A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales
11 Sep 2015-Willdenowia (Botanischer Garten und Botanisches Museum Berlin-Dahlem)-Vol. 45, Iss: 3, pp 281-383
TL;DR: A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the Caryophyllales, a major lineage of flowering plants with approximately 12500 species in 39 families.
Abstract: The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world.
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TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.
7,299 citations
University of Camerino1, University of Pisa2, University of Pavia3, University of Cagliari4, University of Genoa5, University of Calabria6, University of Turin7, University of Florence8, Sapienza University of Rome9, University of Palermo10, National Museum of Natural History11, University of Trieste12, University of Naples Federico II13, Seconda Università degli Studi di Napoli14, University of Perugia15
TL;DR: An updated inventory of the vascular flora alien to Italy, providing details on the occurrence at regional level, is presented in this paper, which includes 1597 species, subspecies, and hybrids, distributed in 725 genera and 152 families; 2 taxa are lycophytes, 11 ferns and fern allies, 33 gymnosperms and 1551 angiosperms.
Abstract: An updated inventory of the vascular flora alien to Italy, providing details on the occurrence at regional level, is presented. The checklist includes 1597 species, subspecies, and hybrids, distributed in 725 genera and 152 families; 2 taxa are lycophytes, 11 ferns and fern allies, 33 gymnosperms, and 1551 angiosperms. 157 taxa are archaeophytes and 1440 neophytes. The alien taxa currently established in Italy are 791 (570 naturalized and 221 invasive), while 705 taxa are casual aliens, 4 are not assessed, 7 are of unknown regional distribution, 47 have not been confirmed in recent times, 3 are considered extinct or possibly extinct in the country, and 40 are doubtfully occurring in Italy. This checklist allows to establish an up-to-date number (9792) of taxa constituting the whole (native and alien) Italian flora.
492 citations
Cites background from "A taxonomic backbone for the global..."
...The systematic order and taxonomic circumscription of the families follow the classification proposed by PPG I (2016) for ferns and fern allies, by Christenhusz et al. (2011) for gymnosperms and by APG IV (2016) for angiosperms, with the exception of Dipsacales (Reveal 2011), Caryophyllales (Hernández-Ledesma et al. 2015) and Boraginales (Luebert et al. 2016)....
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...…follow the classification proposed by PPG I (2016) for ferns and fern allies, by Christenhusz et al. (2011) for gymnosperms and by APG IV (2016) for angiosperms, with the exception of Dipsacales (Reveal 2011), Caryophyllales (Hernández-Ledesma et al. 2015) and Boraginales (Luebert et al. 2016)....
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TL;DR: In this article, a phylogenetic analysis of nucleotide sequence data from the plastic rbcL gene indicates that both carnivory and stereotyped trap forms have arisen independently in different lineages of angiosperms.
Abstract: The carnivorous habit in flowering plants represents a grade of structural organization. Different morphological features associated with the attraction, trapping, and digestion of prey characterize a diversity of specialized forms, including the familiar pitcher and flypaper traps. Phylogenetic analysis of nucleotide sequence data from the plastic rbcL gene indicates that both carnivory and stereotyped trap forms have arisen independently in different lineages of angiosperms. Furthermore, these results demonstrate that flypaper traps share close common ancestry with all other trap forms. Recognition of these patterns of diversification may provide ideal, naturally occurring systems for studies of developmental processes underlying macromorphological evolution in angiosperms.
268 citations
TL;DR: A well-resolved and well-supported phylogeny of the Caryophyllales is recovered that was largely congruent with previous estimates of this order and provides improved support for the phylogenetic position of several key families within this clade.
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TL;DR: It is found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data.
Abstract: Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.].
84 citations
References
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TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.
7,299 citations
Journal Article•
5,035 citations
"A taxonomic backbone for the global..." refers background in this paper
...Didiereaceae radlk. sec. aPG (2009). a family with six genera and 20 species (Bruyns & al....
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...2004 sec. aPG (2009)....
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...Molluginaceae Bartl. sec. aPG (2009). a family with nine genera and c. 90 species mainly distributed in southern africa, but also found in the tropics around the world. the circumscription has been problematic and some of the taxa formerly assigned to Molluginaceae are now considered as members of…...
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...– type: Suessenguthiella scleranthoides (sond.) friedrich Montiaceae raf. sec. aPG (2009). a family with 13 genera and around 200 species distributed around the world (nyffeler & eggli 2010a). the species of this family are traditionally considered as members of Portulacaceae; however, molecular…...
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...Physenaceae takht. sec. aPG (2009). a monogeneric family with two species endemic to madagascar (dickison 2003). traditionally, the only genus Physena was placed in Capparales/Capparaceae (e.g. Pax & Hoffmann 1936) or Flacourtiaceae (e.g. Perrier de la Bâthie 1946)....
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Journal Article•
3,673 citations
TL;DR: Halophytes, plants that survive to reproduce in environments where the salt concentration is around 200 mm NaCl or more, constitute about 1% of the world's flora and research should be concentrated on a number of 'model' species that are representative of the various mechanisms that might be involved in tolerance.
Abstract: Halophytes, plants that survive to reproduce in environments where the salt concentration is around 200 mM NaCl or more, constitute about 1% of the worlds flora. Some halophytes show optimal growth in saline conditions; others grow optimally in the absence of salt. However, the tolerance of all halophytes to salinity relies on controlled uptake and compartmentalization of Na+, K+ and Cl- and the synthesis of organic compatible solutes, even where salt glands are operative. Although there is evidence that different species may utilize different transporters in their accumulation of Na+, in general little is known of the proteins and regulatory networks involved. Consequently, it is not yet possible to assign molecular mechanisms to apparent differences in rates of Na+ and Cl- uptake, in root-to-shoot transport (xylem loading and retrieval), or in net selectivity for K+ over Na+. At the cellular level, H+-ATPases in the plasma membrane and tonoplast, as well as the tonoplast H+-PPiase, provide the transmembrane proton motive force used by various secondary transporters. The widespread occurrence, taxonomically, of halophytes and the general paucity of information on the molecular regulation of tolerance mechanisms persuade us that research should be concentrated on a number of model species that are representative of the various mechanisms that might be involved in tolerance.
2,127 citations
TL;DR: Two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups indicate that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling.
Abstract: We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study.
1,976 citations