø JH, Spanu I, Thevenet J, Tollefsrud MM, Turion N, Vendramin GG, Villar M, von Arx G, Westin J, Fady B, Myking T, Valladares F, Aravanopoulos FA, Cavers S. The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species. Gigascience 2021; 10:6177710. [PMID: 33734368 PMCID: PMC7970660 DOI: 10.1093/gigascience/giab010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/07/2020] [Accepted: 02/03/2021] [Indexed: 11/14/2022] Open
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.
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Affiliation(s)
- Lars Opgenoorth
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany.,Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Benjamin Dauphin
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Raquel Benavides
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Katrin Heer
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Paraskevi Alizoti
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | | | - Ricardo Alía
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Olivier Ambrosio
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Albet Audrey
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Francisco Auñón
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Camilla Avanzi
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Evangelia Avramidou
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Francesca Bagnoli
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Evangelos Barbas
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Cristina C Bastias
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, UMR 5175, 34090, Montpellier, France
| | - Catherine Bastien
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Dept ECOFA, 45075, Orléans, France
| | - Eduardo Ballesteros
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Giorgia Beffa
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Frédéric Bernier
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Henri Bignalet
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Guillaume Bodineau
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), GBFOR, 45075, Orléans, France
| | - Damien Bouic
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Sabine Brodbeck
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - William Brunetto
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Jurata Buchovska
- Vytautas Magnus University, Studentu Street 11, 53361, Akademija, Lithuania
| | - Melanie Buy
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Ana M Cabanillas-Saldaña
- Departamento de Agricultura, Ganadería y Medio Ambiente, Gobierno de Aragón, P. Mª Agustín 36, 50071, Zaragoza, Spain
| | - Bárbara Carvalho
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Nicolas Cheval
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - José M Climent
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Marianne Correard
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Eva Cremer
- Bavarian Institute for Forest Genetics, Forstamtsplatz 1, 83317, Teisendorf, Germany
| | | | - Fernando Del Caño
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Jean-Luc Denou
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Nicolas di Gerardi
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Bernard Dokhelar
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | | | - Anne Eskild Nilsen
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Anna-Maria Farsakoglou
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Patrick Fonti
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), 57001, Thermi, Greece
| | - José M García Del Barrio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Olivier Gilg
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | | | - René Graf
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Alan Gray
- UK Centre for Ecology and Hydrology, Bush Estate Penicuik, EH26 0QB, Edinburgh, UK
| | - Delphine Grivet
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | | | - Enja Hollenbach
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Agathe Hurel
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Bernard Issehut
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Florence Jean
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Veronique Jorge
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), ONF, BIOFORA, 45075, Orléans, France
| | - Arnaud Jouineau
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Jan-Philipp Kappner
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Katri Kärkkäinen
- Natural Resources Institute Finland, Paavo Havaksentie 3, 90014, University of Oulu, Finland
| | - Robert Kesälahti
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Florian Knutzen
- Bavarian Institute for Forest Genetics, Forstamtsplatz 1, 83317, Teisendorf, Germany
| | - Sonja T Kujala
- Natural Resources Institute Finland, Paavo Havaksentie 3, 90014, University of Oulu, Finland
| | - Timo A Kumpula
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Mariaceleste Labriola
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Celine Lalanne
- INRAE, Univsité de Bordeaux, BIOGECO, 33770, Cestas, France
| | - Johannes Lambertz
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Martin Lascoux
- Department of Ecology & Genetics, EBC, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Vincent Lejeune
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), GBFOR, 45075, Orléans, France
| | | | - Joseph Levillain
- Université de Lorraine, AgroParisTech, INRAE, SILVA, 54000, Nancy, France
| | - Mirko Liesebach
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - David López-Quiroga
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Benjamin Meier
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Ermioni Malliarou
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Jérémy Marchon
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Nicolas Mariotte
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Antonio Mas
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933, Móstoles, Spain
| | - Helge Meischner
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Célia Michotey
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), URGI, Versailles, France
| | - Pascal Milesi
- Department of Ecology & Genetics, EBC, Science for Life Laboratory, Uppsala University, 75236, Uppsala, Sweden
| | - Sandro Morganti
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Daniel Nievergelt
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Eduardo Notivol
- Centro de Investigación y Tecnología Agroalimentaria de Aragón - Unidad de Recursos Forestales (CITA), Avda. Montañana 930, 50059, Zaragoza, Spain
| | - Geir Ostreng
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Birte Pakull
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - Annika Perry
- UK Centre for Ecology and Hydrology, Bush Estate Penicuik, EH26 0QB, Edinburgh, UK
| | - Andrea Piotti
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | | | - Nicolas Poinot
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Mehdi Pringarbe
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Luc Puzos
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Tanja Pyhäjärvi
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Annie Raffin
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - José A Ramírez-Valiente
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Christian Rellstab
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Dourthe Remi
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France
| | - Sebastian Richter
- Philipps University Marburg, Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany
| | - Juan J Robledo-Arnuncio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Sergio San Segundo
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Outi Savolainen
- University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu, Finland
| | - Silvio Schueler
- Austrian Research Centre for Forests (BFW), Seckendorff-Gudent-Weg 8, 1131, Wien, Austria
| | - Volker Schneck
- Thünen Institute of Forest Genetics, Eberswalder Chaussee 3a, 15377, Waldsieversdorf, Germany
| | - Ivan Scotti
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural branch of RAS, 8 Marta St. 202, 620144, Ekaterinburg, Russia
| | - Lenka Slámová
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Jørn Henrik Sønstebø
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Ilaria Spanu
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Jean Thevenet
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Mari Mette Tollefsrud
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Norbert Turion
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy
| | - Marc Villar
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), ONF, BIOFORA, 45075, Orléans, France
| | - Georg von Arx
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | | | - Bruno Fady
- Institut National de Recherche en Agriculture, Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Tor Myking
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Fernando Valladares
- LINCGlobal, Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Filippos A Aravanopoulos
- Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement, 54124, Thessaloniki, Greece
| | - Stephen Cavers
- UK Centre for Ecology and Hydrology, Bush Estate Penicuik, EH26 0QB, Edinburgh, UK
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de Pedro M, Riba M, González-Martínez SC, Seoane P, Bautista R, Claros MG, Mayol M. Demography, genetic diversity and expansion load in the colonizing species Leontodon longirostris (Asteraceae) throughout its native range. Mol Ecol 2021; 30:1190-1205. [PMID: 33452714 DOI: 10.1111/mec.15802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 12/25/2022]
Abstract
Unravelling the evolutionary processes underlying range expansions is fundamental to understand the distribution of organisms, as well as to predict their future responses to environmental change. Predictions for range expansions include a loss of genetic diversity and an accumulation of deleterious alleles along the expansion axis, which can decrease fitness at the range-front (expansion load). In plants, empirical studies supporting expansion load are scarce, and its effects remain to be tested outside a few model species. Leontodon longirostris is a colonizing Asteraceae with a widespread distribution in the Western Mediterranean, providing a particularly interesting system to gain insight into the factors that can enhance or mitigate expansion load. In this study, we produced a first genome draft for the species, covering 418 Mbp (~53% of the genome). Although incomplete, this draft was suitable to design a targeted sequencing of ~1.5 Mbp in 238 L. longirostris plants from 21 populations distributed along putative colonization routes in the Iberian Peninsula. Inferred demographic history supports a range expansion from southern Iberia around 40,000 years ago, reaching northern Iberia around 25,000 years ago. The expansion was accompanied by a loss of genetic diversity and a significant increase in the proportion of putatively deleterious mutations. However, levels of expansion load in L. longirostris were smaller than those found in other plant species, which can be explained, at least partially, by its high dispersal ability, the self-incompatible mating system, and the fact that the expansion occurred along a strong environmental cline.
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Affiliation(s)
| | - Miquel Riba
- CREAF, Cerdanyola del Vallès, Spain.,Univ. Autònoma Barcelona, Cerdanyola del Vallès, Spain
| | | | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, and Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Málaga, Spain.,CIBER de Enfermedades Raras (CIBERER), Málaga, Spain.,Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain
| | - Rocío Bautista
- Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain
| | - Manuel Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, and Institute for Mediterranean and Subtropical Horticulture (IHSM-CSIC-UMA), Málaga, Spain.,CIBER de Enfermedades Raras (CIBERER), Málaga, Spain.,Institute of Biomedical Research in Malaga (IBIMA), IBIMA-RARE, Málaga, Spain.,Andalusian Platform for Bioinformatics-SCBI, Universidad de Málaga, Málaga, Spain.,Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Málaga, Spain
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12
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Jaramillo-Correa JP, Bagnoli F, Grivet D, Fady B, Aravanopoulos FA, Vendramin GG, González-Martínez SC. Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse. Mol Ecol 2020; 29:4797-4811. [PMID: 33063352 DOI: 10.1111/mec.15684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022]
Abstract
Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e., evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across 177 gene-loci in a circum-Mediterranean conifer (Pinus pinea L.) that represents one of the most extreme cases of genetic pauperization in widespread outbreeding taxa. We found very little genetic variation in both hypervariable nuclear microsatellites (SSRs) and gene-loci, which translated into genetic diversity estimates one order of magnitude lower than those previously reported for pines. Such values were consistent with a strong population decline that began some ~1 Ma. Comparisons with the related and parapatric maritime pine (Pinus pinaster Ait.) revealed reduced rates of adaptive evolution (α and ωa ) and a significant accumulation of genetic load. It is unlikely that these are the result from differences in mutation rate or linkage disequilibrium between the two species; instead they are the presumable outcome of contrasting demographic histories affecting both the speed at which these taxa accumulate genetic diversity, and the global efficacy of selection. Future studies, and programs for conservation and management, should thus start testing for the effects of genetic load on fitness, and integrating such effects into predictive models.
