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Valdés-Florido A, Valcárcel V, Maguilla E, Díaz-Lifante Z, Andrés-Camacho C, Zeltner L, Coca-de-la-Iglesia M, Medina NG, Arroyo J, Escudero M. The interplay between climatic niche evolution, polyploidy and reproductive traits explains plant speciation in the Mediterranean Basin: a case study in Centaurium (Gentianaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1439985. [PMID: 39184574 PMCID: PMC11344271 DOI: 10.3389/fpls.2024.1439985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/19/2024] [Indexed: 08/27/2024]
Abstract
Speciation and diversification patterns in angiosperms are frequently shaped by niche evolution. Centaurium Hill is a Mediterranean genus with ca. 25 species, of which 60% are polyploids (tetra- and hexaploids), distributed mainly in the Mediterranean Basin and in areas with temperate and arid climates of Asia, Europe, North-Central Africa and North America. The evolutionary history of this genus has been studied using morphological, biogeographical and molecular approaches, but its climatic niche characterization and its relation with genome evolution (chromosome number and ploidy level) has not been addressed yet. Thus, this study aims to identify the role of the evolution of climatic niche, ploidy level, life cycle and floral traits in the diversification of Centaurium. Climatic niche characterization involved estimating present climate preferences using quantitative data and reconstructing ancestral niches to evaluate climatic niche shifts. The evolution of climatic niche towards selective optima determined by ploidy level (three ploidy levels) and different binary traits (polyploidy, floral size, floral display, herkogamy and life cycle) was addressed under the Ornstein-Uhlenbeck model. Chromosome number evolution was inferred using the ChromoSSE model, testing if changes are clado- or anagenetic. Chromosome number evolution and its link with cladogenesis, life cycle and floral traits was modeled on the phylogeny. The reconstruction of the ancestral niches shows that Centaurium originated in a mild climate and diversified to both humid and cold as well as to dry and warmer climates. Niche conservatism was estimated in the climatic niche of the ancestors, while the climatic niche of the current taxa experienced transitions from their ancestors' niche. Besides, the evolution of climatic niche towards multiple selective optima determined by the studied traits was supported, life cycle optima receiving the highest support. The reconstruction of chromosome number transitions shows that the rate of speciation process resulting from chromosomal changes (chromosomal cladogenesis) is similar to that of non-chromosomal cladogenesis. Additionally, dependent evolution of floral size, floral display and herkogamy with chromosome number variation was supported. In conclusion, polyploidization is a crucial process in the Mediterranean region that assisted speciation and diversification into new areas with different climates, entailing niche shifts and evolution of reproductive strategies.
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Affiliation(s)
- Ana Valdés-Florido
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
| | - Zoila Díaz-Lifante
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Cristina Andrés-Camacho
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Louis Zeltner
- Laboratoire de Botanique Evolutive, Université de Neuchâtel, Neuchâtel, Switzerland
| | | | - Nagore G. Medina
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Arroyo
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Marcial Escudero
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
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Vaz de Sousa D, Greve M, Oberlander KC. Friends without benefits: Extensive cytotype sympatry and polyploid persistence in an African geophyte. AMERICAN JOURNAL OF BOTANY 2024; 111:e16291. [PMID: 38439133 DOI: 10.1002/ajb2.16291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 03/06/2024]
Abstract
PREMISE Polyploidy is a major factor in plant adaptation and speciation. Multiple mechanisms contribute to autopolyploid frequency within populations, but uncertainties remain regarding mechanisms that facilitate polyploid establishment and persistence. Here we aimed to document and predict cytotype distributions of Oxalis obliquifolia Steud. ex A. Rich. across Gauteng, South Africa, and test for evidence of possible mechanisms, including morphological, phenological, and reproductive traits, that may potentially facilitate polyploid persistence. METHODS Over 320 O. obliquifolia plants from 25 sites were cytotyped using flow cytometry, and DNA ploidy was confirmed using meiotic chromosome squashes. Cytotypes were mapped and correlations with abiotic variables assessed using ordinations. To assess morphological and phenological associations with cytotype, we grew multiple cytotypes in a common garden, measured phenotypic traits and compared them using linear models and discriminant analyses. Intercytotype reproductive isolation was assessed using crossing experiments, and AMOVAs based on ITS DNA sequences tested for cytogeographic structure. RESULTS Six cytotypes were identified, and most sites had multiple cytotypes. Abiotic variables were not predictive of cytotype distribution. A clear gigas effect was present. Differences in flower size and phenology suggested pollinator interactions could play a role in polyploid persistence. Intercytotype crosses produced seed at low frequency. DNA data suggested diploids and polyploids were largely reproductively isolated in situ, and polyploidization events were not frequent enough to explain high cytotype sympatry. CONCLUSIONS Diploids and polyploids are behaving as separate species, despite little observable niche differentiation and non-zero potential intercytotype seed set. Tests on biotic interactions and intercytotype F1 fitness may provide insights into diploid and polyploid coexistence.
