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Zhou R, Qin X, Hou J, Liu Y. Research progress on Brassicaceae plants: a bibliometrics analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1285050. [PMID: 38357268 PMCID: PMC10864531 DOI: 10.3389/fpls.2024.1285050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
The Brassicaceae is a worldwide family that produces ornamental flowers, edible vegetables, and oilseed plants, with high economic value in agriculture, horticulture, and landscaping. This study used the Web of Science core dataset and the CiteSpace bibliometric tool to quantitatively visualize the number of publications, authors, institutions, and countries of 3139 papers related to Brassicaceae plants from 2002 to 2022. The keywords and references were divided into two phases: Phase 1 (2002-2011) and Phase 2 (2012-2022) for quantitative and qualitative analysis. The results showed: An average annual publication volume of 149 articles, with an overall fluctuating upward trend; the research force was mainly led by Professor Ihsan A. Al-shehbaz from Missouri Botanical Garden; and the United States had the highest number of publications. In the first phase, research focused on the phylogeny of Brassicaceae plants, while the second phase delved into diverse research based on previous studies, research in areas such as polyploidy, molecular technique, physiology, and hyperaccumulator has been extended. Based on this research, we propounded some ideas for future studies on Brassicaceae plants and summarized the research gaps.
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Affiliation(s)
- Ruixue Zhou
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xinsheng Qin
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Junjun Hou
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yining Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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Kaya Y, Aydın ZU, Cai X, Wang X, Dönmez AA. Genome-wide characterization of two Aubrieta taxa: Aubrieta canescens subsp. canescens and Au. macrostyla (Brassicaceae). AOB PLANTS 2022; 14:plac035. [PMID: 36196394 PMCID: PMC9521481 DOI: 10.1093/aobpla/plac035] [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: 03/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Aubrieta canescens complex is divided into two subspecies, Au. canescens subsp. canescens, Au. canescens subsp. cilicica and a distinct species, Au. macrostyla, based on molecular phylogeny. We generated a draft assembly of Au. canescens subsp. canescens and Au. macrostyla using paired-end shotgun sequencing. This is the first attempt at genome characterization for the genus. In the presented study, ~165 and ~157 Mbp of the genomes of Au. canescens subsp. canescens and Au. macrostyla were assembled, respectively, and a total of 32 425 and 31 372 gene models were predicted in the genomes of the target taxa, respectively. We corroborated the phylogenomic affinity of taxa with some core Brassicaceae species (Clades A and B) including Arabis alpina. The orthology-based tree suggested that Aubrieta species differentiated from A. alpina 1.3-2.0 mya (million years ago). The genome-wide syntenic comparison of two Aubrieta taxa revealed that Au. canescens subsp. canescens (46 %) and Au. macrostyla (45 %) have an almost identical syntenic gene pair ratio. These novel genome assemblies are the first steps towards the chromosome-level assembly of Au. canescens and understanding the genome diversity within the genus.
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Affiliation(s)
| | - Zübeyde Uğurlu Aydın
- Molecular Plant Systematic Laboratory (MOBIS), Department of Biology, Faculty of Science, Hacettepe University, Ankara 06800, Turkey
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ali A Dönmez
- Molecular Plant Systematic Laboratory (MOBIS), Department of Biology, Faculty of Science, Hacettepe University, Ankara 06800, Turkey
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Chen H, German DA, Al-Shehbaz IA, Yue J, Sun H. Phylogeny of Euclidieae (Brassicaceae) based on plastome and nuclear ribosomal DNA data. Mol Phylogenet Evol 2020; 153:106940. [PMID: 32818597 DOI: 10.1016/j.ympev.2020.106940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 01/19/2023]
Abstract
Euclidieae, a morphologically diverse tribe in the family Brassicaceae (Cruciferae), consists of 29 genera and more than 150 species distributed mainly in Asia. Prior phylogenetic analyses on Euclidieae are inadequate. In this study, sequence data from the plastid genome and nuclear ribosomal DNA of 72 species in 27 genera of Euclidieae were used to infer the inter- and intra-generic relationships within. The well-resolved and strongly supported plastome phylogenies revealed that Euclidieae could be divided into five clades. Both Cymatocarpus and Neotorularia are polyphyletic in nuclear and plastome phylogenies. Besides, the conflicts of systematic positions of three species of Braya and two species of Solms-laubachia s.l. indicated that hybridization and or introgression might have happened during the evolutionary history of the tribe. Results from divergence-time analyses suggested an early Miocene origin of Euclidieae, and it probably originated from the Central Asia, Pamir Plateau and West Himalaya. In addition, multiple ndh genes loss and pseudogenization were detected in eight species based on comparative genomic study.
