RAD locus allele frequencies

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)

BayeScan analyses of comparisons of live and dead bottlenose dolphins

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)

Stacks analysis of common bottlenose dolphin RAD sequences

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

Fisher’s Exact Test for differences in allele frequency between live and dead bottlenose dolphins

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

Smoothed 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 direction

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

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

Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations

Plumage microorganism communities of tidal marsh sparrows

Summary: Microorganism communities can shape host phenotype evolution but are often comprised of thousands of taxa with varied impact on hosts. Identification of taxa influencing host evolution relies on first describing microorganism communities and acquisition routes. Keratinolytic (keratin-degrading) microorganisms are hypothesized to be abundant in saltmarsh sediments and to contribute to plumage evolution in saltmarsh-adapted sparrows. Metabarcoding was used to describe plumage bacterial (16S rRNA) and fungal (ITS) communities in three sparrow species endemic to North America’s Atlantic coast saltmarshes. Results describe limited within-species variability and moderate host species-level patterns in microorganism diversity and community composition. A small percentage of overall microorganism diversity was comprised of potentially keratinolytic microorganisms, warranting further functional studies. Distinctions between plumage and saltmarsh sediment bacteria, but not fungal, communities were detected, suggesting multiple bacterial acquisition routes and/or vertebrate host specialization. This research lays groundwork for future testing of causal links between microorganisms and avian host evolution

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals

Cammen KM, Andrews KR, Carroll EL, et al. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. Journal of Heredity. 2016;107(6):481-495

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals

The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs