DOI: 10.5061/dryad.8931zcrxc
title: SNP datasets from invasive Bombus terrestris on Tasmania, Australia

description: Invasive species are predicted to adjust their morphological,
 physiological, and life-history traits to adapt to their non-native
 environments. Although a loss of genetic variation during invasion may
 restrict local adaptation, introduced species often thrive in novel
 environments. Despite being founded by just a few individuals, the
 bumblebee Bombus terrestris (Hymenoptera: Apidae) has successfully spread
 across the island of Tasmania (Australia) in less than 30 years, becoming
 abundant and competitive with native pollinators. We use RADseq to
 investigate what neutral and adaptive genetic processes associated with
 environmental and morphological variation allow B. terrestris to thrive as
 an invasive species in Tasmania. Across 15 sites, we found high gene flow
 with low genetic diversity, significant isolation-by-distance, and spatial
 variation in effective migration rates. A longitudinal band of restricted
 migration was evident across the mid-central region of Tasmania,
 corresponding to sites with high elevation, pastural land, low wind speeds
 and low precipitation seasonality. Tajima’s D indicated a recent
 population expansion for central sites extending from the south to the
 north of the island. Significant selection signatures were found for loci
 in relation to precipitation, wind speed, and wing loading. Candidate loci
 were annotated to genes with functions related to cuticle water retention
 and insect flight muscle stability. Understanding how a genetically
 impoverished invasive bumblebee has rapidly adapted to a novel island
 environment provides further understanding about the evolutionary
 processes that determine successful insect invasions and the potential for
 invasive hymenopteran pollinators to spread globally.
description: Wild <em>B.
 terrestris</em> workers were sampled from 16 locations across the
 Australian continental island state of Tasmania and subsequently extracted
 for DNA (DNeasy Blood and Tissue extraction kit (Qiagen) and sent for
 RADseq at to Floragenex, Inc. (Portland, OR, USA). Samples were
 individually sequenced on an Illumina HighSeq 4000, generating 150bp
 paired-end reads with an average depth of coverage between 12–112x per
 sample. 
description: # SNP datasets
 [https://doi.org/10.5061/dryad.8931zcrxc](https://doi.org/10.5061/dryad.8931zcrxc) The three SNP datasets are VCF files and consists of 160 *Bombus terrestris* samples. ## Description of the data and file structure Dataset 1 (TAS\_bombus\_dataset1.vcf.gz) consists of 35,836 SNPs and was generated for neutral genetic clustering analyses. Setting in populations in STACKS were *-R 0.80, --write-single-snp*, *--hwe 0.05 and --min-mac 2*. The dataset was also pruned for SNPs in linkage-disequilibrium using the *--indep-pairwise 50* (window size), *5* (step size), and *0.2* (r<sup>^2</sup> threshold) option in *Plink v.1.9*. Dataset 2 (TAS\_bombus\_dataset2.vcf.gz) (90,396 SNPs) was filtered identically to dataset 1 except it included all SNPs per locus in order to reconstruct the full haplotype information. This dataset was used for fineRADstructure analysis. Dataset 3 (TAS\_bombus\_dataset3.vcf.gz) (33,832 SNPs) was generated for selection analyses (*-R 0.80, --write-single-snp*, *--min-maf 0.05 and --min-mac 2*), whereby loci in linkage disequilibrium were not pruned, but a single SNP per RAD tag was retained. For all three datasets full-siblings has been removed (*--relatedness2* filter in VCFtools). Individuals with high missing data and low read depth were removed (*populations*: *-R 0.5, --hwe 0.05*). Data quality was checked using the *--missing-indv* and *--site-mean-depth* options in VCFtools. ##