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Rurik I, Melichárková A, Gbúrová Štubová E, Kučera J, Kochjarová J, Paun O, Vďačný P, Slovák M. Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:753-765. [PMID: 38217489 DOI: 10.1111/tpj.16630] [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: 09/08/2023] [Revised: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 01/15/2024]
Abstract
Specific ecological conditions in the high mountain environment exert a selective pressure that often leads to convergent trait evolution. Reticulations induced by incomplete lineage sorting and introgression can lead to discordant trait patterns among gene and species trees (hemiplasy/xenoplasy), providing a false illusion that the traits under study are homoplastic. Using phylogenetic species networks, we explored the effect of gene exchange on trait evolution in Soldanella, a genus profoundly influenced by historical introgression. At least three features evolved independently multiple times: the single-flowered dwarf phenotype, dysploid cytotype, and ecological generalism. The present analyses also indicated that the recurring occurrence of stoloniferous growth might have been prompted by an introgression event between an ancestral lineage and a still extant species, although its emergence via convergent evolution cannot be completely ruled out. Phylogenetic regression suggested that the independent evolution of larger genomes in snowbells is most likely a result of the interplay between hybridization events of dysploid and euploid taxa and hostile environments at the range margins of the genus. The emergence of key intrinsic and extrinsic traits in snowbells has been significantly impacted not only by convergent evolution but also by historical and recent introgression events.
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Affiliation(s)
- Ivan Rurik
- Department of Zoology, Comenius University Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Andrea Melichárková
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
| | - Eliška Gbúrová Štubová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
- Slovak National Museum, Natural History Museum, Vajanského nábrežie 2, 810 06, Bratislava, Slovak Republic
| | - Jaromír Kučera
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
| | - Judita Kochjarová
- Department of Phytology, Faculty of Forestry, Technical University Zvolen, Masarykova 24, 960 53, Zvolen, Slovak Republic
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Peter Vďačný
- Department of Zoology, Comenius University Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
- Department of Botany, Charles University, Benátská 2, 128 01, Prague, Czech Republic
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2
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Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.
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Affiliation(s)
| | - Giada Ferrari
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | | | | | - Kanae Nishii
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
- School of Biological Sciences University of Edinburgh Edinburgh United Kingdom
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3
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Vera-Paz SI, Granados Mendoza C, Díaz Contreras Díaz DD, Jost M, Salazar GA, Rossado AJ, Montes-Azcué CA, Hernández-Gutiérrez R, Magallón S, Sánchez-González LA, Gouda EJ, Cabrera LI, Ramírez-Morillo IM, Flores-Cruz M, Granados-Aguilar X, Martínez-García AL, Hornung-Leoni CT, Barfuss MH, Wanke S. Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage. FRONTIERS IN PLANT SCIENCE 2023; 14:1205511. [PMID: 37426962 PMCID: PMC10326849 DOI: 10.3389/fpls.2023.1205511] [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: 04/13/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]
Abstract
Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.
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Affiliation(s)
- Sandra I. Vera-Paz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Daniel D. Díaz Contreras Díaz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Andrés J. Rossado
- Laboratorio de Sistemática de Plantas Vasculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia A. Montes-Azcué
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rebeca Hernández-Gutiérrez
- Departament of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, United States
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis A. Sánchez-González
- Museo de Zoología “Alfonso L. Herrera”, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric J. Gouda
- Botanical Garden, Utrecht University, Utrecht, Netherlands
| | - Lidia I. Cabrera
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - María Flores-Cruz
- Departamento El Hombre y su Ambiente, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Xochimilco, Mexico City, Mexico
| | - Xochitl Granados-Aguilar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana L. Martínez-García
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Investigaciones Biológicas, Herbario HGOM, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Hidalgo, Mexico
| | - Claudia T. Hornung-Leoni
- Centro de Investigaciones Biológicas, Herbario HGOM, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Hidalgo, Mexico
| | - Michael H.J. Barfuss
- Departament of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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4
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Reginato M. A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 2022; 10:e14525. [PMID: 36523475 PMCID: PMC9745922 DOI: 10.7717/peerj.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily assembled and constitutes the bulk of phylogenetic information generated in these studies. Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use, such endeavor remains neglected. Causes might include the trade-off between libraries with few reads and species with large genomes (i.e., missing data caused by low coverage), but also might relate to the lack of pipelines for data assembling. Methods A pipeline and its companion R package designed to automate the recovery of low copy nuclear markers from genome skimming libraries are presented. Additionally, a series of analyses aiming to evaluate the impact of key assembling parameters, reference selection and missing data are presented. Results A substantial amount of putative low copy nuclear loci was assembled and proved useful to base phylogenetic inference across the libraries tested (4 to 11 times more data than previously assembled plastomes from the same libraries). Discussion Critical aspects of assembling low copy nuclear markers from genome skims include the minimum coverage and depth of a sequence to be used. More stringent values of these parameters reduces the amount of assembled data and increases the relative amount of missing data, which can compromise phylogenetic inference, in turn relaxing the same parameters might increase sequence error. These issues are discussed in the text, and parameter tuning through multiple comparisons tracking their effects on support and congruence is highly recommended when using this pipeline. The skimmingLoci pipeline (https://github.com/mreginato/skimmingLoci) might stimulate the use of genome skims to recover nuclear loci for direct phylogenetic use, increasing the power of genome skimming data to resolve phylogenetic relationships, while reducing the amount of sequenced DNA that is commonly wasted.
