Maternal genomic variability of the wild boar (Sus scrofa) reveals the uniqueness of East‐Caucasian and Central Italian populations

The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian (n = 8), European (n = 64), and North African (n = 5) wild boar. Our analyses provided evidence of unique lineages in the East‐Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the presence of old maternal lineages in two Southern glacial refugia (i.e., Caucasus and the Italian peninsula), as a legacy of an ancient wave of colonization of Southern Europe from an Eastern origin.     

Current status of the Sardinian partridge (<Emphasis Type="Italic">Alectoris barbara</Emphasis>) assessed by molecular markers

Four Alectoris species inhabit the Mediterranean area, where they represent important gamebirds subject to human manipulations. The Sardinian partridge is peculiar in Europe, in that it belongs to the African species Alectoris barbara. Nevertheless, no comprehensive study has as yet investigated its genetic status as regards both the extant levels of genetic diversity and the possible contamination due to introgressive hybridization with other Mediterranean species. For the purposes of this study, we analyzed 65 samples of Sardinian partridges, 40 of which came from the wild population and 25 from captive stocks. No one of them showed a mtDNA polymerase chain reaction restriction fragment length polymorphism haplotype assigned to another species than A. barbara, thus, ruling out a possible introgression in the maternal line. In addition, we compared these samples with 94 partridges from other circum-Mediterranean populations using a set of eight chicken (Gallus gallus) microsatellites. A low level of genetic variation was observed in the Sardinian population (H _E = 0.310; k _AR = 2.69), comparable only to that observed in the Sicilian rock partridge (A. graeca). The comparison with the Tunisian population showed that its present genetic composition is consistent with a historical introduction from North Africa, showing possible effects of a post-introductional genetic drift. Bayesian tests assigned all but one individuals with >90% probability to A. barbara, thus, providing evidence that no or only a few exotic Alectoris genes have introgressed into Sardinian partridges.     

Fine-scale genetic structure suggests low levels of short-range gene flow in a wolf population of the Italian Apennines

We investigated local gene flow in a high-density wolf (Canis lupus) population of the Italian Apennines, where no effective barrier to wolf dispersal was present. From 1998 to 2004 we examined wolf carcasses and non-invasively collected samples, focusing on three mountain districts, separated by two valleys, where wolf packs showed high spatial stability. Using nine autosomal microsatellites we successfully genotyped 177 samples, achieving the identification of 74 wolves. Genetic relatedness steeply decreased with increasing distance between sampling areas, thus suggesting that short-distance interpack migration is infrequent in this population. In addition, no individual from a central pack under intensive monitoring was sampled in the range of the surrounding packs over a 4-year period. The limited short-distance gene flow resulted in a cryptic genetic structure, which was revealed by Bayesian analysis. A different genetic cluster was found in each of the three mountain areas, and a small proportion of first-generation immigrants was detected. Overall, the present study suggests that local genetic differentiation in Italian wolves might arise from high spatial stability of packs and can be favoured by a combination of long-range dispersal, the attitude to mate between unrelated individuals and a high young mortality rate.     

Trophic niche overlap and wild ungulate consumption by red fox and wolf in a mountain area in Italy

Red fox (Vulpes vulpes) and wolf (Canis lupus) are two widespread opportunistic predators living in simpatry in many areas. Nonetheless, scarce information are available on their trophic interactions. We investigated food habits of these two carnivores in a mountain area in Italy and assessed the extent of their trophic niche overlap, focusing on the consumption of wild ungulates. Thereby we analyzed the content of 669 red fox scats and 253 wolf scats collected between May 2008 and April 2009. Red foxes resulted to have a more than three times higher niche breadth than wolves. Vegetables, small mammals, wild ungulates, and invertebrates were major items (altogether 92% of volume) of the red fox annual diet. On the contrary wolf annual diet relied on wild ungulates (94% of volume) with wild boar (Sus scrofa) being the main food item. The degree of trophic niche overlap between the two species was found to be low (Pianka's O = 0.356). Diet variation between the warm and the cold seasons was limited in both species, and higher in red fox than in wolf. The two canids appeared to use wild ungulates unevenly being the former more selective for younger preys, smaller in size (newborn piglets and roe deer Capreolus capreolus fawns), whereas the latter exhibited a preference for medium-sized and large ungulates (10–35 kg wild boar and adult roe deer). Even if wild ungulates represent the main shared food category, the different use of age/weight classes by the two predators, together with their possible consumption as carrions by red fox, suggests a very limited trophic competition between wolf and red fox.This study represents a contribution to the knowledge of trophic interaction in predator–prey systems where sympatric carnivores are present.     

Novel Y‐chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations

Y‐chromosome markers are important tools for studying male‐specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non‐human mammals is often hampered by the lack of Y‐specific polymorphic markers. We identified new male‐specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5–10 alleles per locus), falling in one duplicated and two single‐copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (H_D = 0.904 ± 0.011 and H_D = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (F_ST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y‐chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.     

Genomic diversity and differentiation of a managed island wild boar population

The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F_ST=0.126–0.138), and from DP (F_ST=0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F_ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.     

Differentiation under isolation and genetic structure of Sardinian hares as revealed by craniometric analysis,mitochondrial DNA and microsatellites

Hares (Lepus capensis Linnaeus 1758) were probably introduced into Sardinia in historical times. Previous studies indicated North Africa as the most likely source area but did not exclude the occurrence of hybridization events with continental brown hares (L. europaeus Pallas 1778) perhaps introduced for hunting purposes. We implemented both morphometric and genetic approaches to verify the genetic isolation of the Sardinian population. Specifically, we conducted a multivariate analysis of craniometric data and analysed 461 bp of the mitochondrial control region and 12 autosomal microsatellites in Sardinian hares, using North African cape hares and European brown hares as reference populations. Sardinian hares displayed a peculiar skull shape. In agreement, both nuclear and mitochondrial markers remarked the distinctiveness of this population. Observed and expected heterozygosity were 0.52 and 0.61, while haplotype and nucleotide diversity were 0.822 and 0.0129. Self‐assignment based on Bayesian cluster analysis was high (average membership 0.98), and no evident signs of introgression from continental brown hares were found. Our results support the hypothesis that the Sardinian hares have been introduced from North Africa, remained genetically isolated since the founding event and evolved independently from the source population. This long‐lasting isolation and the consequent genetic drift resulted in a differentiation, perhaps accompanied by an adaptation to local environmental conditions.     

Molecular Approaches Revealing Prehistoric, Historic, or Recent Translocations and Introductions of Hares (Genus Lepus) by Humans

Although only of medium size, and thus of little nutritional value compared to big game such as mammoths and ungulates, hares (Lepus spp.) probably have always been a food source for humans, as documented in archaeological finds. Nowadays, hares, particularly such species as the brown hare (L. europaeus), are among the most important game species in many European countries. For hunting, perhaps religious reasons, and in connection with certain myths, hares have been and are still being intentionally translocated. Ancient translocations by humans can be inferred from the presence of hares on islands that had no mainland connections, at least during the Pleistocene, the major evolutionary period of the genus Lepus. We review some of the literature on anthropogenic translocations of hares. We focus on three examples [the brown hare (L. europaeus), the Corsican hare (L. corsicanus), and the Sardinian hare (L. capensis)], where some molecular data could be used to trace the translocation routes and possible origins of introduced hare populations. Certain molecular marker systems, such as sequences of the hypervariable part I (HV-1) of the mitochondrial control region, show high variability in hare species and are thus promising for tracing both recent and ancient origins of translocated hares. Some other molecular marker systems as well as caveats connected with the use of such marker systems in the genus Lepus are also discussed.     

Y-chromosome microsatellite variation in Italian wolves: A contribution to the study of wolf-dog hybridization patterns

One major concern in wolf (Canis lupus) conservation is the risk of genetic contamination due to crossbreeding with domestic dogs. Although genetic monitoring of wolf populations has become widely used, the behavioural mechanisms involved in wolf-dog hybridization and the detrimental effects of genetic introgression are poorly known. In this study we analysed Y-chromosome microsatellite variation in the recovering Italian wolf population and detected strikingly different allele frequencies between wolves and dogs. Four Y haplotypes were found in 74 analysed male wolves, and all of them were present in a focus wolf population in the Apennines. On the other hand, only 1 haplotype was found in the recolonizing wolf population from the Western Alps. The most common haplotype in a sample of domestic dogs, was also found in 5 wolves, 2 of which revealing a signature of recent hybridization. Moreover, another suspect hybrid carried a private haplotype of possible canine origin. These results give support to the idea that female wolves can breed with male stray dogs in the wild. The Y-chromosome variation in Italian wolves contrasts with the previously observed lack of mitochondrial variation. Further investigations are needed to clarify at what extent historical or recent wolf-dog hybridization events may have contributed to the observed haplotype diversity. In conclusion, the two molecular markers employed in this study represent effective means to trace directional genetic introgression into the wolves male lineage and have the noteworthy advantage of being suitable for analyses on low-quality DNA samples.