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Affiliation(s)
- Hongliang Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Laboratory of Systematics & Evolutionary Botany and Biodiversity, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Lenin Ave. 61, Barnaul 656049, Russia
| | | | - Jipei Yue
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Koch MA, Möbus J, Klöcker CA, Lippert S, Ruppert L, Kiefer C. The Quaternary evolutionary history of Bristol rock cress (Arabis scabra, Brassicaceae), a Mediterranean element with an outpost in the north-western Atlantic region. ANNALS OF BOTANY 2020; 126:103-118. [PMID: 32211750 PMCID: PMC7304472 DOI: 10.1093/aob/mcaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/19/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Bristol rock cress is among the few plant species in the British Isles considered to have a Mediterranean-montane element. Spatiotemporal patterns of colonization of the British Isles since the last interglacial and after the Last Glacial Maximum (LGM) from mainland Europe are underexplored and have not yet included such floristic elements. Here we shed light on the evolutionary history of a relic and outpost metapopulation of Bristol rock cress in the south-western UK. METHODS Amplified fragment length polymorphisms (AFLPs) were used to identify distinct gene pools. Plastome assembly and respective phylogenetic analysis revealed the temporal context. Herbarium material was largely used to exemplify the value of collections to obtain a representative sampling covering the entire distribution range. KEY RESULTS The AFLPs recognized two distinct gene pools, with the Iberian Peninsula as the primary centre of genetic diversity and the origin of lineages expanding before and after the LGM towards mountain areas in France and Switzerland. No present-day lineages are older than 51 ky, which is in sharp contrast to the species stem group age of nearly 2 My, indicating severe extinction and bottlenecks throughout the Pleistocene. The British Isles were colonized after the LGM and feature high genetic diversity. CONCLUSIONS The short-lived perennial herb Arabis scabra, which is restricted to limestone, has expanded its distribution range after the LGM, following corridors within an open landscape, and may have reached the British Isles via the desiccated Celtic Sea at about 16 kya. This study may shed light on the origin of other rare and peculiar species co-occurring in limestone regions in the south-western British Isles.
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Affiliation(s)
- Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Johanna Möbus
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Clara A Klöcker
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Stephanie Lippert
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Laura Ruppert
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
| | - Christiane Kiefer
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, Heidelberg, Germany
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Balpinar N. The biological activities of Arabis alpina L. subsp. brevifolia (DC.) Cullen against food pathogens. OPEN CHEM 2018. [DOI: 10.1515/chem-2018-0104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractIn this study, in vitro biological activities of both methanol and ethanol extracts of Arabis alpina subsp. brevifolia were investigated. Also, the phenolic components of this plant was examined in this study. The extracts were tested against the eight strains of food pathogens for their antimicrobial activities by utilizing minimum inhibitory concentration (MIC) and disc diffusion assay. The non-enzymatic antioxidant activities were determined according to scavenging of the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). The phenolic compounds were analyzed by high performance liquid chromatography (HPLC). The main component was ellagic acid for the methanol extract of stem-leaf, rutin for the ethanol extract of stem-leaf, and 2,5-dihydroxybenzoic acid for the methanol and ethanol extracts of fruit-flower. The ethanolic extracts of leaves revealed antibacterial activities against Salmonella Typhimurium (7 mm) while the ethanolic extracts of flowers demonstrated no activity against the test pathogens. The methanolic extracts of leaf-flower showed antibacterial activities against S. Typhimurium (7 mm). No activity was observed against C. albicans. The MIC value for four test bacteria was 13000 μg/mL. The ethanol extracts of A. alpina subsp. brevifolia exhibited the highest DPPH inhibition (76%). This study showed that A. alpina subsp. brevifolia possesses antioxidant and antimicrobial activities.
