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  • 1.
    Beimforde, Christina
    et al.
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Feldberg, Kathrin
    Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
    Nylinder, Nylinder
    Swedish Museum of Natural History, Department of Botany.
    Rikkinen, Jouko
    Department of Biosciences, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland.
    Tuovila, Hanna
    Department of Biosciences, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland.
    Dörfelt, Heinrich
    Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.
    Gube, Matthias
    Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.
    Jackson, Daniel
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Reitner, Joachim
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Seyfullah, Leyla
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Schmidt, Alexander
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, no 78, p. 386-398Article in journal (Refereed)
    Abstract [en]

    The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualisticassociations such as mycorrhizae and lichens have evolved in this group, which are regarded as keyinnovations that supported the evolution of land plants. Only a few attempts have been made to date theorigin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack ofsatisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycetefossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils representfive major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes,and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 andRPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibrationpoints solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with aBayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician,followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuousdiversification was unaffected by mass extinctions. We suggest that the ecological diversity within eachlineage ensured that at least some taxa of each group were able to survive global crises and rapidlyrecovered.

  • 2. Bengtson, Annika
    et al.
    Nylinder, Stephan
    Swedish Museum of Natural History, Department of Botany.
    Karis, Per Ola
    Anderberg, Arne A.
    Swedish Museum of Natural History, Department of Botany.
    Evolution and diversification related to rainfall regimes: diversification patterns in the South African genus Metalasia (Asteraceae-Gnaphalieae).2015In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 42, no 1, p. 121-131Article in journal (Refereed)
    Abstract [en]

    Aim. The Cape region is known for its exceptional species richness, although much remains unknown regarding the appearance of the modern Cape flora. One explanation is that floral diversification was influenced by the establishment of winter rainfall/summer arid conditions hypothesized to have occurred towards the end of the Miocene. We studied the evolution and diversification of the plant genus Metalasia (Asteraceae–Gnaphalieae), with the aim of testing whether radiation patterns may have been influenced by the climatic changes.

    Location. South Africa, with emphasis on the south-west.

    Methods. The radiation of Metalasia was investigated using two approaches: a species diffusion approach, which estimated the ancestral areas by means of a relaxed random walk while sampling from extant distributions; and a discrete approach, in which distributions were defined according to the phytogeographical centres of the Cape region. Secondarily derived clock rates from an earlier Gnaphalieae study were used for calibration purposes.

    Results. Our analyses date Metalasia to approximately 6.9 Ma, after the Miocene–Pliocene boundary and the establishment of the winter rainfall/summer arid conditions. Metalasia consists of two sister clades: Clade A and Clade B. Clade B, which is endemic to the winter rainfall area, is estimated to have diversified c. 6.4 Ma, whereas Clade A, with a main distribution in the all-year rainfall area, is considerably younger, with a crown group age estimated to 3.3 Ma. Diversification rates suggest an early rapid speciation, with rates decreasing through time both for Metalasia and for clades A and B separately. Ancestral area estimations show a possible scenario for the radiation of Metalasia to its current diversity and distribution, with no conflict between results inferred from diffusion or discrete methods.

    Main conclusions. The diversification of Metalasia is estimated to have begun after the establishment of the winter rainfall/summer arid conditions, consistent with its radiation having been influenced by changes in the climatic regime.

  • 3.
    de Sousa, Filipe
    et al.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Bertrand, Yann J. K.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Nylinder, Nylinder
    Swedish Museum of Natural History, Department of Botany.
    Oxelman, Bengt
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Eriksson, Jonna S.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Pfeil, Bernard E.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 10Article in journal (Refereed)
    Abstract [en]

    Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research,including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionaryhistory of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies.Identification of the processes causing this genealogical incongruence is essential for the inference of a correct speciesphylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtainedacross different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogeneticproperties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-basedgene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternativeproves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level andallows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided,and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants ispresented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made availableand can be used in further probe development for sequence-capture of the same markers.

