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Keywords:

  • conservation genetics;
  • nuclear DNA

The Eurasian black vulture (Aegypius monachus) has experienced a severe decline during the last two centuries and is globally classified as near-threatened. This has led to the extinction of many traditional breeding areas in Europe and resulted in the present patchy distribution (Iberian and Balkan peninsulas) in the Western Palearctic. In the present study, we describe the current genetic status of the European populations using both mitochondrial cytochrome b sequences and nuclear microsatellite markers, comparing with those found in Asia (Mongolia and Caucasus region). Although, mitochondrial (mt)DNA revealed a relatively low genetic variability (haplotype diversity), no evidence of genome-wide genetic erosion exists because nuclear diversity exhibits normal levels and strong differentiation. A highly philopatric dispersal behaviour must be invoked to explain the existence of a clear pattern that revealed by the phylogeographic analysis, which indicates a sharp East–West clinal distribution and an allopatric differentiation. The distribution of mtDNA haplotypes one in the Iberian population and two in Balkan population and the significance divergence at nuclear loci fulfill the definitions of those populations as evolutionary significant units. We discuss how management strategies should aim at the maintenance (or increase) of current genetic variability levels, suggesting that independent conservation plans are urgently required to protect these two breeding European populations from extinction. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 859–872.