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FIGURE 1 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 1. Maximum likelihood mitochondrial phylogeny of the Naja melanoleuca complex. Node support values indicate % bootstrap support; support values for the most distal nodes not shown. Country abbreviations: CAR = Central African Republic, DRC = Democratic Republic of Congo, KZN = KwaZulu-Natal Province, South Africa, RoC = Republic of Congo. Mitochondrial candidate species (CS) are shown in the same colours as in Figures 2–4. For specimen information see Appendix 1.

FIGURE 5 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 5. Naja (Boulengerina) guineensis sp. nov. Left and top right: holotype, MNHN 1921.0485, dorsal and ventral view and side view of head. Note extensive mottling of throat and anterior ventral side and limited posterior extent of lighter ventral markings. Bottom right: live adult specimen measuring approximately 200 cm total length, from Sekondi-Takoradi, Western Region, Ghana, displaying dark suffusion of throat and anterior venter (not preserved; photo L. Chirio).

FIGURE 4 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 4. Ordination of individual specimens and OTU centroids of four of the mitochondrially defined candidate species of the N. melanoleuca complex along the first two canonical variates. CS5-peroescobari was omitted due to the small available sample size. Canonical variates 1 and 2 account for 57.9 and 22.8% of total variance, respectively. Enlarged symbols indicate OTU centroids.

FIGURE 3 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 3. Ordination of individual specimens in a Principal Coordinates Analysis of standardised multilocus distances of PRLR and UBN1 scnDNA sequence data. (a) All specimens; (b) Analysis repeated under exclusion of CS2 and CS3.

FIGURE 8 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 8. Naja (Boulengerina) melanoleuca. Adult specimens from Yaoundé, Cameroon (left—photo J.-F. Trape) and Tsibilé, Gabon (right—photo L. Chirio). Note the diffuse but distinct hood mark that is often present in this species, and the combination of broad main bands and narrow accessory bands on the ventral side.

FIGURE 9 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 9. Naja (Boulengerina) subfulva. Variation in colour and pattern. Top left: specimen from Kakamega, western Kenya, illustrating the typically deep black and white specimens with strong facial markings from the periphery of Lake Victoria. Bottom left: specimen from Chuka, Mount Kenya, Kenya, illustrating an extreme of the brown forebody and reduced facial pigmentation typical of the species in much of its range. Photos W. Wüster, courtesy Royjan Taylor / Bio-Ken snake farm live collection, Watamu, Kenya. Right: specimen from Bamenda, Cameroon, representing the form described by Stucki-Stirn (1979) as Naja melanoleuca aurata. Note the indistinct ventral bands and the lack of accessory ventral bands, as is typical of this species. Photo J.-F. Trape.

FIGURE 7 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 7. Naja (Boulengerina) savannula sp. nov. Top row and bottom left: holotype, MNHN 2018.0002. Bottom right: live specimen from Kindia, Guinea, showing conspicuous, broad dorsal bands and ventral banding, including narrow accessory bands (not vouchered). Photos J.-F. Trape.

FIGURE 2 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)

FIGURE 2. Haplotype networks for single copy nuclear loci. (a) PRLR; (b) UBN1. Small black circles indicate unsampled haplotypes.

Figure 5 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 5. Phylogenetic relations of the ITS1–5.8S rDNA–ITS2–LSU rDNA sequences of Opalinida by the maximum likelihood (ML) method. The numbers 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. The tree is rooted considering the Protoopalina sequences at the basal position according to the results obtained in the phylogenetic analysis of the SSU rDNA sequences. New sequences are noted in bold.

Figure 4 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Figure 4. Opalinata subtree showing the results of the TimeTree analysis inferred by applying the RelTime method to the SSU rDNA phylogenetic tree calculated by the maximum parsimony method. Three sets of calibrations including a total of seven time points were combined to obtain the TimeTree (set A* 'sequence evolution'* included three calibration points with uniform distributions; set B* 'host class constraints'* included two maximum time calibration points; and set C* 'host family constraints'* included two maximum time calibration points; see main text for further details); diamonds indicate calibration points included within the Opalinata subtree. Divergence time estimates and their 95% credibility intervals (magenta bars) are indicated in each node. Images showing the evolution of continents are from Scotese (2016).

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.

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.

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.