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Affiliation(s)
- N. Balpinar
- Department of Biology, Faculty of Arts and Science, Mehmet Akif Ersoy University, Burdur15030, Turkey
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Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing. Int J Mol Sci 2018; 19:ijms19020602. [PMID: 29463014 PMCID: PMC5855824 DOI: 10.3390/ijms19020602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 02/01/2023] Open
Abstract
Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta, A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, A. nipponica and A. stelleri, differ at similar levels to possible maternal donor species A. flagellosa, which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while A. nipponica and A. flagellosa were more similar to each other than to A. hirsuta. This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian Arabis species.
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German DA, Koch MA. Eutrema salsugineum (Cruciferae) new to Mexico: a surprising generic record for the flora of Middle America. PHYTOKEYS 2017:13-21. [PMID: 28228683 PMCID: PMC5301981 DOI: 10.3897/phytokeys.76.9731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/12/2016] [Indexed: 05/14/2023]
Abstract
The paper reports Eutrema salsugineum as a novelty to the flora of Mexico and Middle America in general. The finding stands ca. 1600 km apart from the closest known locality in the Rocky Mountains of Colorado, USA. The species is considered native to NW Mexico and its late discovery in the region is presumably explained by its tiny habit, early flowering time, and subephemeral life cycle. The phylogenetic position of this Mexican population in a haplotype network based on the chloroplast DNA fragment psbA-trnH confirms this hypothesis and also suggests, in contrast to the previously held viewpoint, multiple colonizations of North American continent from Asia.
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Affiliation(s)
- Dmitry A. German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
- South-Siberian Botanical Garden, Altai State University, Lenin Str. 61, 656049 Barnaul, Russia
| | - Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
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Koch MA, Karl R, German DA. Underexplored biodiversity of Eastern Mediterranean biota: systematics and evolutionary history of the genus Aubrieta (Brassicaceae). ANNALS OF BOTANY 2017; 119:39-57. [PMID: 27941091 PMCID: PMC5218375 DOI: 10.1093/aob/mcw204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/08/2016] [Accepted: 08/23/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Aubrieta is a taxonomically difficult genus from the Brassicaceae family with approximately 20 species centred in Turkey and Greece. Species boundaries and their evolutionary history are poorly understood. Therefore, we analysed bio- and phylogeographic relationships and evaluated morphological variation to study the evolution of this genus. METHODS Phylogenetic analyses of DNA sequence variation of nuclear-encoded loci and plastid DNA were used to unravel phylogeographic patterns. Morphometric analyses were conducted to study species delimitation. DNA sequence-based mismatch distribution and climate-niche analyses were performed to explain various radiations in space and time during the last 2·5 million years. KEY RESULTS Species groups largely show non-overlapping distribution patterns in the eastern Mediterranean and Asia Minor. We recognized 20 species and provide evidence for overlooked species, thereby highlighting taxonomical difficulties but also demonstrating underexplored species diversity. The centre of origin of Aubrieta is probably Turkey, from which various clades expanded independently towards Asia Minor, south to Lebanon and west to Greece and the Balkans during the Pleistocene. CONCLUSIONS Pleistocene climatic fluctuations had a pronounced effect on Aubrieta speciation and radiation during the last 1·1 million years in the Eastern Mediterranean and Asia Minor. In contrast to many other Brassicaceae, speciation processes did not involve excessive formation of polyploids, but displayed formation of diploids with non-overlapping present-day distribution areas. Expansions from the Aubrieta centre of origin and primary centre of species diversity showed adaptation trends towards higher temperature and drier conditions. However, later expansion and diversification of taxa from within the second centre of species diversity in Greece started ∼0·19 Mya and were associated with a general transition of species adaptation towards milder temperatures and less dry conditions.