  • 4.
    Nilsson, R Henrik
    et al.
    GU.
    Hyde, Kevin D.
    Pawlowska, Julia
    Ryberg, Martin
    Tedersoo, Leho
    Aas, Anders Bjornsgard
    Alias, Siti A.
    Alves, Artur
    Anderson, Cajsa Lisa
    Antonelli, Alexandre
    Arnold, A. Elizabeth
    Bahnmann, Barbara
    Bahram, Mohammad
    Bengtsson-Palme, Johan
    Berlin, Anna
    Branco, Sara
    Chomnunti, Putarak
    Dissanayake, Asha
    Drenkhan, Rein
    Friberg, Hanna
    Froslev, Tobias Guldberg
    Halwachs, Bettina
    Hartmann, Martin
    Henricot, Beatrice
    Jayawardena, Ruvishika
    Jumpponen, Ari
    Kauserud, Havard
    Koskela, Sonja
    Kulik, Tomasz
    Liimatainen, Kare
    Lindahl, Bjorn D.
    Lindner, Daniel
    Liu, Jian-Kui
    Maharachchikumbura, Sajeewa
    Manamgoda, Dimuthu
    Martinsson, Svante
    Neves, Maria Alice
    Niskanen, Tuula
    Nylinder, Nylinder
    Swedish Museum of Natural History, Department of Botany.
    Pereira, Olinto Liparini
    Pinho, Danilo Batista
    Porter, Teresita M.
    Queloz, Valentin
    Riit, Taavi
    Sanchez-Garcia, Marisol
    de Sousa, Filipe
    Stefanczyk, Emil
    Tadych, Mariusz
    Takamatsu, Susumu
    Tian, Qing
    Udayanga, Dhanushka
    Unterseher, Martin
    Wang, Zheng
    Wikee, Saowanee
    Yan, Jiye
    Larsson, Ellen
    Larsson, Karl-Henrik
    Koljalg, Urmas
    Abarenkov, Kessy
    Improving ITS sequence data for identification of plant pathogenic fungi2014In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 67, no 1, p. 11-19Article in journal (Refereed)
    Abstract [en]

    Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results - a total of 31,954 changes - are incorporated in and made available through the UNITE database for molecular identification of fungi (including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

  • 5.
    Nylinder, Stephan
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Anderberg, Arne Alfred
    Swedish Museum of Natural History, Department of Botany.
    Phylogeny of the Inuleae (Asteraceae) with special emphasis on the Inuleae-Plucheinae.2015In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 64, no 1, p. 110-130Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships in the tribe Inuleae (Asteraceae, sunflower family) are elucidated based on a concatenated set of nuclear (ETS, ITS), and chloroplast data (ndhF, trnL-F, trnH-psbA), analysed by Bayesian and parsimony methods. Extensive sampling of representatives from both subtribes Inuleae-Inulinae and Inuleae-Plucheinae establish their reciprocal monophyly, and result in the first-ever resolved molecular phylogeny of the Inuleae-Plucheinae with new insights into the relationships and morphological character distributions between genera and among species. Of the 31 accepted genera in the Inuleae-Plucheinae, only Pseudoblepharispermum is not represented in this study, 12 monotypic genera are placed in the phylogeny, 13 genera are shown to be monophyletic, and only 5 of the remaining 18 genera are revealed to be polyphyletic. The implications for the nomenclature status of the monotypic and polyphyletic genera are discussed, together with a descriptive review of morphological characters traditionally used to circumscribe the genera in this subtribe.

  • 6.
    Nylinder, Stephan
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Lemey, Philippe
    KU Leuven, Rega Institute.
    de Bruyn, Mark
    Bangor University, Biological Sciences.
    Suchard, Mark
    UCLA, Human Genetics.
    Pfeil, Bernard
    University of Gothenburg, Biological and Environmental Sciences.
    Walsh, Neville
    National Herbarium of Victoria.
    Anderberg, Arne
    Swedish Museum of Natural History, Department of Botany.
    On the Biogeography of Centipeda: A Species Tree Diffusion Approach2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, no 63, p. 178-191Article in journal (Refereed)
    Abstract [en]

    Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging dueto the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms ofgeography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plantgenus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampledfrom its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previouslypublished substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipedacorrelates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral speciesshow a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly andsoutherly groups since ∼840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event(∼20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the GreatVictoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. Theresult indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. Thisstudy contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers asignificant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult todescribe geography in terms of discrete areas.

  • 7.
    Nylinder, Stephan
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Razafimandimbison, Sylvain
    Swedish Museum of Natural History, Department of Botany.
    Anderberg, Arne Alfred
    Swedish Museum of Natural History, Department of Botany.
    From Namib around the world: biogeography of the Inuleae-Plucheinae (Asteraceae)2016In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 43, p. 1705-1716Article in journal (Refereed)
    Abstract [en]