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Affiliation(s)
- Juan P Jaramillo-Correa
- Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Francesca Bagnoli
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain
| | - Bruno Fady
- INRAE, Unité de Recherche Écologie des Forêts Méditerranéennes (URFM), Avignon, France
| | - Filippos A Aravanopoulos
- Laboratory of Forest Genetics and Tree Breeding, Department of Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Giovanni G Vendramin
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, Italy
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13
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Valdés-Correcher E, Bourdin A, González-Martínez SC, Moreira X, Galmán A, Castagneyrol B, Hampe A. Leaf chemical defences and insect herbivory in oak: accounting for canopy position unravels marked genetic relatedness effects. Ann Bot 2020; 126:865-872. [PMID: 32463869 PMCID: PMC7539359 DOI: 10.1093/aob/mcaa101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Highly controlled experiments document that plant genetic diversity and relatedness can shape herbivore communities and patterns of herbivory. Evidence from the field is, however, scarce and inconsistent. We assessed whether a genetic signal underlying herbivory can be detected in oak woodlands when accounting for variation at smaller (within-tree) and larger (among-stand) scales. METHODS We tested relationships between tree genetic relatedness, leaf chemical defences and insect herbivory for different canopy layers in 240 trees from 15 pedunculate oak (Quercus robur) forest stands. We partitioned sources of variability in herbivory and defences among stands, individuals and branches. KEY RESULTS Leaf defences, insect herbivory and their relationship differed systematically between the upper and the lower tree canopy. When accounting for this canopy effect, the variation explained by tree genetic relatedness rose from 2.8 to 34.1 % for herbivory and from 7.1 to 13.8 % for leaf defences. The effect was driven by markedly stronger relationships in the upper canopy. CONCLUSIONS Our findings illustrate that considerable effects of the host plant genotype on levels of leaf chemical defences and associated insect herbivory can be detected in natural tree populations when within-individual variation is properly accounted for.
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Affiliation(s)
| | | | | | - Xoaquín Moreira
- Misión Biológica de Galicia (MBG-CSIC), Pontevedra, Galicia, Spain
| | - Andrea Galmán
- Misión Biológica de Galicia (MBG-CSIC), Pontevedra, Galicia, Spain
| | | | - Arndt Hampe
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France
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14
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Martínez-Sancho E, Slámová L, Morganti S, Grefen C, Carvalho B, Dauphin B, Rellstab C, Gugerli F, Opgenoorth L, Heer K, Knutzen F, von Arx G, Valladares F, Cavers S, Fady B, Alía R, Aravanopoulos F, Avanzi C, Bagnoli F, Barbas E, Bastien C, Benavides R, Bernier F, Bodineau G, Bastias CC, Charpentier JP, Climent JM, Corréard M, Courdier F, Danusevicius D, Farsakoglou AM, García Del Barrio JM, Gilg O, González-Martínez SC, Gray A, Hartleitner C, Hurel A, Jouineau A, Kärkkäinen K, Kujala ST, Labriola M, Lascoux M, Lefebvre M, Lejeune V, Le-Provost G, Liesebach M, Malliarou E, Mariotte N, Matesanz S, Michotey C, Milesi P, Myking T, Notivol E, Pakull B, Piotti A, Plomion C, Pringarbe M, Pyhäjärvi T, Raffin A, Ramírez-Valiente JA, Ramskogler K, Robledo-Arnuncio JJ, Savolainen O, Schueler S, Semerikov V, Spanu I, Thévenet J, Tollefsrud MM, Turion N, Veisse D, Vendramin GG, Villar M, Westin J, Fonti P. Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe. Sci Data 2020; 7:114. [PMID: 32242054 PMCID: PMC7118108 DOI: 10.1038/s41597-020-0447-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Elisabet Martínez-Sancho
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland.
| | - Lenka Slámová
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Sandro Morganti
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Claudio Grefen
- Philipps-Universität Marburg, Department of Biology, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Barbara Carvalho
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Benjamin Dauphin
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Christian Rellstab
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Felix Gugerli
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Lars Opgenoorth
- Philipps-Universität Marburg, Department of Biology, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Katrin Heer
- Philipps-Universität Marburg, Department of Biology, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Florian Knutzen
- Bavarian Office for Forest Seeding and Planting - ASP, Forstamtsplatz 1, 83317, Teisendorf, Germany
| | - Georg von Arx
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Fernando Valladares
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Stephen Cavers
- Centre for Ecology and Hydrology NERC, EH26 0QB, Edinburgh, United Kingdom
| | - Bruno Fady
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Ricardo Alía
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Filippos Aravanopoulos
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Camilla Avanzi
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Francesca Bagnoli
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Evangelos Barbas
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Catherine Bastien
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Raquel Benavides
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Frédéric Bernier
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Guillaume Bodineau
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Cristina C Bastias
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Jean-Paul Charpentier
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - José M Climent
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Marianne Corréard
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Florence Courdier
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | | | - Anna-Maria Farsakoglou
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - José M García Del Barrio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Olivier Gilg
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | | | - Alan Gray
- Centre for Ecology and Hydrology NERC, EH26 0QB, Edinburgh, United Kingdom
| | | | - Agathe Hurel
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Arnaud Jouineau
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Katri Kärkkäinen
- Natural Resources Institute Finland, University of Oulu, Paavo Havaksen tie 3, 90014, Oulu, Finland
| | - Sonja T Kujala
- Natural Resources Institute Finland, University of Oulu, Paavo Havaksen tie 3, 90014, Oulu, Finland
| | - Mariaceleste Labriola
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Martin Lascoux
- Department of Ecology & Genetics, EBC, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Marlène Lefebvre
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Vincent Lejeune
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Grégoire Le-Provost
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Mirko Liesebach
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - Ermioni Malliarou
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Nicolas Mariotte
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933, Móstoles, Spain
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Center, Science for Life Laboratory, Uppsala University, Norbyvägen, 18 D, 752 36, Uppsala, Sweden
| | - Tor Myking
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Eduardo Notivol
- Centro de Investigación y Tecnología Agroalimentaria de Aragón - Unidad de Recursos Forestales (CITA), Avda. Montañana 930, 50059, Zaragoza, Spain
| | - Birte Pakull
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Christophe Plomion
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Mehdi Pringarbe
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Tanja Pyhäjärvi
- University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Annie Raffin
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - José A Ramírez-Valiente
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Juan J Robledo-Arnuncio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Outi Savolainen
- University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Silvio Schueler
- Austrian Research Centre for Forests (BFW), Seckendorff-Gudent-Weg 8, 1131, Wien, Austria
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural branch of RAS, 8 Marta St. 202, 620144, Ekaterinburg, Russia
| | - Ilaria Spanu
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Jean Thévenet
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Mari Mette Tollefsrud
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933, Móstoles, Spain
| | - Norbert Turion
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Dominique Veisse
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Marc Villar
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | | | - Patrick Fonti
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
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15
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Martínez-Sancho E, Slámová L, Morganti S, Grefen C, Carvalho B, Dauphin B, Rellstab C, Gugerli F, Opgenoorth L, Heer K, Knutzen F, von Arx G, Valladares F, Cavers S, Fady B, Alía R, Aravanopoulos F, Avanzi C, Bagnoli F, Barbas E, Bastien C, Benavides R, Bernier F, Bodineau G, Bastias CC, Charpentier JP, Climent JM, Corréard M, Courdier F, Danusevicius D, Farsakoglou AM, Del Barrio JMG, Gilg O, González-Martínez SC, Gray A, Hartleitner C, Hurel A, Jouineau A, Kärkkäinen K, Kujala ST, Labriola M, Lascoux M, Lefebvre M, Lejeune V, Le-Provost G, Liesebach M, Malliarou E, Mariotte N, Matesanz S, Michotey C, Milesi P, Myking T, Notivol E, Pakull B, Piotti A, Plomion C, Pringarbe M, Pyhäjärvi T, Raffin A, Ramírez-Valiente JA, Ramskogler K, Robledo-Arnuncio JJ, Savolainen O, Schueler S, Semerikov V, Spanu I, Thévenet J, Mette Tollefsrud M, Turion N, Veisse D, Vendramin GG, Villar M, Westin J, Fonti P. The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe. Sci Data 2020; 7:1. [PMID: 31896794 PMCID: PMC6940356 DOI: 10.1038/s41597-019-0340-y] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/21/2019] [Indexed: 11/12/2022] Open
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.