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5
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Vera-Paz SI, Díaz Contreras Díaz DD, Jost M, Wanke S, Rossado AJ, Hernández-Gutiérrez R, Salazar GA, Magallón S, Gouda EJ, Ramírez-Morillo IM, Donadío S, Granados Mendoza C. New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy. FRONTIERS IN PLANT SCIENCE 2022; 13:924922. [PMID: 35982706 PMCID: PMC9378858 DOI: 10.3389/fpls.2022.924922] [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: 04/20/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Full plastome sequences for land plants have become readily accessible thanks to the development of Next Generation Sequencing (NGS) techniques and powerful bioinformatic tools. Despite this vast amount of genomic data, some lineages remain understudied. Full plastome sequences from the highly diverse (>1,500 spp.) subfamily Tillandsioideae (Bromeliaceae, Poales) have been published for only three (i.e., Guzmania, Tillandsia, and Vriesea) out of 22 currently recognized genera. Here, we focus on core Tillandsioideae, a clade within subfamily Tillandsioideae, and explore the contribution of individual plastid markers and data categories to inform deep divergences of a plastome phylogeny. We generated 37 high quality plastome assemblies and performed a comparative analysis in terms of plastome structure, size, gene content and order, GC content, as well as number and type of repeat motifs. Using the obtained phylogenetic context, we reconstructed the evolution of these plastome attributes and assessed if significant shifts on the evolutionary traits' rates have occurred in the evolution of the core Tillandsioideae. Our results agree with previously published phylogenetic hypotheses based on plastid data, providing stronger statistical support for some recalcitrant nodes. However, phylogenetic discordance with previously published nuclear marker-based hypotheses was found. Several plastid markers that have been consistently used to address phylogenetic relationships within Tillandsioideae were highly informative for the retrieved plastome phylogeny and further loci are here identified as promising additional markers for future studies. New lineage-specific plastome rearrangements were found to support recently adopted taxonomic groups, including large inversions, as well as expansions and contractions of the inverted repeats. Evolutionary trait rate shifts associated with changes in size and GC content of the plastome regions were found across the phylogeny of core Tillandsioideae.
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Affiliation(s)
- Sandra I. Vera-Paz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel D. Díaz Contreras Díaz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Andrés J. Rossado
- Laboratorio de Sistemática de Plantas Vasculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Rebeca Hernández-Gutiérrez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, United States
| | - Gerardo A. Salazar
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric J. Gouda
- Botanical Garden, Utrecht University, Utrecht, Netherlands
| | | | - Sabina Donadío
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Buenos Aires, Argentina
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
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6
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Tavares MM, Ferro M, Leal BSS, Palma‐Silva C. Speciation with gene flow between two Neotropical sympatric species (
Pitcairnia
spp.: Bromeliaceae). Ecol Evol 2022; 12:e8834. [PMID: 35509614 PMCID: PMC9055293 DOI: 10.1002/ece3.8834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Marília Manuppella Tavares
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Milene Ferro
- Departamento de Biologia Geral e Aplicada Universidade Estadual Paulista Rio Claro Brazil
| | - Bárbara Simões Santos Leal
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Clarisse Palma‐Silva
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
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7
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Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzmán-Jacob V, Krömer T, Lexer C, Paun O, Leroy T. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Mol Ecol Resour 2021; 22:927-945. [PMID: 34606683 PMCID: PMC9292372 DOI: 10.1111/1755-0998.13523] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
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Affiliation(s)
- Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Margot Paris
- Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany
| | - Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Norma Rivera
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Valeria Guzmán-Jacob
- Biodiversity, Macroecology and Biogeography, University of Goettingen, Göttingen, Germany
| | - Thorsten Krömer
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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