Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations.

Large carnivores can either directly influence ungulate populations or indirectly affect their behaviour. Knowledge from European systems, in contrast to North American systems, on how this might lead to cascading effects on lower trophic levels is virtually absent. We studied whether wolves Canis lupus via density-mediated and behaviorally-mediated effects on their ungulate prey species influence patterns of browsing and tree regeneration inside the Białowieża National Park, Poland. Browsing intensity of tree saplings (height class  150 cm), irrespective of tree species or forest type, was lower inside a wolf core area (50.5%) where predator presence is highest, than in the remainder of the wolf pack's home range (58.3%). Additionally, browsing intensity was reduced when the amount of coarse woody debris (CWD), which can act as a 'ungulate escape impediment', increased (within 5-m radius) inside the wolf core area. No relationship existed outside the core area. As a result, the proportion of trees growing out of herbivore control increased more strongly with increasing amount of CWD inside compared to outside the wolf core area. This suggests that next to direct effects of wolves on ungulate density caused by a higher predation pressure inside the core area, risk effects are important and are enhanced by habitat characteristics. These results indicate that behaviorally-mediated effects of predators on prey can become more important than density-mediated effects in affecting lower trophic levels. This is the first study we are aware of, that shows CWD can create fine-scale risk effects on ungulates with the potential for cascading effects of large predators on patterns of tree regeneration for a European forest system. This knowledge broadens the discussion on how the impact of large predators on ecosystem functioning depends on the physical landscape, by illustrating these effects for a system which largely contrasts in this respect to the North American systems.

Population genetics and phylogeography of the African buffalo (Syncerus caffer) are inferred from genetic diversity at mitochondrial D-loop hypervariable region I sequences and a Y-chromosomal microsatellite. Three buffalo subspecies from different parts of Africa are included. Nucleotide diversity of the subspecies Cape buffalo at hypervariable region I is high, with little differentiation between populations. A mutation rate of 13-18% substitutions/million years is estimated for hypervariable region I. The nucleotide diversity indicates an estimated female effective population size of 17 000-32 000 individuals. Both mitochondrial and Y-chromosomal diversity are considerably higher in buffalo from central and southwestern Africa than in Cape buffalo, for which several explanations are hypothesized. There are several indications that there was a late middle to late Pleistocene population expansion in Cape buffalo. This also seems to be the period in which Cape buffalo evolved as a separate subspecies, according to the net sequence divergence with the other subspecies. These two observations are in agreement with the hypothesis of a rapid evolution of Cape buffalo based on fossil data. Additionally, there appears to have been a population expansion from eastern to southern Africa, which may be related to vegetation changes. However, as alternative explanations are also possible, further analyses with autosomal loci are needed.

Aim  In recent decades there has been a marked decline in the numbers of African lions (Panthera leo), especially in West Africa where the species is regionally endangered. Based on the climatological history of western Africa, we hypothesize that West and Central African lions have a unique evolutionary history, which is reflected by their genetic makeup. Location  Sub‐Saharan Africa and India, with special focus on West and Central Africa. Method  In this study 126 samples, throughout the lion’s complete geographic range, were subjected to phylogenetic analyses. DNA sequences of a mitochondrial region, containing cytochrome b, tRNAPro, tRNAThr and the left part of the control region, were analysed. Results  Bayesian, maximum likelihood and maximum parsimony analyses consistently showed a distinction between lions from West and Central Africa and lions from southern and East Africa. West and Central African lions are more closely related to Asiatic lions than to the southern and East African lions. This can be explained by a Pleistocene extinction and subsequent recolonization of West Africa from refugia in the Middle East. This is further supported by the fact that the West and Central African clade shows relatively little genetic diversity and is therefore thought to be an evolutionarily young clade. Main conclusions  The taxonomic division between an African and an Asian subspecies does not fully reflect the overall genetic diversity within lions. In order to conserve genetic diversity within the species, genetically distinct lineages should be prioritized. Understanding the geographic pattern of genetic diversity is key to developing conservation strategies, both for in situ management and for breeding of captive stocks.

The applicability of bovine autosomal microsatellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per marker was 5.0 (SE = 0.2) and the mean heterozygosity per marker was 0.61 (SE = 0.03). Considering the overall high level of polymorphism, it was concluded that most bovine microsatellite markers are applicable in African buffalo.