DOI: 10.5061/dryad.rfj6q57h3
title: The genomic response to urbanization in the damselfly Ischnura elegans

description: The complex and rapid environmental changes brought about by urbanization
 pose significant challenges to organisms. The multifaceted effects of
 urbanization often make it difficult to define and pinpoint the very
 nature of adaptive urban phenotypes. In such situations, scanning genomes
 for regions differentiated between urban and non-urban populations may be
 an attractive approach. Here, we investigated the genomic signatures of
 adaptation to urbanization in the damselfly Ischnura elegans sampled from
 31 rural and urban localities in three geographic regions: southern and
 northern Poland, and southern Sweden. Genome-wide variation was assessed
 using more than 370,000 single nucleotide polymorphisms (SNPs) genotyped
 by ddRADseq. Associations between SNPs and the level of urbanization were
 tested using two genetic environment association methods: LFMM and
 BayPass. While we found numerous candidate SNPs and a highly significant
 overlap between candidates identified by the two methods within the
 geographic regions, there was a distinctive lack of repeatability between
 the geographic regions both at the level of individual SNPs and of genomic
 regions. However, we found “synapse organization” at the top of the
 functional categories enriched among the genes located in the proximity of
 the candidate urbanization SNPs. Interestingly, the overall significance
 of “synapse organization” was built up by the accretion of different genes
 associated with candidate SNPs in different geographic regions. This
 finding is consistent with the highly polygenic nature of adaptation,
 where the response may be achieved through a subtle adjustment of allele
 frequencies in different genes that contribute to adaptive phenotypes.
 Taken together, our results point to a polygenic adaptive response in the
 nervous system, specifically implicating genes involved in synapse
 organization, which mirrors the findings from several genomic and
 behavioral studies of adaptation to urbanization in other taxa. 
description: SNP genotypes obtained using RAD-seq and the associated
 metadata.
description: # The genomic response to urbanization in the damselfly Ischnura elegans
 [https://doi.org/10.5061/dryad.rfj6q57h3](https://doi.org/10.5061/dryad.rfj6q57h3) ## Description of the data and file structure The dataset contains **metainformation** in two files: samples.txt * sample: RADseq sample * individual\_id: individual code * pop: population acronym * cov: coverage from gstacks * n\_missing: number of genotypes missing following the final filtering as described in the paper * fr\_missing: fraction of genotypes missing following the final filtering as described in the paper localities.txt * locality: locality full name * pop: population acronym * region: geographic region * urbanization score: as described in the paper * AMeanT: region standardized mean annual temperature as described in the paper Full locality information can be added to samples by joining on the pop field. **SNP genotypes** are in: aut\_AND\_X\_DP\_GQ\_F\_MISSING\_0\_5.vcf.gz - VCF file containing SNPs on scaffolds assigned to chromosomes, following quality filtering as described in the paper; sample IDs correspond to those in samples.txt plink\_files.tar.gz - plink .ped and .map files with genotypes used for GEA analyses as described in the paper; sample ids correspond to those in samples.txt. The naming scheme is as follows: {"", "Pl\_N", "Pl\_S", "Se\_S"}\_{"non\_inv\_aut\_AND\_X", "inv\_ch5", "inv\_XL", "inv\_XR"}\*, where the first part is the regional origin of the dataset, with "" for the full dataset, while the second part is the genomic region: noninverted and the there regions of putative polymorphic inversions as described in the paper.