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Affiliation(s)
- Elisabet Martínez-Sancho
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland.
| | - Lenka Slámová
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Sandro Morganti
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Claudio Grefen
- Philipps-Universität Marburg, Department of Biology, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Barbara Carvalho
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Benjamin Dauphin
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Christian Rellstab
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Felix Gugerli
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Lars Opgenoorth
- Philipps-Universität Marburg, Department of Biology, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Katrin Heer
- Philipps-Universität Marburg, Department of Biology, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Florian Knutzen
- Bavarian Office for Forest Seeding and Planting - ASP, Forstamtsplatz 1, 83317, Teisendorf, Germany
| | - Georg von Arx
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Fernando Valladares
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Stephen Cavers
- Centre for Ecology and Hydrology NERC, EH26 0QB, Edinburgh, United Kingdom
| | - Bruno Fady
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Ricardo Alía
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Filippos Aravanopoulos
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Camilla Avanzi
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Francesca Bagnoli
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Evangelos Barbas
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Catherine Bastien
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Raquel Benavides
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Frédéric Bernier
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Guillaume Bodineau
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Cristina C Bastias
- Department of Biogeography and Global Change, National Museum of Natural Sciences MNCN-CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Jean-Paul Charpentier
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - José M Climent
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Marianne Corréard
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Florence Courdier
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | | | - Anna-Maria Farsakoglou
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - José M García Del Barrio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Olivier Gilg
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | | | - Alan Gray
- Centre for Ecology and Hydrology NERC, EH26 0QB, Edinburgh, United Kingdom
| | | | - Agathe Hurel
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Arnaud Jouineau
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Katri Kärkkäinen
- Natural Resources Institute Finland, University of Oulu, Paavo Havaksen tie 3, 90014, Oulu, Finland
| | - Sonja T Kujala
- Natural Resources Institute Finland, University of Oulu, Paavo Havaksen tie 3, 90014, Oulu, Finland
| | - Mariaceleste Labriola
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Martin Lascoux
- Department of Ecology & Genetics, EBC, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Marlène Lefebvre
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Vincent Lejeune
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Grégoire Le-Provost
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Mirko Liesebach
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - Ermioni Malliarou
- Laboratory of Forest Genetics and Tree Breeding, School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Nicolas Mariotte
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933, Móstoles, Spain
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Center, Science for Life Laboratory, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden
| | - Tor Myking
- Division of Forestry and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), P.O. Box 115, 1431, Ås, Norway
| | - Eduardo Notivol
- Centro de Investigación y Tecnología Agroalimentaria de Aragón - Unidad de Recursos Forestales (CITA), Avda. Montañana 930, 50059, Zaragoza, Spain
| | - Birte Pakull
- Thünen Institute of Forest Genetics, Sieker Landstr. 2, 22927, Grosshansdorf, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Christophe Plomion
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - Mehdi Pringarbe
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Tanja Pyhäjärvi
- University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Annie Raffin
- Institut National de la Recherche Agronomique (INRA), route d'Arcachon 69, 33610, Cestas, France
| | - José A Ramírez-Valiente
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Juan J Robledo-Arnuncio
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR), Ctra. de la Coruña km 7.5, 28040, Madrid, Spain
| | - Outi Savolainen
- University of Oulu, Pentti Kaiteran katu 1, 90014, Oulu, Finland
| | - Silvio Schueler
- Austrian Research Centre for Forests (BFW), Seckendorff-Gudent-Weg 8, 1131, Wien, Austria
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural branch of RAS, 8 Marta St. 202, 620144, Ekaterinburg, Russia
| | - Ilaria Spanu
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Jean Thévenet
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Mari Mette Tollefsrud
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933, Móstoles, Spain
| | - Norbert Turion
- Institut National de la Recherche Agronomique (INRA), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France
| | - Dominique Veisse
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources, National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Marc Villar
- Institut National de la Recherche Agronomique (INRA), Avenue de la Pomme de pin 2163, 45075, Orléans, France
| | | | - Patrick Fonti
- Swiss Federal Institute for Forest Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
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16
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Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua. Genetics 2019; 212:815-835. [PMID: 31113811 PMCID: PMC6614902 DOI: 10.1534/genetics.119.302045] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022] Open
Abstract
Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.
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Affiliation(s)
- Paris Veltsos
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
| | - Kate E Ridout
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
- Department of Plant Sciences, University of Oxford, OX1 3RB, United Kingdom
- Department of Oncology, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Melissa A Toups
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
- Department of Integrative Biology, University of Texas, Austin, 78712 Texas
| | | | - Aline Muyle
- Laboratoire Biométrie et Biologie Évolutive (UMR 5558), CNRS/Université Lyon 1, 69100 Villeurbanne, France
| | - Olivier Emery
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
| | - Pasi Rastas
- University of Helsinki, Institute of Biotechnology, 00014, Finland
| | - Vojtech Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200 Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200 Brno, Czech Republic
| | | | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, OX1 3RB, United Kingdom
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
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Mutke S, Vendramin GG, Fady B, Bagnoli F, González-Martínez SC. Molecular and Quantitative Genetics of Stone Pine (Pinus pinea). Sustainable Development and Biodiversity 2019. [DOI: 10.1007/978-3-319-96454-6_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Wachowiak W, Zaborowska J, Łabiszak B, Perry A, Zucca GM, González-Martínez SC, Cavers S. Molecular signatures of divergence and selection in closely related pine taxa. Tree Genet Genomes 2018; 14:83. [PMID: 30930708 PMCID: PMC6404648 DOI: 10.1007/s11295-018-1296-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/01/2018] [Accepted: 10/10/2018] [Indexed: 06/09/2023]
Abstract
Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at 79 nuclear gene fragments (1212 SNPs) in 16 populations (153 individuals) of the closely related, but phenotypically and ecologically distinct, pine taxa Pinus mugo, P. uliginosa and P. uncinata across their European distributions. Simultaneously, mitochondrial DNA markers, which are maternally inherited in pines and distributed by seeds at short geographic distance, were used to assess genetic relationships of the focal populations and taxa. The majority of nuclear loci showed homogenous patterns of variation between the taxa due to a high number of shared SNPs and haplotypes, similar levels of polymorphism, and low net divergence. However, against this common genetic background and an overall low population structure within taxa at mitochondrial markers, we identified several genes showing signatures of selection, accompanied by significant intra- and interspecific divergence. Our results indicate that loci involved in species divergence may be involved in intraspecific local adaptation.
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Affiliation(s)
- Witold Wachowiak
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Julia Zaborowska
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Bartosz Łabiszak
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Annika Perry
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
| | - Giovanni M. Zucca
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
| | | | - Stephen Cavers
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
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Ruiz Daniels R, Taylor RS, Serra-Varela MJ, Vendramin GG, González-Martínez SC, Grivet D. Inferring selection in instances of long-range colonization: The Aleppo pine (Pinus halepensis) in the Mediterranean Basin. Mol Ecol 2018; 27:3331-3345. [PMID: 29972881 DOI: 10.1111/mec.14786] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 05/31/2018] [Accepted: 06/14/2018] [Indexed: 01/03/2023]
Abstract
Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase in genetic drift at the edges of range expansions ("allele surfing") can be a confounding factor. To address this potential issue, we first assess the long-range colonization history of the Aleppo pine across the Mediterranean Basin, using molecular markers. We then look for single nucleotide polymorphisms (SNPs) involved in local adaptation using: (a) environmental correlation methods (bayenv2), focusing on bioclimatic variables important for the species' adaptation (i.e., temperature, precipitation and water availability); and (b) FST -related methods (pcadapt). To assess the rate of false positives caused by the allele surfing effect, these results are compared with results from simulated SNP data that mimics the species' past range expansions and the effect of genetic drift, but with no selection. We find that the Aleppo pine shows a previously unsuspected complex genetic structure across its range, as well as evidence of selection acting on SNPs involved with the response to bioclimatic variables such as drought. This study uses an original approach to disentangle the confounding effects of drift and selection in range margin populations. It also contributes to the increased evidence that plant populations are able to adapt to new environments despite the expected accumulation of deleterious mutations that takes place during long-range colonizations.
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Affiliation(s)
- Rose Ruiz Daniels
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
| | | | - María Jesús Serra-Varela
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Department of Plant Production and Forest Resources, University of Valladolid, Palencia, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino, FI, Italy
| | - Santiago C González-Martínez
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
- BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Madrid, Spain
- Sustainable Forest Management Research Institute, INIA, University of Valladolid, Palencia, Spain
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Olsson S, Pinosio S, González-Martínez SC, Abascal F, Mayol M, Grivet D, Vendramin GG. De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses. Plant Mol Biol 2018; 97:337-345. [PMID: 29850988 DOI: 10.1007/s11103-018-0742-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/25/2018] [Indexed: 06/08/2023]
Abstract
We provide novel genomic resources for Taxus baccata in the form of a reference transcriptome, SSR and SNP markers, and orthologous single-copy genes, useful for phylogenomic and population genomic applications. English yew (T. baccata) is the only European representative of the Taxaceae family, a conifer group originated in the Jurassic period. The wide extent of environmental heterogeneity within the species' range, together with its long presence in Europe, make English yew an ideal species to investigate adaptive evolution in conifers. To enlarge the genomic resources available for this species, we used Illumina short read sequencing followed by de novo assembly to build the transcriptome of English yew. In addition to a fully annotated transcriptome as well as large sets of new potential SSR and SNP markers for T. baccata, we provide a data set of orthologous single-copy genes across three Taxus species using Picea sitchensis as outgroup, and discuss ortholog uses and limitations for phylogenomic and population genomic applications.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Sara Pinosio
- Istituto di Genomica Applicata (IGA), Via J. Linussio, 51, 33100, Udine, Italy
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, 50019, Sesto Fiorentino, FI, Italy
| | - Santiago C González-Martínez
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Federico Abascal
- Human Genetics Department, Sandhu Group, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Maria Mayol
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, 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.
