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Karbstein K, Kösters L, Hodač L, Hofmann M, Hörandl E, Tomasello S, Wagner ND, Emerson BC, Albach DC, Scheu S, Bradler S, de Vries J, Irisarri I, Li H, Soltis P, Mäder P, Wäldchen J. Species delimitation 4.0: integrative taxonomy meets artificial intelligence. Trends Ecol Evol 2024; 39:771-784. [PMID: 38849221 DOI: 10.1016/j.tree.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/20/2023] [Accepted: 11/08/2023] [Indexed: 06/09/2024]
Abstract
Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.
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Affiliation(s)
- Kevin Karbstein
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany.
| | - Lara Kösters
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Ladislav Hodač
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Martin Hofmann
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany
| | - Elvira Hörandl
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Salvatore Tomasello
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Natascha D Wagner
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Brent C Emerson
- Institute of Natural Products and Agrobiology (IPNA-CSIC), Island Ecology and Evolution Research Group, 38206 La Laguna, Tenerife, Canary Islands, Spain
| | - Dirk C Albach
- Carl von Ossietzky-Universität Oldenburg, Institute of Biology and Environmental Science, 26129 Oldenburg, Germany
| | - Stefan Scheu
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany; University of Göttingen, Centre of Biodiversity and Sustainable Land Use (CBL), 37073 Göttingen, Germany
| | - Sven Bradler
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany
| | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, 37077 Göttingen, Germany; University of Göttingen, Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany; University of Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, 37077 Göttingen, Germany
| | - Iker Irisarri
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Centre for Molecular Biodiversity Research, Phylogenomics Section, Museum of Nature, 20146 Hamburg, Germany
| | - He Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Chenshan Botanical Garden, 201602 Shanghai, China
| | - Pamela Soltis
- University of Florida, Florida Museum of Natural History, 32611 Gainesville, USA
| | - Patrick Mäder
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Ecology and Evolution, Philosophenweg 16, 07743 Jena, Germany
| | - Jana Wäldchen
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
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2
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Barker MS, Jiao Y, Glennon KL. Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy. AMERICAN JOURNAL OF BOTANY 2024; 111:e16395. [PMID: 39164922 DOI: 10.1002/ajb2.16395] [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: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024]
Abstract
All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants.
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Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, 85721, AZ, USA
| | - Yuannian Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kelsey L Glennon
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Ramirez‐Castillo R, Palma‐Rojas C, Seguel PJ, Grusz AL, Araya‐Jaime C. Unfurling an improved method for visualizing mitotic chromosomes in ferns. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11588. [PMID: 39184202 PMCID: PMC11342230 DOI: 10.1002/aps3.11588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/09/2024] [Accepted: 02/05/2024] [Indexed: 08/27/2024]
Abstract
Premise Cytotaxonomy employs chromosome visualization to study organismal relationships and evolution. Despite the critical value of cytogenetic data, cytotypes are lacking for many plant groups. Here, we present an improved approach for visualizing mitotic chromosomes in ferns, a key lineage of land plants, using the dividing cells of unfurling croziers (fiddleheads). Methods and Results Our modified mitotic chromosome preparation incorporates a brief pectinase-cellulase pretreatment, as well as colchicine fixation and the Feulgen reaction to improve the staining and separation of mitotic chromosomes. To demonstrate this easy and efficient assessment, we determined the sporophytic (2n) chromosome number for three fern species: Cheilanthes mollis (2n = 60), Cheilanthes hypoleuca (2n = 120), and Nephrolepis cordifolia (2n = 82). Conclusions The new method presented here improves visualizations of mitotic chromosomes from the dividing nuclei of young fern croziers. Fiddleheads are widely accessible in nature and in living collections worldwide, and this modified approach increases their suitability for fern cytotaxonomic studies.
