DOI: 10.5061/dryad.gtht76hvx
title: Data from: Environmental and anthropogenic factors mediating the functional connectivity of the mesquite lizard along the eastern Trans-Mexican Volcanic Belt

description: Functional connectivity, the extent to which a landscape facilitates or
 impedes the dispersal of individuals across the landscape, is a key factor
 for the survival of species. Anthropogenic activities such as
 urbanization, agriculture, and roads, negatively impact functional
 connectivity of most species, particularly low-vagility species like
 lizards. Here, we examine how a landscape modified by anthropogenic
 activities affects the functional connectivity, at both broad and fine
 scales, of a widely distributed generalist lizard Sceloporus grammicus in
 the eastern Trans-Mexican Volcanic Belt, Mexico. We estimated for the
 first time the species genetic structure, gene flow, and functional
 connectivity in agricultural and forest zones using genomic data, a
 comprehensive landscape characterization, and novel methods including
 gravity models. Our results showed marked genetic differentiation across
 the study region but also that functional connectivity is maintained for
 tens of kilometers despite S. grammicus low vagility. Specifically, we
 found that substrate and air temperature facilitated connectivity over
 broad and fine scales, respectively, while agricultural cover, relative
 humidity, and slope were important for connectivity and gene flow.
 Contrastingly, forest cover and roads favored (broad-scale) and limited
 (fine-scale) connectivity, likely associated with movement facilitated by
 small forest patches and with thermoregulation. Altogether, these results
 support that S. grammicus alternates its thermoregulatory behavior
 depending on the distance traveled and the habitat environmental
 conditions, and that it can disperse through relatively modified
 landscapes, mainly using agricultural zones. The information obtained is
 crucial to understanding the response of lizards to current anthropogenic
 pressures and their potential to adapt.
description: See the main manuscript for a detailed method.
description: # Assembled GBS data (vcf file) of the mesquite lizard Sceloporus
 grammicus anaylzed.
 [https://doi.org/10.5061/dryad.gtht76hvx](https://doi.org/10.5061/dryad.gtht76hvx) This repository includes the genomic data of the mesquite lizard *Sceloporus gramicus* (95 samples) in **vcf format** (Seloporus_grammicus ddRadSeq obtained). ## Description of the data and file structure Library preparation and sequencing were performed at the University of Wisconsin Biotechnology Center using the paired-end ddRAD protocol (Peterson et al., 2012) and the restriction enzymes PstI and BfaI. Samples were sequenced on an Illumina NovaSeq line to obtain 151-bp paired reads. The paired-end ddRAD library for the 95 lizards generated 468,301,806 raw reads. The sequencing lane retained an average of 91.82% of the reads and had an average quality score of 35.5, indicating appropriate sequencing. We used FASTQC v.0.11.9 to assess data quality and demultiplexed using process_radtags included in Stacks v.2.6. We removed adapters and reads with Phred quality &lt;20, trimmed reads to 126 bp length with Trimmomatic v.0.36, and removed reads with kmers using kmer_filter in Stacks v.2.6.