| | - Giovanni G Vendramin
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, 50019, Sesto Fiorentino, FI, Italy
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Veltsos P, Cossard G, Beaudoing E, Beydon G, Savova Bianchi D, Roux C, C González-Martínez S, R Pannell J. Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. Genes (Basel) 2018; 9:E277. [PMID: 29844299 PMCID: PMC6027223 DOI: 10.3390/genes9060277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Abstract
Dioecious plants vary in whether their sex chromosomes are heteromorphic or homomorphic, but even homomorphic sex chromosomes may show divergence between homologues in the non-recombining, sex-determining region (SDR). Very little is known about the SDR of these species, which might represent particularly early stages of sex-chromosome evolution. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, a species with homomorphic sex chromosomes and mild Y-chromosome degeneration. We used RNA sequencing (RNAseq) to identify new Y-linked markers for M. annua. Twelve of 24 transcripts showing male-specific expression in a previous experiment could be amplified by polymerase chain reaction (PCR) only from males, and are thus likely to be Y-linked. Analysis of genome-capture data from multiple populations of M. annua pointed to an additional six male-limited (and thus Y-linked) sequences. We used these markers to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequences, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests that it is enriched for repeats, has low gene density, and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which we estimate to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, both in absolute terms and relative to their genome sizes. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Department of Biology, Jordan Hall, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA.
| | - Guillaume Cossard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel Beaudoing
- Faculty of Biology and Medicine, University of Lausanne, Bâtiment Génopode, 1014 Lausanne, Switzerland.
| | - Genséric Beydon
- National Centre for Genomic Resources (CNRGV), 24 Chemin de Borde Rouge-Auzeville-CS52627, 31326 Castanet Tolosan Cedex, France.
| | | | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- CNRS, University of Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Santiago C González-Martínez
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- BIOGECO, INRA, University of Bordeaux, 33610 Cestas, France.
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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Mosca E, Di Pierro EA, Budde KB, Neale DB, González-Martínez SC. Environmental effects on fine-scale spatial genetic structure in four Alpine keystone forest tree species. Mol Ecol 2018; 27:647-658. [PMID: 29274175 DOI: 10.1111/mec.14469] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 12/22/2022]
Abstract
Genetic responses to environmental changes take place at different spatial scales. While the effect of environment on the distribution of species' genetic diversity at large geographical scales has been the focus of several recent studies, its potential effects on genetic structure at local scales are understudied. Environmental effects on fine-scale spatial genetic structure (FSGS) were investigated in four Alpine conifer species (five to eight populations per species) from the eastern Italian Alps. Significant FSGS was found for 11 of 25 populations. Interestingly, we found no significant differences in FSGS across species but great variation among populations within species, highlighting the importance of local environmental factors. Interannual variability in spring temperature had a small but significant effect on FSGS of Larix decidua, probably related to species-specific life history traits. For Abies alba, Picea abies and Pinus cembra, linear models identified spring precipitation as a potentially relevant climate factor associated with differences in FSGS across populations; however, models had low explanatory power and were strongly influenced by a P. cembra outlier population from a very dry site. Overall, the direction of the identified effects is according to expectations, with drier and more variable environments increasing FSGS. Underlying mechanisms may include climate-related changes in the variance of reproductive success and/or environmental selection of specific families. This study provides new insights on potential changes in local genetic structure of four Alpine conifers in the face of environmental changes, suggesting that new climates, through altering FSGS, may also have relevant impacts on plant microevolution.
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Affiliation(s)
- Elena Mosca
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige, Italy.,Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Erica A Di Pierro
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige, Italy
| | | | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
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Gleiser G, Chybicki IJ, González-Martínez SC, Aizen MA. Phenological match drives pollen-mediated gene flow in a temporally dimorphic tree. Plant Biol (Stuttg) 2018; 20:93-100. [PMID: 29063726 DOI: 10.1111/plb.12651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
Variation in flowering phenology is common in natural populations, and is expected to be, together with inter-mate distance, an important driver of effective pollen dispersal. In populations composed of plants with temporally separated sexual phases (i.e. dichogamous or heterodichogamous populations), pollen-mediated gene flow is assumed to reflect phenological overlap between complementary sexual phases. In this study, we conducted paternity analyses to test this hypothesis in the temporally dimorphic tree Acer opalus. We performed spatially explicit analyses based on categorical and fractional paternity assignment, and included tree size, pair-wise genetic relatedness and morph type as additional predictors. Because differences between morphs in flowering phenology may also influence pollination distances, we modelled separate pollen dispersal kernels for the two morphs. Extended phenological overlap between male and female phases (mainly associated with inter-morph crosses) resulted in higher siring success after accounting for the effects of genetic relatedness, morph type and tree size, while reduced phenological overlap (mainly associated with intra-morph crosses) resulted in longer pollination distances achieved. Siring success also increased in larger trees. Mating patterns could not be predicted by phenology alone. However, as heterogeneity in flowering phenology was the single morph-specific predictor of siring success, it is expected to be key in maintaining the temporal dimorphism in A. opalus, by promoting not only a prevalent pattern of inter-morph mating, but also long-distance pollination resulting from intra-morph mating events.
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Affiliation(s)
- G Gleiser
- Laboratorio Ecotono, INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - I J Chybicki
- Department of Genetics, Kazimierz Wielki University, Bydgoszcz, Poland
| | | | - M A Aizen
- Laboratorio Ecotono, INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
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Grivet D, Avia K, Vaattovaara A, Eckert AJ, Neale DB, Savolainen O, González-Martínez SC. High rate of adaptive evolution in two widespread European pines. Mol Ecol 2017; 26:6857-6870. [PMID: 29110402 DOI: 10.1111/mec.14402] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022]
Abstract
Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ωa ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ωa . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.
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Affiliation(s)
- Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain
| | - Komlan Avia
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, Roscoff, France.,UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, Roscoff, France
| | - Aleksia Vaattovaara
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland.,Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
| | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
| | - Outi Savolainen
- Department of Ecology and Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Madrid, Spain.,Sustainable Forest Management Research Institute, INIA - University of Valladolid, Palencia, Spain.,BIOGECO, INRA, Univ. Bordeaux, Cestas, France
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Torroba-Balmori P, Budde KB, Heer K, González-Martínez SC, Olsson S, Scotti-Saintagne C, Casalis M, Sonké B, Dick CW, Heuertz M. Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species. PLoS One 2017; 12:e0182515. [PMID: 28771629 PMCID: PMC5542443 DOI: 10.1371/journal.pone.0182515] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/08/2017] [Indexed: 01/08/2023] Open
Abstract
The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
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Affiliation(s)
- Paloma Torroba-Balmori
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
| | | | - Katrin Heer
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Conservation Biology and Ecology, University of Marburg, Marburg, Germany
| | - Santiago C. González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
| | | | | | - Bonaventure Sonké
- Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Smithsonian Tropical Research Institute, Republic of Panama
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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Budde KB, González-Martínez SC, Navascués M, Burgarella C, Mosca E, Lorenzo Z, Zabal-Aguirre M, Vendramin GG, Verdú M, Pausas JG, Heuertz M. Increased fire frequency promotes stronger spatial genetic structure and natural selection at regional and local scales in Pinus halepensis Mill. Ann Bot 2017; 119:1061-1072. [PMID: 28159988 PMCID: PMC5604561 DOI: 10.1093/aob/mcw286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/13/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS The recurrence of wildfires is predicted to increase due to global climate change, resulting in severe impacts on biodiversity and ecosystem functioning. Recurrent fires can drive plant adaptation and reduce genetic diversity; however, the underlying population genetic processes have not been studied in detail. In this study, the neutral and adaptive evolutionary effects of contrasting fire regimes were examined in the keystone tree species Pinus halepensis Mill. (Aleppo pine), a fire-adapted conifer. The genetic diversity, demographic history and spatial genetic structure were assessed at local (within-population) and regional scales for populations exposed to different crown fire frequencies. METHODS Eight natural P. halepensis stands were sampled in the east of the Iberian Peninsula, five of them in a region exposed to frequent crown fires (HiFi) and three of them in an adjacent region with a low frequency of crown fires (LoFi). Samples were genotyped at nine neutral simple sequence repeats (SSRs) and at 251 single nucleotide polymorphisms (SNPs) from coding regions, some of them potentially important for fire adaptation. KEY RESULTS Fire regime had no effects on genetic diversity or demographic history. Three high-differentiation outlier SNPs were identified between HiFi and LoFi stands, suggesting fire-related selection at the regional scale. At the local scale, fine-scale spatial genetic structure (SGS) was overall weak as expected for a wind-pollinated and wind-dispersed tree species. HiFi stands displayed a stronger SGS than LoFi stands at SNPs, which probably reflected the simultaneous post-fire recruitment of co-dispersed related seeds. SNPs with exceptionally strong SGS, a proxy for microenvironmental selection, were only reliably identified under the HiFi regime. CONCLUSIONS An increasing fire frequency as predicted due to global change can promote increased SGS with stronger family structures and alter natural selection in P. halepensis and in plants with similar life history traits.
