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Sochor M, Šarhanová P, Duchoslav M, Konečná M, Hroneš M, Trávníček B. Plant kleptomaniacs: geographical genetic patterns in the amphi-apomictic Rubus ser. Glandulosi (Rosaceae) reveal complex reticulate evolution of Eurasian brambles. ANNALS OF BOTANY 2024; 134:163-178. [PMID: 38549558 PMCID: PMC11161565 DOI: 10.1093/aob/mcae050] [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: 01/23/2024] [Accepted: 03/27/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND AND AIMS Rubus ser. Glandulosi provides a unique model of geographical parthenogenesis on a homoploid (2n = 4x) level. We aim to characterize evolutionary and phylogeographical patterns in this taxon and shed light on the geographical differentiation of apomicts and sexuals. Ultimately, we aim to evaluate the importance of phylogeography in the formation of geographical parthenogenesis. METHODS Rubus ser. Glandulosi was sampled across its Eurasian range together with other co-occurring Rubus taxa (587 individuals in total). Double-digest restriction site-associated DNA sequencing (ddRADseq) and modelling of suitable climate were used for evolutionary inferences. KEY RESULTS Six ancestral species were identified that contributed to the contemporary gene pool of R. ser. Glandulosi. Sexuals were introgressed from Rubus dolichocarpus and Rubus moschus in West Asia and from Rubus ulmifolius agg., Rubus canescens and Rubus incanescens in Europe, whereas apomicts were characterized by alleles of Rubus subsect. Rubus. Gene flow between sexuals and apomicts was also detected, as was occasional hybridization with other taxa. CONCLUSIONS We hypothesize that sexuals survived the last glacial period in several large southern refugia, whereas apomicts were mostly restricted to southern France, whence they quickly recolonized Central and Western Europe. The secondary contact of sexuals and apomicts was probably the principal factor that established geographical parthenogenesis in R. ser. Glandulosi. Sexual populations are not impoverished in genetic diversity along their borderline with apomicts, and maladaptive population genetic processes probably did not shape the geographical patterns.
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Affiliation(s)
- Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, 783 71 Olomouc, Czech Republic
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Petra Šarhanová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Martin Duchoslav
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michaela Konečná
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michal Hroneš
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Bohumil Trávníček
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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Xu Y, Li Y, Chen Y, Wang L, Xue B, Zhang X, Song W, Guo W, Wu W. Comparative Analysis of Complete Chloroplast Genomes of Rubus in China: Hypervariable Regions and Phylogenetic Relationships. Genes (Basel) 2024; 15:716. [PMID: 38927652 PMCID: PMC11202638 DOI: 10.3390/genes15060716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
With more than 200 species of native Rubus, China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese Rubus species (including varieties) from three of the eight sections reported in China, i.e., the sections Chamaebatus, Idaeobatus, and Malachobatus. Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 Rubus species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these Rubus plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: trnH-psbA, trnK-rps16, rps16-trnQ-psbK, petN-psbM, trnT-trnL, petA-psbJ, rpl16 intron, ndhF-trnL, and ycf1. Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these Rubus species. All sampled Rubus species formed a monophyletic group; however, sections Idaeobatus and Malachobatus were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within Rubus.
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Affiliation(s)
- Yufen Xu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Yongquan Li
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Yanzhao Chen
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Longyuan Wang
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Bine Xue
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Xianzhi Zhang
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wenpei Song
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wei Wu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
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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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Sochor M, Duchoslav M, Forejtová V, Hroneš M, Konečná M, Trávníček B. Distinct geographic parthenogenesis in spite of niche conservatism and a single ploidy level: A case of Rubus ser. Glandulosi (Rosaceae). THE NEW PHYTOLOGIST 2024; 242:1348-1362. [PMID: 38407427 DOI: 10.1111/nph.19618] [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: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Asexual organisms often differ in their geographic distributions from their sexual relatives. This phenomenon, termed geographic parthenogenesis, has long been known, but the underlying factors behind its diverse patterns have been under dispute. Particularly problematic is an association between asexuality and polyploidy in most taxa. Here, we present a new system of geographic parthenogenesis on the tetraploid level, promising new insights into this complex topic. We used flow cytometric seed screen and microsatellite genotyping to characterise the patterns of distribution of sexuals and apomicts and genotypic distributions in Rubus ser. Glandulosi across its range. Ecological modelling and local-scale vegetation and soil analyses were used to test for niche differentiation between the reproductive groups. Apomicts were detected only in North-western Europe, sexuals in the rest of the range in Europe and West Asia, with a sharp borderline stretched across Central Europe. Despite that, we found no significant differences in ecological niches. Genotypic richness distributions suggested independence of the reproductive groups and a secondary contact. We argue that unless a niche differentiation (resulting from polyploidy and/or hybridity) evolves, the main factors behind the patterns of geographic parthenogenesis in plants are phylogeographic history and neutral microevolutionary processes, such as clonal turnover.
