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Stubbs RL, Theodoridis S, Mora-Carrera E, Keller B, Potente G, Yousefi N, Jay P, Léveillé-Bourret É, Choudhury RR, Celep F, Kochjarová J, Conti E. The genomes of Darwin's primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries. THE NEW PHYTOLOGIST 2024; 241:911-925. [PMID: 37921572 DOI: 10.1111/nph.19361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Introgression is an important source of genetic variation that can determine species adaptation to environmental conditions. Yet, definitive evidence of the genomic and adaptive implications of introgression in nature remains scarce. The widespread hybrid zones of Darwin's primroses (Primula elatior, Primula veris, and Primula vulgaris) provide a unique natural laboratory for studying introgression in flowering plants and the varying permeability of species boundaries. Through analysis of 650 genomes, we provide evidence of an introgressed genomic region likely to confer adaptive advantage in conditions of soil toxicity. We also document unequivocal evidence of chloroplast introgression, an important precursor to species-wide chloroplast capture. Finally, we provide the first evidence that the S-locus supergene, which controls heterostyly in primroses, does not introgress in this clade. Our results contribute novel insights into the adaptive role of introgression and demonstrate the importance of extensive genomic and geographical sampling for illuminating the complex nature of species boundaries.
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Affiliation(s)
- Rebecca L Stubbs
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, 60325, Germany
| | - Emiliano Mora-Carrera
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Étienne Léveillé-Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montreal, QC, H1X 2B2, Canada
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Kırıkkale, 71450, Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of Forestry, Technical University in Zvolen, Zvolen, 96001, Slovak Republic
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
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2
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Indira Cervantes-Díaz C, Patiño-Conde V, González-Rodríguez A, Quesada M, Cuevas E. Molecular and morphological evidence of hybridization between two dimorphic sympatric species of Fuchsia (Onagraceae). AOB PLANTS 2024; 16:plad089. [PMID: 38213511 PMCID: PMC10783250 DOI: 10.1093/aobpla/plad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/16/2023] [Indexed: 01/13/2024]
Abstract
Hybridization is commonly reported in angiosperms, generally based on morphology, and in few cases confirmed by molecular markers. Fuchsia has a long tradition of ornamental cultivars with different hybrids produced by artificial crosses, so natural hybridization between sympatric Fuchsia species could be common. Natural hybridization between F. microphylla and F. thymifolia was tested using six newly developed microsatellites for F. microphylla in addition to other molecular markers with codominant and maternal inheritance. Geometric morphometrics of leaves and floral structures were also used to identify putative hybrids. Hybrids showed a different degree of genetic admixture between both parental species. Chloroplast DNA (cpDNA) sequences indicated that hybridization occurs in both directions, in fact, some of the hybrids showed new haplotypes for cpDNA and ITS (internal transcriber spacer of nuclear ribosomal RNA genes) sequences. The morphology of hybrid individuals varied between the two parental species, but they could be better identified by their leaves and floral tubes. Our study is the first to confirm the hybridization in natural populations of Fuchsia species and suggests that hybridization has probably occurred repeatedly throughout the entire distribution of the species. Phylogeographic analysis of both species will be essential to understanding the impact of hybridization throughout their complete distribution.
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Affiliation(s)
- Cinthya Indira Cervantes-Díaz
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo 58000, Morelia, Michoacán, México
| | - Violeta Patiño-Conde
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
| | - Mauricio Quesada
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
| | - Eduardo Cuevas
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58190, Michoacán, México
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo 58000, Morelia, Michoacán, México
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Zou TT, Lyu ST, Jiang QL, Shang SH, Wang XF. Pre- and post-pollination barriers between two exotic and five native Sagittaria species: Implications for species conservation. PLANT DIVERSITY 2023; 45:456-468. [PMID: 37601545 PMCID: PMC10435913 DOI: 10.1016/j.pld.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 08/22/2023]
Abstract
Anthropogenic introduction of species has resulted in a breakdown of geographical barriers and hybridization in previously allopatric species. Thus, examining hybridization proneness of exotic species contributes to revealing its potential threat. Moreover, reproductive barriers may be strengthened or weakened due to long-term geographical isolation for these newly sympatric species. However, few studies have evaluated multiple barriers between alien and native species. In this study, we quantified the importance of four pre-pollination barriers (phenological, floral traits, pollen production, and floral constancy) and four post-pollination barriers (pollen-pistil incompatibility, seed set, seed viability, and seedling survival) between two introduced and five native Sagittaria species. Results showed that introduced S. platyphylla was cross-compatible with two native species, whereas introduced S. montevidensis was incapable of hybridizing with any native species. Different barriers were asymmetric within species pairs and multiple barriers acted in concert to maintain species boundaries. Post-pollination barriers contributed more to total reproductive isolation in native species, whereas pre-pollination barriers played a stronger role in total reproductive isolation for two introduced species. Seed set was the only barrier that was positively correlated with genetic distance. Our results provide a perspective to better understand reproductive barriers for secondary contact species. We highlight the importance of monitoring hybridization events before human introduction and the possible conservation strategies to remove invasive species with hybridization proneness.
