DOI: 10.5061/dryad.fttdz08pg
title: Panmixia across elevation in thermally sensitive Andean dung beetles

description: Janzen’s seasonality hypothesis predicts that organisms inhabiting
 environments with limited climatic variability will evolve a reduced
 thermal tolerance breadth compared with organisms experiencing greater
 climatic variability. In turn, narrow tolerance breadth may select against
 dispersal across strong temperature gradients, such as those found across
 elevation. This can result in narrow elevational ranges and generate a
 pattern of isolation-by-environment, or neutral genetic differentiation
 correlated with environmental variables that is independent of geographic
 distance. We tested for signatures of isolation-by-environment across
 elevation using genome-wide SNP data from five species of Andean dung
 beetles (subfamily Scarabaeinae) with well-characterized, narrow thermal
 physiologies and narrow elevational distributions. Contrary to our
 expectations, we found no evidence of population genetic structure
 associated with elevation and little signal of isolation-by-environment.
 Further, elevational ranges for four of five species appear to be at
 equilibrium and show no evidence of demographic constraints at range
 limits. Taken together, these results suggest physiological constraints on
 dispersal may primarily operate outside of a stable realized niche, and
 point to a lower bound on the spatial scale of local adaptation.
description: 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 <i>de novo
 </i>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. 
description: 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.  <strong>data.zip: </strong>zipped archive of all intermediate (processed) data files, including locality information, PCA results, ABC results, BEDASSLE output, and data frames for plotting. <strong>vcfs.zip:</strong> zipped archive of .vcf files for each species (with MAF filter) <strong>abc_vcfs.zip:</strong> zipped archive of .vcf files for each species for ABC (without MAF filter)