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Affiliation(s)
- Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Robert Karl
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Dmitry A German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
- South-Siberian Botanical Garden, Altai State University, Lenina Street 61, 656049 Barnaul, Russia
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Özüdoğru B, Fırat M. Arabis watsonii (P.H.Davis) F.K.Mey.: An overlooked cruciferous species from eastern Anatolia and its phylogenetic position. PHYTOKEYS 2016; 75:57-68. [PMID: 28127244 PMCID: PMC5234537 DOI: 10.3897/phytokeys.75.10568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Arabis watsonii (P.H.Davis) F.K.Mey. was initially reported as Thlaspi watsonii P.H.Davis in Flora of Turkey. Although F.K.Meyer transferred this species to Arabis L., this species has been overlooked and treated as Thlaspi L. in relevant literature for Flora of Turkey. In this study this species was evaluated using molecular (nuclear ITS and plastidic trnL-F sequences) and morphological data. Results clearly show that Arabis watsonii is sister to the Arabis hirsuta aggregate and its relatives. In conclusion, our results increased the number of known Arabis species in Turkey to 23. Furthermore, detailed description and distribution of the species are given and a new IUCN threat category for Arabis watsonii is proposed.
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Affiliation(s)
- Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, Ankara Turkey
| | - Mehmet Fırat
- Department of Biology, Faculty of Education, Yüzüncü Yıl University, Van, Turkey
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Herden T, Hanelt P, Friesen N. Phylogeny of Allium L. subgenus Anguinum (G. Don. ex W.D.J. Koch) N. Friesen (Amaryllidaceae). Mol Phylogenet Evol 2015; 95:79-93. [PMID: 26639102 DOI: 10.1016/j.ympev.2015.11.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 01/26/2023]
Abstract
The disjunct distribution of the subgenus Anguinum of the genus Allium makes it a good candidate to test models of Northern hemisphere biogeography. Here we conduct phylogenetic analysis with the nuclear marker ITS and three different chloroplast markers (rps16 intron, rbcL-atpB spacer, rpl32-trnL spacer). Divergence time estimations (Beast) relying on published ITS substitution rates and ancestral range reconstructions were calculated to elucidate the biogeographical history of the subgenus. Additionally we compiled distribution maps for all species with data taken from the literature, herbariums and data from field observations. The main radiation of the subgenus took place in the last one million years and is still going on. They have their origins in the mid Miocene in East Asia and were highly influenced by the climate fluctuations in the Pliocene/Pleistocene period. Conflicting tree topologies between nuclear and cpDNA markers of Allium tricoccum Solander indicate that the species is of hybridogenous origin. Cloning the ITS sequence revealed the parental copies and confirmed our conclusion. One originated from the Eurasian and the other from the East Asian clade. We were able to show that it reached North America most likely via the Beringia around 2.5mya (95% HPD of 0.35-5.26mya). Our data suggest that Allium victorialis L. is only distributed in mountain pastures in Europe as it forms a well-supported clade in the ITS tree. In the analysis of the molecular markers we found two distinct types of Allium ochotense Prokh. and we suggest splitting the species based on Prokhanov's (1930) proposal. Taxonomical remarks and an identification key to all species of the subgenus Anguinum is provided.
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Affiliation(s)
- Tobias Herden
- Botanical Garden of the University of Osnabrueck, Albrechtstrasse 29, 49076 Osnabrueck, Germany
| | - Peter Hanelt
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), OT Gartersleben, Corrensstraße 3, 06466 Stadt Seeland, Germany
| | - Nikolai Friesen
- Botanical Garden of the University of Osnabrueck, Albrechtstrasse 29, 49076 Osnabrueck, Germany.
