Worldwide genetic relationships of pigs as inferred from X chromosome SNPs

The phylogeography of the porcine X chromosome has not been studied despite the unique characteristics of this chromosome. Here, we genotyped 59 single nucleotide polymorphisms (SNPs) in 312 pigs from around the world, representing 39 domestic breeds and wild boars in 30 countries. Overall, widespread commercial breeds showed the highest heterozygosity values, followed by African and American populations. Structuring, as inferred from F_ST and analysis of molecular variance, was consistently larger in the non‐pseudoautosomal (NPAR) than in the pseudoautosomal regions (PAR). Our results show that genetic relationships between populations can vary widely between the NPAR and the PAR, underscoring the fact that their genetic trajectories can be quite different. NPAR showed an increased commercial‐like genetic component relative to the PAR, probably because human selection processes to obtain individuals with high productive parameters were mediated by introgressing boars rather than sows.     

Spatial genetic structure and historical demography of East Asian wild boar

Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511 bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.     

Overabundant wild ungulate populations in Europe: management with consideration of socio-ecological consequences

1. Throughout recent years, ungulates have experienced significant increases in numbers and geographic range sizes in Europe, becoming locally overabundant populations in some regions. Changes in legislation regarding poaching, abandonment of land and re-naturalisation of habitats, and decreasing numbers of hunters, among other things, have led to alarming scenarios in wild ungulate biology. Although ungulates bring some financial benefits for ecosystems and society through tourism and hunting, the problems associated with populations that are no longer controlled can outweigh the advantages. Damage to forestry and agriculture, ungulate-vehicle collisions, and diseases are among the most concerning problems related to ungulate overabundance.
2. To deal with these problems and to decide on the best management strategy to apply, it is essential to have tools available to monitor populations with an integrative approach based on ecological change indicators, and to assess population and ecosystem status. Furthermore, in a globalised world, people’s opinions matter, and sociological studies regarding human perception of wild mammals must take place in order to allow proper management, including consideration of people’s expectations as well as animal and ecosystem needs. Successful and unsuccessful management strategies have already been attempted, and the knowledge of consequences over time enables an adaptive approach.
3. Management of ungulate populations is a complex subject, and each case should be studied, analysing the cost_performance balance of measures to be taken, and ensuring ongoing financial means to carry out and continue with successful ecosystem management strategies. Multidisciplinary teams should be built, including biologists, veterinarians, stakeholders, sociologists, and others, to deal with the management of European wild ungulate populations.

     

Divergence time estimates of East Asian and European pigs based on multiple near complete mitochondrial DNA sequences

The time since the divergence of European and East Asian domestic pigs and wild boars has been estimated in several phylogenetic analyses, generally based on partial mitochondrial sequences or on a small number of complete mtDNA sequences. In the present study, we obtained a refined estimate of this divergence time based on a set of 32 near‐complete mtDNA sequences from wild and domestic pigs of European and Asian types, including 14 new and 18 previously published sequences. A weighted average for different functional mtDNA components resulted in an estimate of 746 000 YBP for the divergence of Asian‐type from European‐type pigs. In addition, our data allowed us to estimate a divergence time between wild and domestic European pigs of 8500 YBP. However, it must be considered cautiously, as most of the estimated values of this sequence divergence were not different from zero, and isolation between wild and domestic pigs has never been complete.