Complete mitogenome of Lepidopygopsis typus, an evolutionarily-distinct, endangered cyprinid fish from the Western Ghats Biodiversity Hotspot: Phylogenetic relationships and implications for conservation.

The mitogenome of Lepidopygopsis typus, an evolutionarily distinct, endangered, cyprinid fish from the Western Ghats Biodiversity Hotspot, was characterized. Total length of the mitogenome was 16,729 bp, and comprised of 13 protein coding, 22 tRNA and two rRNA genes. Thirteen protein coding genes contributed a total nucleotide length of 11,408 bp, which coded for a total of 3794 amino acids and accounting for 68.2 % of the mitogenome. A maximum likelihood phylogenetic tree based on mitogenomes of members of cyprinid subfamilies Torinae, Schizothoracinae and Schizopygopsinae, recovered L. typus in a well-resolved clade of Torinae with members of the Western Ghats endemic genus Hypselobarbus as sister taxa. Selection analysis suggested that the branch of L. typus and Hypselobarbus spp. was under intensified selection with reference to other members of Torinae. There were 19 codons under diversifying selection in L. typus, which could be the result of positive selection for adapting to high-altitude, upstream tributaries of Periyar River, where the species has a restricted distribution. With respect to Hypselobarbus spp., L. typus was under relaxed selection with about 68 % of codons experiencing neutral evolution. Restricted distribution, low population size and relaxation in selection can likely trigger extinction in L. typus, and therefore urgent conservation and monitoring plans are required to secure the future of this evolutionary distinct, and globally endangered species.

Biogeography and evolutionary history of Puntius sensu lato (Teleostei: Cyprinidae) in Sri Lanka.

Sri Lanka's biota is derived largely from Southeast Asian lineages which immigrated via India following its early-Eocene contact with Laurasia. The island is now separated from southeastern India by the 30 km wide Palk Strait which, during sea-level low-stands, was bridged by the 140 km-wide Palk Isthmus. Consequently, biotic ingress and egress were mediated largely by the climate of the isthmus. Because of their dependence on perennial aquatic habitats, freshwater fish are useful models for biogeographic studies. Here we investigate the timing and dynamics of the colonization of-and diversification on-Sri Lanka by a group of four closely-related genera of cyprinid fishes (Puntius sensu lato). We construct a molecular phylogeny based on two mitochondrial and two nuclear gene markers, conduct divergence timing analyses and ancestral-range estimations to infer historical biogeography, and use haplotype networks to discern phylogeographic patterns. The origin of Puntius s.l. is dated to ~ 20 Ma. The source of diversification of Puntius s.l. is Sri Lanka-Peninsular India. Species confined to perhumid rainforests show strong phylogeographic structure, while habitat generalists show little or no such structure. Ancestral range estimations for Plesiopuntius bimaculatus and Puntius dorsalis support an 'Out of Sri Lanka' scenario. Sri Lankan Puntius s.l. derive from multiple migrations across the Palk Isthmus between the early Miocene and the late Pleistocene. Species dependent on an aseasonal climate survived aridification in rainforest refugia in the island's perhumid southwest and went on to recolonize the island and even southern India when pluvial conditions resumed. Our results support an historical extinction of Sri Lanka's montane aquatic fauna, followed by a recent partial recolonization of the highlands, showing also that headwater stream capture facilitated dispersal across basin boundaries.

A new diminutive subterranean eel loach species of the genus Pangio (Teleostei: Cobitidae) from Southern India.

A second subterranean species of Pangio is described from an old dug-out well in Kerala, Southern India. The new species, Pangio pathala is unique within the genus in possessing the highest number (27) of caudal vertebrae. Pangio pathala is distinguished from P. bhujia, the only subterranean Pangio species known so far, in having four pectoral-fin rays (vs. three), five anal-fin rays (vs. six), 67 vertebrae (40 abdominal and 27 caudal vertebrae) (vs. 6263), and a raw genetic distance of 8.18.7% in the mitochondrial cytochrome oxidase subunit 1 gene. This paper also provides an additional record of Pangio bhujia from a location 40 km south of the type locality.

Contracaecum nematode parasites in hillstream loaches of the Western Ghats, India.