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Affiliation(s)
| | | | - Pedro Jara Seguel
- Núcleo de Estudios Ambientales, Facultad de Recursos NaturalesUniversidad Católica de TemucoTemucoChile
| | - Amanda L. Grusz
- University of Minnesota DuluthDuluth55812MinnesotaUSA
- National Museum of Natural HistorySmithsonian InstitutionWashington, D.C.20013USA
| | - Cristian Araya‐Jaime
- Departamento de BiologíaUniversidad de La SerenaLa SerenaChile
- Instituto Multidisciplinario de Investigación y Posgrado Universidad de La SerenaLa SerenaChile
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Bradican JP, Tomasello S, Vollmer J, Hörandl E. Converging forms: an examination of sub-Arctic, circumarctic, and Central Asian Ranunculus auricomus agg. populations. FRONTIERS IN PLANT SCIENCE 2024; 15:1415059. [PMID: 38952845 PMCID: PMC11215153 DOI: 10.3389/fpls.2024.1415059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/21/2024] [Indexed: 07/03/2024]
Abstract
Introduction Phenotypic complexity in species complexes and recently radiated lineages has resulted in a diversity of forms that have historically been classified into separate taxa. Increasingly, with the proliferation of high-throughput sequencing methods, additional layers of complexity have been recognized, such as frequent hybridization and reticulation, which may call into question the previous morphological groupings of closely related organisms. Methods We investigated Northern European, Asian, and Beringian populations of Ranunculus auricomus agg. with phylogenomic analysis of 736 genes and 27,586 SNPs in order to deduce the interrelatedness and hybrid origin of this phenotypically and taxonomically complicated group from Europe characterized by a history of hybridization, polyploidy, apomixis, and recent radiation. The ploidy levels and the reproductive mode of the Northern European populations were assessed via flow cytometric seed screening. In addition, in order to examine the phenotypic plasticity of the dwarf forms previously described as species and summarized as the Ranunculus monophyllus group, we conducted climate chamber experiments under cold (northern) and warm (temperate) conditions. Results The Northern European populations are tetra- to hexaploid and propagate primarily through apomixis. The complex is characterized by highly reticulate relationships. Genetic differentiation of the main clusters has occurred between the above-mentioned geographical regions. We find evidence for the hybrid origin of the taxa in these areas with differing genomic contributions from the geographically nearest European sexual progenitor species. Furthermore, polyphyly in the taxa of the R. monophyllus group is supported. Experiments show low lability in the traits associated with the R. monophyllus group. Discussion We conclude that multiple adaptations of hybrids to colder climates and shorter vegetation periods have shaped the phenotypes of the R. monophyllus group, and we suggest a formal classification as nothotaxa within the R. auricomus group.
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Affiliation(s)
- John Paul Bradican
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
- Georg-August University School of Sciences (GAUSS), University of Göttingen, Göttingen, Germany
| | - Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Judith Vollmer
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
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Braglia L, Ceschin S, Iannelli MA, Bog M, Fabriani M, Frugis G, Gavazzi F, Gianì S, Mariani F, Muzzi M, Pelella E, Morello L. Characterization of the cryptic interspecific hybrid Lemna×mediterranea by an integrated approach provides new insights into duckweed diversity. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3092-3110. [PMID: 38387000 PMCID: PMC11103106 DOI: 10.1093/jxb/erae059] [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: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Lemnaceae taxonomy is challenged by the particular morphology of these tiny free-floating angiosperms. Although molecular taxonomy has helped clarify the phylogenetic history of this family, some inconsistency with morphological data leads to frequent misclassifications in the genus Lemna. Recently, the finding that Lemna japonica is an interspecific hybrid between Lemna minor and Lemna turionifera provided a clear explanation for one such taxonomic question. Here we demonstrated that L. minor is also capable of hybridizing with Lemna gibba, generating a cryptic but widespread taxon in the Mediterranean area. The nothotaxon Lemna ×mediterranea is described and compared with clones of the putative parental species L. minor and L. gibba. Genetic analysis by nuclear and plastid markers, as well as genome size measurement, revealed that two different cytotypes, diploid and triploid, originated by at least two independent hybridization events. Despite high overall similarity, morphometrical, physiological, and biochemical analyses showed an intermediate position of L. ×mediterranea between its parental species in most qualitative and quantitative characters, and also separation of the two hybrid cytotypes by some criteria. These data provide evidence that hybridization and polyploidization, driving forces of terrestrial plant evolution, contribute to duckweed genetic diversity and may have shaped the phylogenetic history of these mainly asexual, aquatic plants.
