Important new records of Pelomedusa species for South Africa and Ethiopia

Because of a recent taxonomic revision, the species identity of helmeted terrapins (Pelomedusa) became unclear in many regions of their wide distribution range. Based on mtDNA sequence data, here we present the first record of Pelomedusa subrufa sensu stricto for the South African province of Mpumalanga. In South Africa, this species was previously known only from a single record in the province of Limpopo. In addition, we provide evidence for the occurrence of at least two distinct Pelomedusa species in Ethiopia. A sample from southern Ethiopia (Omo Region) turned out as P. neumanni, while another sample from Koka Lake (Oromia Region, central Ethiopia) represents P. somalica. Also a historical museum specimen from Ethiopia, most likely collected south of the Shebelle River (Oromia Region), belongs to P. somalica. However, these two Ethiopian specimens of P. somalica represent highly distinct genetic lineages, which may actually correspond to two different species

Diversity, distribution and conservation of the terrestrial reptiles of Oman (Sauropsida, Squamata)

All authors: Salvador Carranza , Meritxell Xipell, Pedro Tarroso, Andrew Gardner, Edwin Nicholas Arnold, Michael D. Robinson, Marc Simó-Riudalbas, Raquel Vasconcelos, Philip de Pous, Fèlix Amat, Jiří Šmíd, Roberto Sindaco, Margarita Metallinou †, Johannes Els, Juan Manuel Pleguezuelos, Luis Machado, David Donaire, Gabriel Martínez, Joan Garcia-Porta, Tomáš Mazuch, Thomas Wilms, Jürgen Gebhart, Javier Aznar, Javier Gallego, Bernd-Michael Zwanzig, Daniel Fernández-Guiberteau, Theodore Papenfuss, Saleh Al Saadi, Ali Alghafri, Sultan Khalifa, Hamed Al Farqani, Salim Bait Bilal, Iman Sulaiman Alazri, Aziza Saud Al Adhoobi, Zeyana Salim Al Omairi, Mohammed Al Shariani, Ali Al Kiyumi, Thuraya Al Sariri, Ahmed Said Al Shukaili, Suleiman Nasser Al Akhzami.In the present work, we use an exceptional database including 5,359 records of 101 species of Oman’s terrestrial reptiles together with spatial tools to infer the spatial patterns of species richness and endemicity, to infer the habitat preference of each species and to better define conservation priorities, with especial focus on the effectiveness of the protected areas in preserving this unique arid fauna. Our results indicate that the sampling effort is not only remarkable from a taxonomic point of view, with multiple observations for most species, but also for the spatial coverage achieved. The observations are distributed almost continuously across the two-dimensional climatic space of Oman defined by the mean annual temperature and the total annual precipitation and across the Principal Component Analysis (PCA) of the multivariate climatic space and are well represented within 17 out of the 20 climatic clusters grouping 10% of the explained climatic variance defined by PC1 and PC2. Species richness is highest in the Hajar and Dhofar Mountains, two of the most biodiverse areas of the Arabian Peninsula, and endemic species richness is greatest in the Jebel Akhdar, the highest part of the Hajar Mountains. Oman’s 22 protected areas cover only 3.91% of the country, including within their limits 63.37% of terrestrial reptiles and 50% of all endemics. Our analyses show that large areas of the climatic space of Oman lie outside protected areas and that seven of the 20 climatic clusters are not protected at all. The results of the gap analysis indicate that most of the species are below the conservation target of 17% or even the less restrictive 12% of their total area within a protected area in order to be considered adequately protected. Therefore, an evaluation of the coverage of the current network of protected areas and the identification of priority protected areas for reptiles using reserve design algorithms are urgently needed. Our study also shows that more than half of the species are still pending of a definitive evaluation by the International Union for Conservation of Nature (IUCN).This work was funded by grants CGL2012-36970, CGL2015-70390-P from the Ministerio de Economía y Competitividad, Spain (cofunded by FEDER) to SC, the project Field study for the conservation of reptiles in Oman, Ministry of Environment and Climate Affairs, Oman (Ref: 22412027) to SC and grant 2014-SGR-1532 from the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya to SC. MSR is funded by a FPI grant from the Ministerio de Economía y Competitividad, Spain (BES-2013-064248); RV, PT and LM were funded by Fundação para a Ciência e Tecnologia (FCT) through post-doc grants (SFRH/BPD/79913/2011) to RV, (SFRH/BPD/93473/2013) to PT and PhD grant (SFRH/BD/89820/2012) to LM, financed by Programa Operacional Potencial Humano (POPH) – Quadro de Referência Estrategico Nacional (QREN) from the European Social Fund and Portuguese Ministerio da Educação e Ciência

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

http://zoobank.org/urn:lsid:zoobank.org:pub:9618FFD9-B836-4450-9BF5-AA2815C8756B

www.mapress.com/zootaxa

Circadian properties of the mathematical model reproduce the RAS-mediated effect on the clock.