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Affiliation(s)
- Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, Olomouc, 78371, Czech Republic
| | - Martin Duchoslav
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Věra Forejtová
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
- Station of Apple Breeding for Disease Resistance, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 313, Prague 6-Lysolaje, 16502, Czech Republic
| | - Michal Hroneš
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Michaela Konečná
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
| | - Bohumil Trávníček
- Plant Biosystematics and Ecology Research Group, Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc, 78371, Czech Republic
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Shah HMS, Singh Z, Kaur J, Hasan MU, Woodward A, Afrifa-Yamoah E. Trends in maintaining postharvest freshness and quality of Rubus berries. Compr Rev Food Sci Food Saf 2023; 22:4600-4643. [PMID: 37661731 DOI: 10.1111/1541-4337.13235] [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: 09/12/2022] [Revised: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023]
Abstract
Blackberries and raspberries, commonly known as Rubus berries, are commercially grown worldwide across different climates. Rubus berries contain wide array of phytochemicals, vitamins, dietary fibers, minerals, and unsaturated fatty acids. Nevertheless, these berries have short storage life which is the major constraint in their supply chains leading to higher postharvest losses. Inappropriate harvest handling, physical bruising, insect pests, and postharvest diseases lower the acceptability of fruit among consumers and other supply chain stakeholders. Additionally, the susceptibility to microbial decay, fruit softening, higher ethylene production, respiratory activity, and increased oxidation of anthocyanins, phenolics, and flavonoids considerably affects the marketability of Rubus berries at domestic and international markets. To date, several postharvest strategies such as cold storage, precooling, modified and controlled atmospheres, anti-ripening chemicals, edible coatings, biological agents, and nonchemical alternatives (heat treatment, ultrasound, irradiations, ozone) have been reported to prolong storage life, ensure food safety, and maintain the nutritional quality of Rubus berries. This review briefly encompasses multiple aspects including harvest maturity indices, regulation of fruit ripening, pre and postharvest factors affecting fruit quality, and an update on postharvest quality preservation by employing postharvest technologies to extend the storage life and maintaining the bioactive compounds in Rubus berries which are lacking in the literature. Accordingly, this review provides valuable information to the industry stakeholders and scientists offering relevant solutions, limitations in the application of certain technologies at commercial scale, highlighting research gaps, and paving the way forward for future investigations.
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Affiliation(s)
| | - Zora Singh
- Horticulture, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Jashanpreet Kaur
- Horticulture, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Mahmood Ul Hasan
- Horticulture, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Andrew Woodward
- Horticulture, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Eben Afrifa-Yamoah
- Horticulture, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
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Cai L, Kreft H, Taylor A, Schrader J, Dawson W, Essl F, van Kleunen M, Pergl J, Pyšek P, Winter M, Weigelt P. Climatic stability and geological history shape global centers of neo- and paleoendemism in seed plants. Proc Natl Acad Sci U S A 2023; 120:e2300981120. [PMID: 37459510 PMCID: PMC10372566 DOI: 10.1073/pnas.2300981120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Assessing the distribution of geographically restricted and evolutionarily unique species and their underlying drivers is key to understanding biogeographical processes and critical for global conservation prioritization. Here, we quantified the geographic distribution and drivers of phylogenetic endemism for ~320,000 seed plants worldwide and identified centers and drivers of evolutionarily young (neoendemism) and evolutionarily old endemism (paleoendemism). Tropical and subtropical islands as well as tropical mountain regions displayed the world's highest phylogenetic endemism. Most tropical rainforest regions emerged as centers of paleoendemism, while most Mediterranean-climate regions showed high neoendemism. Centers where high neo- and paleoendemism coincide emerged on some oceanic and continental fragment islands, in Mediterranean-climate regions and parts of the Irano-Turanian floristic region. Global variation in phylogenetic endemism was well explained by a combination of past and present environmental factors (79.8 to 87.7% of variance explained) and most strongly related to environmental heterogeneity. Also, warm and wet climates, geographic isolation, and long-term climatic stability emerged as key drivers of phylogenetic endemism. Neo- and paleoendemism were jointly explained by climatic and geological history. Long-term climatic stability promoted the persistence of paleoendemics, while the isolation of oceanic islands and their unique geological histories promoted neoendemism. Mountainous regions promoted both neo- and paleoendemism, reflecting both diversification and persistence over time. Our study provides insights into the evolutionary underpinnings of biogeographical patterns in seed plants and identifies the areas on Earth with the highest evolutionary and biogeographical uniqueness-key information for setting global conservation priorities.
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Affiliation(s)
- Lirong Cai
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Göttingen37077, Germany
| | - Holger Kreft
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Göttingen37077, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen37077, Germany
- Campus-Institute Data Science, Göttingen37077, Germany
| | - Amanda Taylor
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Göttingen37077, Germany
| | - Julian Schrader
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Göttingen37077, Germany
- School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Wayne Dawson
- Department of Biosciences, Durham University, DurhamDH1 3LE, United Kingdom
| | - Franz Essl
- Division of Bioinvasions, Global Change & Macroecology, University Vienna, Vienna1030, Austria
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Konstanz78464, Germany
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou318000, China
| | - Jan Pergl
- Czech Academy of Sciences, Institute of Botany, Department of Invasion Ecology, Průhonice252 43, Czech Republic
| | - Petr Pyšek
- Czech Academy of Sciences, Institute of Botany, Department of Invasion Ecology, Průhonice252 43, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague128 44, Czech Republic
| | - Marten Winter
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Leipzig04103, Germany
| | - Patrick Weigelt
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Göttingen37077, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen37077, Germany
- Campus-Institute Data Science, Göttingen37077, Germany
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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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Habib S, Gong Y, Dong S, Lindstrom A, William Stevenson D, Liu Y, Wu H, Zhang S. Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia, an Australian endemic genus of Cycadales. ANNALS OF BOTANY 2022; 130:671-685. [PMID: 36111957 PMCID: PMC9670756 DOI: 10.1093/aob/mcac117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/14/2022] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. METHODS We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. KEY RESULTS The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5-6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. CONCLUSIONS This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.
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Affiliation(s)
- Sadaf Habib
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Anders Lindstrom
- Global Biodiversity Conservancy 144/124 Moo 3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi 20250, Thailand
| | | | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
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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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10
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Zhang K, Yin Y, Yi S, Li H. Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus quinquefoliolatus T.T.Yu & L.T.Lu (family Rosaceae). Mitochondrial DNA B Resour 2022; 7:1364-1366. [PMID: 35903303 PMCID: PMC9318300 DOI: 10.1080/23802359.2022.2098859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rubus quinquefoliolatus T.T.Yu & L.T.Lu is a climbing shrub belonging to the Rosaceae family. It is widely distributed in the provinces of Yunnan and Guizhou in China. In this study, we sequenced the first complete chloroplast genome (cpDNA) sequence of R. quinquefoliolatus. The results showed a genome length of 156,489 bp, which is composed of a large single-copy (LSC) of 86,103 bp, small single-copy (SSC) of 18,844 bp, and two inverted repeats of 25,771 bp each. The whole chloroplast genome encodes 131 genes, including 86 coding sequences, 37 tRNAs, and eight rRNAs. Phylogenetic analysis revealed that R. quinquefoliolatus is closely related to R. lineatus and R. pentagonus.
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Affiliation(s)
- Ke Zhang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, PR China
| | - Yongfei Yin
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, PR China
| | - Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, PR China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, PR China
| | - Haitao Li
- Yunnan Branch Institute of Medicinal Plant, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong, PR China
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11
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Meng Q, Manghwar H, Hu W. Study on Supergenus Rubus L.: Edible, Medicinal, and Phylogenetic Characterization. PLANTS (BASEL, SWITZERLAND) 2022; 11:1211. [PMID: 35567211 PMCID: PMC9102695 DOI: 10.3390/plants11091211] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural "supergenus" for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies.
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Affiliation(s)
- Qinglin Meng
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
| | - Weiming Hu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Q.M.); (H.M.)
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12
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Yu J, Fu J, Fang Y, Xiang J, Dong H. Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus. BMC Genomics 2022; 23:32. [PMID: 34991463 PMCID: PMC8740016 DOI: 10.1186/s12864-021-08225-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Rubus is the largest genus of the family Rosaceae and is valued as medicinal, edible, and ornamental plants. Here, we sequenced and assembled eight chloroplast (cp) genomes of Rubus from the Dabie Mountains in Central China. Fifty-one Rubus species were comparatively analyzed for the cp genomes including the eight newly discovered genomes and forty-three previously reported in GenBank database (NCBI). RESULTS The eight newly obtained cp genomes had the same quadripartite structure as the other cp genomes in Rubus. The length of the eight plastomes ranged from 155,546 bp to 156,321 bp with similar GC content (37.0 to 37.3%). The results indicated 133-134 genes were annotated for the Rubus plastomes, which contained 88 or 89 protein coding genes (PCGs), 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Among them, 16 (or 18) of the genes were duplicated in the IR region. Structural comparative analysis results showed that the gene content and order were relatively preserved. Nucleotide variability analysis identified nine hotspot regions for genomic divergence and multiple simple sequences repeats (SSRs), which may be used as markers for genetic diversity and phylogenetic analysis. Phylogenetic relationships were highly supported within the family Rosaceae, as evidenced by sub-clade taxa cp genome sequences. CONCLUSION Thus, the whole plastome may be used as a super-marker in phylogenetic studies of this genus.
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Affiliation(s)
- Jiaojun Yu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Jun Fu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Yuanping Fang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China
| | - Hongjin Dong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang Normal University, Huanggang, Hubei, China.
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Xingang Road No. 146, Huanggang, 438000, Hubei, China.
