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

TL;DR

This paper presents the genome of the endangered Indus River dolphin, revealing low genetic diversity and adaptations to freshwater life.

Contribution

The study provides the first genome assembly of the Indus River dolphin and identifies genes linked to freshwater adaptation and low heterozygosity.

Findings

The Indus River dolphin has very low heterozygosity (0.0218%) due to historical bottlenecks and inbreeding.

Genes related to skin adaptations and immune responses show signs of positive selection, suggesting freshwater adaptation.

The species diverged from other dolphins around 31.2 million years ago, placing it in a more basal evolutionary position.

Abstract

The Indus River dolphin (
Platanista minor
) is a highly endangered freshwater dolphin endemic to the Indus River system of the Indian subcontinent. We reported a de novo 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
Lipotes vexillifer
). 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%).

The Indus River dolphin (
Platanista minor
) is a highly endangered freshwater dolphin endemic to the Indus River system of the Indian subcontinent. We reported a relatively high‐quality de novo genome assembly of it. We revealed the low heterozygosity as well as the molecular mechanisms underlying its adaptation and evolution.

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