DOI: 10.5061/dryad.qbzkh18sz
title: Data for: Desert landscape features influencing the microgeographic genetic structure of Nelson’s pocket mouse Chaetodipus nelsoni

description: Elucidating the factors that drive the genetic patterns of natural
 populations is key in evolutionary biology, ecology, and conservation.
 Hence, it is crucial to understand the role that environmental features
 play in species' genetic diversity and structure. Landscape genetics
 measures functional connectivity and evaluates the effects of landscape
 composition, configuration, and heterogeneity on microevolutionary
 processes. Deserts constitute one of the world’s most widespread biomes
 and exhibit a striking heterogeneity of microhabitats, yet few landscape
 genetics studies have been performed with rodents in deserts. We evaluated
 the relationship between landscape and functional connectivity, at a
 microgeographic scale, of the Nelson’s pocket mouse Chaetodipus nelsoni in
 the Mapimí Biosphere Reserve (Chihuahuan desert). We used
 single-nucleotide polymorphisms and characterized the landscape based on
 on-site environmental data and from Landsat satellite images. We
 identified two distinct genetic clusters shaped by elevation, vegetation,
 and soil. The high elevation group showed higher connectivity in the
 elevated zones (1250-1350 m), with scarce vegetation and predominantly
 rocky soils; whereas that of the Low elevation group was at &lt;1200
 m, with denser vegetation and sandy soils. These genetic patterns are
 likely associated with the species’ locomotion type, feeding strategy, and
 building of burrows. Interestingly, we also identified morphological
 differences, where hind foot size was significantly smaller in individuals
 from High elevation compared to Low elevation, suggesting the possibility
 of ecomorphs associated with habitat differences and potential local
 adaptation processes, which should be explored further. These findings
 improve our understanding of the genetics and ecology of C. nelsoni and
 other desert rodents.
description: Sampling individuals in the wild. Tissue samples for extracting
 DNA. Library preparation and sequencing were performed at the University
 of Wisconsin Biotechnology Center (UWBC) following a Genotyping by
 sequencing approach. Libraries were prepared using the ApeKI enzyme
 (cutting site: C[AT]G) and sequenced on a single lane of an Illumina
 Hi-Seq 2500 with single-end 101 bp reads. A <em>de novo</em>
 assembly was performed using raw data processed with ipyrad (Eaton and
 Overcast 2020; https://ipyrad.readthedocs.io/en/master/). We further
 processed our data using VCFtools v.0.1.13 (see publication for the
 bioinformatics description).
description: # Data for: Desert landscape features influencing the microgeographic
 genetic structure of Nelson’s pocket mouse *Chaetodipus nelsoni*
 [https://doi.org/10.5061/dryad.qbzkh18sz](https://doi.org/10.5061/dryad.qbzkh18sz) ## Description of the data and file structure This repository includes four data sets Inquires to: [gissellap11@gmail.com](mailto:gissellap11@gmail.com) ### Files and variables #### - chaeto\_67\_2pop\_718snps : snp data for the 67 filtered individuals and 718 snps * chaeto_67_popK.str: str file format with 67 individuals * chaeto__def.str: str file with the final data set used for genomic analysis * chaeto95.vcf: raw data from GBS ApeKI enzyme single-end 101 bp reads **Description:** Input files for population genetic analyses (raw and filtered genomic data files) ## Code/software NA