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14
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Kosiński P, Maliński T, Nobis M, Rojek-Jelonek M, Tomaszewski D, Dering M, Zieliński J. Rubuskaznowskii (Rosaceae), a new bramble species from south-central Poland. PHYTOKEYS 2021; 185:27-41. [PMID: 34819779 PMCID: PMC8604876 DOI: 10.3897/phytokeys.185.71193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Based on field research in south-central Poland, supplemented with a review of herbarium materials, we identified a stable bramble biotype with a range large enough (190 km distance between the outermost stands) to be described as a new regional agamic species, Rubuskaznowskii sp.nov. It belongs to the series Subthyrsoidei(sect. Corylifolii). Although R.kaznowskii has a unique combination of features, it can be potentially mistaken for R.gothicus. It differs from the latter species in many aspects, including: pruinose primocanes, denser indumentum of the abaxial leaf surface, and more curved prickles on the petiole. R.kaznowskii has mainly been observed on rusty soils, in habitats of mixed coniferous and mixed broadleaf forests, usually in sunny places, along forest margins and roads, in clearings and roadside thickets.
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Affiliation(s)
- Piotr Kosiński
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, PolandInstitute of Dendrology, Polish Academy of SciencesKórnikPoland
- Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, PolandPoznań University of Life SciencesPoznańPoland
| | - Tomasz Maliński
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, PolandJagiellonian UniversityKrakowPoland
| | - Marcin Nobis
- Department of Plant Taxonomy, Phytogeography & Paleobotany, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, PolandUniversity of Silesia in KatowiceKatowicePoland
| | - Magdalena Rojek-Jelonek
- Institute of Biology, Biotechnology, and Environmental Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, PolandInstitute of Dendrology, Polish Academy of SciencesPoznanPoland
| | - Dominik Tomaszewski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, PolandInstitute of Dendrology, Polish Academy of SciencesKórnikPoland
| | - Monika Dering
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, PolandInstitute of Dendrology, Polish Academy of SciencesKórnikPoland
- Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, PolandJagiellonian UniversityKrakowPoland
| | - Jerzy Zieliński
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, PolandInstitute of Dendrology, Polish Academy of SciencesKórnikPoland
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15
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Lyu R, He J, Luo Y, Lin L, Yao M, Cheng J, Xie L, Pei L, Yan S, Li L. Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:745988. [PMID: 34712260 PMCID: PMC8545901 DOI: 10.3389/fpls.2021.745988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/22/2021] [Indexed: 05/23/2023]
Abstract
Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.
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Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lele Lin
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Shuangxi Yan
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Liangqian Li
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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16
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Carter KA, Liston A, Bassil NV, Alice LA, Bushakra JM, Sutherland BL, Mockler TC, Bryant DW, Hummer KE. Target Capture Sequencing Unravels Rubus Evolution. FRONTIERS IN PLANT SCIENCE 2019; 10:1615. [PMID: 31921259 PMCID: PMC6933950 DOI: 10.3389/fpls.2019.01615] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/15/2019] [Indexed: 05/09/2023]
Abstract
Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.
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Affiliation(s)
- Katherine A. Carter
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Aaron Liston
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Nahla V. Bassil
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Lawrence A. Alice
- Department of Biology, Western Kentucky University, Bowling Green, KY, United States
| | - Jill M. Bushakra
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Brittany L. Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Todd C. Mockler
- Mockler Lab, Donald Danforth Plant Sciences Center, St. Louis, MO, United States
| | - Douglas W. Bryant
- Mockler Lab, Donald Danforth Plant Sciences Center, St. Louis, MO, United States
| | - Kim E. Hummer
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
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17
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Yang J, Pak JH, Maki M, Kim SC. Multiple origins and the population genetic structure of Rubus takesimensis (Rosaceae) on Ulleung Island: Implications for the genetic consequences of anagenetic speciation. PLoS One 2019; 14:e0222707. [PMID: 31536553 PMCID: PMC6752786 DOI: 10.1371/journal.pone.0222707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/05/2019] [Indexed: 11/19/2022] Open
Abstract
To determine the origin and genetic consequences of anagenesis in Rubus takesimensis on Ulleung Island, Korea, we compared the genetic diversity and population structure of R. takesimensis with those of its continental progenitor R. crataegifolius. We broadly sampled a total of 315 accessions in 35 populations and sequenced five noncoding regions of chloroplast DNA. Rubus takesimensis emerged as nonmonophyletic and several geographically diverse continental populations were likely responsible for the origin of R. takesimensis; the majority of R. takesimensis accessions were sisters to the clade containing accessions of R. crataegifolius, primarily from the Korean peninsula, while rare accessions from three populations shared common ancestors with the ones from the southern part of the Korean peninsula, Jeju Island, and Japan. A few accessions from the Chusan population originated independently from the Korean peninsula. Of 129 haplotypes, 81 and 48 were found exclusively in R. crataegifolius and R. takesimensis, respectively. We found unusually high genetic diversity in two regions on Ulleung Island and no geographic population structure. For R. crataegifolius, two major haplotype groups were found; one for the northern mainland Korean peninsula, and the other for the southern Korean peninsula and the Japanese archipelago. Compared with populations of R. crataegifolius sampled from Japan, much higher haplotype diversity was found in populations from the Korean peninsula. The patterns of genetic consequences in R. takesimensis need to be verified for other endemic species based on chloroplast DNA and independent nuclear markers to synthesize emerging patterns of anagenetic speciation on Ulleung Island.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Gyeongsangbuk-do, Korea