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Munkert J, Costa C, Budeanu O, Petersen J, Bertolucci S, Fischer G, Müller-Uri F, Kreis W. Progesterone 5β-reductase genes of the Brassicaceae family as function-associated molecular markers. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:1113-22. [PMID: 26108256 DOI: 10.1111/plb.12361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/22/2015] [Indexed: 05/12/2023]
Abstract
This study aimed to define progesterone 5β-reductases (P5βR, EC 1.3.99.6, enone 1,4-reductases) as function-associated molecular markers at the plant family level. Therefore cDNAs were isolated from 25 Brassicaceae species, including two species, Erysimum crepidifolium and Draba aizoides, known to produce cardiac glycosides. The sequences were used in a molecular phylogeny study. The cladogram created is congruent to the existing molecular analyses. Recombinant His-tagged forms of the P5βR cDNAs from Aethionema grandiflorum, Draba aizoides, Nasturtium officinale, Raphanus sativus and Sisymbrium officinale were expressed in E. coli. Enone 1,4-reductase activity was demonstrated in vitro using progesterone and 2-cyclohexen-1-one as substrates. Evidence is provided that functional P5βRs are ubiquitous in the Brassicaceae. The recombinant P5βR enzymes showed different substrate preferences towards progesterone and 2-cyclohexen-1-one. Sequence comparison of the catalytic pocket of the P5βR enzymes and homology modelling using Digitalis lanata P5βR (PDB ID: 2V6G) as template highlighted the importance of the hydrophobicity of the binding pocket for substrate discrimination. It is concluded that P5βR genes or P5βR proteins can be used as valuable function-associated molecular markers to infer taxonomic relationship and evolutionary diversification from a metabolic/catalytic perspective.
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Affiliation(s)
- J Munkert
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - C Costa
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - O Budeanu
- University of the Academy of Sciences of Moldova, Chisinau, Moldova Republic
| | - J Petersen
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - S Bertolucci
- Agriculture Department, Universidade Federal de Lavras, Lavras, Brazil
| | - G Fischer
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - F Müller-Uri
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - W Kreis
- Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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12
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Mandáková T, Schranz ME, Sharbel TF, de Jong H, Lysak MA. Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:785-93. [PMID: 25864414 DOI: 10.1111/tpj.12849] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/24/2015] [Accepted: 04/01/2015] [Indexed: 05/19/2023]
Abstract
Chromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we have used comparative chromosome painting (CCP) to reconstruct the pathways of descending and ascending dysploidy in the genus Boechera (tribe Boechereae, Brassicaceae). We describe the origin and structure of three Boechera genomes and establish the origin of the previously described aberrant Het and Del chromosomes found in Boechera apomicts with euploid (2n = 14) and aneuploid (2n = 15) chromosome number. CCP analysis allowed us to reconstruct the origin of seven chromosomes in sexual B. stricta and apomictic B. divaricarpa from the ancestral karyotype (n = 8) of Brassicaceae lineage I. Whereas three chromosomes (BS4, BS6, and BS7) retained their ancestral structure, five chromosomes were reshuffled by reciprocal translocations to form chromosomes BS1-BS3 and BS5. The reduction of the chromosome number (from x = 8 to x = 7) was accomplished through the inactivation of a paleocentromere on chromosome BS5. In apomictic 2n = 14 plants, CCP identifies the largely heterochromatic chromosome (Het) being one of the BS1 homologues with the expansion of pericentromeric heterochromatin. In apomictic B. polyantha (2n = 15), the Het has undergone a centric fission resulting in two smaller chromosomes - the submetacentric Het' and telocentric Del. Here we show that new chromosomes can be formed by a centric fission and can be fixed in populations due to the apomictic mode of reproduction.
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Affiliation(s)
- Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, CZ-62500, Czech Republic
| | - M Eric Schranz
- Plant Systematics Group, Wageningen University (WU), Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Timothy F Sharbel
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Hans de Jong
- Laboratory of Genetics, Wageningen UR PSG, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, CZ-62500, Czech Republic
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Zarrei M, Talent N, Kuzmina M, Lee J, Lund J, Shipley PR, Stefanović S, Dickinson TA. DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus. AOB PLANTS 2015; 7:plv045. [PMID: 25926325 PMCID: PMC4480070 DOI: 10.1093/aobpla/plv045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/18/2015] [Indexed: 05/03/2023]
Abstract
DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication of hawthorn materials in natural health products.
