Data from: Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Manthey JD, Moyle RG

Date Published: June 2, 2015

DOI: http://dx.doi.org/10.5061/dryad.8hm4p

 

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Title Sitta_FASTQ
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Description FASTq sequences for all individuals used in the study (part 1/3).
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Title Sitta_FASTQ2
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Description FASTq sequences for all individuals used in the study (part 2/3).
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Title Sitta_FASTQ3
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Description FASTq sequences for all individuals used in the study (part 3/3).
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Title bayenv2 files
Downloaded 72 times
Description BayEnv2 input and output files. sitta4.env and sitta7.env are environment files for max. temp. of warmest month and min. precip. of driest month for each population. bf_environ files are the output of the program. Also included is the SNP frequency matrix, a file to link SNPs with their locus name, and the covariance matrix calculated in BayEnv2.
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Title bayescan files
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Description Infile and output from BayeScan analyses. Also included is a file associating SNPs with their locus names.
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Title BEDASSLE files
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Description Input and output BEDASSLE files. Genetic data for each population are in the allele.counts and sample.sizes files. Environmental data matrices are located in the .csv files. Output is in R object files. Included are two replicates of output using the PCA-based environmental data (Sitta1_BB_MCMC and Sitta2_BB_MCMC files) and two replicates using temperature and precipitation data as environmental data (Sitta_66_2var files).
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Title FASTA_BLAST
Downloaded 65 times
Description FASTA file of consensus sequences containing all SNPs used in the study and BLAST+ results of these loci.
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Title LFMM files
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Description Input used in LFMM analyses including genetic (sitta.lfmm) and environmental (sitta.lfmm.env) data for each individual.
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Title Model_Points
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Description Training and testing points used for ecological niche modeling.
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Title Sitta_Data
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Description Characteristics of sky islands, including area of forest cover, distance to the niche centroid, distance to Mogollon Rim and Sierra Madre Occidental, and distance to nearest mainland.
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Title Pairwise comparisons
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Description Pairwise comparisons of geographic (distance.km) and environmental (distance.e) distances between populations and genetic differentiation (FST) between populations. Genetic differentiation is based on STACKS output using eight different settings. m1, m5, m10, and m15 indicate stats when changing the minimum read depth for loci to be included in the dataset with a minimum of two individuals per population. limited and 90% indicate when more restrictive sampling is necessary for SNPs to be included (as described in the manuscript). select and no_select indicate genetic differentiation when only loci under selection are included or loci under selection are excluded, respectively.
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Title STACKS_output
Downloaded 61 times
Description STACKS output. Included are the catalog.tags file, a population map, a whitelist of loci used in the main analyses, and output of the populations module for eight settings (as described in pairwise comparisons data upload). Each directory includes an FST summary, summary statistics per locus and overall, and all SNP data (in STRUCTURE format).
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When using this data, please cite the original publication:

Manthey JD, Moyle RG (2015) Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach. Molecular Ecology 24(14): 3628–3638. http://dx.doi.org/10.1111/mec.13258

Additionally, please cite the Dryad data package:

Manthey JD, Moyle RG (2015) Data from: Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8hm4p
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