Gharial genomes reveal ancient and recent population decline

The gharial (Gavialis gangeticus), a freshwater crocodylian endemic to the Indian subcontinent, has suffered catastrophic population declines both in the deep past and in recent centuries. A new genomic study, published in BMC Genomic Data, presents the first genome-wide analysis of the Critically Endangered species and shows that its largest surviving population carries extremely low genetic diversity, shaped by demographic collapses on multiple timescales.

The researchers worked with a single high-coverage whole-genome sequence together with ddRAD data from 21 individuals sampled across five nesting sites along the Chambal River. Their measurements revealed exceptionally low genomic diversity in this population: Watterson’s theta was 0.0008 ± 0.0001 (mean ± SD) and nucleotide diversity was 0.00036 ± 0.00005, both substantially lower than values reported for other extant crocodylians.

Analyses of population genomic structure indicated weak, partially resolved structuring among the sampled animals. Individuals from the site known as Radi formed a distinct group, whereas individuals from the other nesting sites showed limited spatial structuring, suggesting that the river’s gharials are not strongly subdivided apart from this one grouping.

Demographic reconstructions uncovered declines in effective population size across multiple timescales. These included an ancient decline occurring roughly 10,000 years ago and a more recent, severe decline within the last approximately 250 years, indicating that the species’ genomic erosion is the product of both deep-time constraints and modern pressures.

Consistent with the recent decline, long runs of homozygosity in the genomes suggest that recent close inbreeding, over roughly the last four generations, rather than ancient demographic history alone, is the primary contributor to contemporary genome-wide homozygosity. Conservation interventions initiated in the mid-1970s have enabled partial recovery of the species, but the findings indicate that ongoing genetic erosion remains a concern. The authors present these results as a critical foundation for genomics-informed conservation planning for the gharial.

Subject of Research: Genome-wide analysis of population decline and low genetic diversity in the Critically Endangered gharial

Article Title: Genomic signatures of ancient and recent population decline in the Critically Endangered gharial (Gavialis gangeticus)

Article References: Sharma, S. P., Hussain, S. A., Ghazi, M. G., Badola, R., & Hussain, S. A. (2026). Genomic signatures of ancient and recent population decline in the Critically Endangered gharial (Gavialis gangeticus). BMC Genomic Data. https://doi.org/10.1186/s12863-026-01483-x

Image Credits: AI Generated

DOI: 10.1186/s12863-026-01483-x

Keywords: gharial, Gavialis gangeticus, genomics, population decline, genetic diversity, inbreeding, Chambal River, crocodylian, conservation, runs of homozygosity, India, effective population size