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zenodo32/100

Figure 3. A in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 3. A* phylogenetic relationships of the SSU rDNA sequences of Opalinata by maximum likelihood (ML) method. The Salpingoeca infusorium AF100941 sequence was used as an outgroup. The number at the nodes represent* respectively* the bootstrap support as computed from 1000 replicates for ML and maximum parsimony methods* and the posterior probability values of the Bayesian analysis. Dashes (–) indicate a different tree topology. The tree is drawn to scale* with branch lengths measured in the number of substitutions per site. New sequences are noted in bold. B* phylogenetic relationships of the SSU rDNA sequences of Opalinata by Bayesian inference; only the subtree corresponding to Opalinata is presented* showing the differences in the branching pattern with respect to the trees obtained by ML and maximum parsimony methods. The numbers at the nodes represent posterior probability values; the probabilities for the nodes without numbers are given in Figure 3A.

opennotspecifiedNov 2023View details →
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Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2–LSU rDNA of Opalinida* The expansion segments (ES#L) containing helices (in red) where there are important differences between genera are annotated. Colour code: yellow* ITS1 region; blue* 5.8S rRNA; magenta* ITS2 region; grey* LSU rRNA.

opennotspecifiedNov 2023View details →
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Figure 1 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 1. Proposed general secondary structure model for the SSU rRNA of Opalinata (Proteromonadida and Opalinida). The expansion segments (ES#S) containing helices (in red) where there are important differences between genera are annotated.

opennotspecifiedNov 2023View details →
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FIGURE 4 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content

FIGURE 4. Leaf cross sections: 1) Sternbergia candida, 2) S. clusiana, 3) S. colchiciflora, 4) S. lutea, 5) S. sicula, 6) S. vernalis.

opennotspecifiedJun 2016View details →
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FIGURE 1 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content

FIGURE 1. Distribution of the genus Sternbergia in Turkey: S.candida, S.clusianȧ, S. colchiciflora, S.lutea, S. sicula, S. vernalis, S.schubertii?.

opennotspecifiedJun 2016View details →
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FIGURE 3 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content

FIGURE 3. Mitotic chromosomes and idiograms of Sternbergia; 4) S. lutea, 5) S. sicula, 6) S. vernalis, (Scale bar = 10μm).

opennotspecifiedJun 2016View details →
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FIGURE 6 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content

FIGURE 6. UPGMA cluster of the considered taxa, based on the morpho-anatomical data matrix presented in Table 3.

opennotspecifiedJun 2016View details →
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FIGURE 2 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content

FIGURE 2. Mitotic chromosomes and idiograms of Sternbergia; 1) S. candida, 2) S. clusiana, 3) S. colchiciflora (Scale bar = 10μm).

opennotspecifiedJun 2016View details →
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FIGURE 5 in Taxonomic remarks on the genus Sternbergia L. (Amaryllidaceae) in Turkey based on leaf anatomy, karyosystematic analysis and nuclear DNA content

FIGURE 5. Leaf cross sections: 1) Sternbergia candida, 2) S. clusiana, 3) S. colchiciflora, 4) S. lutea, 5) S. sicula, 6) S. vernalis. (e: epidermis, s: stomata, pp: palisade parenchyma, sp: spongy parenchyma, ls: laticifer systems) (scale bar 0.1 mm).

opennotspecifiedJun 2016View details →
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FIGURE 1 in A new circumscription of the Mediterranean genus Anacyclus (Anthemideae, Asteraceae) based on plastid and nuclear DNA markers

FIGURE 1. Consensus tree (50% majority-rule) from Bayesian inference of the combined ITS + psbA-trnH dataset. Posterior probability values (PP) are indicated along branches (values below 0.50 are not shown). Colours of branches indicate tribal classification of the taxa. Phylogenetic placement of Anacyclus core species (Western Mediterranean species, WM) and Eastern Mediterranean (EM) species is highlighted in grey.

opennotspecifiedMay 2018View details →
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FIGURE 1 in Phylogenetic Analysis of the Genus Pohlia (Bryophyta, Bryaceae) Using Chloroplast and Nuclear Ribosomal DNA

FIGURE 1. The strict consensus tree obtained from the combined (rps4, trnL-F, atpB-rbcL, trnG and ITS) dataset. Numbers above branches indicate bootstrap values from Bayesian inference analysis (=0.5), maximum likelihood analysis (=50%) and maximum parsimony analysis (=50%).

opennotspecifiedMay 2018View details →
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FIGURE 3 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data

FIGURE 3. Bayesian maximum clade reliability trees based on combined nuclear At103 and chloroplast rps16, trnL-F datasets for Dracaena, Sansevieria, and selected outgroups. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP. Long branches were shortened by half their length (indicated by \\).

opennotspecifiedNov 2018View details →
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FIGURE 2 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data

