title: Genomic diversity and differentiation of a managed island wild boar population.
abstract: 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 (FST=0.126-0.138), and from DP (FST=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, FST 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.
authors.affiliation: Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy.|Department of Chemistry and Bioscience, Faculty of Engineering and Science, Section of Biology and Environmental Science, Aalborg East, Denmark.
authors.forename: L
authors.initials: L
authors.lastname: Iacolina
authors.affiliation: Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Scandura
authors.affiliation: Braunschweig, Zoological Institute, Braunschweig, Germany.
authors.forename: D J
authors.initials: DJ
authors.lastname: Goedbloed
authors.affiliation: Wageningen University, Animal Breeding and Genomics Centre, Wageningen, the Netherlands.|Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
authors.forename: P
authors.initials: P
authors.lastname: Alexandri
authors.affiliation: Wageningen University, Animal Breeding and Genomics Centre, Wageningen, the Netherlands.
authors.forename: R P M A
authors.initials: RP
authors.lastname: Crooijmans
authors.affiliation: Durham Evolution and Ancient DNA, Durham University, Department of Archaeology, Durham, UK.
authors.forename: G
authors.initials: G
authors.lastname: Larson
authors.affiliation: The Roslin Institute, R(D)SVS, University of Edinburgh, Division of Genetics and Genomics, Midlothian, UK.
authors.forename: A
authors.initials: A
authors.lastname: Archibald
authors.affiliation: Department of Science for Nature and Environmental Resources, University of Sassari, Sassari, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Apollonio
authors.affiliation: University of Illinois, Laboratory of Comparative Genomics, Urbana, IL, USA.
authors.forename: L B
authors.initials: LB
authors.lastname: Schook
authors.affiliation: Wageningen University, Animal Breeding and Genomics Centre, Wageningen, the Netherlands.
authors.forename: M A M
authors.initials: MA
authors.lastname: Groenen
authors.affiliation: Wageningen University, Animal Breeding and Genomics Centre, Wageningen, the Netherlands.
authors.forename: H-J
authors.initials: HJ
authors.lastname: Megens
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005060:Europe; D005828:Genetics, Population; D005838:Genotype; D062312:Islands; D007558:Italy; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics*