DOI: 10.5061/dryad.1jwstqk43
title: Data from: Comparative landscape genomics reveals species-specific spatial patterns and suggests human-aided dispersal in a global hotspot for biological invasions

description: Biological invasions are a growing threat to native ecosystems, and
 genomic studies have become an increasingly useful tool for invasive
 species management by providing the ability to identify spatial population
 structure in the invaded range. In this study, we compared the spatial
 genetic structure of two ecologically distinct non-native lizard species
 both established and widespread throughout South Florida, a global hotspot
 for reptile invasions. We used an individual-based sampling approach to
 collect genetic samples of Agama picticauda, a rock specialist native to
 West Africa, and Basiliscus vittatus, a riparian specialist from Central
 and South America. We collected specimens across Miami-Dade County (the
 original site of introduction) and then genotyped ~4,000 single nucleotide
 polymorphisms (SNPs) for each species. Both species exhibited fine-scale
 population structure at distances &lt;5 km for A. picticauda and
 &lt;10 km for B. vitattus, but at the county scale B. vittatus showed
 much stronger spatial structure compared to A. picticauda. Landscape
 genomic analysis revealed no significant landscape influence on A.
 picticauda genetic differentiation, while for B. vittatus low canopy cover
 was the best predictor of genetic connectivity. The genetic structure of
 both species may suggest human-aided dispersal is driving long distance
 movements, and A. picticauda appear more susceptible to these events
 likely due to their affinity for highly urbanized areas. By identifying
 variable dispersal patterns among two ecologically distinct species, we
 hope that this study will help combat the spread of these or similar
 species as they continue to arrive at urban centers across the
 globe. 
description: Genomic DNA was extracted from tissues (liver or muscle) using
 Qiagen’s DNeasy Blood and Tissue Extraction kit (Qiagen, Hilden, Germany),
 following the standard extraction protocol. DNA quality was checked by
 running 100 ng of each sample on a 1% agarose gel to confirm intact,
 unfragmented DNA. DNA samples were sent to University of
 Wisconsin-Madison’s Biotechnology Center DNA Sequencing Facility for
 genotyping-by-sequencing using the restriction enzyme ApeKI for both
 species (following enzyme optimization). SNPs were called using the
 non-reference genome version of the Universal Network Enabled Analysis Kit
 (UNEAK) pipeline (Lu et al. 2013) implemented in Tassel 3.0 (Bradbury et
 al. 2007). This pipeline trims reads to 64 bp, merges identical reads into
 tags within each barcoded individual, and uses pairwise alignment to
 identify tag pairs with 1 bp mismatch (while probabilistically correcting
 sequencing errors using the error tolerance rate parameter set to 0.05).
 This resulted in 388,535 SNPs for A. picticauda and 497,346 SNPs for
 <em>B. vittatus</em>. These candidate SNPs were further
 filtered to only those present in &gt;90% of individuals and those
 with &gt;5% minor allele frequency, which left a final dataset of
 4,446 and 3,952 SNPs for <em>A. picticauda</em> and
 <em>B. vittatus</em>, respectively, that was used for all
 analyses.
description: # Comparative landscape genomics reveals species-specific spatial patterns
 and suggests human-aided dispersal in a global hotspot for biological
 invasions
 [https://doi.org/10.5061/dryad.1jwstqk43](https://doi.org/10.5061/dryad.1jwstqk43) ## Description of the data and file structure Data provided includes fastq files for two lizard species, *Agama picticauda* and *Basiliscus vittatus*, and a metadata file with the date, coordinates and species tied to each matching ID in the fastq files. Genomic samples were extracted from the tissues of individuals captured in their invasive range in Miami-Dade County, Florida and fastq files are a result of genotyping-by-sequencing method. ### Files and variables #### File: sample\_metadata.xlsx **Description:** Metadata ##### Variables * Date: The date the individual was captured. NA represents samples that were acquired from colleagues and date is unknown. * LAT: The latitudinal coordinate of the site the individual was captured at (in decimal degrees). * LONG: The longitudinal coordinate of the site the individual was captured at (in decimal degrees). * ID: The matching sample ID in the fastq files. * Species: The species the sample is from. "Agama" = *Agama picticauda* and "Basilisk" = *Basiliscus vittatus* #### File: Searcy\_Aug4\_2020\_GBS\_S15\_L001\_R1\_001.fastq.gz **Description:** Raw sequencing outputs from genotyping-by-sequencing, Read 1. #### File: Searcy\_Aug4\_2020\_GBS\_S15\_L001\_R2\_001.fastq.gz **Description:** Raw sequencing outputs from genotyping-by-sequencing, Read 2.