Aim  To investigate the phylogeographical patterns of red deer (Cervus elaphus) in Europe, and to disentangle the influence of ancient (e.g. Pleistocene ice ages) from more recent processes (e.g. human translocations). Location  Europe. Methods  In this study we provide by far the most extensive analysis of genetic structure in European red deer, based on analyses of variation at two mitochondrial markers (cyt b and D‐loop) in a large number of individuals from 39 locations. Relationships of mitochondrial DNA haplotypes were determined using minimum spanning networks and phylogenetic analyses. Population structure was examined by analyses of molecular variance. Historical processes shaping the present patterns were inferred from nested clade analysis and nucleotide diversity statistics. Results  Within Europe, we detected three deeply divergent mitochondrial DNA lineages. The three lineages displayed a phylogeographical pattern dividing individuals into western European, eastern European and Mediterranean (Sardinia, Spain and Africa) groups, suggesting contraction into three separate refugia during the last glaciation. Few haplotypes were shared among these three groups, a finding also confirmed by FST values. Calculations of divergence times suggest that the groups probably split during the Pleistocene. Main conclusions  The observed pattern is interpreted to result from isolation in different refugia during the last glaciation. The western and eastern European lineages could be linked to an Iberian and Balkan refugium, respectively. The third lineage might originate from a Sardinian or African refugium. We link local phylogeographical patterns observed in Europe to the post‐glacial recolonization process, shaped by the geographical localization of refugia and barriers to gene flow. Regardless of the importance of red deer as a game species and the tradition of translocating red deer in Europe, we detected few individuals that did not match the trichotomous pattern, suggesting that translocations have occurred mainly at smaller spatial scales.

Red deer Cervus elaphus of the endangered populations from Sardinia and Mesola Wood, northern Italy, were analysed for genetic variation at 531 bp of the mitochondrial control region and 12 polymorphic nuclear microsatellite loci. A phylogenetic analysis was conducted including additional data from the literature to gain insight into the phylogeographical origin of the Sardinian subspecies C. e. corsicanus . Microsatellite variation was low in both populations but Sardinia showed comparatively high variability at the control region. Management recommendations are discussed. In particular, the Mesola red deer, the only remaining indigenous Italian population, ought to be managed to increase the effective population size and should be subdivided into two or more populations. As to the phylogeography of the Sardinian population, microsatellite data favoured mainland Italy as the place of origin in that Sardinia and Mesola showed the smallest distance values and were paired together in trees with high bootstrap support. However, the mitochondrial data only partially confirmed this conclusion but showed great similarity between Sardinian and Spanish red deer. Possible explanations for this discrepancy and general limits of mitochondrial sequences in resolving demographic and biogeographical processes of the recent past are discussed.

Samples from 69 British red deer Cervus elaphus scoticus from seven populations in Scotland and England were analysed with respect to variability within and differentiation among stocks using 11 polymorphic microsatellite loci and 439 bp of the mitochondrial control region. The results clearly showed the effects of anthropogenic factors on British red deer. On the whole, variability values were within the species' reported range. The island population of Islay, Scotland, however, while showing average microsatellite variability, exhibited no mitochondrial variation at all. One microsatellite locus was monomorphic in three Scottish populations (Islay, Dunachton and Achnacarry). Overall and pairwise F ST values indicate considerable differentiation among the populations studied, but Dunachton and Achnacarry, two adjacent populations free from recorded introductions, showed only a little differentiation and were paired in trees based on genetic distances. In terms of variability, no statistically significant differences were observed between island and mainland populations and the overall test of isolation by distance was negative. Possible reasons for the genetic patterns observed, such as differences in human impact on the populations, are discussed.

Three mainland and two island roe deer (Capreolus capreolus) populations with a total sample size of 105 individuals from Schleswig-Holstein, northern Germany, were analysed with regard to genetic variability within and differentiation among populations as revealed by eight allozyme loci known to be polymorphic in roe deer, eight microsatellite loci and 404 bp of the mitochondrial control region. Surprisingly, the allozymes were completely monomorphic, but microsatellite and control region variability were high. Hypotheses as to demographic reasons for the variability patterns found, including bottlenecks, founder effects and translocations, are put forward. There were no statistically significant differences between the island and the mainland populations in terms of genetic variability as measured by expected heterozygosity, inbreeding coefficient and allelic richness. The correlations of the various variability indices were not statistically significant after Bonferroni correction. Nevertheless, there was a clear tendency for differentiation indices to yield concordant results for microsatellite and mitochondrial markers.

