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.

Areas of sympatry and hybridization of closely related species can be difficult to assess through morphological differences alone. Species which coexist and are similar morphologically may be distinguished only with molecular techniques. The roe deer (Capreolus spp.) is a meso-mammal having a Palaearctic distribution, with two closely related species: the European C. capreolus and the Siberian C. pygargus. We analysed mtDNA sequences from 245 individuals, sampled through all the entire range of the genus, to investigate the distribution of genetic lineages and outline phylogeographical patterns. We found that: (1) a C. pygargus lineage occurs in Poland and Lithuania, much farther west than the area which so far was believed its westernmost limit; (2) no haplotype of this C. pygargus lineage matches any found in East Europe and Asia -this should rule out human introductions and may indicate Pleistocene-Holocene migrations from the east; (3) no geographical structuring of C. pygargus lineages occurs, questioning the existence of putative subspecies; (4) several genetic lineages of C. capreolus can be recognized, consistent with the existence of two subspecies, respectively in central-southern Italy and southern Spain. Coalescence times suggest that intraspecific variation in C. capreolus and C. pygargus developed approximately 100-10 kya. The extant mitochondrial lineages pre-dated the Last Glacial Maximum. Capreolus pygargus must have moved westward to Central Europe, where at least one genetic lineage still survives, coexisting with C. capreolus.

The extant taxa of central and northern Europe are commonly believed to derive from Pleistocene ancestors, who moved to the north from three separate glacial refugia: the Iberian and Italian peninsulae, as well as the southern Balkans. The issue of postglacial dispersal patterns was addressed through the investigation of population structure and phylogeography of the European roe deer, Capreolus capreolus . The genetic diversity in 376 individuals representing 14 allegedly native populations across their European range was assessed, using ten autosomal microsatellite loci and restriction fragment length polymorphisms of the mitochondrial D-loop and NADH dehydrogenase 1 gene segments. Our results suggest the existence of three major genetic lineages of roe deer in Europe. One comprises populations in the south-western limit of the species' distribution (i.e. Iberia), where an internal substructure splits a northern from a southern sublineage. A second lineage includes populations of southern and eastern Europe, as well as a separate sublineage sampled in central-southern Italy, where the existence of the subspecies Capreolus c. italicus was supported. In central-northern Europe, a third lineage is present, which appeared genetically rather homogeneous, although admixed, and equally divergent from both the eastern and western lineages. Current patterns of intraspecific genetic variation suggest that postglacial recolonization routes of this cervid to northern Europe could be due to range expansion from one or more refugia in central-eastern Europe, rather than proceeding from the Mediterranean areas.

1. Despite it being the most abundant mountain dwelling ungulate of Europe and the Near East, the taxonomy, systematics and biology of the chamois are still imperfectly known. Although neither species of chamois is at risk, several subspecies are threatened (Rupicapra rupicapra cartusiana, Rupicapra rupicapra tatrica and Rupicapra rupicapra balcanica; Rupicapra pyrenaica ornata. Rupicapra rupicapra asiatica is data-deficient but probably threatened). 2.A life history with apparently contradictory relationships between survival, sexual dimorphism and mating system suggests a unique survival strategy not yet fully understood. Over the last century, morphologic, biometric, behavioural and genetic features have been studied to shed light on the phylogeography and monophyly or polyphyly of the chamois as well as on the number of existing species and subspecies of the genus Rupicapra. 3. The dispersal hypothesis, according to which R. rupicapra migrated westward from eastern Europe in the Quaternary, confining R. pyrenaica to the southernmost regions of Europe, has been recently called into question by some molecular analyses that yielded contradictory results. 4. In spite of subtleties relevant to each method of analysis, an overall evaluation of differences between the R. rupicapra and the R. pyrenaica groups strongly supports the functional separation of the taxa into two species. 5. Further studies on the ecology of chamois, as well as on the epidemiology of severe diseases, e.g. sarcoptic mange, are needed to improve the management of viable populations. 6. Before translocations and reintroductions are carried out, the risk of hybridization leading to genetic extinction should be evaluated.