A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set (original) (raw)
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Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences
Botanical Journal of …, 2000
A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18s rDNA (1855 bp), rbcl. (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early-branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schisandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well-supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well-supported eudicot clade, the early-diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise * Correspondence to 0. E. Soltis.
Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences
Annals of the Missouri …, 1997
A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18s rDNA (1855 bp), rbcl. (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early-branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schisandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well-supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well-supported eudicot clade, the early-diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise * Correspondence to 0. E. Soltis.
Willdenowia, 2015
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.
Botanical journal of the Linnean Society, 2003
A revised and updated classification for the families of the flowering plants is provided. Newly adopted orders include Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales. Pertinent literature published since the first APG classification is included, such that many additional families are now placed in the phylogenetic scheme. Among these are Hydnoraceae (Piperales), Nartheciaceae (Dioscoreales), Corsiaceae (Liliales), Triuridaceae (Pandanales), Hanguanaceae (Commelinales), Bromeliacae, Mayacaceae and Rapateaceae (all Poales), Barbeuiaceae and Gisekiaceae (both Caryophyllales), Geissolomataceae, Strasburgeriaceae and Vitaceae (unplaced to order, but included in the rosids), Zygophyllaceae (unplaced to order, but included in eurosids I), Bonnetiaceae, Ctenolophonaceae, Elatinaceae, Ixonanthaceae, Lophopyxidaceae, Podostemaceae (Malpighiales), Paracryphiaceae (unplaced in euasterid II), Sladeniaceae, Pentaphylacaceae (Ericales) and Cardiopteridaceae (Aquifoliales). Several major families are recircumscribed. Salicaceae are expanded to include a large part of Flacourtiaceae, including the type genus of that family; another portion of former Flacourtiaceae is assigned to an expanded circumscription of Achariaceae. Euphorbiaceae are restricted to the uniovulate subfamilies; Phyllanthoideae are recognized as Phyllanthaceae and Oldfieldioideae as Picrodendraceae. Scrophulariaceae are recircumscribed to include Buddlejaceae and Myoporaceae and exclude several former members; these are assigned to Calceolariaceae, Orobanchaceae and Plantaginaceae. We expand the use of bracketing families that could be included optionally in broader circumscriptions with other related families; these include Agapanthaceae and Amaryllidaceae in Alliaceae s.l. , Agavaceae, Hyacinthaceae and Ruscaceae (among many other Asparagales) in Asparagaceae s.l. , Dichapetalaceae in Chrysobalanaceae, Turneraceae in Passifloraceae, Erythroxylaceae in Rhizophoraceae, and Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae and Valerianaceae in Caprifoliaceae s.l.
Phylogenomics of the plant family Araceae
The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer . However, phylogenetic ambiguity near the root of the tree precludes answering questions about the early evolution of the family. We use Illumina sequencing technology and reference based assembly to resolve the remaining questions in the deep phylogeny of Araceae. We sampled 32 genera and obtained 7 from GenBank (including an outgroup), representing 42 of 44 major clades described in . A subsequent phylogenomic analysis based on mitochondrial data was performed to test congruence between plastid and mitochondrial data for phylogenetic inference. Plastid sequences produced strongly supported phylogenies. In contrast, mitochondrial phylogenies were weakly supported and incongruent with chloroplast data (Templeton test, p 6 0.0001), although several smaller clades were recovered. New strongly-supported clades seen here are: (1) Anubias and Montrichardia, excluding Calla, form a clade that is sister to the Zantedeschia clade; (2) the South African genus Zantedeschia is sister to the Old World Anchomanes clade; and (3) within the Zantedeschia clade, Philodendron is sister to the rest. Calla and Schismatoglottis form a clade at the base of one of two major clades in Aroideae based on complete chloroplast sequences. Although statistical support is weak, morphological and cytological features support this topology.
Myrtaceae Revisited: A Reassessment of Infrafamilial Groups
American Journal of Botany, 2001
Cladistic analyses are presented of matK sequence data as well as a nonmolecular database for an identical set of exemplar species chosen to represent the core genera or groups of genera in Myrtaceae. Eleven robust clades are recognized on the molecular data. Polyphyly of the previously recognized Metrosideros and Leptospermum alliances is confirmed, and several smaller informal taxonomic groupings are recognized from among the members of the former alliance, i.e., the Tristania, Tristaniopsis, Metrosideros, and Lophostemon groups. The nonmolecular analysis provides only limited resolution of relationships. A degree of congruence exists between the two analyses in that two separate fleshy-fruited clades, the Acmena and Myrtoid groups, are identified, as are the Eucalypt and Tristania groups, and Psiloxylon and Heteropyxis are the first lineages to diverge in both analyses. A combined analysis recognized all 11 clades that received strong support from the molecular data. A high level of homoplasy is revealed in many of the nonmolecular characters when they are examined against the combined estimate of phylogeny.
Angiosperm phylogeny: 17 genes, 640 taxa
American Journal of Botany, 2011
Premise of the study : Recent analyses employing up to fi ve genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses.
A tabular comparison of the classifications of the supraordinal and ordinal groups of angiosperms of the APG III (2009) and Takhtajan (2009) is presented. The linear sequence of the Divisions, Classes, Subclasses, Superorders, Orders and Families is that of the APG. The APG III provided a new model of Phylogenetic (= cladistic) classification. The framework of supraordinal informal (rankless) groups such as Magnoliids, and Campanulinids fully resolved. All the accepted names of the familes are listed in alphabetical sequence (excluding order of that Santalales). Under the supraordinal groups there are the presence of a number of families (32) without their proper assignment to orders, as their ordinal positions are still unclear to the APG III. For the present purpose two supraordinal groups such as 'Basal families' and 'Proeudicots' and 12 additional ordinal names are optionally adopted with quotation-mark ("_"), /, question mark (?) and parenthesis. Nevertheless, there are four ordinal positions which remain unnamed. Monocots are placed between the Magnoliids and the Eudicots. The APG III has recognized 14 'new' orders and updated 19 orders with new consignment of families. They have emended (re-circumscribed, expanded or restricted) 48 families. There are 70 families in parenthesis below the updated families with which these families may be merged or relegated. The APG III has widely shifted 28 families and deleted about 46 popular families in favour of other broadly circumscribed families. Fourteen obsolete families are reintroduced along with a fresh list of'taxa incertae sedis' of two (2) families and three (3 genera).
Botanical Journal of the Linnean Society, 2009
A revised and updated classification for the families of flowering plants is provided. Many recent studies have yielded increasingly detailed evidence for the positions of formerly unplaced families, resulting in a number of newly adopted orders, including Amborellales, Berberidopsidales, Bruniales, Buxales, Chloranthales, Escalloniales, Huerteales, Nymphaeales, Paracryphiales, Petrosaviales, Picramniales, Trochodendrales, Vitales and Zygophyllales. A number of previously unplaced genera and families are included here in orders, greatly reducing the number of unplaced taxa; these include Hydatellaceae (Nymphaeales), Haptanthaceae (Buxales), Peridiscaceae (Saxifragales), Huaceae (Oxalidales), Centroplacaceae and Rafflesiaceae (both Malpighiales), Aphloiaceae, Geissolomataceae and Strasburgeriaceae (all Crossosomatales), Picramniaceae (Picramniales), Dipentodontaceae and Gerrardinaceae (both Huerteales), Cytinaceae (Malvales), Balanophoraceae (Santalales), Mitrastemonaceae (Ericales) and Boraginaceae (now at least known to be a member of lamiid clade). Newly segregated families for genera previously understood to be in other APG-recognized families include Petermanniaceae (Liliales), Calophyllaceae (Malpighiales), Capparaceae and Cleomaceae (both Brassicales), Schoepfiaceae (Santalales), Anacampserotaceae, Limeaceae, Lophiocarpaceae, Montiaceae and Talinaceae (all Caryophyllales) and Linderniaceae and Thomandersiaceae (both Lamiales). Use of bracketed families is abandoned because of its unpopularity, and in most cases the broader circumscriptions are retained; these include Amaryllidaceae, Asparagaceace and Xanthorrheaceae (all Asparagales), Passifloraceae (Malpighiales), Primulaceae (Ericales) and several other smaller families. Separate papers in this same volume deal with a new linear order for APG, subfamilial names that can be used for more accurate communication in Amaryllidaceae s.l., Asparagaceace s.l. and Xanthorrheaceae s.l. (all Asparagales) and a formal supraordinal classification for the flowering plants.