Genes & Genomics

, Volume 41, Issue 12, pp 1417–1430 | Cite as

Distinct evolution of toll-like receptor signaling pathway genes in cetaceans

  • Ran Tian
  • Inge Seim
  • Zepeng Zhang
  • Ying Yang
  • Wenhua Ren
  • Shixia XuEmail author
  • Guang YangEmail author
Research Article



The relatively rapid spread and diversity of marine pathogens posed an initial and ongoing challenge for cetaceans (whales, dolphins, and porpoises), descendants of terrestrial mammals that transitioned from land to sea approximately 56 million years ago. Toll-like receptors (TLRs) play important roles in regulating immunity against pathogen infections by detecting specific molecular patterns and activating a wide range of downstream signaling pathways. The ever-increasing catalogue of mammalian genomes offers unprecedented opportunities to reveal genetic changes associated with evolutionary and ecological processes.


This study aimed to explore the molecular evolution of TLR signaling pathway genes in cetaceans.


Genes involved in the TLR signaling pathway were retrieved by BLAST searches using human coding sequences as queries. We tested each gene for positive selection along the cetacean branches using PAML and Hyphy. Physicochemical property changes of amino acids at all positively selected residues were assessed by TreeSAAP and visualized with WebLogo. Bovine and dolphin TLR4 was assessed using human embryonic kidney cell line HEK293, which lacks TLR4 and its co-receptor MD-2.


We demonstrate that eight TLR signaling pathway genes are under positive selection in cetaceans. These include key genes in the response to Gram-negative bacteria: TLR4, CD14, and LY96 (MD-2). Moreover, 41 out of 65 positively selected sites were inferred to harbor substitution that dramatically changes the physicochemical properties of amino acids, with most of them situated in or adjacent to functional regions. We also found strong evidence that positive selection occurred in the lineage of the Yangtze finless porpoise, likely reflecting relatively recent adaptions to a freshwater milieu. Species-specific differences in TLR4 response were observed between cetacean and terrestrial species. Cetacean TLR4 was significantly less responsive to lipopolysaccharides from a terrestrial E. coli strain, possibly a reflection of the arms race of host–pathogen co-evolution faced by cetaceans in an aquatic environment.


This study provides further impetus for studies on the evolution and function of the cetacean immune system.


Toll-like receptor signaling pathway TLR4 Cetaceans Molecular evolution Positive selection Ligand responsiveness 



This work was financially supported by the National Key Program of Research and Development, Ministry of Science and Technology of China (Grant no. 2016YFC0503200 to G.Y. and S.X.), the Key Project of the National Natural Science Foundation of China (NSFC) (Grant no. 31630071 to G.Y.), the National Natural Science Foundation of China (NSFC) (Grant nos. 31570379 and 31772448 to S.X; Grant no. 31872219 to W.R.), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the China Postdoctoral Science Foundation (Grant no. 2018M642278 to R.T.).

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

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The authors consent to publish and copyright transfer.

Supplementary material

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Supplementary material 1 (PDF 467 kb)
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Supplementary material 2 (XLSX 13 kb)
13258_2019_861_MOESM3_ESM.docx (23 kb)
Supplementary material 3 (DOCX 23 kb)


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Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  1. 1.Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
  2. 2.Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
  3. 3.Comparative and Endocrine Biology Laboratory, Translational Research Institute–Institute of Health and Biomedical Innovation, School of Biomedical SciencesQueensland University of TechnologyBrisbaneAustralia

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