FIGURE 2. Bayesian maximum clade credibility trees based on nuclear At103 (A) and chloroplast rps16, trnL-F (B) datasets for Dracaena and Sansevieria. Outgroups were trimmed from the Figure. The values above the branch represent the maximum parsimony bootstrap percentage (BS), and the ones below are the Bayesian posterior probability (PP). Bold branches indicate strong support, interpreted as ≥ 70 BS and ≥ 95 PP.

opennotspecifiedNov 2018View details →
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FIGURE 1 in Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data

FIGURE 1. Representative morphological diversity in the dracaenoid genera, Dracaena and Sansevieria. A, Dracaena draco subsp. draco, Spain, Canary Islands, Tenerife, Icod de los Vinos; B, D. konaensis, origin: USA, Hawai'i, Big Island, Kona coast, in cultivation at Kew (Acc. No. 2008-239); C, D. arborea, Gabon, Woleu-Ntem Rd, Mitzic to Njole; D, D. laxissima, São Tomé and Príncipe, São Nicolau; E, D. goldieana, origin: Gabon, in cultivation at Kew (Acc. No. 1990-2300); F, D. aubryana, Gabon, Woleu-Ntem Rd Mitzic to Njole; G, Sansevieria frequens, Kenya, Laikipia District, Ngare Ndare Farm (type locality); H, S. aethiopica, Namibia, 74 km from Windhoek, on road to Walvis Bay; I, S. fischeri, Kenya, Munda, 18.9 km NE of Mwatate on Taveta road; J, S. pinguicula, Kenya, by Kowi airstrip, north bank of Tiva Lugga; K, S. ascendens, Kenya, Coast Province, Kwale District, around base of Taru Hill (type locality); L, S. kirkii var. pulchra, in cultivation (private collection, Miami, FL). Photographs by A, L. Mucina; B, I. Willey; C, E–F, T.H.J. Damen; D, J.J.F.E. de Wilde; G-K, L. E. Newton; L, S. Zona.

opennotspecifiedNov 2018View details →
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Table 2 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

<p><b>Table 2.</b> Primers used for PCRs and sequencing (F* forward; R* reverse).</p><table><tbody><tr><th><b>Primer</b></th><th><b>Sequence</b></th><th><b>Reference</b></th></tr></tbody><tbody><tr><th>MedlinA (F)</th><td>5 <i>ʹ</i> -AACCTGGTTGATCCTGCCAGT-3%</td><td>Medlin <i>et al.</i> (1988)</td></tr><tr><th>MedlinB (R)</th><td>5 <i>ʹ</i> -TGATCCTTCTGCAGGTTCACCTAC-3%</td><td>Medlin <i>et al.</i> (1988)</td></tr><tr><th>SSU-LSU-F (F)</th><td>5 <i>ʹ</i> -TCGCACCTACCGATTGGATG-3%</td><td>This study</td></tr><tr><th>SSU-LSU-R (R)</th><td>5 <i>ʹ</i> -GAAAAGATAACTCTTCCTAG-3%</td><td>This study</td></tr><tr><th>M28S-F (F)</th><td>5 <i>ʹ</i> -TAGCCCTGAAAATGGATGGCGCT-3%</td><td>This study</td></tr><tr><th>28S-4R (R)</th><td>5 <i>ʹ</i> -TTCTGACTTAGAGGCGTTCAG-3%</td><td>Moreira <i>et al.</i> (2007)</td></tr></tbody></table>

opennotspecifiedNov 2023View details →
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Table 1 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

