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Bobo‐Pinilla J, Nieto Lugilde D, Terrab A, Balao F, Peñas J. Spatially explicit assessment of genetic variation to inform conservation effort for an endangered Mediterranean conifer,
Cedrus atlantica. Ecol Evol 2022; 12:e9613. [PMCID: PMC9745260 DOI: 10.1002/ece3.9613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Javier Bobo‐Pinilla
- Department of Botany and Plant Physiology University of Salamanca Salamanca Spain
- Biobanco de ADN Vegetal, Edificio Multiusos I+D+i Salamanca Spain
| | - Diego Nieto Lugilde
- Departmento de Botánica, Ecología y Fisiología Vegetal Universidad de Córdoba Córdoba Spain
| | - Anass Terrab
- Departamento de Biología Vegetal y Ecología, Facultad de Biología Universidad de Sevilla Sevilla Spain
| | - Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología Universidad de Sevilla Sevilla Spain
| | - Julio Peñas
- Department of Botany University of Granada Granada Spain
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Di Santo LN, Hoban S, Parchman TL, Wright JW, Hamilton JA. Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation. Mol Ecol 2022; 31:4622-4639. [PMID: 35822858 DOI: 10.1111/mec.16615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
Abstract
Understanding the contribution of neutral and adaptive evolutionary processes to population differentiation is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to identify loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation within both Torrey pine populations, reflecting consistently low effective population sizes across time, and limited genetic differentiation, suggesting maintenance of gene flow between populations following divergence. However, genome scans identified more than 2000 candidate SNPs potentially under divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, evidence for adaptive differentiation suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.
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Affiliation(s)
- Lionel N Di Santo
- North Dakota State University, Department of Biological Sciences, Fargo, ND, USA
| | | | | | - Jessica W Wright
- USDA- Forest Service, Pacific Southwest Research Station, Davis, CA, USA
| | - Jill A Hamilton
- North Dakota State University, Department of Biological Sciences, Fargo, ND, USA.,Pennsylvania State University, Department of Ecosystem Science and Management, University Park, PA, USA
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A Change in Conservation Status of Pachyphytum caesium (Crassulaceae), a Threatened Species from Central Mexico Based on Genetic Studies. BIOLOGY 2022; 11:biology11030379. [PMID: 35336753 PMCID: PMC8945335 DOI: 10.3390/biology11030379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Species decline has accelerated in recent decades, with rare species often being the first to go extinct, mainly due to low population sizes. This study worked with Pachyphytum cesium (Crassulaceae), an endemic species from central Mexico threatened by human activities and climate change. To increase our knowledge of the species, we analyze the diversity and genetic structure of all known populations of P. caesium to change their current genetic status and propose conservation strategies. The results indicate that this species presents low to moderate levels of genetic diversity and incipiently structured populations due to low genetic flow. We found that genetic parameters are essential to the conservation strategies and status vulnerability reclassification. Based on our results, we propose reclassifying the conservation status of the species in danger of extinction; hence a series of conservation strategies are provided to prevent its disappearance. Abstract Genetic studies in rare species are important to determine their patterns of genetic diversity among populations and implement conservation plans aimed to reduce extinction risks. Pachyphytum caesium is an endemic species with extremely small populations in central Mexico. This work analyzes the diversity and genetic structure of Pachyphytum cesium (Crassulaceae) to change the conservation status and propose conservation strategies. Twelve dominant ISSR markers were used to describe the genetic diversity of all known populations. Additionally, we carried out two simulations to explore how the loss of individuals or the local populations extinction affect the genetics parameters of the species. The average results indicated moderate levels of genetic diversity (number of alleles = 89.7 ± 3.9, expected heterozygosity = 0.212 ± 0.0, and percentage of polymorphic loci = 56.1 ± 3.9), parameters that decreased significantly when simulations were performed in P. caesium. Additionally, a genetic structure of the populations was found with low gene flow (Nm = 0.92). Genetic parameters are negatively affected by the loss of individuals and the local extinction of populations. Based on our results, we propose to reclassify the conservation status of the species in danger of extinction, hence a series of conservation strategies are provided to prevent its disappearance.
