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Predictive models of habitat suitability for the Common Crane Grus grus in a wintering area of southern Portugal were derived using logistic multiple regression and Geographic Information Systems. The study area was characterized by landscape variables and surveyed uniformly for the presence of cranes. The most important variables were distance to roosts, to open Holm Oak woods and to villages, and the occurrence of unpaved roads, shrubby vegetation, slope and orchards. Two models were built, the second having one variable fewer than the first. The selection of the best model was based on statistical and biological criteria. Crane distribution was negatively related to: distance to open Holm Oak Quercus rotundifolia woods and roosts. Additionally, unsuitable vegetation and orchard areas are avoided. In these areas movement is difficult, food availability is reduced and the risk of predation increased. We also found that villages and roads were avoided; disturbance is a significant factor for this species. Some management guidelines are proposed for the area: (1) maintenance of open Holm Oak woodlands, (2) incentives to avoid the abandonment of traditional agriculture and pastoral use of the area, which would lead to an increase of shrubby vegetation areas, (3) preservation of suitable roosting places and (4) management of new patches of forest and orchards

Aim: Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be safely differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting. Location: Morocco. Taxon: Spiny-footed lizard (Acanthodactylus erythrurus), Squamata: Lacertidae. Methods: Using 323 samples from 40 localities, we identified genetic discontinuities within A. erythrurus based on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks). Result: A. erythrurus is characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 8.5 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases. Main conclusions: The genetic diversity of A. erythrurus originates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations within A. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.