DOI: 10.5061/dryad.f1vhhmh92
title: Data from: Population genomic insights into recent nutria (<em>Myocastor coypus</em>) invasion dynamics

description: Nutria (Myocastor coypus) are semi‐aquatic rodents native to South
 America, introduced to the USA for fur farming during the early twentieth
 century. This species' herbivory can cause extensive damage to
 agriculture and wetland ecosystems. Although declared eradicated from
 California, USA, in the 1970s, nutria populations were recently discovered
 in the state's Central Valley and subsequently in the Sacramento–San
 Joaquin Delta, areas of significant agricultural and conservation
 importance. We report the use of a combination of nuclear
 single-nucleotide polymorphisms (SNPs) and mitochondrial (mtDNA;
 cytochrome b locus) markers to characterize the source and demographic
 history of the current invasion, to inform eradication efforts. Our study
 is the first to develop a SNP dataset for nutria, utilizing 6809 loci to
 characterize genetic diversity in comparison to several potential source
 populations. Multivariate analysis and Bayesian clustering of the SNP
 dataset found the greatest similarity to invasive nutria in central
 Oregon, USA, with minimal genetic differentiation in the Central Valley,
 excluding the leading edges of the invasion. Cytochrome b sequencing
 yielded a single contemporary California haplotype shared with nutria in
 Oregon and Washington, as well as in museum samples from California fur
 farms that predated eradication. Mantel tests found genetic
 differentiation between nutria in the Central Valley was best explained by
 ecological distance along rivers, while estimated effective migration
 surface (EEMS) analysis indicated gene flow was characterized by
 infrequent dispersal followed by rapid expansion in large, protected areas
 of emergent wetland habitat. These combined findings suggest contemporary
 California nutria represent a recent introduction that underwent rapid
 expansion. Our data further support treating the Central Valley as a
 single eradication unit while investing additional resources in targeting
 dispersal corridors to best achieve management goals. This study presents
 the first characterization of a regional nutria invasion within the larger
 context of global population and phylogenetics.
description: # Data from: Population genomic insights into recent nutria (*Myocastor
 coypus*) invasion dynamics Dataset DOI:
 [10.5061/dryad.f1vhhmh92](https://doi.org/10.5061/dryad.f1vhhmh92) ##
 Description of the data and file structure VCF files (RADseq SNP dataset)
 and FASTA files (mitochondrial Cyt b and D-loop) Individual FASTQ files
 can be found on NCBI's Sequence Read Archive: BioProject PRJNA1328208
 (accession numbers SAMN51307640-SAMN51307946). Novel mitochondrial
 sequences were uploaded to NCBI GenBank under accession numbers
 PX240733-35.\ Sample metadata can be found in the supplemental materials
 (Table S1) of the publication. ### Files and variables #### File:
 finalRADseq_filtered_all.vcf **Description:** final filtered dataset with
 all 6809 SNP loci and all individuals. This was used for all analyses
 except for the "private allele" analyses described below. In
 some instances this VCF was subsampled by individual for computational
 efficiency or to avoid sample size biases - see supplemental materials
 (Table S1) of publication for individuals included in the EEMS, RAxML
 phylogenetics, PCoA in Fig. 5A, and Structure analyses. #### File:
 priv_allelesEvsW_CA.vcf **Description:** filtered dataset with 403 SNP
 loci which were identified as containing private alleles within the East
 (Louisiana, Maryland, Texas and Virginia; 87 loci) or West (Oregon and
 Washington; 316 loci) regions of the USA. Following identification of
 private alleles, California samples were added back to the dataset to
 determine the relationship between California and other USA nutria
 populations. ## Code/software *
 [https://github.com/cdfwWildlifeGenetics/publications/tree/main/Ahrens%20et%20al.%202025%20Evol%20Appl%20nutria](https://github.com/cdfwWildlifeGenetics/publications/tree/main/Ahrens%20et%20al.%202025%20Evol%20Appl%20nutria) ## Access information Other publicly accessible locations of the data: * NCBI's Sequence Read Archive: BioProject PRJNA1328208 (accession numbers SAMN51307640-SAMN51307946) Data was derived from the following sources: * GBS RADseq - Illumina HiSeq5000 * Sanger sequencing for mitochondrial data