Nematode parasites of the family Anisakidae infect definitive hosts, such as fish-eating birds and mammals, through primary intermediate hosts like copepods and secondary intermediate hosts like fishes. However, consumption of raw or undercooked fish can lead to nematode infection called anisakidosis in humans. We observed the presence of nematode infection in hillstream loaches of families Cobitidae and Nemacheilidae available for human consumption in the local markets in the northern parts of Western Ghats, India. Scanning electron micrograph and genetic identification employing mitochondrial cytochrome oxidase subunit II, identified the nematode to the genus Contracaecum. Histology of infected host revealed the presence of the parasite in muscles. Antioxidant enzyme analysis of host liver suggested that infection leads to oxidative stress in the fish. We suspect that a gradual increase in parasite infection of the loaches in the last decade could be attributed to various anthropogenic stressors that are altering riverine habitats. Since loaches are consumed by tribal people who often prepare the fish without degutting and possibly undercooked, there is a potential threat of human infection.

Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India.

The phylogenetic diversity of cultivable actinobacteria isolated from sponges (Haliclona spp.) and associated intertidal zone environments along the northern parts of the western coast of India were studied using 16S rRNA gene sequences. A subset of randomly selected actinobacterial cultures were screened for three activities, namely predatory behaviour, antibacterial activity and enzyme inhibition. We recovered 237 isolates from the phylum Actinobacteria belonging to 19 families and 28 genera, which could be attributed to 95 putative species using maximum-likelihood partition and 100 putative species using Bayesian partition in Poisson tree processes. Although the trends in the discovery of actinobacterial genera isolated from sponges were consistent with previous studies from different study areas, we provide the first report of nine actinobacterial species from sponges. We observed widespread non-obligate epibiotic predatory behaviour in eight actinobacterial genera and we provide the first report of predatory activity in Brevibacterium , Glutamicibacter , Micromonospora , Nocardiopsis , Rhodococcus and Rothia . Sponge-associated actinobacteria showed significantly more predatory behaviour than environmental isolates. While antibacterial activity by actinobacterial isolates mainly affected Gram-positive target bacteria with little or no effect on Gram-negative bacteria, predation targeted both Gram-positive and Gram-negative prey with equal propensity. Actinobacterial isolates from both sponges and associated environments produced inhibitors of serine proteases and angiotensin-converting enzyme. Predatory behaviour was strongly associated with inhibition of trypsin and chymotrypsin. Our study suggests that the sponges and associated environments of the western coast of India are rich in actinobacterial diversity, with widespread predatory activity, antibacterial activity and production of enzyme inhibitors. Understanding the diversity and associations among various actinobacterial activities - with each other and the source of isolation - can provide new insights into marine microbial ecology and provide opportunities to isolate novel therapeutic agents.

Poor groundwater governance threatens ancient subterranean fishes.

Groundwater depletion is a significant global issue, but its impact on the often-enigmatic subterranean biodiversity and its conservation remains poorly understood. In the Western Ghats biodiversity hotspot of India, poor governance of groundwater resources is threatening its evolutionarily distinct subterranean freshwater fauna, some taxa of which represent Gondwanan relics.

Combining payment for crop damages and reward for productivity to address wildlife conflict.

Conflict caused by wild herbivores damaging crops is an almost universal problem in conservation. We designed and implemented a game-theory-based system for supporting farmers whose crops were being heavily damaged by wild herbivores. In this community-operated system, farmers self-report their production, which is endorsed by neighboring farmers. The average deficit in production is compensated for by a payment that is directly proportional to the average deficit in production of the group and to the individual farmer's productivity. As a result, farmers are compensated for the average damage (support) and rewarded for individual productivity (reward) (i.e., support cum reward [SuR]). The design of the game is such that only honest reporting gives maximum returns. Farmers who underreport receive less payment because the SuR amount is proportionate to their self-reported productivity. The endorsing farmers, in their own self-interest, prevent overreporting. The system involves multiple game situations, the combined result of which is a stable strategy based on honesty and hard work. In 2 villages along the western boundary of Tadoba Andhari Tiger Reserve in central India, we tested the system with 75 farmers over 6 crop seasons. After a few initial attempts to cheat, honesty prevailed throughout the group. Average crop productivity increased 2.5-fold, in spite of damage, owing to increased effort by farmers. Apart from wildlife conflict resolution, the model offers a promising alternative to crop insurance and a potential behavioral green revolution in agriculture.

Combinación entre el Pago por Daños a Cultivos y la Recompensa por Productividad para Abordar el Conflicto con la Fauna Resumen El conflicto causado por herbívoros silvestres que dañan los cultivos es casi un problema universal para la conservación. Diseñamos e implementamos un sistema basado en la teoría de juegos para apoyar a los agricultores cuyos cultivos estuvieran siendo dañados considerablemente por los herbívoros silvestres. En este sistema operado comunitariamente, los agricultores reportan por sí mismos su producción, la cual es endosada por los agricultores vecinos. El déficit promedio en la producción se compensa con un pago que es directamente proporcional al déficit promedio en la producción del grupo y a la productividad individual del agricultor. Como resultado, los agricultores son compensados por el daño promedio (apoyo) y recompensados por la productividad individual (recompensa) (es decir, apoyo con recompensa [SuR]). El diseño del juego es tal que solamente la declaración honesta otorga la máxima ganancia. Los agricultores que declaren menos de lo dañado reciben menor pago porque la cantidad SuR es proporcional a su productividad auto declarada. Los agricultores que los endosan, por interés propio, previenen que haya declaraciones por encima de lo realmente producido. El sistema involucra varias situaciones de juego, cuyo resultado combinado es una estrategia estable basada en la honestidad y el trabajo duro. En dos aldeas ubicadas a lo largo de la frontera occidental de la Reserva de Tigres Tadoba Andhari en el centro de la India, pusimos a prueba este sistema con 75 agricultores durante seis temporadas de cultivo. Después de algunos intentos iniciales por hacer trampa, la honestidad prevaleció en todo el grupo. La productividad promedio de cultivos incrementó 2.5 veces su cantidad inicial a pesar del daño, esto debido al incremento en el esfuerzo de los agricultores. Además de la solución del conflicto con la fauna, el modelo ofrece una alternativa prometedora al aseguramiento de cultivos y una potencial revolución verde en el comportamiento agrícola.

Phylogenetic position and relationships of mountain loaches (Teleostei: Balitoridae) of the Western Ghats as revealed by CO1 sequences.

The teleostean family Balitoridae comprises small-sized freshwater fishes adapted to swift-flowing torrential mountain streams in South and South-East Asia. Little is known about their molecular phylogenetics and evolutionary biogeography, and much of the scientific literature that references them is focused on morphological taxonomy. In this paper, we generate CO1 sequences for the endemic balitorid lineages of the Western Ghats (WG) Hotspot in India, particularly for the endemic genera, Bhavania, Ghatsa and Travancoria. Integration of these data into a phylogeny revealed that the endemic WG genera together form a well-supported monophyletic clade that shows, subject to our limited taxon sampling, a sister-group relationship to the Southeast Asian genus Pseudohomaloptera. Three WG endemic species of the genus Balitora, namely B. chipkali, B. jalpalli and B. laticauda, though morphologically distinct, have low genetic divergence and barcode gap, suggestive of recent speciation. Interestingly, a fourth WG endemic, B. mysorensis, formed a clade with two species of Balitora from Eastern-Himalaya and Indo-Burma. We also show that all available CO1 sequences assigned to WG endemic balitorid genera in GenBank are misidentifications, and provide diagnostic characters for the accurate identification of these taxa in the future.

Indoreonectes telanganaensis, a new species of loach (Teleostei: Nemacheilidae) from the Godavari Basin of India.

A new species of hill-stream loach, Indoreonectes telanganaensis, is described from a seasonal tributary of the Godavari River at Maisamma Loddi, within the Kawal Tiger Reserve, Telangana State, India. The new species is distinguished from its congeners by a combination of characters including caudal peduncle as long as deep; eye large, its diameter about one-fifth head length; pectoral fin as long as head; nasal barbel reaching the middle of the eye; dorsal-fin origin on vertical through pelvic-fin origin; and bars on the lateral side of the body well defined and wide. We also provide multivariate morphometric, and DNA analysis based on the mitochondrial cytochrome b gene sequence to support the distinction of the new species.

Aenigmachannidae, a new family of snakehead fishes (Teleostei: Channoidei) from subterranean waters of South India.