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Affiliation(s)
- Ting-Ting Zou
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Sen-Tao Lyu
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qi-Lin Jiang
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shu-He Shang
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiao-Fan Wang
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Mora‐Carrera E, Stubbs RL, Keller B, Léveillé‐Bourret É, de Vos JM, Szövényi P, Conti E. Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species. Mol Ecol 2023; 32:61-78. [PMID: 34761469 PMCID: PMC10078681 DOI: 10.1111/mec.16270] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/29/2022]
Abstract
The repeated transition from outcrossing to selfing is a key topic in evolutionary biology. However, the molecular basis of such shifts has been rarely examined due to lack of knowledge of the genes controlling these transitions. A classic example of mating system transition is the repeated shift from heterostyly to homostyly. Occurring in 28 angiosperm families, heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, usually self-incompatible floral morphs. Conversely, homostyly is characterized by a single, self-compatible floral morph with reduced separation of male and female organs, facilitating selfing. Here, we investigate the origins of homostyly in Primula vulgaris and its microevolutionary consequences by integrating surveys of the frequency of homostyles in natural populations, DNA sequence analyses of the gene controlling the position of female sexual organs (CYPᵀ), and microsatellite genotyping of both progeny arrays and natural populations characterized by varying frequencies of homostyles. As expected, we found that homostyles displace short-styled individuals, but long-style morphs are maintained at low frequencies within populations. We also demonstrated that homostyles repeatedly evolved from short-styled individuals in association with different types of loss-of-function mutations in CYPᵀ. Additionally, homostyly triggers a shift to selfing, promoting increased inbreeding within and genetic differentiation among populations. Our results elucidate the causes and consequences of repeated transitions to homostyly within species, and the putative mechanisms precluding its fixation in P. vulgaris. This study represents a benchmark for future analyses of losses of heterostyly in other angiosperms.
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Affiliation(s)
- Emiliano Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Rebecca L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Étienne Léveillé‐Bourret
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Département de Sciences BiologiquesInstitut de Recherche en Biologie VégétaleUniversité de MontréalMontréalQuébecCanada
| | - Jurriaan M. de Vos
- Department of Environmental Sciences – BotanyUniversity of BaselBaselSwitzerland
| | - Peter Szövényi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
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5
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Stubbs RL, Theodoridis S, Mora‐Carrera E, Keller B, Yousefi N, Potente G, Léveillé‐Bourret É, Celep F, Kochjarová J, Tedoradze G, Eaton DAR, Conti E. Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot. THE NEW PHYTOLOGIST 2023; 237:656-671. [PMID: 36210520 PMCID: PMC10099377 DOI: 10.1111/nph.18525] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.
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Affiliation(s)
- Rebecca L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am Main60325Germany
| | - Emiliano Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Étienne Léveillé‐Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV)Université de MontréalQuébecH1X 2B2Canada
| | - Ferhat Celep
- Department of Biology, Faculty of Arts and SciencesKırıkkale UniversityKırıkkale71450Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of ForestryTechnical University in ZvolenZvolen96001Slovak Republic
| | - Giorgi Tedoradze
- Department of Plant Systematics and Geography, Institute of BotanyIlia State UniversityTbilisi0105Georgia
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNY10027USA
| | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
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Christie K, Fraser LS, Lowry DB. The strength of reproductive isolating barriers in seed plants: Insights from studies quantifying premating and postmating reproductive barriers over the past 15 years. Evolution 2022; 76:2228-2243. [PMID: 35838076 PMCID: PMC9796645 DOI: 10.1111/evo.14565] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 01/22/2023]
Abstract
Speciation is driven by the evolution of reproductive isolating barriers that reduce, and ultimately prevent, substantial gene flow between lineages. Despite its central role in evolutionary biology, the process can be difficult to study because it proceeds differently among groups and may occur over long timescales. Due to this complexity, we typically rely on generalizations of empirical data to describe and understand the process. Previous reviews of reproductive isolation (RI) in flowering plants have suggested that prezygotic or extrinsic barriers generally have a stronger effect on reducing gene flow compared to postzygotic or intrinsic barriers. Past conclusions have rested on relatively few empirical estimates of RI; however, RI data have become increasingly abundant over the past 15 years. We analyzed data from recent studies quantifying multiple pre- and postmating barriers in plants and compared the strengths of isolating barriers across 89 taxa pairs using standardized RI metrics. Individual prezygotic barriers were on average stronger than individual postzygotic barriers, and the total strength of prezygotic RI was approximately twice that of postzygotic RI. These findings corroborate that ecological divergence and extrinsic factors, as opposed to solely the accumulation of genetic incompatibilities, are important to speciation and the maintenance of species boundaries in plants. Despite an emphasis in the literature on asymmetric postmating and postzygotic RI, we found that prezygotic barriers acted equally asymmetrically. Overall, substantial variability in the strengths of 12 isolating barriers highlights the great diversity of mechanisms that contribute to plant diversification.
