DOI: 10.5061/dryad.9ghx3ffr2
title: Limited evidence for genetic differentiation or adaptation in two amphibian species across replicated rural-urban gradients

description: Urbanization leads to complex environmental changes and poses multiple
 challenges to organisms. Amphibians are highly susceptible to the effects
 of urbanization, with land use conversion, habitat destruction, and
 degradation ranked as the most significant threats. Consequently,
 amphibians are declining in urban areas, in both population numbers and
 abundance, however, the effect of urbanization on population genetic
 parameters remains unclear. Here, we studied the genomic response to
 urbanization in two widespread European species, the common toad Bufo bufo
 (26 localities, 480 individuals), and the smooth newt Lissotriton vulgaris
 (30 localities, 516 individuals) in three geographic regions: southern and
 northern Poland and southern Norway. We assessed genome-wide SNP variation
 using RADseq (ca. 42 and 552 thousand SNPs in B. bufo and L. vulgaris,
 respectively) and adaptively relevant major histocompatibility complex
 (MHC) class I and II genes. The results linked most of the genetic
 differentiation in both marker types to regional (latitudinal) effects,
 which also correspond to historical biogeography. Further, we did not find
 any association between genetic differentiation when comparing urban and
 rural populations at local scales for either species. However, urban
 smooth newts have lower levels of within-population genome-wide diversity,
 suggesting higher susceptibility to the negative effects of urbanization.
 A decreasing level of genetic diversity linked to increasing urbanization
 was also found for MHC II in smooth newts, while the relationship between
 MHC class I diversity and urbanization differed between geographic
 regions. We did not find any effects of urbanization on MHC diversity in
 the toad populations. Although two genetic environment association
 analyses of genome-wide data, LFMM and BayPass, revealed numerous (219 in
 B. bufo and 7040 in L. vulgaris) SNPs statistically associated with
 urbanization, we found a marked lack of repeatability between geographic
 regions, suggesting a complex and multifaceted response to natural
 selection elicited by life in the city.
description: # Limited evidence for genetic differentiation or adaptation in two
 amphibian species across replicated rural-urban gradients
 [https://doi.org/10.5061/dryad.9ghx3ffr2](https://doi.org/10.5061/dryad.9ghx3ffr2) RADseq SNP data, MHC genotypes, as well as sample and locality information for all samples and data used in the study ## Description of the data and file structure ### Information about samples and localities *samples.txt* * species: species * 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* * species: species * locality: locality acronym * latitude: latitude * longitude: longitude * region: geographic region * urbanization score: scoring as described in the paper Full locality information can be added to samples by joining on the pop field. ### RADseq SNP genotypes are in: ***Bufo bufo*** *Bufo_filtered_renamedCHR_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 *Bufo_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. "ALL" - entire dataset, "NO" - Norway, "PL_N" - northern Poland, "PL_S" - southern Poland, "PLALL" - northern and southern Poland combined. ***Lissotriton vulgaris*** *filtered_DP_GQ_F_MISSING_0_5.vcf.gz* VCF file containing SNPs identified in RAD loci, following quality filtering as described in the paper; sample IDs correspond to those in samples.txt *Lisso_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. "ALL" - entire dataset, "NO" - Norway, "PL_N" - northern Poland, "PL_S" - southern Poland, "PLALL" - northern and southern Poland combined. Note that one population in Oslo, Norway, likely suffered an extreme founder event, and this population was excluded from ALL and NO datasets ("_noU1") ### MHC **MHC sequences** Sequences of all MHC alleles are in files: *Bufo_MHC_I_allele_seq.fas* *Bufo_MHC_II_allele_seq.fas* *Lisso_MHC_I_allele_seq.fas* *Lisso_MHC_II_allele_seq.fas* **MHC genotypes** MHC genotypes, for each species and MHC class are in the files: *Bufo_MHC_I_genotypes.txt* *Bufo_MHC_II_genotypes.txt* *Lisso_MHC_I_genotypes.txt* *Lisso_MHC_II_genotypes.txt* Genotypes form a rectangular matrix with individuals in rows, alleles in columns, and allele presence-absence indicated as 1/0. Column locality allows linking these data to localities.txt.