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

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

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

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

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

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

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

Table 7. List of nomenclatural acts.<table><tbody><tr><th>Taxon nameb</th><th>Previous name</th><th>Comments</th></tr><tr><th>Opalina Purkinje & Valentin * 1835 (= Cepedea Metcalf * 1920)</th></tr></tbody><tbody><tr><th>Opalina acuta (Delvinquier* Markus & Passmore* 1993) comb. nov.</th><td>Cepedea acuta Delvinquier * Markus & Passmore* 1992</td><td></td></tr><tr><th>Opalina affinis Nazaretskaja * 1922</th><td>Cepedea affinis (Nazaretskaja* 1922) Walton* 1964</td><td></td></tr><tr><th>Opalina africana (Tuzet & Zuber-Vogeli* 1954) comb. nov.</th><td>Cepedea africana Tuzet & Zuber-Vogeli * 1954</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina amygdala (Boisson* 1965) Delvinquier et al. * 1991</th><td>Cepedea amygdala Boisson * 1965</td><td>Proposed as synonym of Opalina foliacea by Affa’a and Lynn (1994)</td></tr><tr><th>Opalina baudinii (Metcalf* 1923) comb. nov.</th><td>Cepedea baudini Metcalf * 1923</td><td></td></tr><tr><th>Opalina boissoni (Tuzet & Knoepffler* 1968) comb. nov.</th><td>Cepedea boissoni Tuzet & Knoepffler * 1968</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina borneonensis (Metcalf* 1923) comb. nov.</th><td>Cepedea borneonensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina buergeri (Metcalf* 1923) comb. nov.</th><td>Cepedea buergeri Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina brumpti (Cordero* 1928) comb. nov.</th><td>Cepedea brumpti Cordero * 1928</td><td></td></tr><tr><th>Opalina cantabrigensis (Metcalf* 1923)</th><td>Cepedea cantabrigensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina celebensis (Metcalf* 1923) comb. nov.</th><td>Cepedea celebensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina ciliata (Metcalf* 1940) comb. nov.</th><td>Cepedea ciliata Metcalf * 1940</td><td></td></tr><tr><th>Opalina crispata (Boisson* 1965) comb. nov.</th><td>Cepedea crispata Boisson * 1965</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina daloalensis (Tuzet & Zuber-Vogeli* 1954) comb. nov.</th><td>Cepedea daloalensis Tuzet & Zuber-Vogeli * 1954</td><td></td></tr><tr><th>Opalina dimidiata Stein * 1860</th><td>Cepedea dimidiata (Stein* 1860) Metcalf* 1923</td><td></td></tr><tr><th>Opalina dolichosoma (Metcalf* 1923) comb. nov.</th><td>Cepedea dolichosoma Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina dracuncula (Boisson* 1957) comb. nov.</th><td>Cepedea dracuncula Boisson * 1957</td><td></td></tr><tr><th>Opalina elongata Gourvitsch * 1926</th><td>Cepedea elongata (Gourvitsch* 1926) Banina* 1962</td><td></td></tr><tr><th>Opalina flava Stokes * 1884</th><td>Cepedea flava (Stokes* 1884) Metcalf* 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina floridensis (Metcalf* 1923) comb. nov.</th><td>Cepedea floridensis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina foliacea (Boisson* 1959) Delvinquier et al. * 1991</th><td>Cepedea foliacea Boisson * 1959</td><td></td></tr><tr><th>Opalina formosae (Metcalf* 1923) comb. nov.</th><td>Cepedea formosae Metcalf * 1923</td><td></td></tr><tr><th>Opalina fujiensis (Metcalf* 1923) comb. nov.</th><td>Cepedea fujiensis Metcalf * 1923</td><td></td></tr><tr><th>Opalina fusiformis (Tuzet & Knoepffler* 1968) comb. nov.</th><td>Cepedea fusiformis Tuzet & Knoepfler * 1968</td><td>Proposed as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina globosa (Metcalf* 1923) comb. nov.</th><td>Cepedea globosa Metcalf * 1923</td><td></td></tr><tr><th>Opalina gracilis (Banina* 1952) comb. nov.</th><td>Cepedea gracilis Banina * 1952</td><td></td></tr><tr><th>Opalina hasseltii (Metcalf* 1940) comb. nov.</th><td>Cepedea hasseltii Metcalf * 1940</td><td></td></tr><tr><th>Opalina hispanica (Metcalf* 1923) comb. nov.</th><td>Cepedea hispanica Metcalf * 1923</td><td>Proposed as synonym of Opalina longa by Metcalf (1940)</td></tr><tr><th>Opalina hosei (Metcalf* 1940) comb. nov.</th><td>Cepedea hosei Metcalf * 1940</td><td></td></tr><tr><th>Opalina hylae (Khan* 1962) comb. nov.</th><td>Cepedea hylae Khan * 1962</td><td></td></tr><tr><th>Opalina lemuriae (Metcalf* 1940) comb. nov.</th><td>Cepedea lemuriae Metcalf * 1940</td><td></td></tr><tr><th>Opalina longa Bezzenberger * 1904</th><td>Cepdea longa (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th>Opalina luzonensis (Metcalf* 1940) comb. nov.</th><td>Cepedea luzonensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina macronucleata (Banina* 1952) comb. nov.</th><td>Cepedea macronucleata Banina * 1952</td><td></td></tr><tr><th>Opalina madagascariensis (Metcalf* 1923) comb. nov.</th><td>Cepedea madagascariensis Metcalf * 1923</td><td>Considered in part as synonym of Opalina affinis by Delvinquier et al. (1993)</td></tr><tr><th>Opalina magna (Metcalf* 1923) comb. nov.</th><td>Cepedea magna Metcalf * 1923</td><td>(= Opalina sudafricana Fantham * 1923) (following Delvinquier et al. 1993)</td></tr><tr><th>Opalina marginata (Amaro* 1964) comb. nov.</th><td>Cepedea marginata Amaro * 1964</td><td></td></tr><tr><th>Opalina metcalfi (Bhatia & Gulati* 1927) comb. nov.</th><td>Cepedea metcalfi Bhatia & Gulati * 1927</td><td></td></tr><tr><th>Opalina mexicana (Metcalf* 1923) comb. nov.</th><td>Cepedea mexicana Metcalf * 1923</td><td></td></tr><tr><th>Opalina microhylae (Metcalf* 1940) comb. nov.</th><td>Cepedea microhylae Metcalf * 1940</td><td></td></tr><tr><th>Opalina minor (Metcalf* 1923) comb. nov.</th><td>Cepedea minor Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina mogyana Carini * 1937</th><td>Cepedea mogyana (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina multiformis (Metcalf* 1923) comb. nov.</th><td>Cepedea multiformis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina obovoidea (Metcalf* 1923) comb. nov.</th><td>Cepedea obovoidea Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina obtrigonoidea Metcalf * 1923</th><td>Cepedea obtrigonoidea (Metcalf* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Opalina occidentalis (Metcalf* 1923) comb. nov.</th><td>Cepedea occidentalis Metcalf * 1923</td><td></td></tr><tr><th>Opalina ophis (Metcalf* 1923) comb. nov.</th><td>Cepedea ophis Metcalf * 1923</td><td></td></tr><tr><th>Opalina parva (Lu* 1945) comb. nov.</th><td>Cepedea parva Lu * 1945</td><td></td></tr><tr><th>Opalina philauti (Uttangi* 1952) comb. nov.</th><td>Cepedea philauti Uttangi * 1952</td><td></td></tr><tr><th>Opalina philippensis (Metcalf* 1940) comb. nov.</th><td>Cepedea philippensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina phrynomantidis (Metcalf* 1923) comb. nov.</th><td>Cepedea phrynomantidis Metcalf * 1923</td><td>Proposed as synonym of Opalina magna by Delvinquier et al. (1993)</td></tr><tr><th>Opalina plata (Metcalf* 1940) comb. nov.</th><td>Cepedea plata Metcalf * 1940</td><td></td></tr><tr><th>Opalina pulchra (Metcalf* 1923) comb. nov.</th><td>Cepedea pulchra Metcalf * 1923</td><td></td></tr><tr><th>Opalina punjagbensis (Bhatia & Gulati* 1927) comb. nov.</th><td>Cepedea punjagbensis Bhatia & Gulati * 1927</td><td></td></tr><tr><th>Opalina rubra Carini * 1937</th><td>Cepedea rubra (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina rugosa Carini * 1937</th><td>Cepedea rugosa (Carini* 1937) Metcalf* 1940</td><td></td></tr><tr><th>Opalina saharana (Metcalf* 1923) comb. nov.</th><td>Cepedea saharana Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina scalpriformis Ghosh * 1918</th><td>Cepedea scalpriformis (Ghosh* 1918) Metcalf* 1940</td><td></td></tr><tr><th>Opalina segmentata (Metcalf* 1923) comb. nov.</th><td>Cepedea segmentata Metcalf * 1923</td><td></td></tr><tr><th>Opalina seychellensis (Metcalf* 1923) comb. nov.</th><td>Cepedea seychellensis Metcalf * 1923</td><td>Proposed for suppression by Earl (1973) b</td></tr><tr><th>Opalina sialkoti (Bathia & Gulati* 1927) comb. nov.</th><td>Cepedea sialkoti Bathia & Gulati * 1927</td><td></td></tr><tr><th>Opalina siamensis (Metcalf* 1940) comb. nov.</th><td>Cepedea siamensis Metcalf * 1940</td><td></td></tr><tr><th>Opalina spinifera (Metcalf* 1923) comb. nov.</th><td>Cepedea spinifera Metcalf * 1923</td><td></td></tr><tr><th>Opalina subcylindrica (Mello* 1932) comb. nov.</th><td>Cepedea subcylindrica Mello * 1932</td><td></td></tr><tr><th>Opalina sudafricana Fantham * 1923</th><td>Cepedea sudafricana (Fantam* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Opalina thiagi (Mello* 1931) comb. nov.</th><td>Cepedea thiagi Mello * 1931</td><td></td></tr><tr><th>Opalina vanniekerkae (Delvinquier* Markus & Passmore* 1993)</th><td>Cepedea vanniekerkae Delvinquier * Markus & Passmore* 1993</td><td></td></tr><tr><th>Opalina virgula Dobell * 1910</th><td>Cepedea virgula (Dobell* 1910) Metcalf* 1940</td><td></td></tr><tr><th>Opalina virguloidea Metcalf * 1923</th><td>Cepedea virguloidea (Metcalf* 1923) Affa’a & Lynn* 1994</td><td></td></tr><tr><th>Protoopalina Metcalf * 1918 (= Bezzenbergeria Earl * 1973)</th><td></td><td></td></tr><tr><th>Protoopalina lanceolata Bezzenberger* 1904</th><td>Bezzenbergeria lanceolata [(Bezzenberger* 1904) Metcalf* 1923] Earl* 1973 Cepedea lanceolata (Bezzenberger* 1904) Metcalf* 1923</td><td></td></tr><tr><th>Protoopalina axoucleata Metcalf * 1923</th><td>Protoopalina japonica Nishi et al. * 2005</td><td>Nomem nudum</td></tr></tbody></table>aThe species Cepedea lanceolatum was listed by Delvinquier and Patterson (1993)* citing Evans et al. (1977) * but without specifying the author and publication year.We have been unable to obtain a copy of the paper by Evans et al. (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 Opalina lanceolata.bEarl (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.

