Data from: When new human-modified habitats favor the expansion of an amphibian pioneer species: evolutionary history of the natterjack toad (Bufo calamita) in a coal basin

Human activities affect microevolutionary dynamics by inducing environmental changes. In particular, land cover conversion and loss of native habitats decrease genetic diversity and jeopardize the adaptive ability of populations. Nonetheless, new anthropogenic habitats can also promote the successful establishment of emblematic pioneer species. We investigated this issue by examining the population genetic features and evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in northern France, where populations can be found in native coastal habitats and coalfield habitats shaped by European industrial history, along with an additional set of European populations located outside this focal area. We predicted contrasting patterns of genetic structure, with newly settled coalfield populations departing from migration–drift equilibrium. As expected, coalfield populations showed a mosaic of genetically divergent populations with short-range patterns of gene flow, and native coastal populations indicated an equilibrium state with an isolation-by-distance pattern suggestive of postglacial range expansion. However, coalfield populations exhibited (i) high levels of genetic diversity, (ii) no evidence of local inbreeding or reduced effective population size and (iii) multiple maternal mitochondrial lineages, a genetic footprint depicting independent colonization events. Furthermore, approximate Bayesian computations suggested several evolutionary trajectories from ancient isolation in glacial refugia during the Pleistocene, with biogeographical signatures of recent expansion probably confounded by human-mediated mixing of different lineages. From an evolutionary and conservation perspective, this study highlights the ecological value of industrial areas, provided that ongoing regional gene flow is ensured within the existing lineage boundaries

poolseq_analyses

R script describing the analyses made in the manuscript

top_SNP_per_hotspot

Coordinates of the top 1 SNP per hotspot (based on KLD values from the SelEstim analysis) on the v2 assembly

X-A_assignment

Coordinates (v2 assembly) of the X chromosome or autosome blocks identified by Jaquiéry et al. 2018 GBE

SelEstim output

Full output from the SelEstim analysis, see the README file for the command used

windows_50k_10k

Results of the sliding window analysis. For each 50kb window (10 kb step size) are given its coordinates, multilocus (overall and pairwise) F_ST estimates, pi_XY estimates, heterozygosity estimates, total number of SNPs within the window and number of SNPs above a given KLD threshold. Outlier windows are defined as windows with at least 10 SNPs with KLD values greater than the 99% quantile

Data from: Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races

Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genome-wide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes. Most of these highly differentiated regions were located on the autosomes and overall differentiation was weaker on the X chromosome. High levels of absolute divergence between races within hotspots suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host plant specialization and ecological isolation in the pea aphid complex

SNP_refcounts.tab

Reference allele count data for each of the 1,588,558 SNPs in each BAM file (2 per host race, ALF: alfalfa, CLO: clover, PEA: Pea). Coordinates on the v2 assembly (SCAFFOLD_POSITION) are given as row names

Contig_coordinates

Contig coordinates on the v2 assembly scaffolds. For each contig are given its start and end positions in the scaffold along with its length

coordinates_CS_salivary_candidates

Genomic coordinates of all chemosensory and salivary candidates (v2 assembly)