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

[https://doi.org/10.5061/dryad.gxd2547sf](https://doi.org/10.5061/dryad.gxd2547sf)

## Description of the data and file structure

This dataset contains both \"raw\" unfiltered vcfs files obtained using the Stacks pipeline and R scripts for regression analyses using maximum-likelihood population effects models. In these models, genetic distance is used as response variable and several demographic, geographic and movement related variables as explanatory variables. Data for explanatory variables were obtained in a previous work. The study area is divided in half by a road; analyses were performed with and without cross-road connections between ponds. Scripts that exclude cross-road connections are identified by the suffix \"*\_no\_crossroad*\".

Scripts and all necessary data are compressed in a .rar file for each sp...