Environmental and anthropogenic factors mediating the functional connectivity of the mesquite lizard along the eastern Trans-Mexican Volcanic Belt

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 de..., See the main manuscript for a detailed method., , # 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. ...

功能连接性（functional connectivity）指景观促进或阻碍个体在景观中扩散的程度，是物种存续的关键因子。城市化、农业活动、道路建设等人为活动会对多数物种的功能连接性造成负面影响，对于扩散能力较弱的物种（如蜥蜴）尤为显著。本研究以墨西哥东跨墨西哥火山带广泛分布的广食性蜥蜴——牧豆树蜥蜴（Sceloporus grammicus）为研究对象，探究人为改造的景观在宏观与细尺度下对其功能连接性的影响。本研究首次利用基因组数据、全面的景观特征表征方法及包括重力模型在内的创新分析手段，估算了农业区与林区内该物种的遗传结构、基因流及功能连接性。研究结果显示，研究区域内存在显著的遗传分化，但该物种的功能连接性可维持数十公里……详细研究方法请参见主文稿。

# 本数据集为经分析的牧豆树蜥蜴（Sceloporus grammicus）组装简化基因组测序（genotyping-by-sequencing，GBS）数据（vcf文件）。
DOI: https://doi.org/10.5061/dryad.gtht76hvx
本仓库包含95份牧豆树蜥蜴（Sceloporus grammicus）的基因组数据，格式为vcf（已获取Sceloporus_grammicus ddRadSeq测序数据）。

## 数据与文件结构说明
本研究的文库构建与测序工作于威斯康星大学生物技术中心完成，采用双端ddRAD（双酶切限制性位点相关DNA测序）方案（Peterson等，2012），限制性内切酶选用PstI与BfaI。所有样本均在Illumina NovaSeq测序平台上进行测序，获取151bp双端测序读段。
95份蜥蜴样本的双端ddRAD文库共产出468,301,806条原始读段。本次测序泳道的有效读段平均占比为91.82%，平均质量值为35.5，表明测序质量达标。
本研究使用FASTQC v.0.11.9评估数据质量，并通过Stacks v.2.6内置的process_radtags工具进行样本拆分（解复用）……