Malpighiales phylogenetics: gaining ground on one of the most recalcitrant clades in the angiosperm tree of life. Am J Bot

Department of Botany, Smithsonian Institution, P.O. Box 37012 NMNH MRC-166, Washington, District of Columbia 20013-7012 USA.
American Journal of Botany (Impact Factor: 2.6). 08/2009; 96(8):1551-70. DOI: 10.3732/ajb.0800207
Source: PubMed


The eudicot order Malpighiales contains ∼16000 species and is the most poorly resolved large rosid clade. To clarify phylogenetic relationships in the order, we used maximum likelihood, Bayesian, and parsimony analyses of DNA sequence data from 13 gene regions, totaling 15604 bp, and representing all three genomic compartments (i.e., plastid: atpB, matK, ndhF, and rbcL; mitochondrial: ccmB, cob, matR, nad1B-C, nad6, and rps3; and nuclear: 18S rDNA, PHYC, and newly developed low-copy EMB2765). Our sampling of 190 taxa includes representatives from all families of Malpighiales. These data provide greatly increased support for the recent additions of Aneulophus, Bhesa, Centroplacus, Ploiarium, and Rafflesiaceae to Malpighiales; sister relations of Phyllanthaceae + Picrodendraceae, monophyly of Hypericaceae, and polyphyly of Clusiaceae. Oxalidales + Huaceae, followed by Celastrales are successive sisters to Malpighiales. Parasitic Rafflesiaceae, which produce the world's largest flowers, are confirmed as embedded within a paraphyletic Euphorbiaceae. Novel findings show a well-supported placement of Ctenolophonaceae with Erythroxylaceae + Rhizophoraceae, sister-group relationships of Bhesa + Centroplacus, and the exclusion of Medusandra from Malpighiales. New taxonomic circumscriptions include the addition of Bhesa to Centroplacaceae, Medusandra to Peridiscaceae (Saxifragales), Calophyllaceae applied to Clusiaceae subfamily Kielmeyeroideae, Peraceae applied to Euphorbiaceae subfamily Peroideae, and Huaceae included in Oxalidales.

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Available from: Charles C Davis, Oct 20, 2015
    • "As molecular phylogenetic analyses of large plant clades have become more common, many have encountered a recurrent problem: major clades are resolved with strong support, but clear, wellsupported relationships among those clades is lacking (''backbone topologies, " e.g., Wurdack and Davis, 2009; Refulio-Rodriguez and Olmstead, 2014; Straub et al., 2014). Resolution of such topologies often has critical implications for character-state inference and taxonomic decisions involving the tip taxa. "
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    ABSTRACT: Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia should be split into several segregate genera.
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    • "Subfamily Medusagynoideae has 2–5 ovules per carpel, and Quiinoideae has 2. More recently, Wurdack and Davis (2009) and Xi et al. (2012) demonstrated a strongly supported ochnoid clade. It is composed of a single accession of Medusagynaceae sister to a strongly supported Quiinaceae (100% bootstrap [BS], 100% posterior probability [PP]), which together form a moderately supported clade (75% BS, 98% PP) that is in turn sister to a well-supported Ochnaceae clade (100% BS, 100% PP). "
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    ABSTRACT: Premise of research. Paleoochna tiffneyi gen. et sp. nov. is described from late Paleocene fossil fruits from Almont (Morton County) and Beicegel Creek (McKenzie County), North Dakota. On the basis of distinctive anatomical and morphological features, these fruits demonstrate strong taxonomic affinities to Ochna and other members of the family Ochnaceae but are distinct at the generic level. Methodology. Fossil fruits were studied with a combination of transmitted and reflected light microscopy from fractured surfaces and with scanning electron microscopy. Extant fruits were sectioned by freehand sectioning with a razor blade and studied with reflected and transmitted light microscopy. Pivotal results. The study documents the first known occurrence of Ochnaceae fruits in the fossil record. They occur as late Paleocene specimens from the Williston Basin of the Western Interior of North America. Specimens are anatomically preserved and provide critical morphological details of systematic value. Like many of the other plants from the well-known Almont/Beicegel Creek flora, Paleoochna has strong affinities to extant genera but cannot be placed in a modern taxon. Along with fossil leaves of Rhabdophyllum (Ochnaceae) of slightly younger age from southeastern North America, Paleoochna corroborates the presence of Ochna-like plants by the Paleogene in North America. Conclusions. The presence of the Ochnaceae, subfamily Ochnoideae, tribe Ochneae, subtribe Ochninae in the Almont/Beicegel Creek flora suggests that some families within Malpighiales were well established in the Western Interior Basin of North America by the late Paleocene. The presence of Paleoochna in the late Paleocene Williston Basin and of Rhabdophyllum leaves in the early Eocene Mississippian Embayment suggests an interesting biogeographic connection for the family between the Western Interior Basin and the Gulf Coast during the Paleogene.
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    • "Owing to scarcity of herbarium material for some species, and technical difficulties, e.g., primer mismatches, degraded templates and possible gene loss (Wurdack & Davis, 2009), not all amplification products were obtained for each taxon. Primer mismatch was addressed using a step-down PCR procedure (Korbie & Mattick, 2008). "
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    ABSTRACT: Nearly half of the species in the large genus Saxifraga belong to Saxifraga sect. Ciliatae, a largely Sino-Himalayan taxon. We report here that evidence from chloroplast DNA sequences (psbA-trnH, trnL-F) and from nuclear sequences (ITS) indicates that this section is monophyletic and composed of at least three main lineages, corresponding to (1) a clade made up of species from S. subsect. Gemmiparae, subsect. Cinerascentes, subsect. Flagellares and subsect. Hemisphaericae, in which the last three subsections are nested in the first; (2) a clade of species belonging to S. subsect. Rosulares (including S. subsect. Serpyllifoliae); and (3) a clade of species belonging to S. subsect. Hirculoideae. Species relationships in S. subsect. Rosulares and subsect. Hirculoideae are not well resolved. A molecular clock analysis indicates that the diversification of S. sect. Ciliatae into its three lineages dates from ca. 9.48 Ma, coinciding with orogenic events associated with one of the most important phases of uplift of the Qinghai-Tibet Plateau. Extensive diversifications within S. subsect. Rosulares and subsect. Hirculoideae have been more recent (ca. 4.51 Ma and 2.12 Ma, respectively), again correlated with Qinghai-Tibet Plateau uplift events and, in the case of S. subsect. Hirculoideae, have occurred at a rate comparable to that seen in the radiation of Hawaiian fruit flies.
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