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Affiliation(s)
- Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay St, Toronto, ON, Canada M5G 0A4
| | - Nadia Talent
- Green Plant Herbarium, Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, Canada M5S 2C6
| | - Maria Kuzmina
- Canadian Centre for DNA Barcoding, 50 Stone Road East, Guelph, ON, Canada N1G 2W1
| | - Jeanette Lee
- 109 Lakeshore Ave., Edgewood, BC, Canada V0G 1J0
| | - Jensen Lund
- Department of Chemistry, I.K. Barber School of Arts and Sciences, The University of British Columbia Okanagan, 3333 University Way, Kelowna, BC, Canada V1V 1V7
| | - Paul R Shipley
- Department of Chemistry, I.K. Barber School of Arts and Sciences, The University of British Columbia Okanagan, 3333 University Way, Kelowna, BC, Canada V1V 1V7
| | - Saša Stefanović
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2 Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, Canada L5L 1C6
| | - Timothy A Dickinson
- Green Plant Herbarium, Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, Canada M5S 2C6 Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2
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Salariato DL, Zuloaga FO, Cano A, Al-Shehbaz IA. Molecular phylogenetics of tribe Eudemeae (Brassicaceae) and implications for its morphology and distribution. Mol Phylogenet Evol 2014; 82 Pt A:43-59. [PMID: 25451804 DOI: 10.1016/j.ympev.2014.09.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/21/2014] [Accepted: 09/19/2014] [Indexed: 01/06/2023]
Abstract
Tribe Eudemeae comprises a morphologically heterogeneous group of genera distributed along the Andes of South America from Colombia southward into southern Chile and Argentina. The tribe currently includes seven genera: Aschersoniodoxa, Brayopsis, Dactylocardamum, Delpinophytum, Eudema, Onuris, and Xerodraba, and exhibits a wide morphological diversification in growth habit, inflorescences, and fruits. However, little is known about the phylogenetic relationships and evolution of the tribe. We present here a molecular phylogeny of representative sampling of all genera, utilizing sequence data from the nuclear ribosomal ITS region and chloroplast regions trnL-F, trnH-psbA, and rps16. Additionally, climatic niches of the tribe and its main lineages, along with the evolution of diagnostic morphological characters, were studied. All analyses confirmed the monophyly of Eudemeae, with the exception of Delpinophytum that was included with genera of the lineage I of Brassicaceae. Eudemeae is divided into two main lineages differentiated by their geographical distribution and climatic niche: the primarily north-central Andean lineage included Aschersoniodoxa, Brayopsis, Dactylocardamum, and Eudema, and the Patagonian and southern Andean lineage included Onuris and Xerodraba. Finally, ancestral-state reconstructions in the tribe generally reveal multiple and independent gains or losses of diagnostic morphological characters, such as growth form, inflorescence reduction, and fruit type. Relevant taxonomic implications stemming from the results are also discussed.
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Affiliation(s)
- Diego L Salariato
- Instituto de Botánica Darwinion (CONICET - ANCEFN), Labardén 200, Casilla de Correo 22, B1642HYD San Isidro, Buenos Aires, Argentina.
| | - Fernando O Zuloaga
- Instituto de Botánica Darwinion (CONICET - ANCEFN), Labardén 200, Casilla de Correo 22, B1642HYD San Isidro, Buenos Aires, Argentina
| | - Asunción Cano
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos (UNMSM), Av. Arenales 1256, Lima 11, Peru; Instituto de Investigación de Ciencias Biológicas, Facultad de Ciencias Biológicas (UNMSM), Av. Venezuela s/n, Lima 1, Peru
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Zarrei M, Stefanović S, Dickinson TA. Reticulate evolution in North American black-fruited hawthorns (Crataegus section Douglasia; Rosaceae): evidence from nuclear ITS2 and plastid sequences. ANNALS OF BOTANY 2014; 114:253-69. [PMID: 24984714 PMCID: PMC4111394 DOI: 10.1093/aob/mcu116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 05/07/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The taxonomic complexity of Crataegus (hawthorn; Rosaceae, Maleae), especially in North America, has been attributed by some to hybridization in combination with gametophytic apomixis and polyploidization, whereas others have considered the roles of hybridization and apomixis to be minimal. Study of the chemical composition and therapeutic value of hawthorn extracts requires reproducible differentiation of entities that may be difficult to distinguish by morphology alone. This study sought to address this by using the nuclear ribosomal spacer region ITS2 as a supplementary DNA barcode; however, a lack of success prompted an investigation to discover why this locus gave unsatisfactory results. METHODS ITS2 was extensively cloned so as to document inter- and intraindividual variation in this locus, using hawthorns of western North America where the genus Crataegus is represented by only two widely divergent groups, the red-fruited section Coccineae and the black-fruited section Douglasia. Additional sequence data from selected loci on the plastid genome were obtained to enhance further the interpretation of the ITS2 results. KEY RESULTS In the ITS2 gene tree, ribotypes from western North American hawthorns are found in two clades. Ribotypes from diploid members of section Douglasia occur in one clade (with representatives of the east-Asian section Sanguineae). The other clade comprises those from diploid and polyploid members of section Coccineae. Both clades contribute ribotypes to polyploid Douglasia. Data from four plastid-derived intergenic spacers demonstrate the maternal parentage of these allopolyploids. CONCLUSIONS Repeated hybridization between species of section Douglasia and western North American members of section Coccineae involving the fertilization of unreduced female gametes explains the observed distribution of ribotypes and accounts for the phenetic intermediacy of many members of section Douglasia.