<p><b>Table 1.</b> Opalinid species investigated in the present study. All localities are from China. Morphological identification of each species was carried out in the articles indicated in the &lsquo;reference&rsquo; column.</p><table><tbody><tr><th><b>Species</b></th><th><b>Host</b></th><th><b>Prevalence</b></th><th><b>Locality</b></th><th><b>Reference</b></th></tr></tbody><tbody><tr><th><i>Opalina undulata</i> Nie* 1935</th><td><i>Fejervarya limnocharis</i> (Gravenhorst* 1829) Iskandar* 1998</td><td>7.7% (22/285)</td><td>Diaocha Lake* Hubei Province</td><td>Li <i>et al.</i> (2018)</td></tr><tr><th><i>Opalina triangulata</i> Metcalf* 1923</th><td><i>F. limnocharis</i></td><td>21.5% (9/42)</td><td>Diaocha Lake* Hubei Province</td><td>Wang <i>et al.</i> (2019)</td></tr><tr><th><i>Opalina japonica</i> Sugiyama* 1920</th><td><i>Rana chensinensis</i> David * 1875</td><td>33.3% (4/12)</td><td>Xinbin County* Liaoning Province</td><td>Unpublished</td></tr><tr><th><i>Opalina obtrigonoidea</i> Metcalf* 1923</th><td><i>Duttaphrynus melanostictus</i> (Schneider* 1799) Frost <i>et al.</i> * 2006</td><td>31.4% (11/35)</td><td>Yubei City* Chongquin Province</td><td>Zhao <i>et al.</i> (2020)</td></tr><tr><th><i>Opalina longa</i> Bezzenberger* 1904 (= <i>Cepedea longa</i>)a</th><td><i>F. limnocharis</i></td><td>35.8% (76/ 212)</td><td>Honghu Lake* Hubei Province</td><td>Li <i>et al.</i> (2017a)</td></tr><tr><th><i>Protoopalina</i> <i>limnocharis</i> Nie * 1932</th><td><i>F. limnocharis</i></td><td>25.6% (32/125)</td><td>Meishan County* Sichuan Province</td><td>Zou <i>et al.</i> (2018)</td></tr><tr><th><i>Protoopalina pingi</i> Nie* 1935</th><td><i>Pelophylax nigromaculatus</i> (Hallowell* 1861) Fei <i>et al.</i> * 2005</td><td>40.4% (42/104)</td><td>Honghu Lake* Hubei Province</td><td>Li <i>et al.</i> (2014)</td></tr><tr><th><i>Zelleriella orientalis</i> Nie* 1935</th><td><i>Microhyla ornate</i> (Dum&eacute;ril &amp; Bibron* 1841) Boulenger* 1882</td><td>16.2% (6/37)</td><td>Nanning City* Guangxi Province</td><td>Unpublished</td></tr><tr><th><i>Zelleriella</i> sp.</th><td><i>Hyla chinensis</i> Gunther * 1858</td><td>11.1% (2/18)</td><td>Sanming City* Fujian Province</td><td>Unpublished</td></tr></tbody></table><p><sup>aThe</sup> initial identification of this species as <i>Cepedea longa</i> followed the proposal by Metcalf (1923). See Discussion section for the justification of the change.</p>

opennotspecifiedNov 2023View details →
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Table 3 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

