Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns

A diverse group of genes are involved in the tooth development of mammals. Several studies, focused mainly on mice and rats, have provided a detailed depiction of the processes coordinating tooth formation and shape. Here we surveyed 236 tooth-associated genes in 39 mammalian genomes and tested for signatures of selection to assess patterns of molecular adaptation in genes regulating mammalian dentition. Of the 236 genes, 31 (∼13.1%) showed strong signatures of positive selection that may be responsible for the phenotypic diversity observed in mammalian dentition. Mammalian-specific tooth-associated genes had accelerated mutation rates compared with older genes found across all vertebrates. More recently evolved genes had fewer interactions (either genetic or physical), were associated with fewer Gene Ontology terms and had faster evolutionary rates compared with older genes. The introns of these positively selected genes also exhibited accelerated evolutionary rates, which may reflect additional adaptive pressure in the intronic regions that are associated with regulatory processes that influence tooth-gene networks. The positively selected genes were mainly involved in processes like mineralization and structural organization of tooth specific tissues such as enamel and dentin. Of the 236 analyzed genes, 12 mammalian-specific genes (younger genes) provided insights on diversification of mammalian teeth as they have higher evolutionary rates and exhibit different expression profiles compared with older genes. Our results suggest that the evolution and development of mammalian dentition occurred in part through positive selection acting on genes that previously had other functions

Western Ghats’ fish fauna in peril: are pseudo conservationist attitudes to be blamed?

Use of threatened species in research – be it for taxonomy, biology or population studies, has always invoked much debate. As a result, the Species Survival Commission of the International Union for Conservation of Nature (IUCN) developed a set of guidelines entitled ‘IUCN Policy Statement on Research Involving Species at Risk of Extinction’ with special reference to scientific collecting of threatened species1

Captivity-induced behaviour and spatial learning abilities in an enigmatic, aquifer-dwelling blind eel, Rakthamichthys digressus

We investigated the impact of captive life on behaviour and learning abilities in an enigmatic, aquifer-dwelling blind eel, Rakthamichthys digressus. Of eight major behavioural traits related to exploration and activity in a novel arena, four were significantly altered by life in captivity. While the startle response upon introduction into the arena and overall swimming away from the walls increased after captivity, inactivity exhibited immediately after the startle and the reaction to an external disturbance decreased. We also observed behavioural syndromes between ‘startle responses’ and ‘horizontal wall following’, and between ‘overall activity’ and ‘vertical wall following’; however, these behavioural syndromes were not altered by maintenance in captivity. Interestingly, this blind-eel failed to learn a simple spatial task in a Y-maze apparatus. Captive-associated behavioural changes in R. digressus may influence their survival after reintroduction into natural habitats, and such changes must be taken into account while developing protocols for ex-situ conservation and subsequent release

Unraveling a 146 Years Old Taxonomic Puzzle: Validation of Malabar Snakehead, Species-Status and Its Relevance for Channid Systematics and Evolution

The current distribution of C. diplogramma and C. micropeltes is best explained by vicariance. The significant variation in the key taxonomic characters and the results of the molecular marker analysis points towards an allopatric speciation event or vicariant divergence from a common ancestor, which molecular data suggests to have occurred as early as 21.76 million years ago. The resurrection of C. diplogramma from the synonymy of C. micropeltes has hence been confirmed 146 years after its initial description and 134 years after it was synonymised, establishing it is an endemic species of peninsular India and prioritizing its conservation value

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Data for "Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited Red Lined Torpedo Barbs endemic to the Western Ghats of India" - Plos_one_June_2013

<p>Dataset for RLTB manuscript - "<strong><em>Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited Red Lined Torpedo Barbs endemic to the Western Ghats of India</em></strong>". Data is submitted by Siby Philip. Authors for the paper are - Lijo John, Siby Philip, Neelesh Dahanukar, Anvar Ali PH, Josin Tharian, Rajeev Raghavan and Agostinho Antunes. (first and second authors are equal contributors, last and second last authors are both corresponding authors).</p> <p>The folder contains - Trace files (ABI files) for the sequences used for the study. The *BEAST xml file used to build the species tree and the ML distance matrix from the sequences.</p> <p>Any other details or help needed regarding the genetic methods/data should be sent to <em>sibyphilips</em> at_the_rate_of <em>gmail</em> DOT com.</p

Data for "Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ"

<p>This zip file "Fish_lateral_line_comparative_genomics_data" contains two folders and two text files.</p> <p> </p> <p>The data contained in them pretains to the manuscript: </p> <p>Siby Philip, João Paulo Machado, Emanuel Maldonado, Vítor Vasconcelos, Stephen J O’Brien, Warren E Johnson, and Agostinho Antunes. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Mol Biol Evol first published online July 27, 2012 doi:10.1093/molbev/mss194 </p> <p> </p> <p>The first folder "nexus_sequence_and_tree_file" contain "nexus" format files for all the 34 genes used in the study, the GBlocks filtered alignment followed by the corresponding phylogenetic tree. This file was used to carry out the HYPHY compartmentalization analysis (see the manuscript for details).</p> <p>The phylogenetic trees were built using PHYML and the best fit nucleotide substitution model was found using MrAIC, which is presented in the text file "MrAIC_AICc_models.txt".</p> <p>The second folder contains the phylogenetic trees used for the PAML analysis of the Postduplication branches, thus there are only 15 trees as specified in the manuscript.</p> <p>The text files contain the MrAIC chosen best fit substitution model (file 1) and the PyCogent Ensembl query script used (file 2; this same script is available in the PyCogent cookbook).</p> <p>any further request for data or detailed results should be addressed to Siby Philip (sibyphilips at gmail dot com).</p

Western Ghats Barb Phylogenetics - Data

<p>This zip file contains data for the upcoming WG Barb phylogenetic revision paper. This file contains the alignment (phylip format) and the best ML tree by GARLI (methods obvious from the paper), the best ML tree with bootstrap probablities and bayesian posterior probablities. The zip file is currently locked (protected) but will be unlocked once the paper is accepted for publication.</p