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Affiliation(s)
- Katharina B. Budde
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
- INRA, Université de Bordeaux, UMR 1202 BIOGECO, 33610 Cestas, France
- For correspondence. E-mail or
| | - Santiago C. González-Martínez
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
- INRA, Université de Bordeaux, UMR 1202 BIOGECO, 33610 Cestas, France
| | | | - Concetta Burgarella
- INRA, UMR 1334 AGAP, 34060 Montpellier, France
- Present address: IRD, UMR DIADE, BP 64501, Montpellier, France
| | - Elena Mosca
- Faculty of Science and Technology, Free University of Bolzano, piazza Università 1, 39100 Bolzano, Italy
| | - Zaida Lorenzo
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
| | - Mario Zabal-Aguirre
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
| | - Giovanni G. Vendramin
- National Research Council, Institute of Biosciences and Bioresources, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), 46113 Moncada (Valencia), Spain
| | - Juli G. Pausas
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), 46113 Moncada (Valencia), Spain
| | - Myriam Heuertz
- INIA Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7·5, 28040 Madrid, Spain
- INRA, Université de Bordeaux, UMR 1202 BIOGECO, 33610 Cestas, France
- For correspondence. E-mail or
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Pérez-Izquierdo L, Zabal-Aguirre M, Flores-Rentería D, González-Martínez SC, Buée M, Rincón A. Functional outcomes of fungal community shifts driven by tree genotype and spatial-temporal factors in Mediterranean pine forests. Environ Microbiol 2017; 19:1639-1652. [DOI: 10.1111/1462-2920.13690] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 01/24/2017] [Accepted: 02/02/2017] [Indexed: 12/01/2022]
Affiliation(s)
| | | | | | | | - Marc Buée
- INRA, UMR1136 INRA Nancy - Université de Lorraine, Interactions Arbres-Microorganismes Labex ARBRE; Champenoux 54280 France
| | - Ana Rincón
- Instituto de Ciencias Agrarias; ICA-CSIC. Serrano 115bis Madrid 28006 Spain
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28
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Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 2017; 26:706-717. [PMID: 27997049 DOI: 10.1111/mec.13963] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022]
Abstract
Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 304 Cheatham Hall, Blacksburg, VA 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, 5-108 Centennial Centre for Interdisciplinary Science, Edmonton, AB T6G2E9, Canada
| | - Bruno Fady
- Mediterranean Forest Ecology (URFM), Institut National de la Recherche Agronomique (INRA), Domaine St Paul, Site Agroparc, 84914 Avignon, France
| | | | - Myriam Heuertz
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Juan-Pablo Jaramillo-Correa
- Institute of Ecology, Universidad Nacional Autonoma de Mexico (UNAM) Circuito Exterior s/n, Apartado Postal 70-275, 04510 Ciudad de México, Mexico City, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna Faculty of Life SciencesRennweg 14, Room 217, A-1030, Vienna, Austria
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 EJ Chapman Drive, Knoxville, TN 37996, USA
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University Jordan Hall Addition 5231, Raleigh, NC 27695, USA
| | - Christophe Plomion
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
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29
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Rodríguez-Quilón I, Santos-del-Blanco L, Grivet D, Jaramillo-Correa JP, Majada J, Vendramin GG, Alía R, González-Martínez SC. Local effects drive heterozygosity-fitness correlations in an outcrossing long-lived tree. Proc Biol Sci 2017; 282:20152230. [PMID: 26631567 DOI: 10.1098/rspb.2015.2230] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Heterozygosity-fitness correlations (HFCs) have been used to understand the complex interactions between inbreeding, genetic diversity and evolution. Although frequently reported for decades, evidence for HFCs was often based on underpowered studies or inappropriate methods, and hence their underlying mechanisms are still under debate. Here, we used 6100 genome-wide single nucleotide polymorphisms (SNPs) to test for general and local effect HFCs in maritime pine (Pinus pinaster Ait.), an iconic Mediterranean forest tree. Survival was used as a fitness proxy, and HFCs were assessed at a four-site common garden under contrasting environmental conditions (total of 16 288 trees). We found no significant correlations between genome-wide heterozygosity and fitness at any location, despite variation in inbreeding explaining a substantial proportion of the total variance for survival. However, four SNPs (including two non-synonymous mutations) were involved in significant associations with survival, in particular in the common gardens with higher environmental stress, as shown by a novel heterozygosity-fitness association test at the species-wide level. Fitness effects of SNPs involved in significant HFCs were stable across maritime pine gene pools naturally growing in distinct environments. These results led us to dismiss the general effect hypothesis and suggested a significant role of heterozygosity in specific candidate genes for increasing fitness in maritime pine. Our study highlights the importance of considering the species evolutionary and demographic history and different spatial scales and testing environments when assessing and interpreting HFCs.
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Affiliation(s)
- Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain
| | - Luis Santos-del-Blanco
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne 1015, Switzerland
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain
| | - Juan Pablo Jaramillo-Correa
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México D.F., Mexico
| | - Juan Majada
- CETEMAS-SERIDA, Sección Forestal, Finca Experimental La Mata, Grado 33820, Spain
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Florence) 50019, Italy
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia 34071, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera A Coruña km 7.5, Madrid 28040, Spain INRA, UMR 1202 Biodiversité Gènes Ecosystèmes (Biogeco), Cestas 33610, France Université de Bordeaux, UMR 1202 Biodiversité Gènes Ecosystèmes (Biogeco), Talence 33170, France
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30
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Olsson S, Seoane-Zonjic P, Bautista R, Claros MG, González-Martínez SC, Scotti I, Scotti-Saintagne C, Hardy OJ, Heuertz M. Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers. Mol Ecol Resour 2016; 17:614-630. [PMID: 27718316 DOI: 10.1111/1755-0998.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy-Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain
| | - Pedro Seoane-Zonjic
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Rocío Bautista
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - M Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, and Plataforma Andaluza de Bioinformática, Universidad de Málaga, calle Severo Ochoa 34, E-29590, Campanillas, Málaga, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France
| | - Ivan Scotti
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Caroline Scotti-Saintagne
- INRA, UR629 URFM, Ecologie des Forêts Méditerranéennes, Site Agroparc, Domaine Saint Paul, F-84914, Avignon Cedex 9, France
| | - Olivier J Hardy
- Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Carretera de A Coruña km 7.5, E-28040, Madrid, Spain.,UMR1202 BioGeCo, INRA, Univ. Bordeaux, 69 route d'Arcachon, F-33610, Cestas, France.,Faculté des Sciences, Evolutionary Biology and Ecology, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, CP 160/12, B-1050, Brussels, Belgium
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31
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Macaya-Sanz D, Heuertz M, Lindtke D, Vendramin GG, Lexer C, González-Martínez SC. Causes and consequences of large clonal assemblies in a poplar hybrid zone. Mol Ecol 2016; 25:5330-5344. [PMID: 27661461 DOI: 10.1111/mec.13850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 11/27/2022]
Abstract
Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this study, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with Populus tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional genotyping-by-sequencing data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed from P. tremula, which may have favoured their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically extended individuals does not threaten population survival.
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Affiliation(s)
- David Macaya-Sanz
- Department of Forest Ecology and Genetics, INIA-Forest Research Centre, Madrid, 28040, Spain.,Department of Biology, West Virginia University, Morgantown, WV, 26505, USA
| | | | - Dorothea Lindtke
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, 1700, Switzerland.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (Florence), 50019, Italy
| | - Christian Lexer
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, 1700, Switzerland.,Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Vienna, A-1030, Austria
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA-Forest Research Centre, Madrid, 28040, Spain. .,BIOGECO, INRA, Univ. Bordeaux, Cestas, 33610, France.
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32
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Rodríguez-Quilón I, Santos-Del-Blanco L, Serra-Varela MJ, Koskela J, González-Martínez SC, Alía R. Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species. Ecol Appl 2016; 26:2254-2266. [PMID: 27755736 DOI: 10.1002/eap.1361] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/26/2016] [Accepted: 04/12/2016] [Indexed: 06/06/2023]
Abstract
Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available.
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Affiliation(s)
- Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain.
| | - Luis Santos-Del-Blanco
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, 1015, Switzerland
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
| | - María Jesús Serra-Varela
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
| | - Jarkko Koskela
- Bioversity International, Via dei Tre Denari 472/a, Maccarese, 00057, Italy
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
- BIOGECO, INRA, University of Bordeaux, Cestas, 33610, France
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera A Coruña km 7.5, Madrid, 28040, Spain
- Sustainable Forest Management Research Institute, University of Valladolid-INIA, Palencia, 34071, Spain
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33
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Vizcaíno-Palomar N, Ibáñez I, González-Martínez SC, Zavala MA, Alía R. Adaptation and plasticity in aboveground allometry variation of four pine species along environmental gradients. Ecol Evol 2016; 6:7561-7573. [PMID: 31110659 PMCID: PMC6512899 DOI: 10.1002/ece3.2153] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 02/22/2016] [Accepted: 03/20/2016] [Indexed: 02/01/2023] Open
Abstract
Plant species aboveground allometry can be viewed as a functional trait that reflects the evolutionary trade-off between above- and belowground resources. In forest trees, allometry is related to productivity and resilience in different environments, and it is tightly connected with a compromise between efficiency-safety and competitive ability. A better understanding on how this trait varies within and across species is critical to determine the potential of a species/population to perform along environmental gradients. We followed a hierarchical framework to assess tree height-diameter allometry variation within and across four common European Pinus species. Tree height-diameter allometry variation was a function of solely genetic components -approximated by either population effects or clinal geographic responses of the population's site of origin- and differential genetic plastic responses -approximated by the interaction between populations and two climatic variables of the growing sites (temperature and precipitation)-. Our results suggest that, at the species level, climate of the growing sites set the tree height-diameter allometry of xeric and mesic species (Pinus halepensis, P. pinaster and P. nigra) apart from the boreal species (P. sylvestris), suggesting a weak signal of their phylogenies in the tree height-diameter allometry variation. Moreover, accounting for interpopulation variability within species for the four pine species aided to: (1) detect genetic differences among populations in allometry variation, which in P. nigra and P. pinaster were linked to gene pools -genetic diversity measurements-; (2) reveal the presence of differential genetic variation in plastic responses along two climatic gradients in tree allometry variation. In P. sylvestris and P. nigra, genetic variation was the result of adaptive patterns to climate, while in P. pinaster and P. halepensis, this signal was either weaker or absent, respectively; and (3) detect local adaptation in the exponent of the tree height-diameter allometry relationship in two of the four species (P. sylvestris and P. nigra), as it was a function of populations' latitude and altitude variables. Our findings suggest that the four species have been subjected to different historical and climatic constraints that might have driven their aboveground allometry and promoted different life strategies.