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Bobo-Pinilla J, Salmerón-Sánchez E, Mota JF, Peñas J. Genetic conservation strategies of endemic plants from edaphic habitat islands: The case of Jacobaea auricula (Asteraceae). J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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N Di Santo L, Hamilton JA. Using environmental and geographic data to optimize ex situ collections and preserve evolutionary potential. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:733-744. [PMID: 32519757 DOI: 10.1111/cobi.13568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 05/26/2023]
Abstract
Maintenance of biodiversity through seed banks and botanical gardens, where the wealth of species' genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections if trade-offs exist among cost, effort, and conserving species evolutionary potential, particularly when genetic data are not available. We evaluated the genetic consequences of population preservation informed by geographic (isolation by distance [IBD]) and environmental (isolation by environment [IBE]) distance for ex situ collections for which population provenance is available. We used 19 genetic and genomic data sets from 15 plant species to assess the proportion of population genetic differentiation explained by geographic and environmental factors and to simulate ex situ collections prioritizing source populations based on pairwise geographic distance, environmental distance, or both. Specifically, we tested the impact prioritizing sampling based on these distances may have on the capture of neutral, functional, or putatively adaptive genetic diversity and differentiation. Individually, IBD and IBE explained limited population genetic differences across all 3 genetic marker classes (IBD, 10-16%; IBE, 1-5.5%). Together, they explained a substantial proportion of population genetic differences for functional (45%) and adaptive (71%) variation. Simulated ex situ collections revealed that inclusion of IBD, IBE, or both increased allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections based on environmental and geographic distance data can optimize genetic variation captured ex situ. For the vast majority of plant species for which there is no genetic information, these data are invaluable to conservation because they can guide preservation of genetic variation needed to maintain evolutionary potential within collections.
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Affiliation(s)
- Lionel N Di Santo
- Department of Biological Sciences, North Dakota State University, Fargo, ND, U.S.A
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, ND, U.S.A
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Garcia-Jacas N, Requena J, Massó S, Vilatersana R, Blanché C, López-Pujol J. Genetic diversity and structure of the narrow endemic Seseli farrenyi (Apiaceae): implications for translocation. PeerJ 2021; 9:e10521. [PMID: 33604159 PMCID: PMC7868069 DOI: 10.7717/peerj.10521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Seseli farrenyi (Apiaceae) is an extremely narrow endemic plant, which is considered as one of the species of most conservation concern in Catalonia (NW Mediterranean Basin). Given the accelerated fragmentation and reduction of population size (of over 90%), the environmental agency of Catalonia is currently preparing a recovery plan that includes reinforcements of the extant populations. The present study is aimed at providing the necessary knowledge to carry out genetically-informed translocations, by using microsatellites as genetic markers. Fourteen microsatellites have been specifically developed for S. farrenyi, of which nine have been used. Besides the extant natural populations, the three ex situ collections that are known to exist of this species have also been studied, as they would be the donor sources for translocation activities. Our main finding is that levels of genetic diversity in the natural populations of S. farrenyi are still high (He = 0.605), most likely as a result of a predominantly outcrossing mating system in combination with the limited time elapsed since the population decline. However, population fragmentation is showing the first genetic signs, as the values of genetic differentiation are relatively high, and two well-differentiated genetic lineages have been found even in such a narrow geographic range. These genetic results provide important information when designing conservation management measures.
