Genomic Signatures of Ancient and Recent Population Decline in the Critically Endangered Gharial (gavialis Gangeticus)

The gharial (Gavialis gangeticus) is a freshwater crocodylian endemic to the Indian subcontinent that has experienced ancient and recent catastrophic declines in population size. Conservation interventions initiated in the mid-1970s have enabled partial recovery of the species. Yet, how ancient and recent demographic declines have shaped contemporary genomic diversity in gharial remains unknown. Here, we present the first genome-wide analysis of the gharial using a single high-coverage whole-genome sequence and ddRAD data from 21 individuals sampled across five nesting sites along the Chambal River. Our results reveal extremely low genomic diversity in the largest gharial population, with Watterson’s θ = 0.0008 ± 0.0001 (mean ± SD) and Nucleotide diversity = 0.00036 ± 0.00005, both substantially lower than those reported for other extant crocodylians. Analyses of population genomic structure indicated weak, partially resolved structuring, with individuals from Radi forming a distinct group, whereas individuals from other sites showed limited spatial structuring. Demographic reconstructions revealed declines in effective population size across multiple timescales, including an ancient decline occurring 10,000 years ago and a more recent severe decline within the last 250 years. Consistent with this recent decline, long ROH suggest that recent close inbreeding ( 4 generations), rather than ancient demographic history alone, is the primary contributor to contemporary genome-wide homozygosity. Overall, these findings reflect both deep-time demographic constraints and ongoing genetic erosion in gharial, providing a critical foundation for genomics-informed conservation planning.