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Affiliation(s)
- Natalia Vizcaíno-Palomar
- Department of Forest Ecology and Genetics Forest Research Centre (INIA) Ctra. A Coruña, km 7.5 28040 Madrid Spain.,Forest Ecology and Restoration Group Department of Life Sciences Universidad de Alcalá Science Building Campus Universitario, 28871 Alcalá de Henares Madrid Spain
| | - Inés Ibáñez
- School of Natural Resources and Environment University of Michigan Ann Arbor Michigan 48109
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics Forest Research Centre (INIA) Ctra. A Coruña, km 7.5 28040 Madrid Spain.,Sustainable Forest Management Research Institute University of Valladolid-INIA Avd. Madrid s/n 34004 Palencia Spain.,BIOGECO, INRA University of Bordeaux 33610 Cestas France
| | - Miguel A Zavala
- Forest Ecology and Restoration Group Department of Life Sciences Universidad de Alcalá Science Building Campus Universitario, 28871 Alcalá de Henares Madrid Spain
| | - Ricardo Alía
- Department of Forest Ecology and Genetics Forest Research Centre (INIA) Ctra. A Coruña, km 7.5 28040 Madrid Spain.,Sustainable Forest Management Research Institute University of Valladolid-INIA Avd. Madrid s/n 34004 Palencia Spain
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34
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Mayol M, Riba M, González-Martínez SC, Bagnoli F, de Beaulieu JL, Berganzo E, Burgarella C, Dubreuil M, Krajmerová D, Paule L, Romšáková I, Vettori C, Vincenot L, Vendramin GG. Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata). New Phytol 2015; 208:973-986. [PMID: 26096330 DOI: 10.1111/nph.13496] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/30/2015] [Indexed: 06/04/2023]
Abstract
Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity.
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Affiliation(s)
| | - Miquel Riba
- CREAF, Cerdanyola del Vallès, 08193, Spain
- Univ Autonòma Barcelona, Cerdanyola del Vallès, 08193, Spain
| | | | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | | | - Concetta Burgarella
- Université Montpellier 2, CNRS UMR, Institut de Sciences de l'Evolution de Montpellier, Montpellier, 5554, France
| | | | - Diana Krajmerová
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ladislav Paule
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ivana Romšáková
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
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35
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Plomion C, Bartholomé J, Lesur I, Boury C, Rodríguez-Quilón I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, de Miguel M, de María N, Cervera MT, Bagnoli F, Isik F, Vendramin GG, González-Martínez SC. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Mol Ecol Resour 2015; 16:574-87. [PMID: 26358548 DOI: 10.1111/1755-0998.12464] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/28/2015] [Accepted: 09/03/2015] [Indexed: 12/18/2022]
Abstract
Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.
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Affiliation(s)
- C Plomion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J Bartholomé
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - I Lesur
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,HelixVenture, F-33700, Mérignac, France
| | - C Boury
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | | | - H Lagraulet
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - F Ehrenmann
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - L Bouffier
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J M Gion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,UMR AGAP, CIRAD, F-33612, Cestas, France
| | - D Grivet
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M de Miguel
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - N de María
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M T Cervera
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - F Bagnoli
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
| | - F Isik
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - G G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
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Cabezas JA, González-Martínez SC, Collada C, Guevara MA, Boury C, de María N, Eveno E, Aranda I, Garnier-Géré PH, Brach J, Alía R, Plomion C, Cervera MT. Nucleotide polymorphisms in a pine ortholog of the Arabidopsis degrading enzyme cellulase KORRIGAN are associated with early growth performance in Pinus pinaster. Tree Physiol 2015; 35:1000-1006. [PMID: 26093373 DOI: 10.1093/treephys/tpv050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and evaluated the predictive performance for genetic merit gain of the most significantly associated genes and single nucleotide polymorphisms (SNPs). We used a second generation 384-SNP array enriched with candidate genes for growth and wood properties to genotype mother trees collected in 20 natural populations covering most of the European distribution of the species. Phenotypic data for total height, polycyclism, root-collar diameter and biomass were obtained from a replicated provenance-progeny trial located in two sites with contrasting environments (Atlantic vs Mediterranean climate). General linear models identified strong associations between growth traits (total height and polycyclism) and four SNPs from the korrigan candidate gene, after multiple testing corrections using false discovery rate. The combined genomic breeding value predictions assessed for the four associated korrigan SNPs by ridge regression-best linear unbiased prediction (RR-BLUP) and cross-validation accounted for up to 8 and 15% of the phenotypic variance for height and polycyclic growth, respectively, and did not improve adding SNPs from other growth-related candidate genes. For root-collar diameter and total biomass, they accounted for 1.6 and 1.1% of the phenotypic variance, respectively, but increased to 15 and 4.1% when other SNPs from lp3.1, lp3.3 and cad were included in RR-BLUP models. These results point towards a desirable integration of candidate-gene studies as a means to pre-select relevant markers, and aid genomic selection in maritime pine breeding programs.
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Affiliation(s)
- José Antonio Cabezas
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Carmen Collada
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain Departamento de Biotecnología, ETSIM, Ciudad Universitaria s/n 28040 Madrid, Spain
| | - María Angeles Guevara
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Nuria de María
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Emmanuelle Eveno
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Ismael Aranda
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Pauline H Garnier-Géré
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Jean Brach
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - María Teresa Cervera
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
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Santos-del-Blanco L, Alía R, González-Martínez SC, Sampedro L, Lario F, Climent J. Correlated genetic effects on reproduction define a domestication syndrome in a forest tree. Evol Appl 2015; 8:403-10. [PMID: 25926884 PMCID: PMC4408150 DOI: 10.1111/eva.12252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/04/2015] [Indexed: 02/03/2023] Open
Abstract
Compared to natural selection, domestication implies a dramatic change in traits linked to fitness. A number of traits conferring fitness in the wild might be detrimental under domestication, and domesticated species typically differ from their ancestors in a set of traits known as the domestication syndrome. Specifically, trade-offs between growth and reproduction are well established across the tree of life. According to allocation theory, selection for growth rate is expected to indirectly alter life-history reproductive traits, diverting resources from reproduction to growth. Here we tested this hypothesis by examining the genetic change and correlated responses of reproductive traits as a result of selection for timber yield in the tree Pinus pinaster. Phenotypic selection was carried out in a natural population, and progenies from selected trees were compared with those of control trees in a common garden experiment. According to expectations, we detected a genetic change in important life-history traits due to selection. Specifically, threshold sizes for reproduction were much higher and reproductive investment relative to size significantly lower in the selected progenies just after a single artificial selection event. Our study helps to define the domestication syndrome in exploited forest trees and shows that changes affecting developmental pathways are relevant in domestication processes of long-lived plants.
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Affiliation(s)
- Luis Santos-del-Blanco
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
- Department of Ecology and Evolution, University of LausanneLausanne, Switzerland
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
| | | | - Francisco Lario
- Vivero de Maceda, Dirección Técnica, TRAGSAMaceda, Ourense, Spain
| | - José Climent
- Department of Forest Ecology and Genetics, INIA-CIFORMadrid, Spain
- Sustainable Forest Management Research InstitutePalencia, Spain
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Berens DG, Braun C, González-Martínez SC, Griebeler EM, Nathan R, Böhning-Gaese K. Fine-scale spatial genetic dynamics over the life cycle of the tropical tree Prunus africana. Heredity (Edinb) 2014; 113:401-7. [PMID: 24849171 PMCID: PMC4220715 DOI: 10.1038/hdy.2014.40] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/09/2022] Open
Abstract
Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.
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Affiliation(s)
- D G Berens
- Department of Ecology, Institute for
Zoology, Johannes Gutenberg-University of Mainz, Mainz,
Germany
- Department of Ornithology, National
Museums of Kenya, Nairobi, Kenya
| | - C Braun
- Department of Ecology, Institute for
Zoology, Johannes Gutenberg-University of Mainz, Mainz,
Germany
| | | | - E M Griebeler
- Department of Ecology, Institute for
Zoology, Johannes Gutenberg-University of Mainz, Mainz,
Germany
| | - R Nathan
- Movement Ecology Lab, Department of
Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Edmond J
Safra Campus, Givat Ram, Jerusalem, Israel
| | - K Böhning-Gaese
- Department of Ecology, Institute for
Zoology, Johannes Gutenberg-University of Mainz, Mainz,
Germany
- Department of Ornithology, National
Museums of Kenya, Nairobi, Kenya
- Biodiversity and Climate Research Centre
(BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt
(Main), Germany
- Department of Biological Sciences, Goethe
University, Frankfurt (Main), Germany
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39
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Csilléry K, Lalagüe H, Vendramin GG, González-Martínez SC, Fady B, Oddou-Muratorio S. Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations. Mol Ecol 2014; 23:4696-708. [PMID: 25156570 DOI: 10.1111/mec.12902] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 01/17/2023]
Abstract
Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors.
