VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data

In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behavior of target species, which can be modeled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1,056 individuals of two anuran and three urodele species (1,732–3,913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework and combined this genetic data with information obtained in a previous two-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results suggest a significant influence of local population sizes on patterns of genetic connectivity at small spatial scales. In addition, movement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level.

Methods
The vcf files available in this dataset were obtained from tissue samples from five syntopic pond-breeding amphibian species: Epidalea calamita, Triturus pygmaeus, Pelophylax perezi, Lissotriton boscai and Pleurodeles waltl. All species were sampled in the same study area, a dehesa pondscape located in the municipality of Alpedrete, Madrid, Spain. Tissue samples consisted in finger clips plus fin clips for Lissotriton boscai. Tissue was digested with proteinase K and DNA was extracted with the Promega Wizard Kit. Libraries were prepared using 3RAD and size selection was performed with Pippin Prep prior to sequencing. Sequenced reads were treated with Stacks to obtain the vcf files. Geographic-, demographic- and movement-related information were obtained in a previous study performed in the same spatial and temporal frame. Genetic distances, available as genetic matrices were obtained with EDENetworks, using filtered .vcf files from ponds with at least 4 individuals.