    We investigated the historical biogeography of the Inuleae–Plucheinae (Asteraceae), a group of arid-adapted plants with partly unresolved generic circumscriptions, in order to understand its origin and spatiotemporal evolutionary history in relation to the Cenozoic climate shifts. Location Global, with highest species diversity in the Southern Hemisphere. The spatiotemporal biogeography of the Plucheinae was estimated by both a discrete method using a set of general distribution areas, and a relaxed random walk based on extant species distributions. The topology was time calibrated using a combination of secondary node ages and secondary derived rates for included loci. Our results indicate the median age of the Plucheinae to be approximately 15.4 Ma. The biogeographical analyses infer an ancestral origin in southern Africa, with the relaxed random walk analysis narrowing the uncertainty down to an area reaching from coastal Namibia to the western Kalahari. Africa was colonized in a (south)western–(north)eastern direction following the spread of arid habitats. Ancestral representatives of the Plucheinae colonized South America on at least three separate occasions (13.0–4.0, 4.3–3.1 and 4.1–3.7 Ma), with one subsequent spread to North America. Australia was colonized three times between 3.6 and 0.4 Ma. Madagascar and the Mascarenes were colonized at least seven times. The origin of the Plucheinae is estimated to the Namib region, with early speciations and radiations concurring with the timing of aridification of southern Africa, following the increase in strength of the Antarctic Circumpolar Current and subsequent formation of the Benguela Upwelling at c. 11.8 Ma. The current biogeographical distribution of the Plucheinae is best explained by several Neogene long-distance dispersal events from tropical Africa.

  • 8.
    Stride, Gail
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Nylinder, Stephan
    Swedish Museum of Natural History, Department of Botany.
    Swenson, Ulf
    Swedish Museum of Natural History, Department of Botany.
    Revisiting the biogeography of Sideroxylon (Sapotaceae) and an evaluation of the taxonomic status of Argania and Spiniluma2014In: Australian Systematic Botany, ISSN 1030-1887, E-ISSN 1446-5701, Vol. 27, no 2, p. 104-118Article in journal (Refereed)
    Abstract [en]

    Biogeography of Sideroxylon (Sapotoideae) and whether the satellite genera Argania and Spiniluma merit recognition are revisited. The hypothesis of an African origin with a subsequent migration to Central America via Europe and the North Atlantic landbridge is challenged. We analysed 58 accessions of trnH-psbA and ITS sequences in a fossil- calibrated, relaxed lognormal clock model with BEAST for phylogenetic and biogeographic inference. Argania spinosa (L.) Skeels from Morocco must be united with Sideroxylon, whereas S. discolor Radcl.-Sm. and S. oxyacanthum Baill. belong to subfamily Chrysophylloideae and may be recognised as Spiniluma. The divergence time estimate suggests that Sideroxylon originated and first diversified in Central America 56.3–52.2 million years ago, contemporaneous with the landbridge, but an archipelago of islands and the Tethys Seaway halted eastward expansion to Africa until c. 20 million years ago, i.e. 25 million years after establishment in Africa. Range expansion of Sideroxylon was therefore not powered by the landbridge, and a long-distance dispersal from Central America to Africa is proposed. The establishment of the Gomphotherium landbridge between Africa and Eurasia at 19 million years ago provided a land-migration route to Europe and Asia, which is reconcilable with the extension of Xantolis into Asia. Sideroxylon has colonised Socotra by over-water dispersal in the Gulf of Aden, Macaronesia, Madagascar and the Mascarene Islands.

  • 9.
    Swenson, Ulf
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Nylinder, Stephan
    Swedish Museum of Natural History, Department of Botany.
    Munzinger, Jérôme
    Sapotaceae biogeography supports New Caledonia being an old Darwinian island2014In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 41, p. 797-809Article in journal (Refereed)
    Abstract [en]

    Aim Panbiogeographers suggest that the biome in New Caledonia is of vicariant origin, dating from the Cretaceous – rather than being the result of repeated dispersal since c. 37 Ma, when the area is postulated to have re-emerged after c. 15 Ma of submergence. Distributions of the plant family Sapotaceae were used as a model system to test this, and to elucidate the probabilities of ancestral areas, all phrased in six hypotheses.

    Location Australasia and the Pacific.

    Methods We used a recently published dataset with extensive sampling (168 terminals) from the subfamily Chrysophylloideae and three nuclear ribosomal DNA markers. Phylogenetic divergence times and ancestral areas were estimated in a Bayesian framework using beast, a relaxed clock method, and with fossil calibration points. Area transition probabilities were modelled using a reversible rate matrix, assigning equal prior probability to each transition between two areas.

    Results Our analyses suggest that Sapotaceae arrived and diversified in New Caledonia nine times during the period 4.2–33.1 Ma. All crown-node radiations occurred in the Miocene or Pliocene, with stem splits reaching back into the Oligocene. Australia and New Guinea are the most likely source areas for Sapotaceae in New Caledonia, but this archipelago has never acted as a stepping stone for Sapotaceae to disperse into the Pacific.

    Main conclusions Repeated dispersal is the only mechanism able to explain the range expansion of Sapotaceae into New Caledonia. The family has successfully colonized the main island nine times since its re-emergence in the Eocene. We reject the panbiogeographical hypotheses that representatives of Sapotaceae in New Caledonia originated in the Cretaceous, differentiated due to vicariance, and were of Pacific origin. We therefore argue that New Caledonia is an old Darwinian island. The Pacific has been colonized repeatedly and terminal lineages are never older than the islands they inhabit (except for Hawaii). Chrysophylloideae extended across Wallace’s Line into Southeast Asia around 20 Ma, when the Australian continent came into juxtaposition with Eurasia.

  • 10.
    Swenson, Ulf
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Nylinder, Stephan
    Swedish Museum of Natural History, Department of Botany.
    Munzinger, Jérôme
    Towards a natural classification of Sapotaceae subfamily Chrysophylloideae in Oceania and Southeast Asia based on nuclear sequence data2013In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 63, p. 746-770Article in journal (Refereed)
    Abstract [en]

    Generic limits within subfamily Chrysophylloideae (Sapotaceae) from Oceania and Southeast Asia are reconciled based on a molecular phylogeny. We analysed sequences of nuclear ribosomal DNA (ETS, ITS) and the nuclear gene RPB2 with BEAST and parsimony jackknifing, using a sample of 168 terminals. Eight morphological characters were traced on a condensed majority-rule consensus tree to identify diagnostic character combinations for the genera. Accepted genera with character support are Magodendron, Pichonia, Planchonella, Pycnandra, Sersalisia, and Van-royena, while Beccariella and Niemeyera require amendment. Beccariella, a widely distributed group, is an illegitimate later homonym and we propose that the genus Pleioluma is resurrected in its place. The Australian genus Niemeyera is paraphyletic, but it is rendered monophyletic by reinstating Amorphospermum for N. antiloga. Beauvisagea, Blabeia, Fontbrunea, and Krausella are all segregates of Planchonella and rejected, while Wokoia is a later synonym of Pichonia. Planchonella baillonii, an endemic species of New Caledonia, is the sole member of an old lineage and firmly placed as the sister to a clade comprising the other congeners. Planchonella sandwicensis, a Hawaiian species, previously proposed to be a distinct genus, is a member of Planchonella. In the Pacific, P. tahitensis (including P. grayana) is a polymorphic species, widely distributed and adapted to a wide range of habitats. We provide a generic key (excluding Xantolis), diagnostic character combinations for all genera, and the necessary taxonomic combinations for Pichonia, Planchonella, Pleioluma, and Sersalisia to render each genus monophyletic.

  • 11. Terra-Araujo, Mario
    et al.
    de Faria, Aparecida
    Vicentini, Alberto
    Nylinder, Nylinder
    Swedish Museum of Natural History, Department of Botany.
    Swenson, Ulf
    Swedish Museum of Natural History, Department of Botany.
    Species tree phylogeny and biogeography of the Neotropical genus Pradosia (Sapotaceae, Chrysophylloideae).2015In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 87, p. 1-13Article in journal (Refereed)
    Abstract [en]

    Recent phylogenetic studies in Sapotaceae have demonstrated that many genera need to be redefined to better correspond to natural groups. The Neotropical genus Pradosia is believed to be monophyletic and includes 26 recognized species. Here we reconstruct the generic phylogeny by a species-tree approach using ∗BEAST, 21 recognized species (36 accessions), sequence data from three nuclear markers (ITS, ETS, and RPB2), a relaxed lognormal clock model, and a fossil calibration. We explore the evolution of five selected morphological characters, reconstruct the evolution of habitat (white-sand vs. clayish soils) preference, as well as space and time by using a recently developed continuous diffusion model in biogeography. We find Pradosia to be monophyletic in its current circumscription and to have originated in the Amazon basin at ∼ 47.5 Ma. Selected morphological characters are useful to readily distinguish three clades. Preferences to white-sand and/or clay are somewhat important for the majority of species, but speciation has not been powered by habitat shifts. Pradosia brevipes is a relative young species (∼ 1.3 Ma) that has evolved a unique geoxylic life strategy within Pradosia and is restricted to savannahs. Molecular dating and phylogenetic pattern indicate that Pradosia reached the Brazilian Atlantic coast at least three times: at 34.4 Ma (P. longipedicellata), at 11.7 Ma (P. kuhlmannii), and at 3.9 Ma (weakly supported node within the red-flowered clade).

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