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Affiliation(s)
- Katalin Csilléry
- UR629, Écologie Forestière Méditerranéenne, INRA, Domaine Saint Paul, Avignon, F-84914, France
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Alía R, Chambel R, Notivol E, Climent J, González-Martínez SC. Environment-dependent microevolution in a Mediterranean pine (Pinus pinaster Aiton). BMC Evol Biol 2014; 14:200. [PMID: 25245540 PMCID: PMC4177426 DOI: 10.1186/s12862-014-0200-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/08/2014] [Indexed: 11/17/2022] Open
Abstract
Background A central question for understanding the evolutionary responses of plant species to rapidly changing environments is the assessment of their potential for short-term (in one or a few generations) genetic change. In our study, we consider the case of Pinus pinaster Aiton (maritime pine), a widespread Mediterranean tree, and (i) test, under different experimental conditions (growth chamber and semi-natural), whether higher recruitment in the wild from the most successful mothers is due to better performance of their offspring; and (ii) evaluate genetic change in quantitative traits across generations at two different life stages (mature trees and seedlings) that are known to be under strong selection pressure in forest trees. Results Genetic control was high for most traits (h2 = 0.137-0.876) under the milder conditions of the growth chamber, but only for ontogenetic change (0.276), total height (0.415) and survival (0.719) under the more stressful semi-natural conditions. Significant phenotypic selection gradients were found in mature trees for traits related to seed quality (germination rate and number of empty seeds). Moreover, female relative reproductive success was significantly correlated with offspring performance for specific leaf area (SLA) in the growth chamber experiment, and stem mass fraction (SMF) in the experiment under semi-natural conditions, two adaptive traits related to abiotic stress-response in pines. Selection gradients based on genetic covariance of seedling traits and responses to selection at this stage involved traits related to biomass allocation (SMF) and growth (as decomposed by a Gompertz model) or delayed ontogenetic change, depending also on the testing environment. Conclusions Despite the evidence of microevolutionary change in adaptive traits in maritime pine, directional or disruptive changes are difficult to predict due to variable selection at different life stages and environments. At mature-tree stages, higher female effective reproductive success can be explained by differences in their production of offspring (due to seed quality) and, to a lesser extent, by seemingly better adapted seedlings. Selection gradients and responses to selection for seedlings also differed across experimental conditions. The distinct processes involved at the two life stages (mature trees or seedlings) together with environment-specific responses advice caution when predicting likely evolutionary responses to environmental change in Mediterranean forest trees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0200-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA-Forest Research Centre (CIFOR), Avda, A Coruña km 7,5, Madrid, Spain.
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Hernández-Serrano A, Verdú M, Santos-Del-Blanco L, Climent J, González-Martínez SC, Pausas JG. Heritability and quantitative genetic divergence of serotiny, a fire-persistence plant trait. Ann Bot 2014; 114:571-7. [PMID: 25008363 PMCID: PMC4204669 DOI: 10.1093/aob/mcu142] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 05/19/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Although it is well known that fire acts as a selective pressure shaping plant phenotypes, there are no quantitative estimates of the heritability of any trait related to plant persistence under recurrent fires, such as serotiny. In this study, the heritability of serotiny in Pinus halepensis is calculated, and an evaluation is made as to whether fire has left a selection signature on the level of serotiny among populations by comparing the genetic divergence of serotiny with the expected divergence of neutral molecular markers (QST-FST comparison). METHODS A common garden of P. halepensis was used, located in inland Spain and composed of 145 open-pollinated families from 29 provenances covering the entire natural range of P. halepensis in the Iberian Peninsula and Balearic Islands. Narrow-sense heritability (h(2)) and quantitative genetic differentiation among populations for serotiny (QST) were estimated by means of an 'animal model' fitted by Bayesian inference. In order to determine whether genetic differentiation for serotiny is the result of differential natural selection, QST estimates for serotiny were compared with FST estimates obtained from allozyme data. Finally, a test was made of whether levels of serotiny in the different provenances were related to different fire regimes, using summer rainfall as a proxy for fire regime in each provenance. KEY RESULTS Serotiny showed a significant narrow-sense heritability (h(2)) of 0·20 (credible interval 0·09-0·40). Quantitative genetic differentiation among provenances for serotiny (QST = 0·44) was significantly higher than expected under a neutral process (FST = 0·12), suggesting adaptive differentiation. A significant negative relationship was found between the serotiny level of trees in the common garden and summer rainfall of their provenance sites. CONCLUSIONS Serotiny is a heritable trait in P. halepensis, and selection acts on it, giving rise to contrasting serotiny levels among populations depending on the fire regime, and supporting the role of fire in generating genetic divergence for adaptive traits.
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Affiliation(s)
- Ana Hernández-Serrano
- CIDE-CSIC, Ctra. Moncada - Nàquera Km. 4·5 (IVIA campus), 46113 Moncada, Valencia, Spain
| | - Miguel Verdú
- CIDE-CSIC, Ctra. Moncada - Nàquera Km. 4·5 (IVIA campus), 46113 Moncada, Valencia, Spain
| | - Luís Santos-Del-Blanco
- INIA-Forest Research Centre, Ctra. A Coruña Km 7·5, 28040 Madrid, Spain Sustainable Forest Management Research Institute, INIA-University of Valladolid, Palencia, Spain Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - José Climent
- INIA-Forest Research Centre, Ctra. A Coruña Km 7·5, 28040 Madrid, Spain Sustainable Forest Management Research Institute, INIA-University of Valladolid, Palencia, Spain
| | - Santiago C González-Martínez
- INIA-Forest Research Centre, Ctra. A Coruña Km 7·5, 28040 Madrid, Spain Department of Ecology and Evolution, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Juli G Pausas
- CIDE-CSIC, Ctra. Moncada - Nàquera Km. 4·5 (IVIA campus), 46113 Moncada, Valencia, Spain
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42
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Pinosio S, González-Martínez SC, Bagnoli F, Cattonaro F, Grivet D, Marroni F, Lorenzo Z, Pausas JG, Verdú M, Vendramin GG. First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill. Mol Ecol Resour 2014; 14:846-56. [PMID: 24450970 DOI: 10.1111/1755-0998.12232] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/15/2014] [Accepted: 01/17/2014] [Indexed: 11/30/2022]
Abstract
Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48,629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34,014 SNPs across species, with a Ka /Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28,236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes.
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Affiliation(s)
- S Pinosio
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Firenze, Italy; IGA Technology Services s.r.l., Via J. Linussio, 51, 33100, Udine, Italy
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43
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Budde KB, Heuertz M, Hernández-Serrano A, Pausas JG, Vendramin GG, Verdú M, González-Martínez SC. In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster). New Phytol 2014; 201:230-241. [PMID: 24015853 DOI: 10.1111/nph.12483] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/28/2013] [Indexed: 05/28/2023]
Abstract
Wildfire is a major ecological driver of plant evolution. Understanding the genetic basis of plant adaptation to wildfire is crucial, because impending climate change will involve fire regime changes worldwide. We studied the molecular genetic basis of serotiny, a fire-related trait, in Mediterranean maritime pine using association genetics. A single nucleotide polymorphism (SNP) set was used to identify genotype : phenotype associations in situ in an unstructured natural population of maritime pine (eastern Iberian Peninsula) under a mixed-effects model framework. RR-BLUP was used to build predictive models for serotiny in this region. Model prediction power outside the focal region was tested using independent range-wide serotiny data. Seventeen SNPs were potentially associated with serotiny, explaining approximately 29% of the trait phenotypic variation in the eastern Iberian Peninsula. Similar prediction power was found for nearby geographical regions from the same maternal lineage, but not for other genetic lineages. Association genetics for ecologically relevant traits evaluated in situ is an attractive approach for forest trees provided that traits are under strong genetic control and populations are unstructured, with large phenotypic variability. This will help to extend the research focus to ecological keystone non-model species in their natural environments, where polymorphisms acquired their adaptive value.
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Affiliation(s)
- Katharina B Budde
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, 28040, Madrid, Spain
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, 28040, Madrid, Spain
| | - Ana Hernández-Serrano
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC/UV/GV), 46113, Moncada, Valencia, Spain
| | - Juli G Pausas
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC/UV/GV), 46113, Moncada, Valencia, Spain
| | - Giovanni G Vendramin
- Plant Genetics Institute, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC/UV/GV), 46113, Moncada, Valencia, Spain
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44
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Mosca E, González-Martínez SC, Neale DB. Environmental versus geographical determinants of genetic structure in two subalpine conifers. New Phytol 2014; 201:180-192. [PMID: 24102203 DOI: 10.1111/nph.12476] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation.