The Mesola red deer Cervus elaphus in the Po delta are the only native red deer population on the Italian mainland and have been the focus of conservationists and wildlife biologists for some time. In our study, we present a genetic analysis of 25 Mesola red deer on the basis of 20 polymorphic microsatellite loci, aiming at estimating the population's genetic diversity and at providing information for a future genetic screening. In addition, we carried out a population viability analysis (PVA) with demographic and life‐history data available from a long‐term population survey, simulating different management scenarios. Genetic diversity was very low compared to the rest of Europe (observed and expected heterozygosity 0.50 and 0.61, respectively), and an overall excess of homozygosity was indicative of inbreeding. Calculations of the probability of identity and genotype mismatch frequencies suggested that between five and seven highly informative loci were sufficient to resolve individuals with reasonable certainty. The PVA yielded a generally poor outlook, but at the same time, it showed that management measures already taken significantly increased population viability. A sensitivity analysis revealed that inbreeding depression and possible catastrophes had a huge impact on the population's prospects. However, the establishment of two subpopulations and successful attempts at reducing the consequences of catastrophic events were able to significantly mitigate the harmful effects of both inbreeding and environmental stochasticity. These results, in particular the splitting of the population, may be of general interest to conservationists dealing with unique threatened populations.

A population genetic analysis based on sequences of the mitochondrial control region in 110 red foxes from five sampling localities in northern Serbia was carried out. The analysis yielded nine different haplotypes. Neither haplotype phylogeny nor their distribution was in accordance with the geographic location of the populations. In particular, the data failed to detect an unequivocal influence of the two big rivers, the Danube and the Tisza, separating the populations studied. Population differentiation was altogether low, without any relationship to the rivers as possible migration barriers. Although the possibility of foxes crossing the rivers over bridges or by swimming, thus keeping up gene flow, cannot be ruled out, it is most probable that the control region sequences are not sensitive enough to resolve small-scale population relationships but rather show patterns determined by stochastic processes such as genetic drift or lineage sorting.

We analysed 131 common impala (Aepyceros melampus melampus) samples from two provinces in South Africa (Limpopo and KwaZulu-Natal) that are separated by the Drakensberg Mountain Range using sequences of the mitochondrial control region and seven polymorphic nuclear microsatellite loci. In line with earlier studies on bovid species, we found very high values of genetic diversity, particularly at the mtDNA locus with an overall nucleotide diversity of 3.6% and an overall haplotype diversity of 0.98. All statistical approaches confirmed a significant population differentiation between Limpopo and KwaZulu-Natal, suggesting that areas of unsuitable habitat caused by the presence of the Drakensberg Range and the Indian Ocean coastal belt act as a barrier to gene flow. Only few individuals with signs of admixed origin were indicative of translocations or rare migration between the two provinces. Combination of our mtDNA data set with those of previous studies on impala from south-western, southern and eastern Africa revealed the highest diversity in South Africa. This is in line with the hypothesis of a southern glacial refuge from which various African ungulate species spread northeast during the Holocene, although in the case of impala further analyses based on larger data sets will be necessary to definitively settle this question.

The two red deer subspecies C. e. corsicanus (Corsican red deer, endemic to the Tyrrhenian islands of Sardinia and Corsica) and C. e. barbarus (Barbary red deer, presently confined to a small area along the Tunisian-Algerian border) are classified by the IUCN as "Endangered" and "Lower risk (near threatened)", respectively (until recently, the Barbary red deer's status was "Vulnerable"). Both subspecies underwent severe bottlenecks in the twentieth century. We review our results on genetic variability and differentiation in these two subspecies at polymorphic microsatellite loci and sequences of the mitochondrial control region and discuss their bearing on conservation and phylogeography. Our analyses yielded very low genetic variability for C. e. corsicanus. The Barbary red deer also showed low variability values in a European comparison, but diversity was not as low as might have been feared in the light of the population's history. Analyses of molecular variance, assignment tests and factorial correspondence analysis did not yield any signs of differentiation among the Tunisian subgroups studied, whereas there was clear evidence of a differentiation between the Sardinian and the Corsican red deer population. The phylogeographic analysis showed close relationships between C. e. corsicanus and autochthonous Italian deer at two unlinked sets of nuclear loci, suggesting as the most likely scenario an introduction of Italian mainland red deer to the Tyrrhenian islands, from where animals were probably translocated to North-Africa.