Dario urops Britz, Ali & Philip, 2012, new species

&lt;i&gt;Dario urops&lt;/i&gt;, new species &lt;p&gt;Figures 1&ndash;2&lt;/p&gt; &lt;p&gt; &lt;b&gt;Holotype&lt;/b&gt;. CRG&mdash;SAC.2012.3.1, 23.8 mm SL, male; India: Karnataka: from a small unnamed stream, off the Barapole tributary of Valapattanam river, 12&deg;00.310&rsquo;N 75&deg;53.408&rsquo;E; 811m asl.; R. Raghavan et al., 30 Jan 2012.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Paratypes.&lt;/b&gt; CRG&mdash;SAC.2012.3.2&ndash;11, 10, 17.1&ndash;23.6 mm SL, same data as holotype. BMNH 1870.5.2.9, 28.5 mm, Wynaad, India, F. Day. BMNH 1889.2.1.3193-7, 5, 16.4&ndash;23.6 mm, Wynaad, India, F. Day.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Diagnosis.&lt;/b&gt; &lt;i&gt;Dario urops&lt;/i&gt; differs from all other species of the genus &lt;i&gt;Dario&lt;/i&gt; by the presence of a conspicuous black caudal blotch on the caudal peduncle (vs. absence), by the presence of a horizontal suborbital stripe (vs. absence), by the anterior dorsal fin lappets in males not extending beyond fin spines (vs. extending considerably beyond spines), and by its vertebral count (14+14&ndash;15= 28&ndash;29 vs 11&ndash;13+12&ndash;14=24&ndash;27). It differs further from &lt;i&gt;D. dario&lt;/i&gt; and &lt;i&gt;D. hysginon&lt;/i&gt; by the absence in males of a dark stripe along the anterior margin of the pelvic fin, and from &lt;i&gt;D. dario&lt;/i&gt; by the absence of bars in males.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Description&lt;/b&gt;. For general appearance see Figs. 1&ndash;2; morphometric data are provided in Table 1.&lt;/p&gt; &lt;p&gt;Body elongate, moderately laterally compressed. Predorsal contour straight to slightly convex, prepelvic contour convex, giving head a pointed appearance. Eye situated in anterior half of head, snout short. Mouth terminal. Angle of jaws situated at vertical through anterior third of eye. Dorsal contour of body slightly arched, convex, less so in females, ventral contour of body straight; both contours slightly converging towards caudal peduncle. Caudal peduncle only slightly attenuated posteriorly.&lt;/p&gt; &lt;p&gt;Lateral-line canal pores present only on head, absent from body. Head canal pores comprise: dentary pores 3 (d1&ndash;d3), anguloarticular pore 1 (aa2), preopercular pores 5 (p1, p2, p4&ndash;p6), nasal pores 2 (n1&ndash;n2), supraorbital pores 3 (f1-f3), extrascapular pores 3 (ex1&ndash;ex3), posttemporal pores 2 (po1&ndash;po2), coronalis pore 1 (cor), lachrymal pores 2 (l1, l3); no infraorbital pores.&lt;/p&gt; &lt;p&gt;Scales ctenoid on sides, cycloid on top of head. Predorsal scales 5 anterior to coronalis pore, 9 posteriorly. Four rows of scales on cheek. Circumpeduncular scales 16. Tubed lateral-line scales absent. Scales in a longitudinal row 28. Scales in transverse row 10.&lt;/p&gt; &lt;p&gt;Dorsal-fin rays XIV+9 (11), XV+8 (3), or XV+9(2). Anal-fin rays III+8 (14) or III+9 (3). Pectoral-fin rays 12 (11) or 13 (6). Pelvic-fin rays I+5 (17). Principal caudal-fin rays 7+7 (14) or 7+6 (3), with 4&ndash;5 dorsal and ventral procurrent rays.&lt;/p&gt; &lt;p&gt;Interradial membranes of spinous dorsal fin projecting as short fin lappets that do not extend much beyond tips of spines. Soft dorsal and anal fins with rounded tips, extending to base of caudal fin only. Pectoral fin reaching to vertical through base of sixth or seventh dorsal-fin spine. Pelvic fin pointed in males, rounded in females, reaching posteriorly to anus or anterior base of anal fin. Caudal fin rounded to subtruncate.&lt;/p&gt; &lt;p&gt;Vertebrae 14+14=28 (1) or 14+15=29 (5).&lt;/p&gt; &lt;p&gt; &lt;b&gt;Coloration.&lt;/b&gt; In preservative (Fig. 1), background colour beige to light brown with several dark brownish to black marks. Preorbital stripe dark brown, well developed in males, less conspicuous in females. Dark brown horizontal suborbital stripe extending from angle of jaw to vertical through posterior margin of orbit, less developed in females. Postorbital stripe dark brown, extending from upper posterior margin of eye towards nape beginning at 12 h to 13 h and running obliquely. Large dark brown blotch present on opercle, well developed in males but fainter in females, extended posterodorsally towards supracleithral area. No cleithral spot. Series of irregular dark marks along back reaching only two scale rows down. Base of each scale on sides of body with a darker area of denser melanophores forming narrow irregular zigzag-shaped bars on caudal peduncle. Prominent caudal blotch present separated from caudal peduncle bars by much lighter anterior halo-like area. Pectoral fin mostly translucent with few melanophores along fin rays and on fin membrane, all other fins dusky. Dorsal-fin and anal-fin membranes in spinous portions with dense aggregations of melanophores, less densely developed on soft fin membranes. Caudal fin with similar densities of melanophores on both fin rays and interradial membranes.&lt;/p&gt; &lt;p&gt;In life (Fig. 2), background colour yellowish beige. Supraorbital and suborbital stripes prominent. Opercle with golden green iridescense covering opercular blotch, but supracleithral extension of blotch prominent. A number of dark brown scales distributed irregularly on nape, along base of dorsal fin along and on side of body. Caudal blotch not always conspicuous. All fins except pectoral fin with a bluish-gray hue.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Distribution&lt;/b&gt;. &lt;i&gt;Dario urops&lt;/i&gt; has been collected so far only from a small stream of the Barapole tributary of Valapattanam River in southern Karnataka (Fig. 3) and from an unspecified location in Wyanad. The Valapattanam is a westward drainage that flows into the Arabian Sea, while the district of Wyanad lies within the Cauvery basin, which drains eastward into the Bay of Bengal.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Etymology&lt;/b&gt;. The species name &lt;i&gt;urops&lt;/i&gt; is derived from the Greek &omicron;&upsi;&rho;ά, tail and ὄ&psi;, eye and refers to the conspicuous eye spot on the caudal peduncle. A noun in apposition.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Remarks&lt;/b&gt;. The unnamed stream in southern Karnataka from which &lt;i&gt;D. urops&lt;/i&gt; was collected is a small clear water stream, up to 10 m wide and 2 m deep, with a bottom formed of a mixture of sand and mud and larger boulders (Fig. 4). Large stands of the aquatic plant &lt;i&gt;Lagenandra&lt;/i&gt; were growing out of the water. &lt;i&gt;Dario urops&lt;/i&gt; was collected mostly from among bundles of tree roots hanging into the water along the edges of the stream and from thicker layers of leaf litter that had accumulated in low current depressions of the stream.&lt;/p&gt;Published as part of &lt;i&gt;Britz, Ralf, Ali, Anvar &amp; Philip, Siby, 2012, Dario urops, a new species of badid fish from the Western Ghats, southern India (Teleostei: Percomorpha: Badidae), pp. 63-68 in Zootaxa 3348&lt;/i&gt; on pages 64-67, DOI: &lt;a href="http://zenodo.org/record/209965"&gt;10.5281/zenodo.209965&lt;/a&gt