DOI: 10.5061/dryad.579kj
title: Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)

description: Harmful algal blooms (HABs), which can be lethal in marine species and
 cause illness in humans, are increasing worldwide. In the Gulf of Mexico,
 HABs of Karenia brevis produce neurotoxic brevetoxins that cause
 large-scale marine mortality events. The long history of such blooms,
 combined with the potentially severe effects of exposure, may have
 produced a strong selective pressure for evolved resistance. Advances in
 next-generation sequencing, in particular genotyping-by-sequencing,
 greatly enable the genomic study of such adaptation in natural
 populations. We used restriction site-associated DNA (RAD) sequencing to
 investigate brevetoxicosis resistance in common bottlenose dolphins
 (Tursiops truncatus). To improve our understanding of the epidemiology and
 aetiology of brevetoxicosis and the potential for evolved resistance in an
 upper trophic level predator, we sequenced pools of genomic DNA from
 dolphins sampled from both coastal and estuarine populations in Florida
 and during multiple HAB-associated mortality events. We sequenced 129 594
 RAD loci and analysed 7431 single nucleotide polymorphisms (SNPs). The
 allele frequencies of many of these polymorphic loci differed
 significantly between live and dead dolphins. Some loci associated with
 survival showed patterns suggesting a common genetic-based mechanism of
 resistance to brevetoxins in bottlenose dolphins along the Gulf coast of
 Florida, but others suggested regionally specific mechanisms of resistance
 or reflected differences among HABs. We identified candidate genes that
 may be the evolutionary target for brevetoxin resistance by searching the
 dolphin genome for genes adjacent to survival-associated SNPs.
description: Stacks analysis of
 common bottlenose dolphin RAD sequencesResults 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.Stacks_results.csvRAD locus allele frequenciesAllele 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).RADallelefreq.csvFisher’s Exact Test for differences in allele frequency between live and dead bottlenose dolphinsResults (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.FishersExactTest.csvBayeScan analyses of comparisons of live and dead bottlenose dolphinsResults 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).BayeScan_results.csvSmoothed pairwise genetic differentiation (FST) and overall nucleotide diversity (pi)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 directionssmoothFst&Pi.csv