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Affiliation(s)
- Luca Braglia
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
| | - Simona Ceschin
- Department of Sciences, University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy
- NBFC-National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - M Adelaide Iannelli
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Salaria Km. 29,300, 00015 Monterotondo, Rome, Italy
| | - Manuela Bog
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, D-17489 Greifswald, Germany
| | - Marco Fabriani
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Salaria Km. 29,300, 00015 Monterotondo, Rome, Italy
| | - Giovanna Frugis
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Salaria Km. 29,300, 00015 Monterotondo, Rome, Italy
| | - Floriana Gavazzi
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
| | - Silvia Gianì
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
| | - Flaminia Mariani
- Department of Sciences, University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy
| | - Maurizio Muzzi
- Department of Sciences, University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy
| | - Emanuele Pelella
- Department of Sciences, University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy
| | - Laura Morello
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
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Wang X, Liao S, Zhang Z, Zhang J, Mei L, Li H. Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1354812. [PMID: 38595762 PMCID: PMC11002808 DOI: 10.3389/fpls.2024.1354812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024]
Abstract
The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.
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Affiliation(s)
- Xiaomei Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuai Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Zhen Zhang
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - Jianhang Zhang
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, China
| | - Li Mei
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hongqing Li
- School of Life Sciences, East China Normal University, Shanghai, China
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Jiang Y, Yang J, Folk RA, Zhao J, Liu J, He Z, Peng H, Yang S, Xiang C, Yu X. Species delimitation of tea plants (Camellia sect. Thea) based on super-barcodes. BMC PLANT BIOLOGY 2024; 24:181. [PMID: 38468197 PMCID: PMC10926627 DOI: 10.1186/s12870-024-04882-3] [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: 10/24/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect. Thea) form a group of morphologically similar species with significant economic value, providing the raw material for tea, which is the most popular nonalcoholic caffeine-containing beverage in the world. Taxonomic challenges have arisen from vague species boundaries in this group. RESULTS Based on the most comprehensive sampling of C. sect. Thea by far (165 individuals of 39 morphospecies), we applied three de novo species delimitation methods (ASAP, PTP, and mPTP) using plastome data to provide an independent evaluation of morphology-based species boundaries in tea plants. Comparing MOTU partitions with morphospecies, we particularly tested the congruence of MOTUs resulting from different methods. We recognized 28 consensus MOTUs within C. sect. Thea, while tentatively suggesting that 11 morphospecies be discarded. Ten of the 28 consensus MOTUs were uncovered as morphospecies complexes in need of further study integrating other evidence. Our results also showed a strong imbalance among the analyzed MOTUs in terms of the number of molecular diagnostic characters. CONCLUSION This study serves as a solid step forward for recognizing the underlying species boundaries of tea plants, providing a needed evidence-based framework for the utilization and conservation of this economically important plant group.
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Affiliation(s)
- Yinzi Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, 39762, MS, USA
| | - Jianli Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Laboratory of Ecology and Evolutionary Biology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, Yunnan, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Zhengshan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Shixiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Chunlei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Xiangqin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Serrano M, Ortiz S. Species Delimitation in a Polyploid Group of Iberian Jasione (Campanulaceae) Unveils Coherence between Cryptic Speciation and Biogeographical Regionalization. PLANTS (BASEL, SWITZERLAND) 2023; 12:4176. [PMID: 38140501 PMCID: PMC10747609 DOI: 10.3390/plants12244176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Groups with morphological stasis are an interesting framework to address putative cryptic species that may be hidden behind traditional taxonomic treatments, particularly when distribution ranges suggest disjunct and environmentally heterogeneous biogeographic patterns. New hypotheses of delimitation of evolutionary independent units can lead to the identification of different biogeographic processes, laying the foundation to investigate their historical and ecological significance. Jasione is a plant genus with a distribution centered in the Mediterranean basin, characterized by significant morphological stasis. Within the western Mediterranean J. gr. crispa species complex, J. sessiliflora s.l. and allied taxa form a distinct group, occupying environmentally diverse regions. At least two ploidy levels, diploid and tetraploid, are known to occur in the group. The internal variability is assessed with phylogenetic tools, viz. GMYC and ASAP, for species delimitation. The results are compared with other lines of evidence, including morphology and cytology. The fitting of distribution patterns of the inferred entities to chorological subprovinces is also used as a biogeographical and environmental framework to test the species hypothesis. Despite the scarcity of diagnostic morphological characters in the group, phylogenetic delimitation supports the description of at least one cryptic species, a narrow endemic in the NE Iberian Peninsula. Moreover, the results support the segregation of a thermophilic group of populations in eastern Iberia from J. sessiliflora. Ploidy variation from a wide geographical survey supports the systematic rearrangement suggested by species delimitation. Taxonomic reorganization in J. sessiliflora s.l. would allow ecological interpretations of distribution patterns in great accordance with biogeographical regionalization at the subprovince level, supporting geobotanical boundaries as a framework to interpret species ecological coherence of cryptic lineages. These results suggest that species differentiation, together with geographic isolation and polyploidization, is associated with adaptation to different environments, shifting from more to less thermophilic conditions. Thus, the recognition of concealed evolutionary entities is essential to correctly interpret biogeographical patterns in regions with a complex geologic and evolutionary history, such as the Mediterranean basin, and biogeographical units emerge as biologically sound frameworks to test the species hypothesis.