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Affiliation(s)
- Damian Vaz de Sousa
- Department of Plant and Soil Science, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa
- H.G.W.J. Schweickerdt Herbarium, Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
| | - Michelle Greve
- Department of Plant and Soil Science, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa
| | - Kenneth C Oberlander
- H.G.W.J. Schweickerdt Herbarium, Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
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Valdés-Florido A, González-Toral C, Maguilla E, Cires E, Díaz-Lifante Z, Andrés-Camacho C, Nieto Feliner G, Arroyo J, Escudero M. Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae). ANNALS OF BOTANY 2024; 134:247-262. [PMID: 38687133 PMCID: PMC11232519 DOI: 10.1093/aob/mcae066] [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: 01/16/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND AND AIMS Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean Basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographical factors. The Mediterranean genus Centaurium (Gentianaceae) comprises ~25 species, of which 60 % are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim to identify the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels. METHODS We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and Neighbor-Net approaches. To identify hybrid taxa, we used PhyloNetworks and the fastSTRUCTURE algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with non-metric multidimensional scaling. KEY RESULTS Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides was also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels. CONCLUSIONS This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.
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Affiliation(s)
- Ana Valdés-Florido
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | | | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, 41013, Spain
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, 33071, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, Mieres, 33600, Spain
| | - Zoila Díaz-Lifante
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | - Cristina Andrés-Camacho
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | | | - Juan Arroyo
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | - Marcial Escudero
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
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Yu Q, Yang FS, Chen YX, Wu H, Ickert-Bond SM, Wang XQ. Diploid species phylogeny and evolutionary reticulation indicate early radiation of Ephedra in the Tethys coast. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2619-2630. [PMID: 37837251 DOI: 10.1111/jipb.13573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra, which has a large genome and rich polyploids, remain a big challenge. Here we reconstructed a transcriptome-based phylogeny of 19 diploid Ephedra species, and explored evolutionary reticulations in this genus represented by 50 diploid and polyploid species, using four low-copy nuclear and nine plastid genes. The diploid species phylogeny indicates that the Mediterranean species diverged first, and the remaining species split into three clades, including the American species (Clade A), E. rhytidosperma, and all other Asian species (Clade B). The single-gene trees placed E. rhytidosperma sister to Clade A, Clade B, or Clades A + B in similar proportions, suggesting that radiation and gene flow likely occurred in the early evolution of Ephedra. In addition, reticulate evolution occurred not only among the deep nodes, but also in the recently evolved South American species, which further caused difficulty in phylogenetic reconstruction. Moreover, we found that allopolyploid speciation was pervasive in Ephedra. Our study also suggests that Ephedra very likely originated in the Tethys coast during the late Cretaceous, and the South American Ephedra species have a single origin by dispersal from Mexico or North America.
