DOI: 10.5061/dryad.jsxksn05z
title: Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine

description: Invasive alien species are a significant threat to both economic and
 ecological systems.  Identifying processes that give rise to
 invasive populations is essential for implementing effective control
 strategies.  We conducted an ancestry analysis of invasive feral
 swine (Sus scrofa, Linnaeus, 1758), a highly destructive ungulate that is
 widely distributed throughout the contiguous United States, to describe
 introduction pathways, sources of newly-emergent populations, and
 processes contributing to an ongoing invasion.  Comparisons of
 high-density single nucleotide polymorphism genotypes for 6,566 invasive
 feral swine to a comprehensive reference set of S. scrofa revealed that
 the vast majority of feral swine were of mixed ancestry, with dominant
 genetic associations to Western heritage breeds of domestic pig and
 European populations of wild boar.  Further, the rapid expansion
 of invasive feral swine over the past 30 years was attributable to
 secondary introductions from established populations of admixed ancestry
 as opposed to direct introductions of domestic breeds or wild
 boar.  Spatially-widespread genetic associations of invasive
 feral swine to European wild boar deviated strongly from historical S.
 scrofa introduction pressure, which was largely restricted to domestic
 pigs with infrequent, localized wild boar releases.  The
 deviation between historical introduction pressure and contemporary
 genetic ancestry suggests wild boar-hybridization may contribute to
 differential fitness in the environment and heightened invasive potential
 for individuals of admixed domestic pig-wild boar ancestry.
description: Feral swine samples were collected throughout the entirety of the
 invaded range within the contiguous US as an extension of damage
 mitigation efforts led by the United States Department of Agriculture
 (USDA) between 2001 and 2017.  Invasive feral swine were genotyped using
 Illumina BeadChip microarrays (San Diego, California) developed for
 porcine (PorcineSNP60 v2, <i>n</i> = 168; Genomic Profiler for
 Porcine HD, <i>n</i> = 6,398, exclusively licensed to
 GeneSeek, a Neogen Corporation, Lincoln, Nebraska; Ramos et al., 2009). 
 Combining genotypes produced across multiple Illumina BeadChips
 microarrays yielded 29,375 common autosomal loci, with all available loci
 retained for subsequent analyses.  Based upon the available loci, we
 removed samples with call rates &lt;95%, thus retaining 6,566 invasive
 feral swine for analysis. We assembled our reference
 set by compiling domestic pig and native wild boar HD SNP genotypes from
 previously published datasets (<i>n</i> = 2,450; Alexandri et
 al., 2017; Burgos-Paz et al., 2013; Goedbloed et al., 2013a; Iacolina et
 al., 2016; Roberts & Lamberson, 2015; Yang et al., 2017), which we
 augmented with novel genotypes produced by our research group
 (<i>n</i> = 566; produced with extraction methods described
 above and genotyped with the Genomic Profiler for Porcine HD (GeneSeek)).
  In order to align with feral swine genotypes, we restricted our reference
 set to datasets similarly produced with either the PorcineSNP60 (v1 and
 v2; Illumina) or Genomic Profiler for Porcine HD (GeneSeek) BeadChip
 microarrays (Ramos et al., 2009). 
description: We present genotype files
 for 6,566 invasive feral swine and 2,516 corresponding <i>Sus
 scrofa</i> reference samples in the *.bed/*.bim/*.fam (binary PED
 file) file format.  All genotypes were produced with Illumina BeadChip
 microarrays (San Diego, California) developed for porcine (PorcineSNP60 v1
 and 2 or Genomic Profiler for Porcine HD,<i> </i>exclusively
 licensed to GeneSeek, a Neogen Corporation, Lincoln, Nebraska).  Many of
 the reference genotypes have been published previously (full citations
 below with abbreviated citations listed in metadata).  Metadata for both
 invasive feral swine and reference samples are presented and correspond to
 more thorough appendices published online that accompany the manuscript
 “Mixed ancestry from wild and domestic lineages contributes to the rapid
 expansion of invasive feral swine.”  R-code is presented that will allow
 users to recreate ancestry analyses with minimal edits required by the
 user (identify local paths) to execute the code. Citations: Alexandri, P., Megens, H.-J., Crooijmans, R. P. M. A., Groenen, M. A. M., Goedbloed, D. J., Herrero-Medrano, J. M., . . . Triantafyllidis, A. (2017). Distinguishing migration events of different timing for wild boar in the Balkans. <i>Journal of Biogeography</i>,<i> 44</i>, 259-270. doi:10.1111/jbi.12861 Burgos-Paz, W., Souza, C. A., Megens, H. J., Ramayo-Caldas, Y., Melo, M., Lemus-Flores, C., . . . Perez-Enciso, M. (2013). Porcine colonization of the Americas: a 60k SNP story. <i>Heredity</i>,<i> 110</i>, 321-330. doi:10.1038/hdy.2012.109 Goedbloed, D. J., Megens, H. J., van Hooft, P., Herrero-Medrano, J. M., Lutz, W., Alexandri, P., . . . Prins, H. H. T. (2013). Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations. <i>Molecular Ecology</i>,<i> 22</i>, 856-866. doi:10.1111/j.1365-294X.2012.05670.x Iacolina, L., Scandura, M., Goedbloed, D. J., Alexandri, P., Crooijmans, R. P. M. A., Larson, G., . . . Megens, H. J. (2016). Genomic diversity and differentiation of a managed island wild boar population. <i>Heredity</i>,<i> 116</i>, 60-67. doi:10.1038/hdy.2015.70 Roberts, K. S., & Lamberson, W. R. (2015). Relationships among and variation within rare breeds of swine. <i>Journal of Animal Science</i>,<i> 93</i>, 3810-3813. doi:10.2527/jas.2015-9001 Yang, B., Cui, L., Perez-Enciso, M., Traspov, A., Crooijmans, R. P. M. A., Zinovieva, N., . . . Megens, H.-J. (2017). Genome-wide SNP data unveils the globalization of domesticated pigs. <i>Genetics Selection Evolution</i>,<i> 49</i>, 71. doi:10.1186/s12711-017-0345-y