<p>(A) Simplified network representation of the mathematical model. The model consists of seven core-clock components (grey boxes) and nine cell cycle components (orange boxes). Activating (green lines) and inhibiting (red lines) interactions known from literature and a potential transcriptional activation (reported in MotifMap) are represented. The dashed red line from MYC to CLOCK/BMAL represents the overall interference with BMAL-mediated transcription by competitive E-box binding. Module 1 consists of the INK4a/RB1/E2F1 pathway (green) and module 2 of the ARF/MDM2/p53 pathway (orange). (B) In silico peak phases of clock genes from the model are consistent with experimental data. The highest mRNA expression intervals (experimental published data) from the core-clock genes <i>Ror</i> (blue), <i>Rev-Erb</i> (red), <i>Bmal</i> (green), <i>Per</i> (purple), <i>Cry</i> (turquoise) and the cytoplasmic and nuclear PER/CRY protein complexes (orange) are depicted in darker colours within the circles. Yellow dots represent the peak of expression as simulated by the model. (C) Shown are in silico expression profiles for the five core-clock genes <i>Bmal</i>, <i>Per</i>, <i>Cry</i>, <i>Ror</i>, and <i>Rev-Erb</i> and for the PER/CRY protein complex. The period was set to 23.65 h and the phase of <i>Bmal</i> to CT21. (D) The model reproduces experimental clock phenotypes qualitatively. In silico expression data show that upon simulation of RAS overexpression, the Ink4a/Arf^+/+ system acquires a longer period and Ink4a/Arf^-/- system a shorter period compared to the corresponding simulated WT system. RAS overexpression was simulated by decreasing the parameter <i>ktt</i> to 0.4 (<i>ktt</i> = 1 WT, <i>ktt</i> < 1 increase of RAS). (E) RAS overexpression increases <i>Ink4a</i> expression levels in silico. WT, wild-type.</p

Predictive classification of cell cycle-fate phenotypes for Ink4a/Arf^+/+ and Ink4a/Arf^-/- MEFs based on the expression of senescence-associated genes can be validated by experimental results.

<p>(A) A set of 32 senescence-related genes derived from the literature clusters according to the knockout of <i>Ink4a/Arf</i>. (B) Two-dimensional representation of the SVM classification based on the expression of the senescence-related genes <i>Rb1</i> and <i>Suv39h1</i> for the three training conditions (represented as squares) and the remaining five predicted conditions (represented as dots). (C) FACS analysis to determine the percentage of cells in each cell cycle phase for the three training conditions (Ink4a/Arf^+/+, Ink4a/Arf^+/++RAS, and Ink4a/Arf^-/-) and two of the predicted conditions (Ink4a/Arf^-/-+RAS and Ink4a/Arf^-/- <i>shBmal1</i>+RAS) (<i>n</i> = 3; mean and SEM). The cell cycle phases were determined by fitting a univariate cell cycle model using the Watson pragmatic algorithm. Shown are representative examples for each condition. Numerical values are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002940#pbio.2002940.s013" target="_blank">S1 Data</a>. FACS, fluorescence-activated cell sorting; MEF, mouse embryonic fibroblasts; PI, propidium iodide.</p

Ink4a/Arf^+/+ and Ink4a/Arf^-/- MEFs show different circadian phenotypes upon RAS overexpression.