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Affiliation(s)
- Miguel Serrano
- Department of Botany, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
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Bradican JP, Tomasello S, Boscutti F, Karbstein K, Hörandl E. Phylogenomics of Southern European Taxa in the Ranunculus auricomus Species Complex: The Apple Doesn't Fall Far from the Tree. PLANTS (BASEL, SWITZERLAND) 2023; 12:3664. [PMID: 37960021 PMCID: PMC10650656 DOI: 10.3390/plants12213664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
The taxonomic status of many Southern European taxa of the Ranunculus auricomus complex remains uncertain despite this region's proximity to the native ranges of the sexual progenitor species of the complex. We investigated whether additional sexual progenitor species are present in the Mediterranean region. Utilizing target enrichment of 736 single-copy nuclear gene regions and flow cytometry, we analyzed phylogenomic relationships, the ploidy level, and the reproductive mode in representatives of 16 populations in Southern Europe, with additional sequence data from herbarium collections. Additionally, phased sequence assemblies from suspected nothotaxa were mapped to previously described sexual progenitor species in order to determine hybrid ancestry. We found the majority of Mediterranean taxa to be tetraploid, with hybrid populations propagating primarily via apomixis. Phylogenomic analysis revealed that except for the progenitor species, the Mediterranean taxa are often polyphyletic. Most apomictic taxa showed evidence of mixed heritage from progenitor species, with certain progenitor genotypes having mapped more to the populations from adjacent geographical regions. Geographical trends were found in phylogenetic distance, roughly following an east-to-west longitudinal demarcation of the complex, with apomicts extending to the southern margins. Additionally, we observed post-hybridization divergence between the western and eastern populations of nothotaxa in Southern Europe. Our results support a classification of apomictic populations as nothotaxa, as previously suggested for Central Europe.
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Affiliation(s)
- John Paul Bradican
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
- Georg-August University School of Sciences (GAUSS), University of Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Francesco Boscutti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 91, 33100 Udine, Italy
| | - Kevin Karbstein
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans Knöll Strasse 10, 07743 Jena, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
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10
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Marinho RC, Mendes-Rodrigues C, Resende-Moreira LC, Lovato MB, Bonetti AM, Oliveira PE. Phylogeography of Eriotheca species complex: insights into the origin and range expansion of apomictic and polyploid trees in Neotropical Savannas. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:457-467. [PMID: 36728131 DOI: 10.1111/plb.13508] [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: 11/11/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Polyploidy and whole genome duplication are major evolutionary drivers in plants. Climate variations during the Pleistocene have influenced distribution and range expansion worldwide. Similar trends have been reported for Cerrado plants, but no attempt has been made to link phylogeography with ploidy and breeding changes. Thus, we aimed to (i) assess ploidy and genome size of Eriotheca estevesiae Carv.-Sobr., and compare it with E. pubescens (Mart.) Schott & Endl. (Both included into the Eriotheca Stellate Trichome Species Complex - ESTSC). (ii) Subsequently, we investigated their phylogeography to see whether genetic structure and range expansion trends were similar to those previously described for the Cerrado biome. Finally (iii), we discuss whether ESTSC phylogeographic patterns could be associated with geographic parthenogenesis processes. Common cytogenetic techniques and flow cytometry were used to confirm chromosome number and genome size of E. estevesiae. We used three cpDNA regions to analyse 14 ESTSC Cerrado populations, for which we also obtained ploidy level and breeding information. We investigated haplotype diversity, population structure and tested neutrality, aiming to reconstruct phylogeographic scenarios. We found three ploidy levels and eight cpDNA haplotypes in ESTSC, one shared by most populations. Haplotype and ploidy distribution corroborated that E. pubescens, the widely distributed polyploid and apomictic species, may have originated from northern diploid and probably sexual E. estevesiae. Matrilinear cpDNA links support the idea that apomixis and polyploidy in ESTSC may have allowed range expansion during the Pleistocene, in a process analogous to the geographic parthenogenesis described elsewhere.