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Affiliation(s)
- Kyle Christie
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824,Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizona86011
| | - Linnea S. Fraser
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
| | - David B. Lowry
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
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Hopkins R. Predicting how pollinator behavior causes reproductive isolation. Ecol Evol 2022; 12:e8847. [PMID: 35462980 PMCID: PMC9019001 DOI: 10.1002/ece3.8847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/06/2022] [Indexed: 11/07/2022] Open
Abstract
Pollinator behavior is an important contributor to plants speciation, yet how variation in pollinator behavior causes variation in reproductive isolation (RI) is largely uncharacterized. Here I present a model that predicts how two aspects of pollinator behavior, constancy and preference, contribute to a barrier to reproduction in plants. This model is motivated by two observations: most co‐occurring plants vary in frequency over space and time, and most plants have multiple pollinators that differ in behavior. Thus, my goal was to understand how relative frequencies of plants and pollinators in a community influence ethological RI between co‐occurring plants. I find that RI for a focal plant generally increases with increasing relative plant frequency, but the shape of this relationship is highly dependent on the strength of pollinator behavior (constancy and preference). Additionally, when multiple pollinators express different behavior, I find that pollinators with stronger preference disproportionately influence RI. But, I show that RI caused by constancy is the average RI predicted from constancy of each pollinator weighted by pollinator frequency. I apply this model to examples of pollinator‐mediated RI in Phlox and in Ipomopsis to predict the relationships between plant frequency and ethological RI in natural systems. This model provides new insights into how and why pollinator specialization causes RI, and how RI could change with changing biological communities.
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Affiliation(s)
- Robin Hopkins
- The Department of Organismic and Evolutionary Biology and The Arnold ArboretumHarvard UniversityBostonMassachusettsUSA
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Abdelaziz M, Muñoz-Pajares AJ, Berbel M, García-Muñoz A, Gómez JM, Perfectti F. Asymmetric Reproductive Barriers and Gene Flow Promote the Rise of a Stable Hybrid Zone in the Mediterranean High Mountain. FRONTIERS IN PLANT SCIENCE 2021; 12:687094. [PMID: 34512685 PMCID: PMC8424041 DOI: 10.3389/fpls.2021.687094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/15/2021] [Indexed: 05/13/2023]
Abstract
Hybrid zones have the potential to shed light on evolutionary processes driving adaptation and speciation. Secondary contact hybrid zones are particularly powerful natural systems for studying the interaction between divergent genomes to understand the mode and rate at which reproductive isolation accumulates during speciation. We have studied a total of 720 plants belonging to five populations from two Erysimum (Brassicaceae) species presenting a contact zone in the Sierra Nevada mountains (SE Spain). The plants were phenotyped in 2007 and 2017, and most of them were genotyped the first year using 10 microsatellite markers. Plants coming from natural populations were grown in a common garden to evaluate the reproductive barriers between both species by means of controlled crosses. All the plants used for the field and greenhouse study were characterized by measuring traits related to plant size and flower size. We estimated the genetic molecular variances, the genetic differentiation, and the genetic structure by means of the F-statistic and Bayesian inference. We also estimated the amount of recent gene flow between populations. We found a narrow unimodal hybrid zone where the hybrid genotypes appear to have been maintained by significant levels of a unidirectional gene flow coming from parental populations and from weak reproductive isolation between them. Hybrid plants exhibited intermediate or vigorous phenotypes depending on the analyzed trait. The phenotypic differences between the hybrid and the parental plants were highly coherent between the field and controlled cross experiments and through time. The highly coherent results obtained by combining field, experimental, and genetic data demonstrate the existence of a stable and narrow unimodal hybrid zone between Erysimum mediohispanicum and Erysimum nevadense at the high elevation of the Sierra Nevada mountains.
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Affiliation(s)
- Mohamed Abdelaziz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- *Correspondence: Mohamed Abdelaziz
| | - A. Jesús Muñoz-Pajares
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Laboratório Associado, Plant Biology, Research Centre in Biodiversity and Genetic Resources, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade Do Porto, Campus Agrário de Vairão, Fornelo e Vairão, Portugal
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | - Modesto Berbel
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - Ana García-Muñoz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - José M. Gómez
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Almeria, Spain
| | - Francisco Perfectti
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
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