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Genetic diversity and phylogeography of Chimaera monstrosa (Linnaeus, 1758) in the Mediterranean Sea: insights from COI mitochondrial DNA analysis

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Abstract

Chimaera monstrosa (Linnaeus, 1758) is a deep-water cartilaginous fish classified as Vulnerable globally and Near Threatened in the Mediterranean by the IUCN, yet its population genetic structure remains poorly characterised across much of its range. Here, we report the first mitochondrial cytochrome c oxidase subunit I (COI) sequences of C. monstrosa from Turkish Mediterranean waters, obtained from five specimens collected as bycatch during commercial bottom trawling at 460–550 m depth in İskenderun Bay. These sequences were analysed together with 60 publicly available COI sequences from the Mediterranean Sea and the Atlantic Ocean using maximum likelihood phylogenetic analysis and TCS haplotype network reconstruction. All Turkish specimens clustered within the Mediterranean clade and were distributed across three haplotypes (H1, H2, and H3), showing close affinity with samples from other Mediterranean localities. Across the full dataset of 65 sequences (596 bp), 30 haplotypes were identified, with high haplotype diversity (Hd = 0.909) and low nucleotide diversity (π = 0.00544). AMOVA revealed strong and significant inter-basin structure (ΦST = 0.682, P < 0.001), with Mediterranean and Atlantic haplotypes forming non-overlapping regional clusters. Neutrality tests produced significantly negative Fu’s Fs (− 22.528, P < 0.001), yet the multimodal mismatch distribution does not support simple demographic expansion; these results are best treated as model-dependent summaries given the geographically structured nature of the dataset. The findings support genetic differentiation between Mediterranean and Atlantic populations of C. monstrosa and suggest that these populations merit independent consideration in future conservation assessments.

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Data availability

The newly generated COI sequences of Chimaera monstrosa are available in GenBank under accession numbers PP977571, PX945310, PX945311, PX945312, and PX945313. Publicly available sequences analysed in this study are listed in Supplementary Table S1 with their accession numbers and source information. Additional data generated and/or analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

We thank the fishing vessel “Ismail Baba” and “Ibrahim Kaptan” crews who contributed to providing the sample used in this study.

Funding

This research was supported by the Research Projects Unit of Fırat University (Project No: SUF.26.02).

Author information

Authors and Affiliations

  1. Department of Marine Biology, Fisheries Faculty, Firat University, 23200, Elazig, Turkey

    Nuri Başusta

  2. Department of Aquaculture and Fish Diseases, Fisheries Faculty, Firat University, 23200, Elazig, Turkey

    Naim Saglam

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  1. Nuri Başusta
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  2. Naim Saglam
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NB: Conceptualisation, Data Curation, Formal Analysis, Investigation, Funding Acquisition, Project Administration, Resources, Writing Original Draft, Review and Editing. NS: Conceptualisation, Formal Analysis, Investigation, Methodology, Supervision, Visualisation, Project Administration, Resources, Writing Original Draft, Review and Editing. All authors have read and agreed to the published version of the manuscript

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Naim Saglam.

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Institutional Review Board Statement

This study did not require specific permits, as all biological samples were obtained as incidental bycatch during routine commercial bottom trawling fishing operations. The specimens were collected from significant depths, and due to the physiological stress associated with rapid decompression during retrieval, they did not survive upon being brought aboard. This research adheres to ethical guidelines by utilising deceased organisms, avoiding intentional harm or additional impact on marine populations. The European Parliament’s fisheries regulation carried out the activity, and the Council applied to the General Fisheries Commission for the Mediterranean (GFCM) Agreement Area and amendments to Council Regulation (EC) No. 1967/2006.

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41598_2026_45984_MOESM1_ESM.docx (download DOCX )

Supplementary Material: Figure S1. Haplotype complexity visualisation and branch diversity of Chimaera monstrosa COI sequences. Table S1. Locality details and accession numbers of sequences analysed in this study.

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Başusta, N., Saglam, N. Genetic diversity and phylogeography of Chimaera monstrosa (Linnaeus, 1758) in the Mediterranean Sea: insights from COI mitochondrial DNA analysis.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-45984-2

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Keywords


  • Chimaera monstrosa
  • Cytochrome c oxidase subunit I (COI)
  • Haplotype network
  • Mediterranean–Atlantic differentiation
  • Molecular phylogeography
  • Population structure

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