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Affiliation(s)
- M Zarrei
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto ON, Canada M5S 3B2 Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto ON, Canada M5S 2C6
| | - S Stefanović
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto ON, Canada M5S 3B2 Department of Biology, University of Toronto Mississauga, 3359 Mississauga Rd, Mississauga ON, Canada L5L 1C6
| | - T A Dickinson
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto ON, Canada M5S 3B2 Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto ON, Canada M5S 2C6
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LI YAN, KONG YAN, ZHANG ZHE, YIN YANQIANG, LIU BIN, LV GUANGHUI, WANG XIYONG. Phylogeny and biogeography of Alyssum (Brassicaceae) based on nuclear ribosomal ITS DNA sequences. J Genet 2014; 93:313-23. [DOI: 10.1007/s12041-014-0362-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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One or three species in Megadenia (Brassicaceae): insight from molecular studies. Genetica 2014; 142:337-50. [PMID: 25027851 DOI: 10.1007/s10709-014-9778-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
Abstract
Megadenia Maxim. is a small genus of the Brassicaceae endemic to East Asia with three disjunct areas of distribution: the eastern edge of the Qinghai-Tibetan Plateau, the Eastern Sayan Mountains in southern Siberia, and Chandalaz Ridge in the southern Sikhote-Alin Mountains. Although distinct species (M. pygmaea Maxim., M. bardunovii Popov, and M. speluncarum Vorob., Vorosch. and Gorovoj) have been described from each area, they have lately been reduced to synonymy with M. pygmaea due to high morphological similarity. Here, we present the first molecular study of Megadenia. Using the sequences of 11 noncoding regions from the cytoplasmic (chloroplast and mitochondrial) and nuclear genomes, we assessed divergence within the genus and explored the relationships between Megadenia and Biscutella L. Although M. bardunovii, M. speluncarum, and M. pygmaea were found to be indiscernible with regard to the nuclear and mitochondrial markers studied, our data on the plastid genome revealed their distinctness and a clear subdivision of the genus into three lineages matching the three described species. All of the phylogenetic analyses of the chloroplast DNA sequences provide strong support for the inclusion of Megadenia and Biscutella in the tribe Biscutelleae. A dating analysis shows that the genus Megadenia is of Miocene origin and diversification within the genus, which has led to the three extant lineages, most likely occurred during the Early-Middle Pleistocene, in agreement with the vicariance pattern. Given the present-day distribution, differences in habitat preferences and in some anatomical traits, and lack of a direct genealogical relationship, M. pygmaea, M. bardunovii, and M. speluncarum should be treated as distinct species or at least subspecies.