<p>(A) Schematic representation of the experimental setup to investigate the influence of RAS on the circadian phenotype via <i>Ink4a/Arf</i>. MEFs from <i>Ink4a/Arf</i> WT (Ink4a/Arf^+/+) and their <i>Ink4a/Arf</i> knock-out littermates (Ink4a/Arf^-/-) were lentivirally transduced with a <i>Bmal1</i>-promoter driven luciferase construct (<i>Bmal1</i>:<i>Luc</i>). To investigate the effect of the core-clock in this cell model system, <i>Bmal1</i> was downregulated by shRNA. The effect of the oncogene RAS was examined by overexpression of RAS. Bioluminescence was measured over five days. Shown are representative data for eight different conditions, as indicated. (B) RAS overexpression leads to an increase of the period in Ink4a/Arf^+/+ MEFs (26.9 h, dark blue) compared to the corresponding control (24.1 h, light blue). (C) RAS overexpression shortens the period of Ink4a/Arf^-/- MEFs (24.0 h, dark red) compared to the corresponding control (21.4 h, light red). RAS overexpression disrupts the circadian clock in <i>Bmal1</i> knock-down conditions in (D) Ink4a/Arf^+/+ MEFs and (E) Ink4a/Arf^-/- MEFs. (F) Summary of circadian period phenotype measurements for Ink4a/Arf^+/+ MEFs and Ink4a/Arf^-/- MEFs with and without RAS overexpression (<i>n</i> = 5; mean and SEM). (G) The cell number of Ink4a/Arf^+/+ MEFs and Ink4a/Arf^-/- MEFs with and without shBmal1 was monitored over five days (<i>n</i> = 3; mean and SEM). Ink4a/Arf^-/- MEFs proliferate faster than their corresponding Ink4a/Arf^+/+ littermates, independent from <i>Bmal1</i> knockdown. (H) The cell cycle arrest phenotypes were estimated by SA-ß-Gal staining in Ink4a/Arf^+/+ MEFs and their Ink4a/Arf^-/- littermates with or without RAS overexpression and <i>Bmal1</i> downregulation. (I) Percentage of SA-ß-Gal staining positive cells (<i>n</i> = 3; mean and SEM). RAS overexpression significantly increased the number of senescent cells in the Ink4a/Arf^+/+ MEFs compared to the WT. There is no effect of <i>Bmal1</i> downregulation in the Ink4a/Arf^-/- cell population. Statistical significance was determined by <i>t</i> test with <i>p</i>-values corrected for multiple testing with the Benjamini and Hochberg method. ***<i>p</i> < 0.001. Numerical values are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002940#pbio.2002940.s013" target="_blank">S1 Data</a>. MEF, mouse embryonic fibroblasts; ND, not defined; n.s., not significant; RAS, rat sarcoma viral oncogene; shRNA, short hairpin RNA; T, period; WT, wild-type.</p

The RAS-mediated effect on the circadian period is dependent on <i>Ink4a/Arf</i>.

<p>The RAS-mediated effect on the circadian period is dependent on <i>Ink4a/Arf</i>.</p

Schematic model of the Ink4a/Arf-RAS interplay and its connections to circadian clock and cell cycle phenotypes.

<p>(A) Overexpression of the oncogene RAS results in a lengthening of the circadian period in WT MEFs and leads to a senescent cell phenotype. (B) Knockout of the tumour suppressor element <i>Ink4a/Arf</i> that connects components of both cellular oscillators, leads to a change in the RAS-induced effect on the clock resulting in a shorter circadian period and proliferation of cells. MEF, mouse embryonic fibroblasts; RAS, rat sarcoma viral oncogene; WT, wild-type.</p

The genome-wide effect of RAS overexpression and Bmal1 downregulation on Ink4a/Arf ^+/+ and Ink4a/Arf ^-/- MEFs can be mirrored by genes from the mathematical model.

<p>(A) The first three principal components as determined by genome-wide expression analysis based on microarray data of Ink4a/Arf^+/+ and Ink4a/Arf^-/- MEFs with different perturbations highlighting the differences between the eight experimental conditions. The arrays cluster in four groups depending on the presence of <i>Ink4a/Arf</i> and RAS overexpression. (B) Based on the four groups determined in the PCA, the top 50 differentially expressed genes across the different experimental conditions were determined. (C) A network connecting 36 out of the topmost 50 differentially expressed genes (orange) to the previously published NCRG (blue) by at most one connecting element (grey) was generated using information from the IntAct database. The genes that are part of the mathematical model are highlighted. An enrichment analysis was performed to determine the most highly represented pathways for the whole network (D) and the set of connecting elements (F). (E) The clustering based on the expression levels of genes from the mathematical model mimics the genome-wide clustering. (G) The expression changes of selected core-clock and cell cycle-related genes upon perturbations by RAS and <i>shBmal1</i> in Ink4a/Arf^+/+ and Ink4a/Arf^-/- MEFs were validated by RT-qPCR and visualised as the log₂ fold change compared to the WT MEFs. Numerical values are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002940#pbio.2002940.s013" target="_blank">S1 Data</a>. MEF, mouse embryonic fibroblasts; NCRG, network of circadian regulated genes.</p