| | - Jae-Hong Pak
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Gyeongsangbuk-do, Korea
- * E-mail: (SCK); (JHP)
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Sendai, Miyagi, Japan
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
- * E-mail: (SCK); (JHP)
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18
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Carman JG, Mateo de Arias M, Gao L, Zhao X, Kowallis BM, Sherwood DA, Srivastava MK, Dwivedi KK, Price BJ, Watts L, Windham MD. Apospory and Diplospory in Diploid Boechera (Brassicaceae) May Facilitate Speciation by Recombination-Driven Apomixis-to-Sex Reversals. FRONTIERS IN PLANT SCIENCE 2019; 10:724. [PMID: 31214233 PMCID: PMC6555261 DOI: 10.3389/fpls.2019.00724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/16/2019] [Indexed: 05/08/2023]
Abstract
Apomixis (asexual seed formation) in angiosperms occurs either sporophytically, through adventitious embryony, or gametophytically, where an unreduced female gametophyte (embryo sac) forms and produces an unreduced egg that develops into an embryo parthenogenetically. Multiple types of gametophytic apomixis occur, and these are differentiated based on where and when the unreduced gametophyte forms, a process referred to as apomeiosis. Apomeiotic gametophytes form directly from ameiotic megasporocytes, as in Antennaria-type diplospory, from unreduced spores derived from 1st division meiotic restitutions, as in Taraxacum-type diplospory, or from cells of the ovule wall, as in Hieracium-type apospory. Multiple types of apomeiosis occasionally occur in the same plant, which suggests that the different types occur in response to temporal and/or spatial shifts in termination of sexual processes and onset timing of apomeiosis processes. To better understand the origins and evolutionary implications of apomixis in Boechera (Brassicaceae), we determined apomeiosis type for 64 accessions representing 44 taxonomic units. Plants expressing apospory and diplospory were equally common, and these generally produced reduced and unreduced pollen, respectively. Apospory and diplospory occurred simultaneously in individual plants of seven taxa. In Boechera, apomixis perpetuates otherwise sterile or semisterile interspecific hybrids (allodiploids) through multiple generations. Accordingly, ample time, in these multigenerational clones, is available for rare meioses to produce haploid, intergenomically recombined male and female gametes. The fusion of such gametes could then produce segmentally autoploidized progeny. If sex re-emerges among such progeny, then new and genomically unique sexual species could evolve. Herein, we present evidence that such apomixis-facilitated speciation is occurring in Boechera, and we hypothesize that it might also be occurring in facultatively apomictic allodiploids of other angiospermous taxa.
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Affiliation(s)
- John G. Carman
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Mayelyn Mateo de Arias
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- Instituto Tecnológico de Santo Domingo, Santo Domingo, Dominican Republic
| | - Lei Gao
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Xinghua Zhao
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- College of Desert Control Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | | | - David A. Sherwood
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Manoj K. Srivastava
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Krishna K. Dwivedi
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
- Caisson Laboratories, Inc., Smithfield, UT, United States
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Bo J. Price
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
| | - Landon Watts
- Plants, Soils and Climate Department, Utah State University, Logan, UT, United States
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19
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Unmack PJ, Adams M, Bylemans J, Hardy CM, Hammer MP, Georges A. Perspectives on the clonal persistence of presumed 'ghost' genomes in unisexual or allopolyploid taxa arising via hybridization. Sci Rep 2019; 9:4730. [PMID: 30894575 PMCID: PMC6426837 DOI: 10.1038/s41598-019-40865-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/20/2019] [Indexed: 01/19/2023] Open
Abstract
Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as ‘ghost species’ after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.
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Affiliation(s)
- P J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - M Adams
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Department of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - J Bylemans
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - C M Hardy
- CSIRO Land and Water, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - M P Hammer
- Museum & Art Gallery of the Northern Territory, Darwin, Northern Territory, 0810, Australia
| | - A Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
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Vegetation classification as a mirror of evolution? Thoughts on the syntaxonomy and management of bramble scrubs of the Prunetalia (Rhamno-Prunetea). Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00199-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AbstractIn Germany and the Netherlands, many bramble scrub associations are distinguished on the basis of the occurrence of Rubus species. The associations belonging to the Prunetalia spinosae Tüxen 1952 are usually assigned to the Pruno-Rubion radulae Weber Osnabr Naturwiss Mitt 3:143–150, 1974, but published tables show inconsistencies in the occurrence of alliance character species. In this paper, we compare synoptic tables from different sources from the Netherlands and Germany. From this comparison, it is concluded that the associations can be divided over two alliances, the Pruno-Rubion radulae in central Europe, and the Pruno-Rubion sprengelii Weber Osnabr Naturwiss Mitt 3:143–150, 1974 in northwest Europe (excluding the UK). The differential species of both these alliances coincide to a considerable degree with the indicator species of the phytogeographical Rubus territories as defined by Haveman et al. (J Biogeogr 43:1360-1371, 2016). As can be deduced from recent molecular studies (Sochor et al. Mol Phylogenet Evol 89:13-27, 2015), these territories have an evolutionary background. This is an effect of the unsaturated distribution areas of a large portion of the very young Rubus agamospecies. The same holds true for the two alliances: although they have a different ecology, we argue that their current distribution areas are not a reflection of this ecology, but both their ecology and distribution area are caused by different evolutionary developments.
