Data from: Population genetic structure of a common host predicts the spread of white-nose syndrome, an emerging infectious disease in bats

Wilder AP, Kunz TH, Sorenson MD

Date Published: September 28, 2015

DOI: http://dx.doi.org/10.5061/dryad.v1v13

 

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Title Myotis cytb parsimony tree
Downloaded 2 times
Description Parsimony tree used to create Myotis lucifugus haplotype network, including outgroups and other Myotis lucifugus sequences downloaded from GenBank. See Key to cytb haplotypes for identification of individual sequences belonging to each haplotype.
Download cytb.parsimonyGB.tree (27.86 Kb)
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Title Key to cytb haplotypes
Downloaded 8 times
Description Sample ID and/or GenBank Accession number of sequences used to generate the cytb parsimony tree. The corresponding haplotype ID used in the tree file, and number of identical sequences belonging to the haplotype are provided.
Download CytbTreeKey.txt (25.74 Kb)
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Title Myotis cytb haplotype sequences
Downloaded 2 times
Description Cytb haplotype sequences (fasta format) used to create haplotype network. See Key to cytb haplotypes for samples and GenBank accession numbers belonging to each haplotype.
Download myluPars.fasta (165.3 Kb)
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Title SNPs from range-wide Myotis lucifugus ddRAD-seq
Downloaded 5 times
Description SNPs (STRUCTURE format) from ddRAD-seq data used in principal component analysis of range-wide samples. The first two columns give the sample name (with allele number) and the sampling locality. Headers for the remaining columns indicate the RAD locus and SNP number. -9 indicates missing data; 0 and 1 indicate indels; 2,3,4,5 indicate A,C,G,T, respectively
Download RADalln5010_84507.stru (106.6 Mb)
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Title ddRAD-seq from hibernating Myotis lucifugus colonies
Downloaded 3 times
Description ddRAD-seq data (nexus format) used to estimate PhiST among hibernating colonies of Myotis lucifugus for risk models of disease spread. Sequences represent unphased, concatenated RAD sequences. Headers indicate the sample name and locality. Only loci with genotype calls for all samples were included.
Download EriskCmplt871RVAPPAL.nex (10.40 Mb)
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Title ddRAD-seq from range-wide Myotis lucifugus
Downloaded 3 times
Description ddRAD-seq data (fasta format) from Myotis lucifugus sampled across their range. Unphased sequences were concatenated for each individual and used to estimate PhiST across sampling localities. Headers indicate sample ID (with allele number) and sampling locality. Only loci with genotype calls for all samples were included.
Download Perfect_Clusters.fasta (42.58 Mb)
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Title Cytb sequences from hibernating Myotis lucifugus colonies
Downloaded 3 times
Description Cytb sequences (fasta format) from hibernating colonies of Myotis lucifugus used to estimate PhiST for risk models of disease spread. Header indicates sample ID and sampling locality.
Download Cytb_Erisk.fasta (70.49 Kb)
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Title Genetic and geographic distance matrix from range-wide ddRAD-seq
Downloaded 6 times
Description Pairwise PhiST of ddRAD-seq (above diagonal) and geographic distance (km; below diagonal) between localities of Myotis lucifugus sampled across their range. The first four columns indicate Region (E=eastern, W=western), Site-type (M=maternity colony, H=hibernaculum, F=foraging site), sample size (N) and sampling locality (Site).
Download RAD_Rangewide.txt (18.83 Kb)
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Title Genetic and geographic distance matrix from range-wide cytb
Downloaded 3 times
Description Pairwise PhiST of cytb (above diagonal) and geographic distance (km; below diagonal) between localities of Myotis lucifugus sampled across their range. The first four columns indicate Region (E=eastern, W=western), Site-type (M=maternity colony, H=hibernaculum, F=foraging site), sample size (N) and sampling locality (Site).
Download Cytb_Rangewide.txt (31.45 Kb)
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Title Genetic and geographic distance matrix for ddRAD-seq among hibernacula
Downloaded 5 times
Description Pairwise PhiST of ddRAD-seq (above diagonal) and geographic distance (km; below diagonal) between hibernating colonies of Myotis lucifugus used in risk models of disease spread. Column 1 gives sample size (N) and column 2 gives sampling locality (Site).
Download RAD_Erisk.txt (1.906 Kb)
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Title Genetic and geographic distance matrix for cytb among hibernacula
Downloaded 3 times
Description Pairwise PhiST of cytb (above diagonal) and geographic distance (km; below diagonal) between hibernating colonies of Myotis lucifugus used in risk models of disease spread. Column 1 gives sample size (N) and column 2 gives sampling locality (Site).
Download Cytb_Erisk.txt (1.936 Kb)
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When using this data, please cite the original publication:

Wilder AP, Kunz TH, Sorenson MD (2015) Population genetic structure of a common host predicts the spread of white-nose syndrome, an emerging infectious disease in bats. Molecular Ecology 24(22): 5495–5506. http://dx.doi.org/10.1111/mec.13396

Additionally, please cite the Dryad data package:

Wilder AP, Kunz TH, Sorenson MD (2015) Data from: Population genetic structure of a common host predicts the spread of white-nose syndrome, an emerging infectious disease in bats. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v1v13
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