# Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria

## TL;DR

This study uses a new dugong genome to uncover genetic adaptations for aquatic life in sirenians and finds evidence of a genetic split in Australian populations.

## Contribution

The study identifies molecular adaptations and gene losses in sirenians linked to aquatic life and provides insights into population divergence in Australian dugongs.

## Key findings

- Sirenian genomes show adaptations in circadian clock and iodide transport genes linked to aquatic herbivory.
- Genetic evidence suggests a population split in Australian dugongs around 10.7 thousand years ago.
- Loss of KCNK18 gene may be linked to cold stress syndrome in sirenians.

## Abstract

Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.

Sirenians are aquatic mammals that originated in Africa ~60 million years ago. Using comparative genomics of a new dugong genome, this study finds genetic adaptations shared by extant sirenians and assessed the diversity of dugongs in Australian waters and the functionally extinct Okinawan dugong.