DOI: 10.5061/dryad.qnk98sfgz
title: Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima

description: Natural and anthropogenic disasters have the capability to cause sudden
 extrinsic environmental changes and long-lasting perturbations including
 invasive species, species expansion, and influence evolution as selective
 pressures force adaption. Such disasters occurred on March 11th 2011, in
 Fukushima, Japan when an earthquake, tsunami, and meltdown of a nuclear
 power plant all drastically reformed anthropogenic land use. Here, we
 demonstrate, using genetic data, how wild boar (Sus scrofa leucomystax)
 have persevered against these environmental changes, including an invasion
 of escaped domestic pigs (Sus scrofa domesticus). Concurrently, we show
 evidence of successful hybridization between pigs and native wild boar in
 this area, however in future offspring, the pig legacy has been diluted
 through time. We speculate that the range expansion dynamics inhibit
 long-term introgression and introgressed alleles will continue to decrease
 at each generation while only maternally inherited organelles will
 persist. Using the gene flow data among wild boar, we assume that
 offspring from hybrid lineages will continue dispersal north at low
 frequencies as climates warm. We conclude that future risks for wild boar
 in this area include intraspecies competition, revitalization of human
 related disruptions, and disease outbreaks.
description: The wild boar muscle samples used were collected from 191 wild
 boar, all of which were morphologically identified as typical wild boar in
 Japan, captured in or nearby the Fukushima evacuated zone from 2015 to
 2018. Additional wild boar samples from the period prior to the 2011
 evacuations, were provided by prefectural hunters, which included 25
 muscle samples from a wild boar population in Ibaraki Prefecture, south of
 Fukushima Prefecture; 10 muscle samples from Yamagata Prefecture and seven
 muscle samples from Miyagi Prefecture, both north of Fukushima Prefecture.
 GPS coordinates, sex, and estimated age based on tooth erosion patterns
 were recorded at the trap sites prior to sampling. Additionally, the birth
 period of wild boar was approximated using sampling year and age data. Ten
 pig muscle samples were obtained from a Fukushima pig slaughterhouse or
 purchased from a Fukushima prefectural meat market in 2016. In total, 243
 samples were assayed for this study. All samples were stored individually
 at −20 °C in 99.5% ethanol until DNA extraction. Total genomic DNA was
 extracted using the Gentra PureGene Blood & Tissue kit (QIAGEN,
 CA, USA), according to manufacturer’s instructions. 
 All data were collected via common practices and genetic
 analysis:  <i>Mitochondrial DNA. </i>The
 mtDNA sequences provide material lineage information and can be used to
 identify wild boar with pig maternal ancestry for many distant
 generations. The mtDNA sequences were obtained from previous literature
 for all samples in this study (Anderson <em>et
 al.</em> 2019, Nagata <em>et al.</em> 2006) In brief,
 the mtDNA control region was successfully amplified and partial sequences
 (713-bp) were determined from all samples. DNA sequencing data was viewed
 from FinchTV chromatogram viewer version 1.5.0 (Geospiza Inc., WA,
 USA). <i>Nuclear microsatellites.
 </i>Nuclear microsatellite (STR) data were analyzed to determine the
 genetic structure of wild boar and the extent of domestic pig
 introgression into the local wild boar population. A total of 24 STR loci
 were selected and genotyped for our study populations based on the allele
 frequencies and the amplification for each of these markers in pure
 species individuals (see Anderson <i>et al.</i> 2020). All 24
 markers were developed by previous studies Rohrer <em>et
 al.</em> 1994, Krause <em>et al.</em> 2002,
 Karlskov-Mortensen <em>et al.</em> 2007; and recommended by
 the Food and Agriculture Organisation of the United Nations database.
 All samples were analyzed as described in Anderson <i>et
 al.</i> 2020. In brief, PCR amplification was performed in 5 μL
 reactions using the QIAGEN Multiplex PCR Kit (QIAGEN, CA, USA) and a
 protocol for fluorescent dye-label [34]. Each sample reaction contained 10
 to 20 ng of genomic template DNA, 2.5 μL of Multiplex PCR Master Mix, 0.1
 μM of forward primer, 0.2 μM of reverse primer, and 0.1 μM of
 fluorescently labeled primer. Product sizes were determined using an ABI
 PRISM 3130 Genetic Analyzer and GeneMapper software (Applied Biosystems,
 MA, USA).
description: Please see the associated manucript, and Supplement, uploaded
 here and available from PRSB when the paper is published. How the datasets
 were used, and replicable analyses can be done. We recommend that future
 studies use this data to assess the fitness of these hybrids (wild boar x
 pig) and better characterize their ecological niche using range expansion
 models and their ecological interactions.