<p><b>Table 3.</b> List of sequences used in the present study. Sequences lacking&gt;100 bases at the 5 <i>ʹ</i> or 3 <i>ʹ</i> ends are shown in parentheses. New sequences are marked in bold.</p><table><tbody><tr><th><b>Sequence/species</b></th><th><b>Accession sequence</b></th></tr><tr><th><b>Number</b></th><th><b>Length</b></th><th><b>GC%</b></th><th><b>Source</b></th></tr><tr><th><b>SSU rDNA</b></th></tr><tr><th>STRAMENOPILES</th></tr><tr><th>OPALINATA</th></tr><tr><th>Opalinida</th></tr><tr><th>(<i>Protoopalina intestinalis</i> (Stein* 1856) Metcalf* 1923)</th></tr></tbody><tbody><tr><th></th><td>AY576545</td><td>1409</td><td>33.6</td><td>Kostka <i>et al.</i> (2004)</td></tr><tr><th>(<i>Protoopalina axonucleata</i> Metcalf * 1923a)</th><td>AB175929</td><td>1263</td><td>32.5</td><td>Nishi <i>et al.</i> (2005)</td></tr><tr><th><i>Protoopalina limnocharis</i></th><td><b>MN625264</b></td><td>1829</td><td>32.2</td><td>This study</td></tr><tr><th><i>Protoopalina pingi</i></th><td><b>MN625266</b></td><td>1830</td><td>32.4</td><td>This study</td></tr><tr><th><i>Zelleriella orientalis</i></th><td><b>MN625263</b></td><td>2143</td><td>26.4</td><td>This study</td></tr><tr><th><i>Zelleriella sp.</i></th><td><b>MN625265</b></td><td>2143</td><td>26.4</td><td>This study</td></tr><tr><th><i>Opalina undulata</i></th><td>MF434114</td><td>2167</td><td>26.8</td><td>Li <i>et al.</i> (2018)</td></tr><tr><th><i>Opalina triangulata</i></th><td>MK872804</td><td>2166</td><td>26.8</td><td>Wang <i>et al.</i> (2019)</td></tr><tr><th><i>Opalina obtrigonoidea</i></th><td>MK970648</td><td>2167</td><td>26.8</td><td>Zhao <i>et al.</i> (2020)</td></tr><tr><th><i>Opalina japonica</i></th><td><b>MN625267</b></td><td>2170</td><td>26.0</td><td>This study</td></tr><tr><th><i>Opalina longa</i></th><td><b>MN625268</b></td><td>2171</td><td>27.7</td><td>This study</td></tr><tr><th>Proteromonadida</th></tr><tr><th><i>Karotomorpha</i> sp.</th><td>DQ431242</td><td>1858</td><td>44.1</td><td>Kostka <i>et al.</i> (2007)</td></tr><tr><th>(<i>Karotomorpha</i> sp.)</th><td>DQ431243</td><td>1424</td><td>46.2</td><td>Kostka <i>et al.</i> (2007)</td></tr><tr><th><i>Proteromonas lacertae</i> Grass&eacute; * 1879</th><td>U37108</td><td>1743</td><td>37.4</td><td>Leipe <i>et al.</i> (1996)</td></tr><tr><th>BLASTOCYSTIDA</th></tr><tr><th><i>Blastocystis cycluri</i> Singh <i>et al.</i> * 1996</th><td>AY266474</td><td>1848</td><td>35.6</td><td>Yoshikawa <i>et al.</i> (2004)</td></tr><tr><th><i>Blastocystis lapemi</i> Teow <i>et al.</i> * 1991 <i>Blastocystis pythoni</i> Singh <i>et al.</i> * 1996</th><td>AY266471 AY266472</td><td>1840 1794</td><td>36.7 39.1</td><td>Yoshikawa <i>et al.</i> (2004) Yoshikawa <i>et al.</i> (2004)</td></tr><tr><th><i>Blastocystis hominis</i> (Swaine &amp; Britain* 1849) Brumpt* 1912</th><td></td><td></td><td></td></tr><tr><th><i>Blastocystis ratti</i> Chen <i>et al.</i> * 1997 PLACIDIDA</th><td>AB023499 AY590114</td><td>1740 1730</td><td>43.6 40.3</td><td>Arisue <i>et al.</i> (2002) Noel <i>et al.</i> (2005)</td></tr><tr><th><i>Placidia cafeteriopsis</i> Moriya <i>et al.</i> * 2002</th><td>JF834161</td><td>1775</td><td>49.4</td><td>Chan YF* Chen CW* Tsai AY* Chiang KP* unpublished</td></tr><tr><th><i>Suigetsumonas clinomigrationis</i> Okamura &amp; Kondo * 2015</th><td></td><td></td><td></td></tr><tr><th><i>Wobblia lunata</i> Moriya <i>et al.</i> * 2000 BICOSOECIDA</th><td>AB976561 AB032606</td><td>1769 1726</td><td>52.0 49.1</td><td>Okamura and Kondo (2015) Moriya <i>et al.</i> (2000)</td></tr><tr><th><i>Bicosoeca petiolata</i> (Stein* 1878) Prinsheim* 1946</th><td></td><td></td><td></td></tr><tr><th></th><td>AY520444</td><td>1809</td><td>48.6</td><td>Cavalier-Smith and Chao (2006)</td></tr><tr><th><i>Cafeteria roenbergensis</i> Fenchel &amp; Patterson * 1988</th><td></td><td></td><td></td></tr><tr><th></th><td>AF174364</td><td>1695</td><td>47.1</td><td>Atkins <i>et al.</i> (2000)</td></tr><tr><th>ALVEOLATA</th></tr><tr><th>APICOMPLEXA</th></tr><tr><th><i>Babesia gibsoni</i> (Patton* 1910)</th><td>KC461261</td><td>1665</td><td>45.5</td><td>Mandal <i>et al.</i> (2015)</td></tr><tr><th><i>Eimeria necatrix</i> Johnson * 1930</th><td>KT184349</td><td>1763</td><td>46.8</td><td>Ogedengbe <i>et al.</i> (2016)</td></tr><tr><th>DINOFLAGELLATA</th></tr><tr><th><i>Blastodinium contortum</i> Chatton * 1908</th><td>DQ317537</td><td>1799</td><td>44.8</td><td>Skovgaard <i>et al.</i> (2007)</td></tr><tr><th><i>Prorocentrum arenarium</i> Faust * 1994</th><td>Y16234</td><td>1788</td><td>46.4</td><td>Grzebyk <i>et al.</i> (1998)</td></tr><tr><th>CILIOPHORA</th></tr><tr><th><i>LItonotus paracygnus</i> Song* 1994</th><td>EU242509</td><td>1635</td><td>42.0</td><td>Gao <i>et al.</i> (2008)</td></tr><tr><th><i>Paramecium buestchlii</i> van As <i>et al.</i> * 1998</th><td>KM091234</td><td>1703</td><td>44.2</td><td>Krenek <i>et al.</i> (2015)</td></tr><tr><th>AMORPHEA</th></tr><tr><th>CHOANOZOA</th></tr><tr><th><i>Salpingoeca infusionum</i> Kent * 1880</th><td>AF100941</td><td>1978</td><td>49.6</td><td>Collins (1998)</td></tr><tr><th><b>ITS region</b> (OPALINATA)</th><td></td><td></td><td></td><td></td></tr><tr><th><i>Protoopalina limnocharis</i></th><td><b>MN630239</b></td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>231</td><td>2.2</td><td></td></tr><tr><th>5.8S</th><td></td><td>154</td><td>35.7</td><td></td></tr><tr><th>ITS2</th><td></td><td>229</td><td>4.4</td><td></td></tr><tr><th><i>Protoopalina pingi</i></th><td><b>MN630241</b></td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>237</td><td>2.1</td><td></td></tr><tr><th>5.8S</th><td></td><td>154</td><td>36.4</td><td></td></tr><tr><th>ITS2</th><td></td><td>218</td><td>4.6</td><td></td></tr><tr><th><i>Zelleriella orientalis</i></th><td><b>MN630236</b></td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>291</td><td>2.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>26.4</td><td></td></tr><tr><th>ITS2</th><td></td><td>285</td><td>2.5</td><td></td></tr><tr><th><i>Zelleriella sp.</i></th><td><b>MN630237</b></td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>290</td><td>2.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>166</td><td>26.5</td><td></td></tr><tr><th>ITS2</th><td></td><td>279</td><td>2.5</td><td></td></tr><tr><th><i>Opalina undulata</i></th><td>MG816209</td><td></td><td></td><td>Li <i>et al.</i> (2018)</td></tr><tr><th>ITS1</th><td></td><td>325</td><td>1.5</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.0</td><td></td></tr><tr><th>ITS2</th><td></td><td>290</td><td>2.4</td><td></td></tr><tr><th><i>Opalina triangulata</i></th><td>MK872803</td><td></td><td></td><td>Wang <i>et al.</i> (2019)</td></tr><tr><th>ITS1</th><td></td><td>292</td><td>1.7</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>284</td><td>1.8</td><td></td></tr><tr><th><i>Opalina obtrigonoidea</i></th><td>MK973090</td><td></td><td></td><td>Zhao <i>et al.</i> (2020)</td></tr><tr><th>ITS1</th><td></td><td>323</td><td>1.6</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>287</td><td>1.7</td><td></td></tr><tr><th><i>Opalina japonica</i></th><td><b>MN630238</b></td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>357</td><td>1.7</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>358</td><td>2.5</td><td></td></tr><tr><th><i>Opalina longa</i></th><td><b>MN630240</b></td><td></td><td></td><td>This study</td></tr><tr><th>ITS1</th><td></td><td>283</td><td>1.8</td><td></td></tr><tr><th>5.8S</th><td></td><td>167</td><td>24.6</td><td></td></tr><tr><th>ITS2</th><td></td><td>261</td><td>2.3</td><td></td></tr><tr><th><b>LSU rDNA</b> (OPALINATA)</th><td></td><td></td><td></td><td></td></tr><tr><th><i>Protoopalina limnocharis</i></th><td><b>MN638759</b></td><td>3652</td><td>26.7</td><td>This study</td></tr><tr><th><i>Protoopalina pingi</i></th><td><b>MN638761</b></td><td>3647</td><td>26.9</td><td>This study</td></tr><tr><th><i>Zelleriella orientalis</i></th><td><b>MN638760</b></td><td>4064</td><td>23.0</td><td>This study</td></tr><tr><th><i>Zelleriella sp.</i></th><td><b>MN638763</b></td><td>4102</td><td>22.8</td><td>This study</td></tr><tr><th><i>Opalina undulata</i></th><td><b>MN638758</b></td><td>4108</td><td>22.8</td><td>This study</td></tr><tr><th><i>Opalina triangulata</i></th><td><b>MN638762</b></td><td>4043</td><td>23.9</td><td>This study</td></tr><tr><th><i>Opalina obtrigonoidea</i></th><td><b>MW504710</b></td><td>4122</td><td>22.5</td><td>This study</td></tr><tr><th><i>Opalina japonica</i></th><td><b>MN638764</b></td><td>4120</td><td>22.4</td><td>This study</td></tr><tr><th><i>Opalina longa</i></th><td><b>MN638765</b></td><td>4096</td><td>23.6</td><td>This study</td></tr></tbody></table><p><sup>aNishi</sup> <i>et al.</i> (2005: 701&ndash;702) indicated that &lsquo;the four sequences from <i>Protoopalina</i> sp. were all identical* although they were isolated at different geographical locations.Futhermore* the genus <i>Protoopalina</i> is presently restricted to the host species <i>Rana nigromaculata</i> in Japan.They commonly retain four relatively large nuclei* show similar morphological characters (Table 1)* and are classified as <i>P.japonica</i> (Hara 1934) &rsquo;. However* the work by Hara (1934) is on the cell morphology and microtubular structures of <i>Protoopalina axonucleata</i> * and he did not mention any other species in his work.According to the statements by Nishi <i>et al.</i> (2005) * their isolates corresponded to the same species studied by Hara (1934) and should be identified as <i>P.axonucleata.</i> The name <i>Protoopalina japonica</i> is a <i>nomen nudum</i> because this species has never been described.</p>