Pronounced organism-wide morphological stasis in evolution has resulted in taxa with unusually high numbers of primitive characters. These 'living fossils' hold a prominent role for our understanding of the diversification of the group in question. Here we provide the first detailed osteological analysis of Aenigmachanna gollum based on high-resolution nano-CT scans and one cleared and stained specimen of this recently described snakehead fish from subterranean waters of Kerala in South India. In addition to a number of derived and unique features, Aenigmachanna has several characters that exhibit putatively primitive conditions not encountered in the family Channidae. Our morphological analysis provides evidence for the phylogenetic position of Aenigmachanna as the sister group to Channidae. Molecular analyses further emphasize the uniqueness of Aenigmachanna and indicate that it is a separate lineage of snakeheads, estimated to have split from its sister group at least 34 or 109 million years ago depending on the fossil calibration employed. This may indicate that Aenigmachanna is a Gondwanan lineage, which has survived break-up of the supercontinent, with India separating from Africa at around 120 mya. The surprising morphological disparity of Aenigmachanna from members of the Channidae lead us to erect a new family of snakehead fishes, Aenigmachannidae, sister group to Channidae, to accommodate these unique snakehead fishes.

Taxonomy and systematics of the 'Maharaja Barbs' (Teleostei: Cyprinidae), with the description of a new genus and species from the Western Ghats, India.

Maharaja Barbs (Teleostei: Cyprinidae), endemic to the high-altitude streams of the northern Western Ghats are currently represented by a single species, Puntius sahyadriensis. Integrative taxonomic analysis of these fishes reveals them to form a distinct clade within the Cyprinidae, for which we propose the name Waikhomia gen. nov. Waikhomia differs from Puntius and other closely related genera by a combination of characters including: barbels absent; last unbranched dorsal-fin ray smooth, with highly segmented apex; total vertebrae 30 (17 abdominal and 13 caudal); post-epiphysial fontanelle absent, frontals elongated, parietals narrow; infraorbital 2-4 large, deep and wide, overlapping cheek and preopercle; opercle not overlapping the interopercle laterally; free uroneural 2 absent; lateral line complete, with 23-25 perforated scales; pelvic fins jet black with tip of fins white; and body coloration consisting of multiple (6-8) spots and blotches on side of body. We also describe a new species of Waikhomia from the west-flowing Kali river system in the northern part of the Western Ghats, India. The new species, Waikhomia hira is distinguished from W. sahyadriensis by a combination of characters including a distinct body coloration, consisting of 7-8 small, rhomboidal spots arranged across the lateral-line scale row; 23--25 perforated lateral line scales; 10 pre-dorsal scales and 2-3 sparsely spaced gill rakers on epibranchial 1. Further, W. hira differs from its sister taxon, W. sahyadriensis, by a raw genetic distance ranging from 4.3-4.9% in partial cytochrome oxidase subunit 1, and 7.0-8.2% in partial cytochrome b genes.

Amazonian invaders in an Asian biodiversity hotspot: Understanding demographics for the management of the armoured sailfin catfish, Pterygoplichthys pardalis in Kerala, India.

Invasion of armoured catfish, Pterygoplichthys spp., is a major threat to global aquatic biodiversity, and developing effective strategies for their control and eradication is both a concern and a research priority. A length-based population assessment of invasive Pterygoplichthys pardalis in southern India, a hotspot for endemic aquatic biodiversity, indicated that rapid growth, high growth performance index and continuous recruitment have aided their successful invasion. Increasing fishing pressure on the adults is not adequate for population management, and only targeting young individuals (<30 cm) will result in overexploitation and population collapse.

Channa rara, a new species of snakehead fish from the Western Ghats region of Maharashtra, India (Teleostei: Labyrinthici: Channidae).

Channa rara, new species, is described from the Jagbudi River in Maharashtra, India. It belongs to the Gachua group and differs from all its members by the possession of one or more ocelli in the posterior part of the dorsal fin in adults (vs. ocelli absent or 1, rarely 2-3 ocelli in juveniles only). It is further distinguished from most species of the C. gachua group by having 6-7 dark concentric bands on the pectoral fins. We review recent descriptions of species of the genus Channa and conclude that C. royi is a synonym of Channa harcourtbutleri, that the diagnosis of C. shingon from C. harcourtbutleri is seriously flawed and that C. torsaensis is not sufficiently diagnosed from C. quinquefasciata. The recently described C. amari is a junior synonym of C. brunnea.

Pangio bhujia, a new, peculiar species of miniature subterranean eel loach lacking dorsal and pelvic fins from India (Teleostei: Cobitidae).

A unique, new species of eel loach, Pangio bhujia, is described from Kerala, India. It is the first species of Pangio to be described from subterranean waters. It possesses several unusual characters including absence of both dorsal and pelvic fins, the presence of only 3 pectoral-fin rays, 6 anal-fin rays and a unique count of 38 precaudal + 24 caudal vertebrae.

The subterranean Aenigmachanna gollum, a new genus and species of snakehead (Teleostei: Channidae) from Kerala, South India.

Aenigmachanna gollum, new genus and species, is described from Kerala, South India. It is the first subterranean species of the family Channidae. It has numerous derived and unique characters, separating it from both the Asian Channa Scopoli and the African Parachanna Teugels Daget. Uniquely among channids, A. gollum has a very slender (maximum body depth only 11.1-11.3% SL), eel-like body (head length 20.8-21.6% SL), large mouth (jaw length 60.4-61.1 % HL), 43-44 anal-fin rays, 83-85 scales in a lateral series, an unusual colour pattern and it lacks pored lateral-line scales on the body and body buoyancy. In addition, it is distinguished by its DNA barcode sequence, which is 15.8-24.2% divergent from other species of the family Channidae. Morphological modifications usually associated with a subterranean life, such as reduction of eyes and enhancement of non-visual senses (taste, smell, mechanosensory systems) are absent in A. gollum. However, it shares with subterranean fishes a slight reduction of its pigmentation in comparison to epigean channids.

Haplotype diversity in medically important red scorpion (Scorpiones: Buthidae: Hottentotta tamulus) from India.

The medically important Indian red scorpion, Hottentotta tamulus, is one of the most poisonous scorpions of Indian subcontinent. We studied the haplotype diversity in eight populations of H. tamulus based on mitochondrial cytochrome oxidase subunit I (COI) partial gene sequence. Analyses revealed 22 haplotypes with a haplotype diversity of 0.941 and nucleotide diversity of 0.023. For the first two codon positions both transition and transversion types of substitutions were equally likely and the test for neutrality was not rejected. However, codon substitution pattern indicated that the gene has experienced purifying selection. Model-based clustering method indicated that the eight populations form three groups that correspond to high, moderate and low rainfall areas, indicating that there is biogeographical separation of haplotypes. Populations from three groups formed distinct clades in maximum likelihood analysis and median joining genetic network and were statistically supported by low within group and high among group variation in analyses of molecular variance. We provide the first account of haplotype diversity in Indian red scorpions and their biogeographical separation.

Demographics of Lagocephalus inermis in the Arabian Sea unveils complex conservation challenges.

The first assessment of the demographics of Lagocephalus inermis, a species associated with pufferfish bites and fishing down the food web in the Arabian Sea, south-west coast of India, was performed based on length structured population dynamics of 1601 individuals caught in commercial fisheries. Analysis revealed that the current level of exploitation is 90% of the predicted exploitation producing maximum relative yield per recruit (Emax ), suggesting high levels of exploitation with potential for significant negative consequences for trophic cascades.

A new syntopic species of small barb from the Western Ghats of India (Teleostei: Cyprinidae).

A new species of the cyprinid genus Pethia is described from the Hiranyakeshi, a tributary of the Krishna River system in the Western Ghats mountain ranges of peninsular India. The new species, Pethia sahit, is syntopic-and shoals together-with Pethia longicauda, a species described recently from the same river. Pethia sahit is distinguished from P. longicauda and its congeners by a combination of characters like, incomplete lateral line with 3-6 pored scales; 19-22 scales in lateral series; 4½ scales between dorsal-fin origin and lateral-line row and 2½ scales between lateral line row and pelvic-fin origin; intercalated scale row originates above and after the 6th scale of the lateral-line scale row; dorsal fin originating behind the pelvic-fin origin; 4+13 abdominal and 12 caudal vertebrae; dorsal, pectoral, pelvic, anal and caudal fins without any bands or spots, deep yellow-orange in color or deep red with a pale tint of orange in mature males; a dark-black vertically elongate humeral spot, overlapping the 4th lateral-line scale, extending over the base of one scale above and below the 4th scale; caudal peduncle spot dark, covering 14th-16th scales in lateral-line scale row. Genetic analysis based on the mitochondrial cytochrome b gene indicates that P. sahit and P. longicauda are not sister taxa. Further, P. sahit has no genetically proximate congener in the Western Ghats region, and differs from known congeners from south and southeast Asia, for which genetic data are available, with genetic distance ranging from 11.8-16.4%.