DOI: 10.5061/dryad.kprr4xhfs
title: Data from: Environmental gradients shape genetic variation in the desert moss, Syntrichia caninervis Mitt. (Pottiaceae)

description: The moss Syntrichia caninervis Mitt. is distributed throughout drylands
 globally, and often anchors ecologically significant communities known as
 biological soil crusts (biocrusts). The species occupies a variety of
 dryland habitats with varying levels of drought and temperature stress,
 suggesting the potential for ecological specialization within S.
 caninervis. Here, we sampled S. caninervis from sites along two elevation
 gradients and used restriction site associated DNA sequencing to compare
 the relative impacts of environmental factors and geospatial distances on
 genetic differentiation in S. caninervis populations. While we found no
 evidence of isolation by distance in our data, one environmental variable,
 mean annual precipitation (MAP), was found to be a positive predictor of
 FST. An ecological association analysis identified 32 SNP alleles that
 covary significantly with MAP, 15 of which fall within the exonic regions
 of genes with annotations suggesting diverse roles in response to
 dehydration stress. Understanding the degree to which genetic variation in
 S. caninervis is associated with environmental factors is key to
 predicting its potential for persistence in the face of global climate
 change, which is predicted to be especially detrimental to desert
 organisms already living at their physiological limits.
description: Samples underwent DNA extraction and double-digestion using the
 restriction enzymes MseI and PstI prior to RADseq. Libraries were
 multiplexed and sequenced in two lanes of a 1x150 Illumina NextSeq 500
 run. Raw fastq sequence data for each sample were submitted to the NCBI
 Sequence Read Archive and are available under BioProject accession number
 PRJNA1002376. <strong>De novo assembly and SNP
 filtering</strong>: Raw fastq sequence data were demultiplexed,
 trimmed to a consistent length of 60 bp, filtered for quality, and
 assembled de novo in STACKS v2. Initial filtering was performed to retain
 loci present in at least 60% of individuals across populations and with a
 minimum minor allele count (mac) of 6 (i.e., minor allele shared by at
 least three individuals). Identical multi-locus genotypes (MLGs) were
 identified in <em>poppr</em>, and the data set was
 subsequently filtered in VCFtools to retain one representative genotype
 per clone and to remove individual samples with more than 20% missing
 data. <strong>Reference-Based Assembly and SNP
 Filtering: </strong>Raw fastq sequence data were demultiplexed,
 trimmed, filtered for quality, and assembled to the <em>S.
 caninervis </em>reference genome using the iPyrad pipeline. iPyrad
 was also used to generate consensus loci across samples and identify SNPs.
 Parameters were set to retain only biallelic loci (max SNPs per locus =
 2), and to enforce the expectation of haploidy in the samples (max
 heterozygotes per consensus sequence = 0; max heterozygous sites per locus
 = 0). VCFtools was used to iteratively filter SNP loci. First, loci
 missing from more than 33% of the samples, or with a mac less than 4
 (i.e., not present in at least two individuals) were removed, as were
 individual samples with more than 50% missing data (122 samples, 18,067
 sites remaining). Next loci with more than 30% missing data in any of the
 populations were identified and filtered out. In
 <em>poppr</em>, identical multi-locus genotypes (MLGs) were
 identified and identical genotypes were subsequently filtered from the
 .vcf file to leave a single representative individual per genotype.
 Individuals from the NV high elevation site were also filtered from the
 data set, as too few (&lt; 5) individuals from this site remained for
 meaningful population genetic inference. Finally, the data set was
 filtered to remove sites on the sex chromosome (n=14), thinned so that all
 loci were separated by at least 2 Kb, and filtered to enforce a minimum
 minor allele frequency of 0.05 (i.e., minor alleles present in at least
 three individuals).
description: # Data from: Environmental gradients shape genetic variation in the desert
 moss, Syntrichia caninervis Mitt. (Pottiaceae)
 [https://doi.org/10.5061/dryad.kprr4xhfs](https://doi.org/10.5061/dryad.kprr4xhfs) ## Description of the data and file structure The data were collected in support of a study on population structure and environmental adaptation in a desert moss, *Syntrichia caninervis*. A total of 180 samples were genotyped through ddRAD-seq and two assemblies, one de novo and one reference-based, were performed. The vcf files generated after SNP calling and filtering for both assemblies are provided here, along with associated metadata.   ### Files and variables #### File: CC30.84\_population\_metadata.txt **Description:** This file contains information on the five populations represented in the SNP data set (CC30.84.vcf) derived from the reference-based assembly in Farah and Fisher (in press). Site data provided for each population include georeference (lat-long) coordinates, elevation in meters, and Mean Annual Precipitation (MAP) in millimeters. The NCBI SRA BioSample accession numbers for individuals from each population that contributed SNP genotype data to CC30.84.vcf are provided as a comma-separated list at the end of each population entry. ##### Variables * POPULATION ID: A brief population identifier that is appended to the sample names associated with the NCBI SRA BioSamples in PRJNA1002376 #### **File: CC30.84.vcf** **Description:** A vcf file generated by iPyrad_v.0.7.29 containing the SNP variant calls for 84 genotypes included in analyses of the reference-based assembly of RADseq loci in Farah and Fisher (in press). The #reference tag indicates the NCBI accession number for the* S. caninervis* reference genome, GCA_016097705.1  #### File: 123.cc147\_population\_metadata.txt **Description:** This file contains information on the six populations represented in the SNP data set (123.cc147.recode.vcf) derived from the reference-based assembly in Farah and Fisher (in press). Site data provided for each population include georeference (lat-long) coordinates, elevation in meters, and Mean Annual Precipitation (MAP) in millimeters. The NCBI SRA BioSample accession numbers for individuals from each population that contributed SNP genotype data to 23.cc147.recode.vcf are provided as a comma-separated list at the end of each population entry. ##### Variables * POPULATION ID: A brief population identifier that is appended to the sample names associated with the NCBI SRA BioSamples in PRJNA1002376  #### File: 123.cc147.recode.vcf **Description:** A vcf file generated by Stacks v2.52 containing the SNP variant calls for 147 genotypes included in analyses of the de novo assembly of RADseq loci in Farah and Fisher (in press).