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Whitton J, Sears CJ, Maddison WP. Co-occurrence of related asexual, but not sexual, lineages suggests that reproductive interference limits coexistence. Proc Biol Sci 2018; 284:rspb.2017.1579. [PMID: 29212720 DOI: 10.1098/rspb.2017.1579] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/03/2017] [Indexed: 02/02/2023] Open
Abstract
We used randomizations to analyse patterns of co-occurrence of sexual and apomictic (asexual) members of the North American Crepis agamic complex (Asteraceae). We expect strong asymmetry in reproductive interactions in Crepis: apomicts produce clonal seeds with no need for pollination and are not subject to reproductive interference from co-occurring relatives. However, because they still produce some viable pollen, apomicts can reduce reproductive success of nearby sexual relatives, potentially leading to eventual local exclusion of sexuals. Consistent with this, randomizations reveal that sexuals are over-represented in isolated sites, while apomicts freely co-occur. Incorporation of taxonomic and phylogenetic evidence indicates that this pattern is not driven by local origins of asexuals. Our evidence that patterns of local co-occurrence are structured by reproductive interference suggests an underappreciated role for these interactions in community assembly, and highlights the need for explicit tests of the relative contributions of ecological and reproductive interactions in generating patterns of limiting similarity.
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Affiliation(s)
- Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher J Sears
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wayne P Maddison
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
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22
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Effects of forest management on biodiversity in temperate deciduous forests: An overview based on Central European beech forests. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2017.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Šarhanová P, Sharbel TF, Sochor M, Vašut RJ, Dančák M, Trávníček B. Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers. ANNALS OF BOTANY 2017; 120:317-328. [PMID: 28402390 PMCID: PMC5737493 DOI: 10.1093/aob/mcx033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/02/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Rubus subgenus Rubus is a group of mostly apomictic and polyploid species with a complicated taxonomy and history of ongoing hybridization. The only polyploid series with prevailing sexuality is the series Glandulosi , although the apomictic series Discolores and Radula also retain a high degree of sexuality, which is influenced by environmental conditions and/or pollen donors. The aim of this study is to detect sources of genetic variability, determine the origin of apomictic taxa and validate microsatellite markers by cloning and sequencing. METHODS A total of 206 individuals from two central European regions were genotyped for 11 nuclear microsatellite loci and the chloroplast trn L- trn F region. Microsatellite alleles were further sequenced in order to determine the exact repeat number and to detect size homoplasy due to insertions/deletions in flanking regions. KEY RESULTS The results confirm that apomictic microspecies of ser. Radula are derived from crosses between sexual series Glandulosi and apomictic series Discolores , whereby the apomict acts as pollen donor. Each apomictic microspecies is derived from a single distinct genotype differing from the parental taxa, suggesting stabilized clonal reproduction. Intraspecific variation within apomicts is considerably low compared with sexual series Glandulosi , and reflects somatic mutation accumulation. While facultative apomicts produce clonal offspring, sexual species are the conduits of origin for new genetically different apomictic lineages. CONCLUSIONS One of the main driving forces of evolution and speciation in the highly apomictic subgenus Rubus in central Europe is sexuality in the series Glandulosi . Palaeovegetation data suggest that initial hybridizations took place over different time periods in the two studied regions, and that the successful origin and spread of apomictic microspecies of the series Radula took place over several millennia. Additionally, the cloning and sequencing show that standard evaluations of microsatellite repeat numbers underestimate genetic variability considering homoplasy in allele size.
