Phylogeny of the hillstream loach genus Mesonoemacheilus reveals widespread diversification through ancient drainage connections in the Western Ghats Biodiversity Hotspot

Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila

The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.

Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification

The mitogenome of an endemic catfish Clarias camerunensis was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accommodates 28 genes, whereas the light strand is constituted by ND6 and eight transfer RNA (tRNA) genes. The C. camerunensis mitochondrial genome is AT biased (56.89%), as showcased in other Clarias species. The comparative analyses revealed that most of the Clarias species have 6 overlapping and 11 intergenic spacer regions. Most of the PCGs were initiated and terminated with the ATG start codon and TAA stop codon, respectively. The tRNAs of C. camerunensis folded into the distinctive cloverleaf secondary structure, except trnS1. The placement of the conserved domains in the control region was similar in all the Clarias species with highly variable nucleotides in CSB-I. Both maximum likelihood and Bayesian-based matrilineal phylogenies distinctly separated all Clarias species into five clades on the basis of their known distributions (South China, Sundaland, Indochina, India, and Africa). The TimeTree analysis revealed that the two major clades (Indo-Africa and Asia) of Clarias species might have diverged during the Paleogene (≈28.66 MYA). Our findings revealed the separation of Indian species (C. dussumieri) and African species (C. camerunensis and Clarias gariepinus) took place during the Paleogene, as well as the South Chinese species (Clarias fuscus) and Sundaland species (Clarias batrachus) splits from the Indochinese species (Clarias macrocephalus) during the Neogene through independent colonization. This pattern of biotic relationships highlights the influence of topography and geological events in determining the evolutionary history of Clarias species. The enrichment of mitogenomic data and multiple nuclear loci from their native range or type locality will confirm the true diversification of Clarias species in African and Asian countries.

Endemicity and radiation in waterfalls of the Western Ghats: The genus Cremnoconchus (Gastropoda: Littorinidae)

Snails of the genus Cremnoconchus - the only freshwater members of the gastropod family Littorinidae - are endemic to the spray zones of numerous waterfalls in the Western Ghats of India. Cremnoconchus consists of nine described and possibly numerous undescribed species as many of these appear to be restricted to specific waterfalls. This is the first attempt at resolving the relationships between the various species in this genus and establishing its monophyly in the family. Further, we also undertake species delimitation analysis to characterize cryptic diversity in this group. Phylogenetic analyses based on nuclear and mitochondrial genes support the monophyly of Cremnoconchus within the family. A fossil-calibrated Bayesian time tree suggests that this freshwater lineage diverged from its marine counterparts around 90.40 million years ago. The separation of Cremnoconchus from its marine ancestors might have been facilitated by the break-up of Gondwana or fluctuating sea levels during this period. Species delimitation analysis retrieved 12 potentially undescribed species in this group. These species formed two distinct clades in the phylogeny, one largely confined to the northern Western Ghats and the other to the central Western Ghats. Species belonging to the northern and central Western Ghats seem to have separated around 56.11 mya, i.e. after the northern Western Ghats were formed. Additionally, spatial isolation due to the patchiness of suitable habitats (waterfalls) and low mobility might have facilitated their diversification.

Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae)

The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.

Ichthyofaunal diversity in the upper-catchment of Kabini River in Wayanad part of Western Ghats, India

We present here a detailed account of the diversity, distribution, threats, and conservation of freshwater fishes in the upper-catchment of the Kabini River in the Wayanad part of the Western Ghats Biodiversity Hotspot.  A total of 136 fish species belonging to 13 orders, 29 families, and 69 genera were recorded.  Order Cypriniformes dominated with five families, 36 genera, and 84 species, and Cyprinidae was the dominant family represented by 51 species within 21 genera.  The true diversity of ichthyofauna in this catchment, is still unclear and requires further exploration and taxonomic studies.  At least 44 species recorded during the study are endemic to the Western Ghats, of which 16 are endemic to the Cauvery River System and two species endemic to the Kabini Catchment.  A total of 20 non-native fish species were recorded from the study area, of which six species were inter-basin (within India) transplants and 14 species were exotic.  Among the native species with confirmed identity, four are Critically Endangered (CR) and nine Endangered (EN) as per the IUCN Red List of Threatened Species.  As a part of the study, we also extend the distribution ranges of Opsarius malabaricus, Laubuka trevori, Opsarius bendelisis, Puntius cauveriensis, Oreichthys coorgensis, Mesonoemacheilus pambarensis, Hypselobarbus curmuca, and Pseudosphromenus cupanus to the Kabini Catchment.  The presence of four species, which were earlier considered to be endemic to the west flowing rivers of the Western Ghats, viz, Laubuka fasciata, Hypselobarbus kurali, Sahyadria denisonii, and Puntius mahecola, in an east flowing stream is reported and discussed.  Deforestation and removal of riparian vegetation, pollution, stream channel modification, sand mining, destructive fishing practices, dams and other impoundments, monsoon fishing, and non-native species are the major threats to freshwater fishes in the region.  Strategies for the conservation of aquatic ecosystems in the Kabini Catchment are discussed.

Genetic structure and demographic history of Indirana semipalmata, an endemic frog species of the Western Ghats, India

The evolutionary potential of a species mainly depends on the level of genetic variation in their populations. Maintenance of gene variation enables populations to adapt more quickly to environmental changes. The geographical gaps also influence the distribution and evolutionary history of many mountain frogs in the world. Hence, a sound knowledge in population genetic structure of a species will help understand its population dynamics and develop conservation strategies. In the context of facing threats to the amphibian fauna of Western Ghats due to habitat loss, we used both mitochondrial and nuclear DNA markers to investigate the genetic structure of an endemic frog species of the Western Ghats (Indirana semipalmata) with restricted distribution. The present study showed the importance of mountain gaps in shaping the species' structuring in the Western Ghats. Though a high genetic diversity was observed for the species when considering a single unit in the southern Western Ghats, the restricted gene flow on/between either side of the Shencottah gap with genetic clustering of the sampled populations may warrant a unique management plan for the species. The habitat fragmentation of the Western Ghats through anthropogenic activities may result in severe setbacks to the survival of the species in the future.