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Affiliation(s)
- R C Marinho
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - C Mendes-Rodrigues
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
- Faculdade de Medicina, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - L C Resende-Moreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M B Lovato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A M Bonetti
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - P E Oliveira
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
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11
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Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex. BIOLOGY 2023; 12:biology12030418. [PMID: 36979110 PMCID: PMC10045763 DOI: 10.3390/biology12030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.
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12
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Wagner ND, Marinček P, Pittet L, Hörandl E. Insights into the Taxonomically Challenging Hexaploid Alpine Shrub Willows of Salix Sections Phylicifoliae and Nigricantes (Salicaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:1144. [PMID: 36904002 PMCID: PMC10005704 DOI: 10.3390/plants12051144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
The complex genomic composition of allopolyploid plants leads to morphologically diverse species. The traditional taxonomical treatment of the medium-sized, hexaploid shrub willows distributed in the Alps is difficult based on their variable morphological characters. In this study, RAD sequencing data, infrared-spectroscopy, and morphometric data are used to analyze the phylogenetic relationships of the hexaploid species of the sections Nigricantes and Phylicifoliae in a phylogenetic framework of 45 Eurasian Salix species. Both sections comprise local endemics as well as widespread species. Based on the molecular data, the described morphological species appeared as monophyletic lineages (except for S. phylicifolia s.str. and S. bicolor, which are intermingled). Both sections Phylicifoliae and Nigricantes are polyphyletic. Infrared-spectroscopy mostly confirmed the differentiation of hexaploid alpine species. The morphometric data confirmed the molecular results and supported the inclusion of S. bicolor into S. phylicifolia s.l., whereas the alpine endemic S. hegetschweileri is distinct and closely related to species of the section Nigricantes. The genomic structure and co-ancestry analyses of the hexaploid species revealed a geographical pattern for widespread S. myrsinifolia, separating the Scandinavian from the alpine populations. The newly described S. kaptarae is tetraploid and is grouped within S. cinerea. Our data reveal that both sections Phylicifoliae and Nigricantes need to be redefined.
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Affiliation(s)
- Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Untere Karspüle 2, D-37073 Göttingen, Germany
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13
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Picks in the Fabric of a Polyploidy Complex: Integrative Species Delimitation in the Tetraploid Leucanthemum Mill. (Compositae, Anthemideae) Representatives. BIOLOGY 2023; 12:biology12020288. [PMID: 36829565 PMCID: PMC9953438 DOI: 10.3390/biology12020288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Based on the results of a preceding species-delimitation analysis for the diploid representatives of the genus Leucanthemum (Compositae, Anthemideae), the present study aims at the elaboration of a specific and subspecific taxonomic treatment of the tetraploid members of the genus. Following an integrative taxonomic approach, species-level decisions on eight predefined morphotaxon hypotheses were based on genetic/genealogical, morphological, ecological, and geographical differentiation patterns. ddRADseq fingerprinting and SNP-based clustering revealed genetic integrity for six of the eight morphotaxa, with no clear differentiation patterns observed between the widespread L. ircutianum subsp. ircutianum and the N Spanish (Cordillera Cantábrica) L. cantabricum and the S French L. delarbrei subsp. delabrei (northern Massif Central) and L. meridionale (western Massif Central). The inclusion of differentiation patterns in morphological (leaf dissection and shape), ecological (climatological and edaphic niches), and geographical respects (pair-wise tests of sympatry vs. allopatry) together with the application of a procedural protocol for species-rank decisions (the 'Wettstein tesseract') led to the proposal of an acknowledgement of the eight predefined morphotaxon hypotheses as six species (two of them with two subspecies). Nomenclatural consequences following from these results are drawn and lead to the following new combinations: Leucanthemum delarbrei subsp. meridionale (Legrand) Oberpr., T.Ott & Vogt, comb. nov. and Leucanthemum ruscinonense (Jeanb. & Timb.-Lagr.) Oberpr., T.Ott & Vogt, comb. et stat. nov.