opencc-zeroDec 2015View details →

dryad32/100

Data from: Molecular evolution of the nuclear factor (erythroid-derived 2)-like 2 gene Nrf2 in Old World fruit bats (Chiroptera: Pteropodidae)

Mammals developed antioxidant systems to defend against oxidative damage in their daily life. Enzymatic antioxidants and low molecular weight antioxidants (LMWAs) constitute major parts of the antioxidant systems. Nuclear factor (erythroid-derived 2)-like 2 (Nrf2, encoded by the Nrf2 gene) is a central transcriptional regulator, regulating transcription, of many antioxidant enzymes. Frugivorous bats eat large amounts of fruits that contain high levels of LMWAs such as vitamin C, thus, a reliance on LMWAs might greatly reduce the need for antioxidant enzymes in comparison to insectivorous bats. Therefore, it is possible that frugivorous bats have a reduced need for Nrf2 function due to their substantial intake of diet-antioxidants. To test whether the Nrf2 gene has undergone relaxed evolution in fruit-eating bats, we obtained Nrf2 sequences from 16 species of bats, including four Old World fruit bats (Pteropodidae) and one New World fruit bat (Phyllostomidae). Our molecular evolutionary analyses revealed changes in the selection pressure acting on Nrf2 gene and identified seven specific amino acid substitutions that occurred on the ancestral lineage leading to Old World fruit bats. Biochemical experiments were conducted to examine Nrf2 in Old World fruit bats and showed that the amount of catalase, which is regulated by Nrf2, was significantly lower in the brain, heart and liver of Old World fruit bats despite higher levels of Nrf2 protein in Old World fruit bats. Computational predictions suggest that three of these seven amino acid replacements might be deleterious to Nrf2 function. Therefore, the results suggest that Nrf2 gene might have experienced relaxed constraint in Old World fruit bats, however, we cannot rule out the possibility of positive selection. Our study provides the first data on the molecular adaptation of Nrf2 gene in frugivorous bats in compensation to the increased levels of LWMAs from their fruit-diet.

dryad32/100

Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a subset of 60 loci in a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories in the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.

opencc-zeroDec 2014View details →