Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)

Cammen KM, Schultz TF, Rosel PE, Wells RS, Read AJ

Date Published: August 18, 2015

DOI: http://dx.doi.org/10.5061/dryad.579kj

 

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Title Stacks analysis of common bottlenose dolphin RAD sequences
Downloaded 16 times
Description Results of Stacks analysis of RAD sequencing data generated from pooled genomic DNA from common bottlenose dolphins sampled along the Florida Gulf of Mexico coastline. Sample pools include live coastal dolphins from the Florida Panhandle (PLC, N=17) and central-west Florida (CWLC, N=26) and live estuarine dolphins from St. Joseph Bay in the Panhandle (PLE, N=12) and Sarasota Bay in central-west Florida (CWLE, N=25). Additional sample pools include samples from bottlenose dolphin strandings (dead samples) during unusual mortality events (UMEs) associated with harmful algal blooms (HABs) in the Panhandle in 1999 (PU99, N=16) and 2004 (PU04, N=35) and during HABs between 1992 and 2006, including a UME in 2005-2006, in central-west Florida (CWU, N=25). Two groups of samples (PLC and CWU) were divided for sequencing into pools of excellent and good quality genomic DNA. PL represents samples from the Florida Panhandle that cannot be definitively attributed to either coastal or estuarine dolphin populations. Stacks parameters are described in the Methods section of Cammen et al. (2015). Chromosome accession numbers refer to scaffolds in the bottlenose dolphin genome: Ttru_1.4/turTru2 (GCA_000151865.2). The spreadsheet includes both the alleles detected at each RAD locus as well as the depth of read coverage within the sample pool for the given alleles. Analyses described in the manuscript were conducted on a subset of these RAD loci that passed additional filters: 1 SNP with a sample-wide minor allele frequency greater than 0.10; present in at least 2 sample pools.
Download Stacks_results.csv (38.74 Mb)
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Title RAD locus allele frequencies
Downloaded 13 times
Description Allele frequencies for 7,431 polymorphic (single SNP) RAD loci that were assessed for an association with bottlenose dolphin survival following exposure to harmful algal blooms. Allele frequencies for each sample pool were calculated based on the proportion of reads sequenced for each SNP variant (see “Stacks analysis of RAD data” Dryad file). Depth indicates the total number of reads per locus and sample pool; sample size indicates the number of individuals sequenced in the sample pool (note this varies for PLC and CWU because individuals of good and excellent quality DNA were separated during library preparation).
Download RADallelefreq.csv (1.235 Mb)
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Title Fisher’s Exact Test for differences in allele frequency between live and dead bottlenose dolphins
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Description Results (p values) of Fisher’s Exact Test for differences in allele frequency between pools of live and dead dolphins. Sample pool abbreviations as in description for “Stacks analysis of common bottlenose dolphin RAD sequences.” Fisher’s exact tests, which were implemented in R, use a contingency table approach to assess deviations from a null hypothesis of no association between genotype and phenotype for each locus independently.
Download FishersExactTest.csv (389.0 Kb)
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Title BayeScan analyses of comparisons of live and dead bottlenose dolphins
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Description Results of BayeScan analyses of comparisons of RADseq allele frequencies between live and dead dolphins. Sample pool abbreviations as in description for “Stacks analysis of common bottlenose dolphin RAD sequences.” BayeScan (v2.1) implements a Bayesian approach to assess evidence for selection at a given locus by comparing population- and locus-specific components of FST across multiple loci (Foll and Gaggioti 2008).
Download BayeScan_results.csv (1.760 Mb)
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Title Smoothed pairwise genetic differentiation (FST) and overall nucleotide diversity (pi)
Downloaded 8 times
Description Smoothed pairwise genetic differentiation (FST) and overall nucleotide diversity (pi) across bottlenose dolphin RAD loci. Sample pool abbreviations as in description for “Stacks analysis of common bottlenose dolphin RAD sequences.” FST was calculated from nucleotide diversity at each population and across the pooled populations, where nucleotide diversity was calculated using allele counts (see equation 2 in Hohenlohe et al. 2010). Accession numbers refer to scaffolds in the killer whale genome (Oorc_1.1, GCA_000331955.2). Smoothed average FST was calculated using a Gaussian function with theta of 150kb and windows truncated at 3σ from centre in both directions
Download smoothFst&Pi.csv (12.49 Mb)
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When using this data, please cite the original publication:

Cammen KM, Schultz TF, Rosel PE, Wells RS, Read AJ (2015) Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus). Molecular Ecology 24(18): 4697–4710. http://dx.doi.org/10.1111/mec.13350

Additionally, please cite the Dryad data package:

Cammen KM, Schultz TF, Rosel PE, Wells RS, Read AJ (2015) Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.579kj
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