Low Heterozygosity and Historical Bottleneck Effect Depicted From the Genome Assembly of the Indus River Dolphin ().

The Indus River dolphin () is a highly endangered freshwater dolphin endemic to the Indus River system of the Indian subcontinent. We reported a assembly and characterization of the draft genome of the Indus River dolphin by using Illumina short-read sequencing technology. Based on this, for the first time, we conducted the comparative genomics study and identified a selection of genes and gene families that have undergone significant positive selection and expansion or contraction, indicating potential molecular mechanisms associated with freshwater adaptation, such as specialized skin features and their derivatives (e.g., hair loss) and immune adaptations. Additionally, this study estimated that the Indus River dolphin diverged nearly 31.2 million years ago from the most recent common ancestor of Delphinidae and Lipotidae, placing it in a more basal position to other freshwater dolphins (e.g., the baiji ). It was suggested that the combined effects of the natural historical bottleneck effect around 40-20 kiloyears ago and anthropogenic activities were the driving factors of inbreeding for this species with very low heterozygosity (0.0218%).