Abstract
A continent‐wide survey of sequence variation in mitochondrial (mt) and nuclear (n) DNA of the endangered great bustard ( Otis tarda ) was conducted to assess the extent of phylogeographic structure in a morphologically monotypic bird. DNA sequence variation in a combined 809 bp segment of the mtDNA genome from 66 individuals from the last six breeding regions showed relatively low levels of intraspecific sequence diversity (π = 0.32%) but significant differences in the regional distribution of 11 haplotypes (Φ ST = 0.49). Despite their exceptional potential for dispersal, a complete and long‐term historical separation between the populations from the Iberian Peninsula (Spain) and mainland Europe (Hungary, Slovakia, Germany, and Russia) was demonstrated. Divergence between populations based on a 3‐bp insertion–deletion polymorphism within the intron region of the nuclear CHD‐Z gene was geographically concordant with the primary subdivision identified within the mtDNA sequences. Inferred aspects of phylogeography were used to formulate conservation recommendations for this endangered species.