opennotspecifiedNov 2023View details →
zenodo32/100

Table 7 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

<p><b>Table 7.</b> List of nomenclatural acts.</p><table><tbody><tr><th><b>Taxon <b>nameb</b></b></th><th><b>Previous name</b></th><th><b>Comments</b></th></tr><tr><th><i>Opalina</i> Purkinje &amp; Valentin * 1835 (= <i>Cepedea</i> Metcalf * 1920)</th></tr></tbody><tbody><tr><th><i>Opalina acuta</i> (Delvinquier* Markus &amp; Passmore* 1993) comb. nov.</th><td><i>Cepedea acuta</i> Delvinquier * Markus &amp; Passmore* 1992</td><td></td></tr><tr><th><i>Opalina affinis</i> Nazaretskaja * 1922</th><td><i>Cepedea affinis</i> (Nazaretskaja* 1922) Walton* 1964</td><td></td></tr><tr><th><i>Opalina africana</i> (Tuzet &amp; Zuber-Vogeli* 1954) comb. nov.</th><td><i>Cepedea africana</i> Tuzet &amp; Zuber-Vogeli * 1954</td><td>Proposed as synonym of <i>Opalina affinis</i> by Delvinquier <i>et al.</i> (1993)</td></tr><tr><th><i>Opalina amygdala</i> (Boisson* 1965) Delvinquier <i>et al.</i> * 1991</th><td><i>Cepedea amygdala</i> Boisson * 1965</td><td>Proposed as synonym of <i>Opalina foliacea</i> by Affa&rsquo;a and Lynn (1994)</td></tr><tr><th><i>Opalina baudinii</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea baudini</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina boissoni</i> (Tuzet &amp; Knoepffler* 1968) comb. nov.</th><td><i>Cepedea boissoni</i> Tuzet &amp; Knoepffler * 1968</td><td>Proposed as synonym of <i>Opalina affinis</i> by Delvinquier <i>et al.</i> (1993)</td></tr><tr><th><i>Opalina borneonensis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea borneonensis</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina buergeri</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea buergeri</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina brumpti</i> (Cordero* 1928) comb. nov.</th><td><i>Cepedea brumpti</i> Cordero * 1928</td><td></td></tr><tr><th><i>Opalina cantabrigensis</i> (Metcalf* 1923)</th><td><i>Cepedea cantabrigensis</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina celebensis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea celebensis</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina ciliata</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea ciliata</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina crispata</i> (Boisson* 1965) comb. nov.</th><td><i>Cepedea crispata</i> Boisson * 1965</td><td>Proposed as synonym of <i>Opalina affinis</i> by Delvinquier <i>et al.</i> (1993)</td></tr><tr><th><i>Opalina daloalensis</i> (Tuzet &amp; Zuber-Vogeli* 1954) comb. nov.</th><td><i>Cepedea daloalensis</i> Tuzet &amp; Zuber-Vogeli * 1954</td><td></td></tr><tr><th><i>Opalina dimidiata</i> Stein * 1860</th><td><i>Cepedea dimidiata</i> (Stein* 1860) Metcalf* 1923</td><td></td></tr><tr><th><i>Opalina dolichosoma</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea dolichosoma</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina dracuncula</i> (Boisson* 1957) comb. nov.</th><td><i>Cepedea dracuncula</i> Boisson * 1957</td><td></td></tr><tr><th><i>Opalina elongata</i> Gourvitsch * 1926</th><td><i>Cepedea elongata</i> (Gourvitsch* 1926) Banina* 1962</td><td></td></tr><tr><th><i>Opalina flava</i> Stokes * 1884</th><td><i>Cepedea flava</i> (Stokes* 1884) Metcalf* 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina floridensis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea floridensis</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina foliacea</i> (Boisson* 1959) Delvinquier <i>et al.</i> * 1991</th><td><i>Cepedea foliacea</i> Boisson * 1959</td><td></td></tr><tr><th><i>Opalina formosae</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea formosae</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina fujiensis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea fujiensis</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina fusiformis</i> (Tuzet &amp; Knoepffler* 1968) comb. nov.</th><td><i>Cepedea fusiformis</i> Tuzet &amp; Knoepfler * 1968</td><td>Proposed as synonym of <i>Opalina affinis</i> by Delvinquier <i>et al.</i> (1993)</td></tr><tr><th><i>Opalina globosa</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea globosa</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina gracilis</i> (Banina* 1952) comb. nov.</th><td><i>Cepedea gracilis</i> Banina * 1952</td><td></td></tr><tr><th><i>Opalina hasseltii</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea hasseltii</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina hispanica</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea hispanica</i> Metcalf * 1923</td><td>Proposed as synonym of <i>Opalina longa</i> by Metcalf (1940)</td></tr><tr><th><i>Opalina hosei</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea hosei</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina hylae</i> (Khan* 1962) comb. nov.</th><td><i>Cepedea hylae</i> Khan * 1962</td><td></td></tr><tr><th><i>Opalina lemuriae</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea lemuriae</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina longa</i> Bezzenberger * 1904</th><td><i>Cepdea longa</i> (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th><i>Opalina luzonensis</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea luzonensis</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina macronucleata</i> (Banina* 1952) comb. nov.</th><td><i>Cepedea macronucleata</i> Banina * 1952</td><td></td></tr><tr><th><i>Opalina madagascariensis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea madagascariensis</i> Metcalf * 1923</td><td>Considered in part as synonym of <i>Opalina affinis</i> by Delvinquier <i>et al.</i> (1993)</td></tr><tr><th><i>Opalina magna</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea magna</i> Metcalf * 1923</td><td>(= <i>Opalina sudafricana</i> Fantham * 1923) (following Delvinquier <i>et al.