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Affiliation(s)
- Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Jèssica Requena
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Sergi Massó
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain.,Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Cèsar Blanché
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
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Bosch M, Herrando-Moraira S, Hoyo AD, López-Pujol J, Massó S, Rosselló JA, Simon J, Blanché C. New conservation viewpoints when plants are viewed at one level higher. Integration of phylogeographic structure, niche modeling and genetic diversity in conservation planning of W Mediterranean larkspurs. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Martín‐Hernanz S, Martínez‐Sánchez S, Albaladejo RG, Lorite J, Arroyo J, Aparicio A. Genetic diversity and differentiation in narrow versus widespread taxa of Helianthemum (Cistaceae) in a hotspot: The role of geographic range, habitat, and reproductive traits. Ecol Evol 2019; 9:3016-3029. [PMID: 30962878 PMCID: PMC6434548 DOI: 10.1002/ece3.4481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/13/2018] [Accepted: 08/03/2018] [Indexed: 11/14/2022] Open
Abstract
Unraveling the relationships between ecological, functional traits and genetic diversity of narrow endemic plants provide opportunities for understanding how evolutionary processes operate over local spatial scales and ultimately how diversity is created and maintained. To explore these aspects in Sierra Nevada, the core of the Mediterranean Betic-Rifean hotspot, we have analyzed nuclear DNA microsatellite diversity and a set of biological and environmental factors (physicochemical soil parameters, floral traits, and community composition) in two strictly endemic taxa from dolomite outcrops of Sierra Nevada (Helianthemum pannosum and H. apenninum subsp. estevei) and two congeneric widespread taxa (H. cinereum subsp. rotundifolium and H. apenninum subsp. apenninum) that further belong to two different lineages (subgenera) of Helianthemum. We obtained rather unexpected results contrasting with the theory: (a) The narrow endemic taxa showed higher values of genetic diversity as well as higher average values of pollen production per flower and pollen-to-ovule ratio than their widespread relatives; and (b) the two taxa of subg. Helianthemum, with larger corollas, approach herkogamy and higher pollen production than the two taxa of subg. Plectolobum, displayed lower genetic diversity and higher values of inbreeding. Altogether, these results disclose how genetic diversity may be affected simultaneously by a large number of intrinsic and extrinsic factors, especially in Pleistocene glacial refugia in mountains where the spatial context harbors a great ecological heterogeneity. On the other hand, differences in mating system and the significant effect of the substrate profile, both being highly diverse in the genus Helianthemum, in the genetic variability illustrate about the importance of these two factors in the diversification and species differentiation of this paradigmatic genus in the Mediterranean and open the field to formulate and test new hypotheses of local adaptation, trait evolution, and habitat diversification.
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Affiliation(s)
- Sara Martín‐Hernanz
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
| | - Sara Martínez‐Sánchez
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
- Present address:
Departamento de Tecnología de la Alimentación y NutriciónUniversidad Católica de MurciaMurciaSpain
| | | | - Juan Lorite
- Departamento de BotánicaUniversidad de GranadaGranadaSpain
| | - Juan Arroyo
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y EcologíaUniversidad de SevillaSevillaSpain
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Peñas J, Barrios S, Bobo-Pinilla J, Lorite J, Martínez-Ortega MM. Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region. PeerJ 2016; 4:e1474. [PMID: 26844014 PMCID: PMC4736990 DOI: 10.7717/peerj.1474] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/14/2015] [Indexed: 11/20/2022] Open
Abstract
Astragalus edulis (Fabaceae) is an endangered annual species from the western Mediterranean region that colonized the SE Iberian Peninsula, NE and SW Morocco, and the easternmost Macaronesian islands (Lanzarote and Fuerteventura). Although in Spain some conservation measures have been adopted, it is still necessary to develop an appropriate management plan to preserve genetic diversity across the entire distribution area of the species. Our main objective was to use population genetics as well as ecological and phylogeographic data to select Relevant Genetic Units for Conservation (RGUCs) as the first step in designing conservation plans for A. edulis. We identified six RGUCs for in situ conservation, based on estimations of population genetic structure and probabilities of loss of rare alleles. Additionally, further population parameters, i.e. occupation area, population size, vulnerability, legal status of the population areas, and the historical haplotype distribution, were considered in order to establish which populations deserve conservation priority. Three populations from the Iberian Peninsula, two from Morocco, and one from the Canary Islands represent the total genetic diversity of the species and the rarest allelic variation. Ex situ conservation is recommended to complement the preservation of A. edulis, given that effective in situ population protection is not feasible in all cases. The consideration of complementary phylogeographic and ecological data is useful for management efforts to preserve the evolutionary potential of the species.