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Karl R, Koch MA. A world-wide perspective on crucifer speciation and evolution: phylogenetics, biogeography and trait evolution in tribe Arabideae. ANNALS OF BOTANY 2013; 112:983-1001. [PMID: 23904444 PMCID: PMC3783230 DOI: 10.1093/aob/mct165] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/29/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Tribe Arabideae are the most species-rich monophyletic lineage in Brassicaceae. More than 500 species are distributed in the majority of mountain and alpine regions worldwide. This study provides the first comprehensive phylogenetic analysis for the species assemblage and tests for association of trait and characters, providing the first explanations for the enormous species radiation since the mid Miocene. METHODS Phylogenetic analyses of DNA sequence variation of nuclear encoded loci and plastid DNA are used to unravel a reliable phylogenetic tree. Trait and ancestral area reconstructions were performed and lineage-specific diversification rates were calculated to explain various radiations in the last 15 Myr in space and time. KEY RESULTS A well-resolved phylogenetic tree demonstrates the paraphyly of the genus Arabis and a new systematic concept is established. Initially, multiple radiations involved a split between lowland annuals and mountain/alpine perennial sister species. Subsequently, increased speciation rates occur in the perennial lineages. The centre of origin of tribe Arabideae is most likely the Irano-Turanian region from which the various clades colonized the temperate mountain and alpine regions of the world. CONCLUSIONS Mid Miocene early diversification started with increased speciation rates due to the emergence of various annual lineages. Subsequent radiations were mostly driven by diversification within perennial species during the Pliocene, but increased speciation rates also occurred during that epoch. Taxonomic concepts in Arabis are still in need of a major taxonomic revision to define monophyletic groups.
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Affiliation(s)
| | - Marcus A. Koch
- Department of Plant Systematics and Biodiversity, Center for Organismal Studies (COS Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
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Kiefer C, Koch MA. A continental-wide perspective: the genepool of nuclear encoded ribosomal DNA and single-copy gene sequences in North American Boechera (Brassicaceae). PLoS One 2012; 7:e36491. [PMID: 22606266 PMCID: PMC3351400 DOI: 10.1371/journal.pone.0036491] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 04/09/2012] [Indexed: 11/30/2022] Open
Abstract
74 of the currently accepted 111 taxa of the North American genus Boechera (Brassicaceae) were subject to pyhlogenetic reconstruction and network analysis. The dataset comprised 911 accessions for which ITS sequences were analyzed. Phylogenetic analyses yielded largely unresolved trees. Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events. Network analyses were superimposed with datasets describing i) geographical distribution, ii) taxonomy, iii) reproductive mode, and iv) distribution history based on phylogeographic evidence. Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale. In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data.
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Affiliation(s)
- Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Heidelberg University, Centre for Organismal Studies Heidelberg, Heidelberg, Germany
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Karl R, Kiefer C, Ansell SW, Koch MA. Systematics and evolution of Arctic-Alpine Arabis alpina (Brassicaceae) and its closest relatives in the eastern Mediterranean. AMERICAN JOURNAL OF BOTANY 2012; 99:778-794. [PMID: 22454383 DOI: 10.3732/ajb.1100447] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The high mountains in southern Anatolia and the eastern Mediterranean are assumed to play a major role as a primary center of genetic diversity and species richness in Eurasia. We tested this hypothesis by focusing on the widespread perennial arctic-alpine Arabis alpina and its sympatrically distributed closest relatives in the eastern Mediterranean. METHODS Plastid (trnL intron, trnL-F intergenic spacer) and nuclear (ITS) DNA sequence analysis was used for phylogenetic reconstruction. Broad-scale plastid haplotype analyses were conducted to infer ancestral biogeographic patterns. KEY RESULTS Five Arabis species, identified from the eastern Mediterranean (Turkey mainland and Cyprus), evolved directly and independently from A. alpina, leaving Arabis alpina as a paraphyletic taxon. These species are not affected by hybridization or introgression, and species divergence took place at the diploid level during the Pleistocene. CONCLUSIONS Pleistocene climate fluctuations produced local altitudinal range-shifts among mountain glacial survival areas, resulting not only in the accumulation of intraspecific genotype diversity but also in the formation of five local species. We also show that the closest sister group of Arabis alpina consists exclusively of annuals/winter annuals and diverged prior to Pleistocene climatic fluctuations during the colonization of the lowland Mediterranean landscape. These findings highlight that Anatolia is not only a center of species richness but also a center for life-history diversification.
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Affiliation(s)
- Robert Karl
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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