The genomic response to urbanization in the damselfly Ischnura elegans
Data files
Oct 05, 2023 version files 1.12 GB
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aut_AND_X_DP_GQ_F_MISSING_0_5.vcf.gz
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localities.txt
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plink_files.tar.gz
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README.md
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samples.txt
Abstract
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.
README: The genomic response to urbanization in the damselfly Ischnura elegans
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.
Methods
SNP genotypes obtained using RAD-seq and the associated metadata.