Comparative genomics and population resequencing elucidate streamlined immune adaptations to aquatic environments in cetaceans

Dongjiao Liu; Jun Liu; Peiyu Xie; Liyuan Zhao; Hui Kang; Qianhui Zeng; Songhai Li; Xianyan Wang; Peijun Zhang

doi:10.59717/j.xinn-life.2026.100245

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Comparative genomics and population resequencing elucidate streamlined immune adaptations to aquatic environments in cetaceans

1.
Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
2.
University of Chinese Academy of Sciences, Beijing 101408, China
3.
Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen 361005, China
4.
Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen 361005, China
5.
These authors contributed equally to this work

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Corresponding authors: pjzhang@idsse.ac.cn (P.Z.); wangxianyan@tio.org.cn (X.W.)
Received Date: January 17, 2026

Accepted Date: March 11, 2026

Published Online: March 30, 2026

The Innovation Life https://doi.org/10.59717/j.xinn-life.2026.100245 | Cite this article

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PUBLIC SUMMARY

PUBLIC SUMMARY
1. Cetaceans possess streamlined MHC regions with reduced gene content and repetitive elements.
  
  Cetaceans maintain conserved MHC structural frameworks.
  
  Class II genes mediated ancestral cetaceans’ aquatic transition, Class I genes drove species diversity.
  
  Cetaceans exhibit aquatic adaptations, including olfactory reduction and metabolic downregulation.
  
  Sousa chinensis exhibit specialized pathogen defense mechanisms and attenuated reproductive gene sets.

ABSTRACT

ABSTRACT

Cetaceans have evolved numerous adaptations to thrive in aquatic environments. In this study, we identified and analyzed the entire MHC regions across cetacean species/populations and their terrestrial counterparts to elucidate immune adaptation strategies to aquatic life. Results reveal cetaceans have evolved a structurally streamlined MHC architecture, marked by reduced repetitive sequences (e.g., loss of BovB, decreased LTRs) and compacted gene content (class II and extended class I regions). Contracted gene sets were involved in olfactory transduction and reproduction. Class II genes were found critical for the initial aquatic transition in ancestral cetaceans, whereas class I genes facilitated subsequent habitat specialization and diversification. Strong signatures of positive selection were detected at both species level (e.g., in DR, TRIM, LTB, MOG genes) and population level (e.g., in DR, TRIM, BTN, DQ genes) within S. chinensis. These findings highlight the pivotal role of MHC-driven adaptations in enabling cetaceans to colonize and thrive in diverse aquatic niches. Collectively, our study provides key insights into the specialized immune evolution underpinning cetacean success in marine environments.
- cetaceans /
- major histocompatibility complex /
- immune adaptation /
- population genetics /
- comparative genomics

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Liu D., Liu J., Xie P., et al. (2026). Comparative genomics and population resequencing elucidate streamlined immune adaptations to aquatic environments in cetaceans. The Innovation Life 4:100245. https://doi.org/10.59717/j.xinn-life.2026.100245

Liu D., Liu J., Xie P., et al. (2026). Comparative genomics and population resequencing elucidate streamlined immune adaptations to aquatic environments in cetaceans. The Innovation Life 4:100245. https://doi.org/10.59717/j.xinn-life.2026.100245

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Comparative genomics and population resequencing elucidate streamlined immune adaptations to aquatic environments in cetaceans

GRAPHICAL ABSTRACT

PUBLIC SUMMARY

ABSTRACT