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

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.