A Genomic Investigation of Divergence Between Tuna Species

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and applied as a reference for population genomic analysis of specimens from 9 localities spanning most of the Blackfin tuna range. Analysis suggested the presence of four weakly differentiated units corresponding to the northwestern Atlantic Ocean, Gulf of Mexico, Caribbean Sea, and southwestern Atlantic Ocean, respectively. Significant spatial autocorrelation of genotypes was observed for specimens collected within 800 km of each other. A high-quality genome assembly generated for the Yellowfin tuna using PacBio and Illumina sequences was scaffolded by a linkage map developed through analysis of the segregation of genome wide Single Nucleotide Polymorphisms in 164 larvae offspring from a single pair produced by controlled breeding. The genome assembly was used as a reference for population genomic analysis of juvenile specimens from the 4 main nursery areas hypothesized in the Atlantic Ocean basin. Analyses corroborated previously reported population subdivision between the east and west Atlantic Ocean, but also suggested subdivision associated with individual nursery areas within the east and west regions. Draft reference assemblies were generated for Albacore, Bigeye and Longtail tunas and used in combination with the Yellowfin and Blackfin tuna genomes obtained in this work and existing assemblies for bluefin tunas in preliminary analyses of genome wide variation between species of the Thunnus genus. Whole-genome derived SNP-based phylogenetic analysis of the Thunnus genus suggests phylogenetic relationships may be more complex than suggested in earlier work based on Restriction-site Associated DNA sequencing or muscle transcriptome sequencing and prompt for further analysis of the genus using a more comprehensive sampling of taxa in each oceanic basin

pdimens/harpy: v0.4.0

<h1>New features</h1> <ul> <li>naibr variant calling now relies on <code>whatshap</code> to back-phase BAM files from a phased VCF for much, much better variant calling</li> <li><code>harpy preflight</code> to do a full suite of file format validations on bam/fastq files prior to running one of the main modules</li> <li>lots more file-check validations and helpful error messages before harpy hands things over to snakemake</li> <li>regular RMarkdown reports have been completely revised using R::Flexdashboard</li> </ul> <h1>bugfixes</h1> <ul> <li>More file checks means fewer downstream errors</li> <li>typos corrected</li> </ul> <h1>breaking changes</h1> <h3>TL;DR: This release pretty much breaks every aspect of the the previous APIs. Pretend you've never used Harpy before</h3> <ul> <li>no more <code>--method</code> flag, instead methods have been submodule-arized into<ul> <li><code>harpy align --method bwa ...</code> is now <code>harpy align bwa ...</code></li> <li><code>harpy align --method ema...</code> is now <code>harpy align ema ....</code></li> <li><code>harpy variants snp --method...</code> is now <code>harpy snp method ....</code> (method = <code>freebayes</code> or <code>mpileup</code>)</li> <li>harpy variants sv --method...<code>is now</code>harpy sv method ....<code>(method =</code>leviathan<code>or</code>naibr`)</li> </ul> </li> <li><code>harpy extra</code> has been made into submodules too, now making:<ul> <li><code>harpy popgroup</code> to create the popgroup file</li> <li><code>harpy stitchparams</code> to create the STITCH parameter file</li> <li><code>harpy hpc</code> to create a SLURM hpc profile</li> </ul> </li> </ul&gt

A Genomic Assessment of Movement and Gene Flow Around the South Florida Vicariance Zone In the Migratory Coastal Blacknose Shark, \u3ci\u3eCarcharinus acronotus\u3c/i\u3e

South Florida has been identified as a genetic break for multiple mobile marine taxa but the mechanisms that impede gene flow largely remain unknown. To understand how South Florida functions as a barrier for blacknose shark, a highly migratory species that has genetically diverged Atlantic and Gulf populations, patterns of genetic variation were assessed in 212 individuals sampled from the Atlantic, eastern Gulf, and Florida Keys at 2213 nuclear-encoded SNP-containing loci. Results support divergence between the Gulf and Atlantic (FST ~ 0.002, P \u3c 0.05), and 51 individuals caught in the Keys were assigned to the Gulf, as compared to only two individuals that assigned to the Atlantic, indicating that Florida Keys is largely composed of Gulf individuals. Further, two to three migrants were identified, all of which were Gulf individuals captured in the Atlantic. The results indicate that South Florida does not prevent individual movement between the Gulf and Atlantic and that the Keys may be a seasonal mixing zone. However, the Gulf and Atlantic remain genetically independent, suggesting that region-specific reproductive behavior/compatibility, or aspects of movement ecology, such as swimming energetics or temperature-driven interannual variability in migratory range, may maintain divergence rather than a physical barrier in South Florida