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14
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Marinček P, Pittet L, Wagner ND, Hörandl E. Evolution of a hybrid zone of two willow species ( Salix L.) in the European Alps analyzed by RAD-seq and morphometrics. Ecol Evol 2023; 13:e9700. [PMID: 36620405 PMCID: PMC9811612 DOI: 10.1002/ece3.9700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 01/06/2023] Open
Abstract
Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise in mountain systems as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. Willows are a large genus of woody plants with an immense capability of interspecific crossing. In this study, the sympatric area of two diploid sister species, S. foetida and S. waldsteiniana in the eastern European Alps, was investigated to study the genomic structure of populations within and outside their contact zone and to analyze congruence of morphological phenotypes with genetic data. Eleven populations of the two species were sampled across the Alps and examined using phylogenetic network and population genetic structure analyses of RAD Seq data and morphometric analyses of leaves. The results showed that a homoploid hybrid zone between the two species was established within their sympatric area. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to not only one of the parental species but also one hybrid population forming a separate lineage. The lack of F1 hybrids indicated a long-term persistence of the hybrid populations. Insignificant isolation by distance suggests that gene flow can act over large geographical scales. Morphometric characteristics of hybrids supported the molecular data and clearly separated populations of the parental species, but showed intermediacy in the hybrid zone populations with a bias toward S. waldsteiniana. The homoploid hybrid zone might have been established via secondary contact hybridization, and its establishment was fostered by the low genetic divergence of parental species and a lack of strong intrinsic crossing barriers. Incomplete ecological separation and the ability of long-distance dispersal of willows could have contributed to the spatial expansion of the hybrid zone.
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Affiliation(s)
- Pia Marinček
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
| | - Loïc Pittet
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
| | - Natascha D. Wagner
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity, and Evolution of Plants (with Herbarium)University of GöttingenGöttingenGermany
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15
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Kozlowski G, Fragnière Y, Clément B, Meade C. Genome Size in the Arenaria ciliata Species Complex (Caryophyllaceae), with Special Focus on A. ciliata subsp. bernensis, a Narrow Endemic of the Swiss Northern Alps. PLANTS (BASEL, SWITZERLAND) 2022; 11:3489. [PMID: 36559611 PMCID: PMC9783149 DOI: 10.3390/plants11243489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The genus Arenaria (Caryophyllaceae) comprises approximately 300 species worldwide; however, to date, just six of these taxa have been investigated in terms of their genome size. The main subject of the present study is the A. ciliata species complex, with special focus on A. ciliata subsp. bernensis, an endemic plant occurring in the Swiss Northern Alps. Altogether, 16 populations and 77 individuals of the A. ciliata complex have been sampled and their genome sizes were estimated using flow cytometry, including A. ciliata subsp. bernensis, A. ciliata s.str., A. multicaulis, and A. gothica. The Arenaria ciliata subsp. bernensis shows the highest 2c-value of 6.91 pg of DNA, while A. gothica showed 2c = 3.69 pg, A. ciliata s.str. 2c = 1.71 pg, and A. multicaulis 2c = 1.57 pg. These results confirm the very high ploidy level of A. ciliata subsp. bernensis (2n = 20x = 200) compared to other taxa in the complex, as detected by our chromosome counting and previously documented by earlier work. The genome size and, thus, also the ploidy level, is stable across the whole distribution area of this taxon. The present study delivers additional support for the taxonomic distinctiveness of the high alpine endemic A. ciliata subsp. bernensis, which strongly aligns with other differences in morphology, phylogeny, phenology, ecology, and plant communities, described previously. In affirming these differences, further support now exists to re-consider the species status of this taxon. Upgrading to full species rank would significantly improve the conservation prospects for this taxon, as, because of its precise ecological adaptation to alpine summit habitats, the A. ciliata subsp. bernensis faces acute threats from accelerated climate warming.
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Affiliation(s)
- Gregor Kozlowski
- Department of Biology and Botanical Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
- Natural History Museum Fribourg, Chemin du Musée 6, CH-1700 Fribourg, Switzerland
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yann Fragnière
- Department of Biology and Botanical Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Benoît Clément
- Department of Biology and Botanical Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Conor Meade
- Molecular Ecology and Biogeography Laboratory, Biology Department, Maynooth University, W23 F2H6 Maynooth, Ireland
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16
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Orantes-Bonilla M, Makhoul M, Lee H, Chawla HS, Vollrath P, Langstroff A, Sedlazeck FJ, Zou J, Snowdon RJ. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation. FRONTIERS IN PLANT SCIENCE 2022; 13:1057953. [PMID: 36466276 PMCID: PMC9716091 DOI: 10.3389/fpls.2022.1057953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 05/26/2023]
Abstract
In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.
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Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Manar Makhoul
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - HueyTyng Lee
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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17
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He L, Hörandl E. Does polyploidy inhibit sex chromosome evolution in angiosperms? FRONTIERS IN PLANT SCIENCE 2022; 13:976765. [PMID: 36212292 PMCID: PMC9541106 DOI: 10.3389/fpls.2022.976765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Dioecy is rare in flowering plants (5-6% of species), but is often controlled genetically by sex-linked regions (SLRs). It has so far been unclear whether, polyploidy affects sex chromosome evolution, as it does in animals, though polyploidy is quite common in angiosperms, including in dioecious species. Plants could be different, as, unlike many animal systems, degenerated sex chromosomes, are uncommon in plants. Here we consider sex determination in plants and plant-specific factors, and propose that constraints created at the origin of polyploids limit successful polyploidization of species with SLRs. We consider the most likely case of a polyploid of a dioecious diploid with an established SLR, and discuss the outcome in autopolyploids and allopolyploids. The most stable system possibly has an SLR on just one chromosome, with a strongly dominant genetic factor in the heterogametic sex (e.g., xxxY male in a tetraploid). If recombination occurs with its homolog, this will prevent Y chromosome degeneration. Polyploidy may also allow for reversibility of multiplied Z or X chromosomes into autosomes. Otherwise, low dosage of Y-linked SLRs compared to their multiple homologous x copies may cause loss of reliable sex-determination at higher ploidy levels. We discuss some questions that can be studied using genome sequencing, chromosome level-assemblies, gene expression studies and analysis of loci under selection.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Göttingen, Germany
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18
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Karbstein K, Tomasello S, Hodač L, Wagner N, Marinček P, Barke BH, Paetzold C, Hörandl E. Untying Gordian knots: unraveling reticulate polyploid plant evolution by genomic data using the large Ranunculus auricomus species complex. THE NEW PHYTOLOGIST 2022; 235:2081-2098. [PMID: 35633497 DOI: 10.1111/nph.18284] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Speciation via hybridization and polyploidization is a major evolutionary force in plant evolution but is still poorly understood for neopolyploid groups. Challenges are attributed to high heterozygosity, low genetic divergence, and missing information on progenitors, ploidy, and reproduction. We study the large Eurasian Ranunculus auricomus species complex and use a comprehensive workflow integrating reduced-representation sequencing (RRS) genomic data to unravel reticulate evolution, genome diversity and composition of polyploids. We rely on 97 312 restriction site-associated DNA sequencing (RAD-Seq) loci, 576 targeted nuclear genes (48 phased), and 71 plastid regions derived from 78 polyploid apomictic taxa and four diploid and one tetraploid putative sexual progenitor species. We applied (phylo)genomic structure, network, and single nucleotide polymorphism (SNP)-origin analyses. Results consistently showed only 3-5 supported and geographically structured polyploid genetic groups, each containing extant sexual and one unknown progenitor species. Combined analyses demonstrated predominantly allopolyploid origins, each involving 2-3 different diploid sexual progenitor species. Young allotetraploids were characterized by subgenome dominance and nonhybrid SNPs, suggesting substantial post-origin but little lineage-specific evolution. The biodiversity of neopolyploid complexes can result from multiple hybrid origins involving different progenitors and substantial post-origin evolution (e.g. homoeologous exchanges, hybrid segregation, gene flow). Reduced-representation sequencing genomic data including multi-approach information is efficient to delimit shallow reticulate relationships.