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Affiliation(s)
- Petra Šarhanová
- Leibniz Institute of Plant Genetics and Crop Research (IPK), Department of Experimental Taxonomy, Corrensstr. 3, D-06466 Gatersleben, Germany
- For correspondence. E-mail
| | - Timothy F. Sharbel
- Leibniz Institute of Plant Genetics and Crop Research (IPK), Department of Experimental Taxonomy, Corrensstr. 3, D-06466 Gatersleben, Germany
- Present address: Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place, suite 1460 Saskatoon, SK S7N 4J8, Canada
| | - Michal Sochor
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, CZ-78371 Olomouc, Czech Republic
| | - Radim J. Vašut
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Martin Dančák
- Department of Ecology and Environmental Sciences, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Bohumil Trávníček
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
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Vargas OM, Ortiz EM, Simpson BB. Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium). THE NEW PHYTOLOGIST 2017; 214:1736-1750. [PMID: 28333396 DOI: 10.1111/nph.14530] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 02/19/2017] [Indexed: 05/21/2023]
Abstract
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
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Affiliation(s)
- Oscar M Vargas
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University Ave, Ann Arbor, MI, 48109, USA
| | - Edgardo M Ortiz
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Beryl B Simpson
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
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Smith JF, Clark JL, Amaya-Márquez M, Marín-Gómez OH. Resolving incongruence: Species of hybrid origin in Columnea (Gesneriaceae). Mol Phylogenet Evol 2017; 106:228-240. [DOI: 10.1016/j.ympev.2016.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/19/2023]
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Li M, Chen S, Zhou R, Fan Q, Li F, Liao W. Molecular Evidence for Natural Hybridization between Cotoneaster dielsianus and C. glaucophyllus. FRONTIERS IN PLANT SCIENCE 2017; 8:704. [PMID: 28536587 PMCID: PMC5422516 DOI: 10.3389/fpls.2017.00704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/18/2017] [Indexed: 05/06/2023]
Abstract
Hybridization accompanied by polyploidization and apomixis has been demonstrated as a driving force in the evolution and speciation of many plants. A good example to study the evolutionary process of hybridization associated with polyploidy and apomixis is the genus Cotoneaster (Rosaceae), which includes approximately 150 species, most of which are polyploid apomicts. In this study, we investigated all Cotoneaster taxa distributed in a small region of Malipo, Yunnan, China. Based on the morphological characteristics, four Cotoneaster taxa were identified and sampled: C. dielsianus, C. glaucophyllus, C. franchetii, and a putative hybrid. Flow cytometry analyses showed that C. glaucophyllus was diploid, while the other three taxa were tetraploid. A total of five low-copy nuclear genes and six chloroplast regions were sequenced to validate the status of the putative hybrid. Sequence analyses showed that C. dielsianus and C. glaucophyllus are distantly related and they could be well separated using totally 50 fixed nucleotide substitutions and four fixed indels at the 11 investigated genes. All individuals of the putative hybrid harbored identical sequences: they showed chromatogram additivity for all fixed differences between C. dielsianus and C. glaucophyllus at the five nuclear genes, and were identical with C. glaucophyllus at the six chloroplast regions. Haplotype analysis revealed that C. dielsianus possessed nine haplotypes for the 11 genes, while C. glaucophyllus had ten, and there were no shared haplotypes between the two species. The putative hybrid harbored two haplotypes for each nuclear gene: one shared with C. dielsianus and the other with C. glaucophyllus. They possessed the same chloroplast haplotype with C. glaucophyllus. Our study provided convincing evidence for natural hybridization between C. dielsianus and C. glaucophyllus, and revealed that all hybrid individuals were derivatives of one initial F1 via apomixes. C. glaucophyllus served as the maternal parent at the initial hybridization event. We proposed that anthropological disturbance provided an opportunity for hybridization between C. dielsianus and C. glaucophyllus, and a tetraploid F1 successfully bred many identical progenies via apomixis. Under this situation, species integrity could be maintained for these Cotoneaster species, but attentions should be kept for this new-born hybrid.
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Affiliation(s)
- Mingwan Li
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Sufang Chen
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
- *Correspondence: Sufang Chen
| | - Renchao Zhou
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Qiang Fan
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Feifei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental SciencesBeijing, China
- College of Life and Environmental Sciences, Minzu University of ChinaBeijing, China
- Feifei Li
| | - Wenbo Liao
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
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Sha LN, Fan X, Wang XL, Dong ZZ, Zeng J, Zhang HQ, Kang HY, Wang Y, Liao JQ, Zhou YH. Genome origin, historical hybridization and genetic differentiation in Anthosachne australasica (Triticeae; Poaceae), inferred from chloroplast rbcL, trnH-psbA and nuclear Acc1 gene sequences. ANNALS OF BOTANY 2017; 119:95-107. [PMID: 28040673 PMCID: PMC5218373 DOI: 10.1093/aob/mcw222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/01/2016] [Accepted: 09/14/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Anthosachne Steudel is a group of allopolyploid species that was derived from hexaploidization between the Asian StY genome Roegneria entity and the Australasia W genome Australopyrum species. Polyploidization and apomixis contribute to taxonomic complexity in Anthosachne Here, a study is presented on the phylogeny and evolutionary history of Anthosachne australasica The aims are to demonstrate the process of polyploidization events and to explore the differentiation patterns of the St genome following geographic isolation. METHODS Chloroplast rbcL and trnH-psbA and nuclear Acc1 gene sequences of 60 Anthosachne taxa and nine Roegneria species were analysed with those of 33 diploid taxa representing 20 basic genomes in Triticeae. The phylogenetic relationships were reconstructed. A time-calibrated phylogeny was generated to estimate the evolutionary history of A. australasica Nucleotide diversity patterns were used to assess the divergence within A. australasica and between Anthosachne and its putative progenitors. KEY RESULTS Three homoeologous copies of the Acc1 sequences from Anthosachne were grouped with the Acc1 sequences from Roegneria, Pseudoroegneria, Australopyrum, Dasypyrum and Peridictyon The chloroplast sequences of Anthosachne were clustered with those from Roegneria and Pseudoroegneria Divergence time for Anthosachne was dated to 4·66 million years ago (MYA). The level of nucleotide diversity in Australasian Anthosachne was higher than that in continental Roegneria A low level of genetic differentiation within the A. australasica complex was found. CONCLUSIONS Anthosachne originated from historical hybridization between Australopyrum species and a Roegneria entity colonized from Asia to Australasia via South-east Asia during the late Miocene. The St lineage served as the maternal donor during the speciation of Anthosachne A contrasting pattern of population genetic structure exists in the A. australasica complex. Greater diversity in island Anthosachne compared with continental Roegneria might be associated with mutation, polyploidization, apomixis and expansion. It is reasonable to consider that A. australasica var. scabra and A. australasica var. plurinervisa should be included in the A. australasica complex.
