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Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima

Citation

Anderson, Donovan et al. (2021), Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima, Dryad, Dataset, https://doi.org/10.5061/dryad.qnk98sfgz

Abstract

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.

Methods

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: 

Mitochondrial DNA. 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 et al. 2019, Nagata et al. 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).

Nuclear microsatellites. 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 et al. 2020). All 24 markers were developed by previous studies Rohrer et al. 1994, Krause et al. 2002, Karlskov-Mortensen et al. 2007; and recommended by the Food and Agriculture Organisation of the United Nations database. All samples were analyzed as described in Anderson et al. 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).

Usage Notes

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. 

Funding

Nippon Life Insurance Foundation

Norges Forskningsråd, Award: 223268/F50