</i> 1993)</td></tr><tr><th><i>Opalina marginata</i> (Amaro* 1964) comb. nov.</th><td><i>Cepedea marginata</i> Amaro * 1964</td><td></td></tr><tr><th><i>Opalina metcalfi</i> (Bhatia &amp; Gulati* 1927) comb. nov.</th><td><i>Cepedea metcalfi</i> Bhatia &amp; Gulati * 1927</td><td></td></tr><tr><th><i>Opalina mexicana</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea mexicana</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina microhylae</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea microhylae</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina minor</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea minor</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina mogyana</i> Carini * 1937</th><td><i>Cepedea mogyana</i> (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th><i>Opalina multiformis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea multiformis</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina obovoidea</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea obovoidea</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina obtrigonoidea</i> Metcalf * 1923</th><td><i>Cepedea obtrigonoidea</i> (Metcalf* 1923) Affa&rsquo;a &amp; Lynn* 1994</td><td></td></tr><tr><th><i>Opalina occidentalis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea occidentalis</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina ophis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea ophis</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina parva</i> (Lu* 1945) comb. nov.</th><td><i>Cepedea parva</i> Lu * 1945</td><td></td></tr><tr><th><i>Opalina philauti</i> (Uttangi* 1952) comb. nov.</th><td><i>Cepedea philauti</i> Uttangi * 1952</td><td></td></tr><tr><th><i>Opalina philippensis</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea philippensis</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina phrynomantidis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea phrynomantidis</i> Metcalf * 1923</td><td>Proposed as synonym of <i>Opalina magna</i> by Delvinquier <i>et al.</i> (1993)</td></tr><tr><th><i>Opalina plata</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea plata</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina pulchra</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea pulchra</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina punjagbensis</i> (Bhatia &amp; Gulati* 1927) comb. nov.</th><td><i>Cepedea punjagbensis</i> Bhatia &amp; Gulati * 1927</td><td></td></tr><tr><th><i>Opalina rubra</i> Carini * 1937</th><td><i>Cepedea rubra</i> (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th><i>Opalina rugosa</i> Carini * 1937</th><td><i>Cepedea rugosa</i> (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th><i>Opalina saharana</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea saharana</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina scalpriformis</i> Ghosh * 1918</th><td><i>Cepedea scalpriformis</i> (Ghosh* 1918) Metcalf* 1940</td><td></td></tr><tr><th><i>Opalina segmentata</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea segmentata</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina seychellensis</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea seychellensis</i> Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th><i>Opalina sialkoti</i> (Bathia &amp; Gulati* 1927) comb. nov.</th><td><i>Cepedea sialkoti</i> Bathia &amp; Gulati * 1927</td><td></td></tr><tr><th><i>Opalina siamensis</i> (Metcalf* 1940) comb. nov.</th><td><i>Cepedea siamensis</i> Metcalf * 1940</td><td></td></tr><tr><th><i>Opalina spinifera</i> (Metcalf* 1923) comb. nov.</th><td><i>Cepedea spinifera</i> Metcalf * 1923</td><td></td></tr><tr><th><i>Opalina subcylindrica</i> (Mello* 1932) comb. nov.</th><td><i>Cepedea subcylindrica</i> Mello * 1932</td><td></td></tr><tr><th><i>Opalina sudafricana</i> Fantham * 1923</th><td><i>Cepedea sudafricana</i> (Fantam* 1923) Affa&rsquo;a &amp; Lynn* 1994</td><td></td></tr><tr><th><i>Opalina thiagi</i> (Mello* 1931) comb. nov.</th><td><i>Cepedea thiagi</i> Mello * 1931</td><td></td></tr><tr><th><i>Opalina vanniekerkae</i> (Delvinquier* Markus &amp; Passmore* 1993)</th><td><i>Cepedea vanniekerkae</i> Delvinquier * Markus &amp; Passmore* 1993</td><td></td></tr><tr><th><i>Opalina virgula</i> Dobell * 1910</th><td><i>Cepedea virgula</i> (Dobell* 1910) Metcalf* 1940</td><td></td></tr><tr><th><i>Opalina virguloidea</i> Metcalf * 1923</th><td><i>Cepedea virguloidea</i> (Metcalf* 1923) Affa&rsquo;a &amp; Lynn* 1994</td><td></td></tr><tr><th><i>Protoopalina</i> Metcalf * 1918 (= <i>Bezzenbergeria</i> Earl * 1973)</th><td></td><td></td></tr><tr><th><i>Protoopalina lanceolata</i> Bezzenberger* 1904</th><td><i>Bezzenbergeria lanceolata</i> [(Bezzenberger* 1904) Metcalf* 1923] Earl* 1973 <i>Cepedea lanceolata</i> (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th><i>Protoopalina axoucleata</i> Metcalf * 1923</th><td><i>Protoopalina japonica</i> Nishi <i>et al.</i> * 2005</td><td>Nomem nudum</td></tr></tbody></table><p><sup>aThe</sup> species <i>Cepedea lanceolatum</i> was listed by Delvinquier and Patterson (1993)* citing Evans <i>et al.</i> (1977) * but without specifying the author and publication year.We have been unable to obtain a copy of the paper by Evans <i>et al.</i> (1977) in order to search for a description or the reference to the original source.Therefore* we have not included this species in the list.If it were to be included* the correct species name would be <i>Opalina lanceolata</i>.</p><p><sup>bEarl</sup> (1973) proposed the suppression of 88 species/subspecies of Opalinida because he deemed them inadequately described:certain characteristics were absent from the original descriptions (such as the length of the falx)* and the descriptions were based on type specimens rather than on populations.</p>

opennotspecifiedNov 2023View details →
dryad32/100

Data from: Nuclear DNA based species delineations of Coccus scale insects in symbiosis with plants and ants, and the role of plant epicuticular wax in structuring associations

We undertook phylogenetic analysis of nuclear DNA to elucidate species boundaries in the symbiotic Coccus scale insects associated with mutualistic Crematogaster ants and Macaranga plants occurring in the ever-wet forests of Southeast Asia. The coccid specimens clustered into ten lineages, each corresponding to a morphospecies assignment. The lineage identified as C. secretus was separated from the Main Clade by an outgroup. We also examined all pairwise associations among the three symbiont guilds to understand how patterns of association were structured. The analyses revealed that each ant, plant or coccid operational (taxonomic) unit often associated with multiple O(T)Us of each of the other two guilds. However, where testing was feasible, a 'preference' for one or sometimes two partner O(T)Us of each guild was often detected. Mutual 'preferences' or 'avoidances' were relatively common among the symbionts, and no conflicts of interest were apparent. The network of preferred partners among all three guilds showed compartmentalization structured by the presence/absence of plant epicuticular wax, suggesting that this feature plays a fundamental role in how the symbionts select partners that best serve their needs. To a lesser degree, the network was also structured by whether the host plant stems were ant-excavated or hollowed naturally.

opencc-zeroDec 2015View details →
dryad32/100

DNA matrix combined (nuclear and indels coded) datasets for Hyptidinae (Lamiaceae)

<p class="CxSpFirst">Hyptidinae, ca. 400 species, is an important component of Neotropical vegetation formations. Members of the subtribe possess flowers arranged in variously modified bracteolate cymes and nutlets with an expanded areole and all share a unique explosive mechanism of pollen release, except for <i>Asterohyptis</i>. In a recent phylogenetic study, the group had its generic delimitations rearranged with the recognition of 19 genera in the subtribe. Although the previous phylogenetic analysis covered almost all the higher taxa in the subtribe, it lacked a broader sampling at the species level. Here we present a new expanded phylogenetic analysis for the subtribe comprising 153 accessions of Hyptidinae sequenced for the nuclear nrITS, nrETS, and waxy regions and the plastid markers<i> trnL-F, trnS-G, trnD-T, </i>and<i> matK</i>. Our results widely support the previous phylogenetic results with some changes in the support and relationship between genera. It also uncovers the need for a new combination of <i>Eriope machrisae </i>in <i>Hypenia</i> and the phylogenetic position of <i>Hyptis</i> sect. <i>Rhytidea</i>, which was demonstrated to be part of <i>Mesosphaerum</i>. The generic delimitation in Hyptidinae is discussed, and we recommend that further studies with more markers are needed to confirm the monophyly of <i>Hyptidendron</i> and <i>Mesosphaerum</i>, as well as to support taxonomic changes on the infrageneric delimitation within <i>Hyptis </i>s. s.</p>

opencc-zeroJul 2021View details →

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Last verified 2026-04-30Open record

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Last verified 2026-04-29Open record

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openneuro
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Last verified 2026-04-29Open record