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Genome wide data recover hierarchical genetic structure and help define conservation units for the threatened Asian Houbara

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Abstract

The Asian Houbara Bustard (Chlamydotis macqueenii), a partially migratory bird from the western and Central Asian steppes, is listed as vulnerable on the IUCN Red List. This study reassesses the species’ genetic structure using modern genomics to identify evolutionary significant units (ESUs). Following the generation of a de novo reference assembly and resequencing data (114 birds, 10 locations), we integrated genetic results, migratory behaviour, and geography to identify eight hierarchically structured ESUs: four near range edges (Yemen, Mongolia, Eastern Kazakhstan, Israel) and four within the central range (Central-Eastern, Central-Western, North Iran, South Iran). Low genetic diversity and recent inbreeding make ESUs on the range periphery (Israel, Mongolia, Yemen) the most genetically threatened, consistent with the central-marginal hypothesis. ESUs do not cluster according to their migrant/non-migrant status. Geographic distance significantly shaped genetic structure, with longitudinal separation (isolation-by-distance along an east–west axis) emerging as the strongest predictor of differentiation, particularly among high-latitude migrant populations. Our findings underscore the importance of integrating genomic, geographic and behavioural criteria to define intraspecific units that effectively address the conservation needs of widespread species with complex evolutionary dynamics.

Data availability

The sequencing data are accessible in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject accession number PRJNA1338100 (sample accessions SRR35788338–SRR35788451).

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Acknowledgements

We are grateful to HH Sheikh Mohamed bin Zayed Al Nahyan, Crown Prince of Abu Dhabi and Founder of the IFHC, HH Sheikh Theyab Bin Mohamed Al Nahyan, Chairman of the IFHC, and HE Mohammed Ahmed Al Bowardi, Deputy Chairman, for their support. This study was conducted under the guidance of Reneco International Wildlife Consultants LLC, a company that manages the IFHC’s conservation programs, such as the National Avian Research Centre. The authors wish to thank the numerous field ecologists from the following organisations for their invaluable efforts in collecting samples over the years: the Emirates Centre for the Conservation of Houbara in Uzbekistan, the Wildlife Science and Conservation Center of Mongolia, the Israel Nature and Heritage Foundation (INHF), and the Israel Nature and Parks Authority (INPA). Special thanks to Joseph Azar for providing ecological insights on the species’ migration, and to Sandra Berthou and Manal Alnaqbi for creating the distribution map.

Funding

Funding was provided by International Funds for Houbara Conservation, Abu Dhabi, UAE.

Author information

Authors and Affiliations

  1. Reneco International Wildlife Consultants LTD, Abu Dhabi, United Arab Emirates

    Thierry Bernard Hoareau, Keiler Arthur Collier, Matthew J. Miller, Yves Hingrat, Eric Le Nuz & Loïc Lesobre

  2. Wildlife Science and Conservation Center of Mongolia, Ulaanbaatar, Mongolia

    Nyambayar Batbayar

  3. Division of Science & Conservation, Israel Nature & Parks Authority, Jerusalem, Israel

    Ohad Hatzofe

  4. Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Haifa, Israel

    Asaf Mayrose

Authors

  1. Thierry Bernard Hoareau
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  2. Keiler Arthur Collier
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  3. Matthew J. Miller
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  4. Yves Hingrat
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  5. Eric Le Nuz
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  6. Nyambayar Batbayar
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  7. Ohad Hatzofe
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  9. Loïc Lesobre
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Contributions

L.L. identified the need for this research and secured funding. T.B.H., LL and YH conceptualised and designed the study with inputs from M.M.J. and K.C. Samples were facilitated or provided by E.L.N., N.B., H.O., A.B. and A.M. T.B.H. and K.C. conducted population genetic analyses. T.B.H. interpreted the results and wrote the manuscript, with inputs from L.L., Y.H., M.M.J. and K.C. All authors contributed to the final revisions of the manuscript.

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Correspondence to
Thierry Bernard Hoareau.

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Hoareau, T.B., Collier, K.A., Miller, M.J. et al. Genome wide data recover hierarchical genetic structure and help define conservation units for the threatened Asian Houbara.
Sci Rep (2026). https://doi.org/10.1038/s41598-025-33691-3

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  • DOI: https://doi.org/10.1038/s41598-025-33691-3

Keywords

  • Adaptive evolutionary conservation
  • Conservation strategy
  • DAPC
  • Partially migratory species
  • Runs of homozygosity
  • Whole genome sequencing

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