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Affiliation(s)
- Elena Mosca
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
| | | | - David B Neale
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
- Department of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA
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Abstract
PREMISE OF THE STUDY Serotiny (delayed seed release with the consequent accumulation of a canopy seedbank) confers fitness benefits in environments with crown-fire regimes. Thus, we predicted that serotiny level should be higher in populations recurrently subjected to crown-fires than in populations where crown-fires are rare. In addition, under a high frequency of fires, space and resources are recurrently available, permitting recruitment around each mother to follow the seed rain shadow. Thus, we also predicted spatial aggregation of serotiny within populations. METHODS We compared serotiny, considering both the proportion and the age of serotinous cones, in populations living in contrasting fire regimes for two iconic Mediterranean pine species (Pinus halepensis, P. pinaster). We framed our results by quantitatively comparing the strength of the fire-serotiny relationship with previous studies worldwide. KEY RESULTS For the two species, populations living under high crown-fire recurrence regimes had a higher serotiny level than those populations where the recurrence of crown-fires was low. For P. halepensis (the species with higher serotiny), populations in high fire recurrence regimes had higher fine-scale spatial aggregation of serotiny than those inhabiting low fire recurrence systems. The strength of the observed fire-serotiny relationship in P. halepensis is among the highest in published literature. CONCLUSIONS Fire regime shapes serotiny level among populations, and in populations with high serotiny, recurrent fires maintain a significant spatial structure for this trait. Consequently, fire has long-term evolutionary implications at different scales, emphasizing its prominent role in shaping the ecology of pines.
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Lindtke D, González-Martínez SC, Macaya-Sanz D, Lexer C. Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations. Heredity (Edinb) 2013; 111:474-85. [PMID: 23860234 PMCID: PMC3833683 DOI: 10.1038/hdy.2013.69] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 06/06/2013] [Accepted: 06/12/2013] [Indexed: 01/30/2023] Open
Abstract
Uncovering the genetic architecture of species differences is of central importance for understanding the origin and maintenance of biological diversity. Admixture mapping can be used to identify the number and effect sizes of genes that contribute to the divergence of ecologically important traits, even in taxa that are not amenable to laboratory crosses because of their long generation time or other limitations. Here, we apply admixture mapping to naturally occurring hybrids between two ecologically divergent Populus species. We map quantitative trait loci for eight leaf morphological traits using 77 mapped microsatellite markers from all 19 chromosomes of Populus. We apply multivariate linear regression analysis allowing the modeling of additive and non-additive gene action and identify several candidate genomic regions associated with leaf morphology using an information-theoretic approach. We perform simulation studies to assess the power and limitations of admixture mapping of quantitative traits in natural hybrid populations for a variety of genetic architectures and modes of gene action. Our results indicate that (1) admixture mapping has considerable power to identify the genetic architecture of species differences if sample sizes and marker densities are sufficiently high, (2) modeling of non-additive gene action can help to elucidate the discrepancy between genotype and phenotype sometimes seen in interspecific hybrids, and (3) the genetic architecture of leaf morphological traits in the studied Populus species involves complementary and overdominant gene action, providing the basis for rapid adaptation of these ecologically important forest trees.
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Affiliation(s)
- D Lindtke
- Unit of Ecology and Evolution, Department of
Biology, University of Fribourg, Fribourg,
Switzerland
| | - S C González-Martínez
- INIA, Forest Research Centre, Department of
Forest Ecology and Genetics, Madrid, Spain
| | - D Macaya-Sanz
- INIA, Forest Research Centre, Department of
Forest Ecology and Genetics, Madrid, Spain
- Technical University of Madrid, ETS Forestry
Engineering, Department of Silviculture, Madrid, Spain
| | - C Lexer
- Unit of Ecology and Evolution, Department of
Biology, University of Fribourg, Fribourg,
Switzerland
- Jodrell Laboratory, Royal Botanic
Gardens, Kew, Richmond, Surrey, UK
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Grivet D, Climent J, Zabal-Aguirre M, Neale DB, Vendramin GG, González-Martínez SC. Adaptive evolution of Mediterranean pines. Mol Phylogenet Evol 2013; 68:555-66. [DOI: 10.1016/j.ympev.2013.03.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 12/10/2012] [Accepted: 03/31/2013] [Indexed: 10/27/2022]
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Alberto FJ, Aitken SN, Alía R, González-Martínez SC, Hänninen H, Kremer A, Lefèvre F, Lenormand T, Yeaman S, Whetten R, Savolainen O. Potential for evolutionary responses to climate change - evidence from tree populations. Glob Chang Biol 2013; 19:1645-61. [PMID: 23505261 PMCID: PMC3664019 DOI: 10.1111/gcb.12181] [Citation(s) in RCA: 373] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 05/18/2023]
Abstract
Evolutionary responses are required for tree populations to be able to track climate change. Results of 250 years of common garden experiments show that most forest trees have evolved local adaptation, as evidenced by the adaptive differentiation of populations in quantitative traits, reflecting environmental conditions of population origins. On the basis of the patterns of quantitative variation for 19 adaptation-related traits studied in 59 tree species (mostly temperate and boreal species from the Northern hemisphere), we found that genetic differentiation between populations and clinal variation along environmental gradients were very common (respectively, 90% and 78% of cases). Thus, responding to climate change will likely require that the quantitative traits of populations again match their environments. We examine what kind of information is needed for evaluating the potential to respond, and what information is already available. We review the genetic models related to selection responses, and what is known currently about the genetic basis of the traits. We address special problems to be found at the range margins, and highlight the need for more modeling to understand specific issues at southern and northern margins. We need new common garden experiments for less known species. For extensively studied species, new experiments are needed outside the current ranges. Improving genomic information will allow better prediction of responses. Competitive and other interactions within species and interactions between species deserve more consideration. Despite the long generation times, the strong background in quantitative genetics and growing genomic resources make forest trees useful species for climate change research. The greatest adaptive response is expected when populations are large, have high genetic variability, selection is strong, and there is ecological opportunity for establishment of better adapted genotypes.
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Affiliation(s)
- Florian J Alberto
- Department of Biology and Biocenter Oulu, University of OuluFIN-90014, Oulu, Finland
- UMR1202 Biodiversité Gènes et Communautés, INRAF-33610, Cestas, France
- UMR1202 Biodiversité Gènes et Communautés, Université de BordeauxF-33410, Talence, France
| | - Sally N Aitken
- Department of Forest and Conservation Sciences and Centre for Forest Conservation Genetics, University of British ColumbiaVancouver, BC V6T 1Z4, Canada
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA - Forest Research CentreE-28040, Madrid, Spain
| | | | - Heikki Hänninen
- Department of Biosciences, University of HelsinkiFIN-00014, Helsinki, Finland
| | - Antoine Kremer
- UMR1202 Biodiversité Gènes et Communautés, INRAF-33610, Cestas, France
- UMR1202 Biodiversité Gènes et Communautés, Université de BordeauxF-33410, Talence, France
| | - François Lefèvre
- URFM, UR629 Ecologie des Forêts Méditerranéennes, INRAF-84914, Avignon, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de MontpellierUMR 5175, F-34293, Montpellier, France
| | - Sam Yeaman
- Department of Forest and Conservation Sciences and Centre for Forest Conservation Genetics, University of British ColumbiaVancouver, BC V6T 1Z4, Canada
- Institute of Biology, Université de NeuchâtelCH-2000, Neuchâtel, Switzerland
| | - Ross Whetten
- Department of Forestry & Environmental Resources, NC State UniversityRaleigh, NC, 27695-8008, USA
| | - Outi Savolainen
- Department of Biology and Biocenter Oulu, University of OuluFIN-90014, Oulu, Finland
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Budde KB, González-Martínez SC, Hardy OJ, Heuertz M. The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa. Heredity (Edinb) 2013; 111:66-76. [PMID: 23572126 DOI: 10.1038/hdy.2013.21] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation-coastal or swamp vs terra firme-in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.
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Affiliation(s)
- K B Budde
- INIA, Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7.5, Madrid, Spain.
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Albaladejo RG, Guzmán B, González-Martínez SC, Aparicio A. Extensive pollen flow but few pollen donors and high reproductive variance in an extremely fragmented landscape. PLoS One 2012; 7:e49012. [PMID: 23152842 PMCID: PMC3495779 DOI: 10.1371/journal.pone.0049012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 10/03/2012] [Indexed: 12/01/2022] Open
Abstract
Analysing pollen movement is a key to understanding the reproductive system of plant species and how it is influenced by the spatial distribution of potential mating partners in fragmented populations. Here we infer parameters related to levels of pollen movement and diversity of the effective pollen cloud for the wind-pollinated shrub Pistacia lentiscus across a highly disturbed landscape using microsatellite loci. Paternity analysis and the indirect KinDist and Mixed Effect Mating models were used to assess mating patterns, the pollen dispersal kernel, the effective number of males (Nep) and their relative individual fertility, as well as the existence of fine-scale spatial genetic structure in adult plants. All methods showed extensive pollen movement, with high rates of pollen flow from outside the study site (up to 73–93%), fat-tailed dispersal kernels and large average pollination distances (δ = 229–412 m). However, they also agreed in detecting very few pollen donors (Nep = 4.3–10.2) and a large variance in their reproductive success: 70% of males did not sire any offspring among the studied female plants and 5.5% of males were responsible for 50% of pollinations. Although we did not find reduced levels of genetic diversity, the adult population showed high levels of biparental inbreeding (14%) and strong spatial genetic structure (Sp = 0.012), probably due to restricted seed dispersal and scarce safe sites for recruitment. Overall, limited seed dispersal and the scarcity of successful pollen donors can be contributing to generate local pedigrees and to increase inbreeding, the prelude of genetic impoverishment.
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Affiliation(s)
- Rafael G Albaladejo
- Department of Plant Biology and Ecology, School of Pharmacy, University of Seville, Seville, Spain.
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