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Affiliation(s)
- Qiong Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fu-Sheng Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Xing Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Stefanie M Ickert-Bond
- Department of Biology and Wildlife & UA Museum of the North, University of Alaska Fairbanks (UAF), Fairbanks, AK, 99775, USA
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Escudero M, Maguilla E, Márquez-Corro JI, Martín-Bravo S, Mayrose I, Shafir A, Tan L, Tribble C, Zenil-Ferguson R. Using ChromEvol to Determine the Mode of Chromosomal Evolution. Methods Mol Biol 2023; 2672:529-547. [PMID: 37335498 DOI: 10.1007/978-1-0716-3226-0_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The ChromEvol software was the first to implement a likelihood-based approach, using probabilistic models that depict the pattern of chromosome number change along a specified phylogeny. The initial models have been completed and expanded during the last years. New parameters that model polyploid chromosome evolution have been implemented in ChromEvol v.2. In recent years, new and more complex models have been developed. The BiChrom model is able to implement two distinct chromosome models for the two possible trait states of a binary character of interest. ChromoSSE jointly implements chromosome evolution, speciation, and extinction. In the near future, we will be able to study chromosome evolution with increasingly complex models.
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Affiliation(s)
- Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Seville, Spain
| | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - José Ignacio Márquez-Corro
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Santiago Martín-Bravo
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Itay Mayrose
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Lu Tan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, China
| | - Carrie Tribble
- School of Life Sciences, University of Hawai`i at Mānoa, Honolulu, HI, USA
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Oyundelger K, Harpke D, Herklotz V, Troeva E, Zheng Z, Li Z, Oyuntsetseg B, Wagner V, Wesche K, Ritz CM. Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia. J Evol Biol 2021; 35:64-80. [PMID: 34792226 DOI: 10.1111/jeb.13960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022]
Abstract
Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping-by-sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 - trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment.
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Affiliation(s)
- Khurelpurev Oyundelger
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Dörte Harpke
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Seeland, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Elena Troeva
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Zhenzhen Zheng
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Zheng Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Viktoria Wagner
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Karsten Wesche
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Christiane M Ritz
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
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Jiménez-Lobato V, Escudero M, Lifante ZD, Camacho CA, de Castro A, Arroyo J. Isolation and characterization of microsatellites markers in Centaurium grandiflorum ssp. boissieri. Mol Biol Rep 2021; 48:8249-8253. [PMID: 34643926 DOI: 10.1007/s11033-021-06764-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Estimating outcrossing/selfing rates and characterizing genetic diversity with microsatellite markers are crucial to understanding the evolution of plant mating systems. METHODS AND RESULTS We developed, optimized and characterized eight new primer pairs for Centaurium grandiflorum ssp. boissieri and transferred them to three subspecies of Centaurium quadrifolium. Two SSR loci were transferred from Sabatia campestris to the four Centaurium taxa. Polymorphisms, He, Ho and H-W deviations were estimated in two populations of C. grandiflorum ssp. boissieri and in seven individuals each of C. quadrifolium ssp. barrelieri, C. quadrifolium ssp. parviflorum and C. quadrifolium ssp. quadrifolium. A total of 80 individuals was used in these experiments. The number of polymorphic loci varied among species from one to ten. A total of 127 alleles was scored. The average number of alleles per locus was 12.7. He was higher than Ho in all sampled populations. Hardy-Weinberg equilibrium was found for some loci in different species. CONCLUSIONS This is the first report of microsatellites successfully amplified in the whole Centaurium genus. They will be valuable for estimating mating system parameters and genetic diversity and exploring their relationships with the wide variation in flower morphology in the genus, especially anther-stigma separation.
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Affiliation(s)
- Vania Jiménez-Lobato
- Laboratorio Nacional de Análisis y Síntesis Ecológica - Campus Costa Grande, Escuela Superior de Desarrollo Sustentable, Universidad Autónoma de Guerrero, Cátedras - CONACYT, Carretera Federal Acapulco - Zihuatanejo, Las Tunas, Tecpan de Galeana, Guerrero, México. .,Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain.
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Zoila Díaz Lifante
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Cristina Andrés Camacho
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Alejandra de Castro
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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