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Affiliation(s)
- Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xiao-Li Wang
- College of Life Sciences, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Zhen-Zhen Dong
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Jin-Qiu Liao
- College of Life Sciences, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Yaan 625014, Sichuan, China
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Sears CJ, Whitton J. A reexamination of the North American Crepis agamic complex and comparison with the findings of Babcock and Stebbins' classic biosystematic monograph. AMERICAN JOURNAL OF BOTANY 2016; 103:1289-99. [PMID: 27313196 DOI: 10.3732/ajb.1600057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 04/12/2016] [Indexed: 05/22/2023]
Abstract
PREMISE OF THE STUDY Babcock and Stebbins coined the term agamic complex in their 1938 monograph of the North American Crepis agamic complex. Despite the historical role that this complex holds in the evolutionary literature, it has not been reexamined in over 75 years. We present a thorough reevaluation of the complex to test hypotheses proposed by Babcock and Stebbins about its origins and spread, the relationships of diploids, and the nature and origins of polyploids. METHODS We used flow cytometry to infer ploidy of roughly 600 samples spanning the morphological and taxonomic diversity of the complex and a phylogenetic analysis of plastid DNA variation to infer maternal relationships among diploids and to infer maternal origins of polyploids. KEY RESULTS We identified populations of all seven recognized diploids plus one new lineage. Phylogenetic analysis of plastid DNA variation in diploids revealed a well-resolved, but moderately supported phylogeny, with evidence for monophyly of the North America Crepis agamic complex and no evidence of widespread homoploid hybridization. Polyploids showed evidence of multiple origins and a pattern of frequent local co-occurrence consistent with repeated colonization of suitable sites. CONCLUSIONS Our findings agree broadly with the distribution and variation of ploidy within and among species described by Babcock and Stebbins. One key difference is finding support for monophyly of North American species, and refuting their hypothesis of polyphyly. Our results provide an explicit phylogenetic framework for further study of this classic agamic complex.
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Affiliation(s)
- Christopher J Sears
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4 Canada
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4 Canada
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Wang Y, Chen Q, Chen T, Tang H, Liu L, Wang X. Phylogenetic Insights into Chinese Rubus (Rosaceae) from Multiple Chloroplast and Nuclear DNAs. FRONTIERS IN PLANT SCIENCE 2016; 7:968. [PMID: 27446191 PMCID: PMC4925702 DOI: 10.3389/fpls.2016.00968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/16/2016] [Indexed: 05/09/2023]
Abstract
Rubus L. is a large and taxonomically complex genus, species of which exhibit apomixis, polyploidy, and frequent hybridization. Most of Chinese Rubus are assigned in two major sections, Idaeobatus and Malachobatus. To explore the phylogenetic relationships within Chinese Rubus, inferences upon three chloroplast DNA (rbcL, rpl20-rps12, and trnG-trnS), nuclear ribosomal ITS, and two low-copy nuclear markers (GBSSI-2 and PEPC) were deduced in 142 Rubus taxa from 17 subsections in 6 sections. nrITS and GBSSI-2 were the most informative among the six DNA regions assessed. Phylogenetic relationships within Rubus were well-resolved by combined nuclear datasets rather than chloroplast markers. The phylogenetic inferences strongly supported that section Idaeobatus was a polyphyletic group with four distant clades. All samples of sect. Malachobatus formed a monophyletic clade, in which R. tsangorum and R. amphidasys of sect. Dalibardastrum, and R. peltatus from subsection Peltati of sect. Idaeobatus were always nested. Rubus pentagonus (2n = 2x = 14) from subsect. Alpestres of sect. Idaeobatus was a sister group to the polyploid sect. Malachobatus, as well as the polytomy of three sect. Cyalctis members. This suggests that some polyploids of Malachobatus might originate from common ancestors, via polyploidization of hybrids between R. pentagonus and sect. Cylactis species. They had experienced species explosion in a short time. Section Dalibardastrum species have potential parental lineages from subsects. Moluccani and Stipulosi of sect. Malachobatus. Based on molecular phylogenies, we also provided recommendations for the taxonomic treatments of four taxa. In addition, our results showed certain incongruence between chloroplast and nuclear markers, which might be due to hybridization and introgression.
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Affiliation(s)
- Yan Wang
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
| | - Tao Chen
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural UniversityChengdu, China
| | - Lin Liu
- Agricultural and Animal Husbandry College of Tibet UniversityLinzhi, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural UniversityChengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural UniversityChengdu, China
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