Taxonomic reasoning: The case of giant wrinkled frog

A recent issue of Current Science carried a correspondence entitled ‘Taxonomic vandalism: The case of the giant wrinkled frog’ by Ranjit Daniels1. The author is critical of a communication authored by us

Nyctibatrachus karnatakaensis nom.nov., a replacement name for the giant wrinkled frog from the Western Ghats

Amphibian research in the Western Ghats looks promising, as 21 new species have been described since 2000. Moreover, it has also provided better insights into the aspects of biogeography, Gondwana relicts and endemism. On the other hand, lack of proper systematics is leading to ambiguities and chaos in amphibian taxonomy. We are presenting a case of a recently described species, Nyctibatrachus hussaini, as an invalid name due to lack of typification and deposition of type specimen in any museum. Here we propose a replacement name for the species – Nyctibatrachus karnatakaensis nom. nov., – as well as holotype designation and vouchering the same in a museum

Lineage delimitation and description of nine new species of bush frogs (Anura: Raorchestes, Rhacophoridae) from the Western Ghats Escarpment

Bush frogs of the genus Raorchestes are distributed mainly in the Western Ghats Escarpment of Peninsular India. The inventory of species in this genus is incomplete and there is ambiguity in the systematic status of species recognized by morphological criteria. To address the dual problem of taxon sampling and systematic uncertainty in bush frogs, we used a large-scale spatial sampling design, explicitly incorporating the geographic and ecological heterogeneity of the Western Ghats. We then used a hierarchical multi-criteria approach by combining mitochondrial phylogeny, genetic distance, geographic range, morphology and advertisement call to delimit bush frog lineages. Our analyses revealed the existence of a large number of new lineages with varying levels of genetic divergence. Here, we provide diagnoses and descriptions for nine lineages that exhibit divergence across multiple axes. The discovery of new lineages that exhibit high divergence across wide ranges of elevation and across the major massifs highlights the large gaps in historical sampling. These discoveries underscore the significance of addressing inadequate knowledge of species distribution, namely the ``Wallacean shortfall'', in addressing the problem of taxon sampling and unknown diversity in tropical hotspots. A biogeographically informed sampling and analytical approach was critical in detecting and delineating lineages in a consistent manner across the genus. Through increased taxon sampling, we were also able to discern a number of well-supported sub-clades that were either unresolved or absent in earlier phylogenetic reconstructions and identify a number of shallow divergent lineages which require further examination for assessment of their taxonomic status

A new species of Philautus Gistel (Amphibia: Anura: Rhacophoridae) from southern Western Ghats, India

A new species of the oriental shrub frog genus Philautus is described from Kakkayam Reserve Forest of Calicut district, Kerala state, in the southern Western Ghats. This species is distinguished from congeners by the combination of characters such as body small, elongate, squat and flat; head arched, wider than long; snout short rounded, equal or sub equal to diameter of eye; canthus rostralis rounded; tympanum indistinct but visible; eyes protruding, pupil with striking golden yellow dentition like marks; belly granular; vocal sac unpigmented; fleshy brown to cream yellow dorsum with two distinct golden yellow lateral bands bordered by dark brown from upper eyelid to the posterior part of flanks. A description of the advertisement calls and ecology and natural history notes are also provided for the new species which so far is only known from the type locality

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Not AvailableEven though cultivated rice is highly sensitive to salinity, significant variability exists in the primary and secondary gene-pool of rice with respect to traits of salinity tolerance. Breeding salinity tolerance rice varieties is imperative due to climate change and increasing rice demand for global population. A meta-analysis of plethora of genomic data and published literature available on various genes/factors associated with response to rice salinity and tolerance can be used to enlist selected candidates genes affecting salinity. Such genes can be utilized to identify potential candidate salinity resistance genes from donor rice genotypes and facilitate their transfer to high yielding varieties of rice through marker-assisted breeding. This approach has tremendous advantage over transgenic approach as no bio-safety or regulatory issues are involved in exploiting the variability. Meta-analyses were performed on three datasets viz., rice microarray data of 166 series comprising of 2586 samples, 1228 published research literature in the last one and half decades and RNA-Seq data of 454 and Illumina from Sequence Retrieval Archive (SRA) at NCBI. Among microarray dataset, six salinity related series were finally selected and multi experiment analysis revealed 2289 differentially expressed genes belonging to 44 gene families. Out of these, 13 families viz., AP2-EREBP, AUX/IAA, bZIP, C2H2, bHLH, C3H, HB, HSF, MYB, MYB-related, NAC, Tify and WRKY were selected. Applying various parameters on the published literature data, 13 genes were selected, of which five were common to the different microarray datasets. From RNA-Seq data, total of 751 differentially expressed genes were obtained from 21 gene families, out of which 11 genes were common with those obtained from microarray data and five genes, viz., AP2-EREBP/DREB, MYB, HSF, bZIP and NAC were common to all the three data sets. Based on the results obtained, a total of 31 meta-analyzed genes have been selected and recommended for use in genetic improvement programs aimed at salinity resistance in rice. The meta-analysis of microarray, RNA-Seq and published literature has been successfully used to select 31 best salinity tolerance associated genes which can be exploited by candidate gene approach for targeted introgression through marker assisted breeding. This approach has multi-fold advantages, as it obviates statutory and ecological issues. Such endeavors are more warranted for combating the key abiotic stresses like salinity, whose effects are increasing due to a changing climate.Indian Council of Agricultural Research, New Delhi “Establishment of National Agricultural Bioinformatics Grid In ICAR” (30(68)/2009/Bio-Informatics/NAIP/O&M dated 31st March, 2010

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Not AvailableBlack pepper (Piper nigrum L.; 2n = 52; Piperaceae), the king of spices, is a perennial, trailing woody flowering vine and has global importance with widespread dietary, medicinal, and preservative uses. It is an economically important germplasm cultivated for its fruit and the major cash crop in >30 tropical countries. Crop production is mainly affected by drought stress. The present study deals with the candidate gene identification from drought‐affected black pepper leaf transcriptome generated by Illumina Hiseq2000. It also aims to mine putative molecular markers (namely SSRs, SNPs, and InDels) and generate primers for them. The identification of transcription factors and pathways involved in drought tolerance is also reported here. De novo transcriptome assembly was performed with trinity assembler. In total, 4914 differential expressed genes, 2110 transcriptional factors, 786 domains and 1137 families, 20,124 putative SSR markers, and 259,236 variants were identified. At2g30105 (unidentified gene containing leucine‐rich repeats and ubiquitin‐like domain), serine threonine protein kinase, Mitogen‐activated protein kinase, Nucleotide Binding Site‐Leucine Rich Repeat, Myeloblastosis‐related proteins, basic helix–loop–helix are all found upregulated and are reported to be associated with plant tolerance against drought condition. All these information are catalogued in the Black Pepper Drought Transcriptome Database (BPDRTDb), freely accessible for academic use at http://webtom.cabgrid.res.in/bpdrtdb/. This database is a good foundation for the genetic improvement of pepper plants, breeding programmes, and mapping population of this crop. Putative markers can also be a reliable genomic resource to develop drought‐tolerant variety for better black pepper productivity.Not Availabl