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Affiliation(s)
- Julio Peñas
- Plant Conservation Unit, Department of Botany, University of Granada, Granada, Spain
| | - Sara Barrios
- Department of Botany, University of Salamanca, Salamanca, Spain
| | - Javier Bobo-Pinilla
- Department of Botany, University of Salamanca, Salamanca, Spain
- Biobanco de ADN Vegetal, Edificio Multiusos I+D+i, Calle Espejo s/n, Salamanca, Spain
| | - Juan Lorite
- Plant Conservation Unit, Department of Botany, University of Granada, Granada, Spain
| | - M. Montserrat Martínez-Ortega
- Department of Botany, University of Salamanca, Salamanca, Spain
- Biobanco de ADN Vegetal, Edificio Multiusos I+D+i, Calle Espejo s/n, Salamanca, Spain
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López-Pujol J, Martinell MC, Massó S, Blanché C, Molero J. <i>Seseli farrenyi</i>: un endemisme empordanès en vies d'extinció? COLLECTANEA BOTANICA 2010. [DOI: 10.3989/collectbot.2010.v29.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Martinell MC, López-Pujol J, Bosch M, Blanché C. Low genetic variability in the rare, recently differentiated Aquilegia paui (Ranunculaceae). BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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The fewer and the better: prioritization of populations for conservation under limited resources, a genetic study with Borderea pyrenaica (Dioscoreaceae) in the Pyrenean National Park. Genetica 2009; 138:363-76. [DOI: 10.1007/s10709-009-9427-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 11/11/2009] [Indexed: 11/26/2022]
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PÉREZ-COLLAZOS ERNESTO, SEGARRA-MORAGUES JOSÉGABRIEL, CATALÁN PILAR. Two approaches for the selection of Relevant Genetic Units for Conservation in the narrow European endemic steppe plant Boleum asperum (Brassicaceae). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.00961.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Segarra-Moragues JG, Iriondo JM, Catalán P. Genetic fingerprinting of germplasm accessions as an aid for species conservation: a case study with Borderea chouardii (Dioscoreaceae), one of the most critically endangered Iberian plants. ANNALS OF BOTANY 2005; 96:1283-92. [PMID: 16230324 PMCID: PMC4247079 DOI: 10.1093/aob/mci280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Molecular markers have changed previous expectations about germplasm collections of endangered plants, as new perspectives aim at holding a significant representation of all the genetic diversity in the studied species to accomplish further conservation initiatives successfully. Borderea chouardii is a critically endangered allotetraploid dioecious member of Dioscoreaceae, known from a single population in the Iberian pre-Pyrenees. This population was reported to be highly structured into two genetically distinct groups of individuals corresponding to their spatial separation along the vertical cliff where it grows. In 1999, the Spanish Government of Aragón launched the first conservation programme for the ex situ preservation of this species, and since then a seed collection has been conserved at the Germplasm Bank of the Universidad Politécnica de Madrid. However, as some seed samples had not been labelled clearly at the time of collection, their origin was uncertain. METHODS Genetic variation in germplasm accessions of B. chouardii was investigated using microsatellite (simple sequence repeat; SSR) markers. KEY RESULTS The 17 primer pairs used detected 62 SSR alleles in the 46 samples analysed from five different germplasm stocks. Eight alleles scored from the wild population were not detected in the germplasm samples analysed. The relatedness of the germplasm samples to the wild subpopulations through neighbour-joining clustering, principal coordinates analysis (PCO) and assignment tests revealed a biased higher representation of the genetic diversity of the lower cliff (43 samples) subpopulation than that of the upper cliff (three samples). CONCLUSIONS The collection of additional samples from the upper cliff is recommended to achieve a better representation of the genetic diversity of this subpopulation. It is also recommended that these stocks should be managed separately according to their distinct microspatial origin in order to preserve the genetic substructuring of the wild population.
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Affiliation(s)
- José Gabriel Segarra-Moragues
- Departamento de Agricultura y Economía Agraria, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, C/Carretera de Cuarte s/n, E-22071 Huesca, Spain.
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