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Affiliation(s)
- Kevin Karbstein
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
- Georg-August University School of Science (GAUSS), University of Göttingen, 37073, Göttingen, Germany
| | - Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Ladislav Hodač
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, 07745, Jena, Germany
| | - Natascha Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Pia Marinček
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Birthe Hilkka Barke
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Claudia Paetzold
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325, Frankfurt (Main), Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
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19
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Roy AK, Chakraborti M, Radhakrishna A, Dwivedi KK, Srivastava MK, Saxena S, Paul S, Khare A, Malaviya DR, Kaushal P. Alien genome mobilization and fixation utilizing an apomixis mediated genome addition (AMGA) strategy in Pennisetum to improve domestication traits of P. squamulatum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2555-2575. [PMID: 35726065 DOI: 10.1007/s00122-022-04138-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
An approach to release 'frozen' variability in apomictic species using sexuality of another species, eventually its utilization in crop improvement and de-novo domestication of crop wild relatives is presented. Pennisetum squamulatum, a secondary gene pool species of pearl millet (P. glaucum), harbours many desirable traits. However, it was neither utilized to improve pearl millet fodder traits nor improvement of its own domestication traits was attempted, due to the complexities of genomes and apomictic reproduction. To overcome this, we followed an Apomixis Mediated Genome Addition (AMGA) strategy and utilized the contrasting reproductive capacities (sexuality and apomixis) of both the species to access the otherwise un-available variability embedded in P. squamulatum. Segregating population of interspecific hybrids exhibited significant variability and heterosis for desired morphological, agronomical, and nutritional traits. Elite apomictic and perennial hybrids were evaluated in breeding trials, and eventually a novel grass cultivar was released for commercial cultivation in India. The performance of newly developed cultivar was superior to other adapted perennial grasses of arid and semi-arid rangelands. Through AMGA, the sexuality of one species was successfully utilized to 'release' the 'frozen' variability embedded in another species. Subsequently, the hybrids representing desirable trait combinations were again 'fixed' utilizing the apomixis alleles from the male parent in a back-and-forth apomixis-sexual-apomixis selection cycle. This study also demonstrated the potential of AMGA to improve crop relatives through genomes introgression as well as de novo domestication of new crops from wild species.
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Affiliation(s)
- A K Roy
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M Chakraborti
- ICAR - National Rice Research Institute, Cuttack, 753006, India
| | - A Radhakrishna
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - K K Dwivedi
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M K Srivastava
- ICAR - Indian Institute of Soybean Research, Indore, 452001, India
| | - S Saxena
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - S Paul
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Aarti Khare
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - D R Malaviya
- ICAR - Indian Institute of Sugarcane Research, Lucknow, 226002, India
| | - P Kaushal
- ICAR - National Institute of Biotic Stress Management, Raipur, 493225, India.
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20
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Serra ADC, Rodrigues CM, Marinho RC, Balao F, Oliveira PE. Interploidy hybridization in Eriotheca gracilipes and E. pubescens (Malvaceae): experimental evidence, genome and stomatal size. RODRIGUÉSIA 2022. [DOI: 10.1590/2175-7860202273078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract Hybridization and changes in ploidy have been associated with shifts from sexuality to apomixis, and may explain isolation among populations and species. Hybrids resulting from interploidy crosses may contribute to a broader understanding of how these populations and species have originated and evolved. Stomatal morphometrics and flow cytometry analyses were carried out for seedlings from different populations of Eriotheca estevesiae, E. gracilipes and E. pubescens, a group of closely related tree species in the Central Brazilian Cerrados. Controlled cross-pollinations between individuals of different cytotypes of E. gracilipes (2n = 2x = 92 and 2n = 6x = 276) and between sexual cytotypes of E. gracilipes (2n = 2x = 92) and E. pubescens (2n = 4x = 184) were performed. Only one viable seed was obtained from interploidy crosses of E. gracilipes. The hybridization between sexual cytotypes did not produce fruits. Genome size analyses indicated that there were apparently no natural hybrids or mixed ploidy populations among the seedlings analyzed. Seedlings stomatal size was consistent with previously reported cytotypes and ploidy levels; and when compared with the stomata of the viable interploidy hybrid of E. gracilipes, indicated a tetraploid, intermediate ploidy level. Although the data suggest the possibility of interploidy hybridization, cytotypes appeared relatively stable and natural interploidy hybridization seems to be uncommon among Eriotheca trees.
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