Panmixia across elevation in thermally sensitive Andean dung beetles
Linck, Ethan; Celi, Jorge; Sheldon, Kimberly (2020), Panmixia across elevation in thermally sensitive Andean dung beetles, Dryad, Dataset, https://doi.org/10.5061/dryad.fttdz08pg
We sampled populations of our five focal species (Deltochilum speciosissimum, Deltochilum tesselatum, Dichotomius podalirius, Dichotomius satanas, Eurysternus affin. flocossus) along two elevational and two horizontal transects on the eastern slope of the Andes Mountains in Napo Province, Ecuador. Our two elevational transects spanned 730 to 1175 m and 1500 to 1950 m in largely undisturbed humid forest, with four sampling localities spaced as close to 125 m apart as possible given local constraints of soil and topography. Our two horizontal transects were each approximately 2 km long, with one transect having four points and the other having two points. Both horizontal transects were located in replicate corridors of montane forest at 2150 m asl separated by a natural barrier, the Cosanga River. No species were shared between the two elevational transects. We extracted genomic DNA from all samples using Qiagen DNeasy kits and the manufacturer’s recommended protocol for insects. To prepare libraries for reduced representation high throughput sequencing, we used a double restriction enzyme digest approach adapted from Gompert et al., 2014. After initially demultiplexing our libraries using our unique barcodes and a Python script implemented in the first step of ipyrad (Eaton, 2014), we assembled sequencing reads and called and filtered variants for each species independently using the dDocent pipeline (v. 2.7.8), a set of bash wrapper scripts optimized for population genomics of nonmodel organisms requiring de novo assemblies (Puritz, Hollenbeck, & Gold, 2014). We then used VCFtools, vcffilter (1.0.0) (https://github.com/vcflib/vcflib), and the dDocent script dDocent_filters to filter this file to high quality SNPs alone.
Uploaded data can be used in conjunction with scripts in the publication's GitHub repository (https://github.com/elinck/scarab_migration) to recreate all figures and results.
data.zip: zipped archive of all intermediate (processed) data files, including locality information, PCA results, ABC results, BEDASSLE output, and data frames for plotting.
vcfs.zip: zipped archive of .vcf files for each species (with MAF filter)
abc_vcfs.zip: zipped archive of .vcf files for each species for ABC (without MAF filter)
National Science Foundation, Award: IOS-1930829