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The gharial (Gavialis gangeticus Gmelin) is a fish-eating specialist crocodylian, endemic to south Asia, and critically endangered in its few remaining wild localities. A secondary gharial population resides in riverine-reservoir habitat adjacent to the Nepal border, within the Katerniaghat Wildlife Sanctuary (KWS), and nests along a 10 km riverbank of the Girwa River. A natural channel shift in the mainstream Karnali River (upstream in Nepal) has reduced seasonal flow in the Girwa stretch where gharials nest, coincident with a gradual loss of nest sites, which in turn was related to an overall shift to woody vegetation at these sites. To understand how these changes in riparian vegetation on riverbanks were related to gharial nesting, we sampled vegetation at these sites from 2017 to 2019, and derived an Enhanced Vegetation Index (EVI) from LANDSAT 8 satellite data to quantify riverside vegetation from 1988 through 2019. We found that sampled sites transitioned to woody cover, the number of nesting sites declined, and the number of nests were reduced by > 40%. At these sites, after the channel shift, woody vegetation replaced open sites that predominated prior to the channel shift. Our findings indicate that the lack of open riverbanks and the increase in woody vegetation at potential nesting sites threatens the reproductive success of the KWS gharial population. This population persists today in a regulated river ecosystem, and nests in an altered riparian habitat which appears to be increasingly unsuitable for the continued successful recruitment of breeding adults. This second-ranking, critically endangered remnant population may have incurred an "extinction debt" by living in a reservoir that will lead to its eventual extirpation.

Microsatellite DNA is among the several molecular tools used for determining genetic variability and inbreeding depression in threatened populations. It has been used extensively for population genetics studies in conservation of crocodilians. Even though single nucleotide polymorphisms have higher precision compared to microsatellite DNA markers, microsatellites offer a cost advantage which is particularly important to researchers in the global south. Here, we review the role of microsatellite DNA as a conservation tool in crocodilians. Employing appropriate keywords in three online databases, we studied 78 publications, where microsatellite DNA had been used to study crocodilian species. We found that 504 species-specific markers were designed for 13, out of a total of 24 crocodilian taxa. Genus Crocodylus had the highest number of species-specific markers and was the most studied taxa using microsatellites. Moreover, microsatellite markers developed for C. porosus were successful in cross amplification of microsatellite markers in 19 other crocodilian species. Microsatellite based studies had highest focus on analyses of multiple populations of a single species. Based on our review of microsatellite based studies on populations of crocodilian species, we recommend that microsatellite DNA markers are an effective conservation tool that can provide critical information on population structures of threatened crocodilian species.

Gharial (Gavialis gangeticus) is a critically endangered fresh water crocodile endemic to the Indian subcontinent. The species has suffered > 95% decline in population and habitat size. A small population of gharials comprising of 50 breeding adults is resident in a 20 Km stretch of the River Girwa in Katerniaghat wildlife sanctuary, India. Gharials in this 20 Km stretch have been genetically isolated since 1976 by a barrage that functions as a barrier to gene flow. A captive rear and release program has been initiated since 1979 under Project Crocodile for restocking declining wild gharial populations. Thousands of gharial eggs were collected from gharial populations at Girwa and Chambal Rivers. Hatchlings from the collected eggs were captive reared at a common location in Kukrail Gharial Centre, India and released back to multiple gharial populations including the isolated population at Girwa. This restocking programme was not preceded by a genetic screening of captive animals or wild populations to identify genetic diversity and genetic structure of both captive and wild animals. In this study we investigate whether release of captive reared gharials into the resident population at Girwa River has prevented genetic isolation caused due to barriers imposed by the barrage. Using a combination of empirical analysis using microsatellite markers and a systematic review of data from previous workers on molecular characterization of gharial populations, we analysed genetic differentiation in gharial populations at Girwa and Chambal. We found similar genetic variability in gharial populations of Girwa and Chambal. There was low inter population genetic differentiation and evidences of genetic migration between the two populations. Our findings indicate that anthropogenic intervention via release of captive animals has compensated for the genetic isolation in Girwa population caused by the barrage.