Résumé
Assessing how genetic diversity is spatially structured underlies many research questions in evolutionary ecology and contributes to understanding the factors implicated in population declines and extirpations, facilitating identification of conservation priorities and decision-making. In this study, we surveyed genomic diversity using genotyping by sequencing in the six subspecies of the midwife toad Alytes obstetricans / almogavarii complex, a group of amphibians from southwestern Europe threatened by habitat loss, climate change and chytridiomycosis. We first illustrate how the structure evident in mitochondrial DNA (mtDNA) and nuclear DNA microsatellites is discordant with the respective distributions of subspecies and patterns of admixture between them. We further document a deeply-divergent mtDNA haplogroup unique to Central Spain that is not reflected by the nuclear diversity, likely corresponding to a ghost mtDNA lineage. Patterns of genetic diversity and structure differ among and within subspecies. The Pyrenean endemics A. a. almogavarii and A. a. inigoi form homogenous genetic groups with high levels of heterozygosity, while the more widespread A. o. pertinax , A. o. boscai and A. o. lusitanicus are geographically structured across the Iberian Peninsula, comprising both genetically diverse and impoverished populations. Finally, A. o. obstetricans probably persisted in a composite glacial refugium north of the Pyrenees, from which it recently expanded across Western Europe, losing much of its genetic variation. Our results should be considered in future red list assessments, management unit delimitation, and ex-situ conservation efforts, and are also relevant to study chytrid epidemiology, for which A. obstetricans has been a model organism for nearly three decades.