title: Genome data from a sixteenth century pig illuminate modern breed relationships.
abstract: Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.
authors.affiliation: Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain.
authors.forename: O
authors.initials: O
authors.lastname: Ramírez
authors.affiliation: 1] Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain [2] Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: W
authors.initials: W
authors.lastname: Burgos-Paz
authors.affiliation: Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain.
authors.forename: E
authors.initials: E
authors.lastname: Casas
authors.affiliation: 1] Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain [2] Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Ballester
authors.affiliation: 1] Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain [2] Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: E
authors.initials: E
authors.lastname: Bianco
authors.affiliation: Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain.
authors.forename: I
authors.initials: I
authors.lastname: Olalde
authors.affiliation: Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain.
authors.forename: G
authors.initials: G
authors.lastname: Santpere
authors.affiliation: Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: V
authors.initials: V
authors.lastname: Novella
authors.affiliation: Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Gut
authors.affiliation: Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain.
authors.forename: C
authors.initials: C
authors.lastname: Lalueza-Fox
authors.affiliation: Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Saña
authors.affiliation: 1] Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain [2] Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain [3] Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Pérez-Enciso
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D005828:Genetics, Population; D016678:Genome; D005838:Genotype; D008297:Male; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013030:Spain; D034421:Sus scrofa / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial