Data from: Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris)

Lanier HC, Massatti R, He Q, Olson LE, Knowles LL

Date Published: July 29, 2015

DOI: http://dx.doi.org/10.5061/dryad.jh2fp

 

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Title Structure and PCA dataset
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Description Dataset used in STRUCTURE and PCA analyses.
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Title Population tree dataset
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Description Concatenated SNP data in phylip format used in population tree analyses
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Title Priors and rules for FastSimCoal2 analyses
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Description Priors and rules input file for analyses in FastSimCoal2
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Title Parameters for FastSimCoal2
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Description Parameter input file for the coalescence simulation program FastSimCoal2.
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Title Observed site frequency spectrum data
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Description Observed site frequency spectrum data used in FastSimCoal2 analyses
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Title FastSimCoal2 results
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Description Summary of results from fifty independent parameter estimations in FASTSIMCOAL2 to achieve the maximum composite likelihood of the joint SFS.
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Title Collared pika location
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Description Coordinate data used in Maxent simulations
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Title Climate data used in ENM (0 kya)
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Description Trimmed climate data (current climates) used to generate niche models in Maxent.
Download 0K_AK_bio_vars_cut.zip (34.33 Mb)
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Title Climate data used in ENM (21 kya)
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Description Trimmed climate data from the Last Glacial Maximum (21 kya) used to generate niche models in Maxent.
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Title Mantel test
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Description Distance data used in mantel tests
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Title Raw genomic data (Allie's Valley)
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Description Raw genomic RadSeq data from individuals in the Allie's Valley population. This zip archive contains 8 gzip compressed fastq files.
Download AlliesValley.zip (660.6 Mb)
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Title Raw genomic data (Anchorage)
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Description Raw genomic RadSeq data from individuals in the Anchorage population. This zip archive contains 6 gzip compressed fastq files.
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Title Raw genomic data (Crescent Creek)
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Description Raw genomic RadSeq data from individuals in the Crescent Creek population. This zip archive contains 7 gzip compressed fastq files.
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Title Raw genomic data (Denali Hwy)
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Description Raw genomic RadSeq data from individuals in the Denali Highway population. This zip archive contains 6 gzip compressed fastq files.
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Title Raw genomic data (Eagle Summit)
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Description Raw genomic RadSeq data from individuals in the Eagle Summit population. This zip archive contains 6 gzip compressed fastq files.
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Title Raw genomic data (Jawbone Lake)
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Description Raw genomic RadSeq data from individuals in the Jawbone Lake population. This zip archive contains 2 gzip compressed fastq files.
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Title Raw genomic data (Lake Kenibuna)
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Description Raw genomic RadSeq data from individuals in the Lake Kenibuna population. This zip archive contains 8 gzip compressed fastq files.
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Title Raw genomic data (Pika Camp)
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Description Raw genomic RadSeq data from individuals in the Pika Camp population. This zip archive contains 8 gzip compressed fastq files.
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Title Raw genomic data (Rock Lake)
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Description Raw genomic RadSeq data from individuals in the Rock Lake population. This zip archive contains 7 gzip compressed fastq files.
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When using this data, please cite the original publication:

Lanier HC, Massatti R, He Q, Olson LE, Knowles LL (2015) Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris). Molecular Ecology 24(14): 3688-3705. http://dx.doi.org/10.1111/mec.13270

Additionally, please cite the Dryad data package:

Lanier HC, Massatti R, He Q, Olson LE, Knowles LL (2015) Data from: Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.jh2fp
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