Migration-related phenotypic divergence is associated with epigenetic modifications in rainbow trout.

Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological and behavioural transition undertaken by juveniles in preparation for seaward migration. O. mykiss is experimentally tractable and displays intra- and interpopulation variation in migration propensity. Migratory individuals can produce nonmigratory progeny and vice versa, indicating a high degree of phenotypic plasticity. One potential way that phenotypic plasticity might be linked to variation in migration-related life history tactics is through epigenetic regulation of gene expression. To explore this, we quantitatively measured genome-scale DNA methylation in fin tissue using reduced representation bisulphite sequencing of F2 siblings produced from a cross between steelhead (migratory) and rainbow trout (nonmigratory) lines. We identified 57 differentially methylated regions (DMRs) between smolt and resident O. mykiss juveniles. DMRs were high in magnitude, with up to 62% differential methylation between life history types, and over half of the gene-associated DMRs were in transcriptional regulatory regions. Many of the DMRs encode proteins with activity relevant to migration-related transitions (e.g. circadian rhythm pathway, nervous system development, protein kinase activity). This study provides the first evidence of a relationship between epigenetic variation and life history divergence associated with migration-related traits in any species.

Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River.

Rainbow Trout, Oncorhynchus mykiss, exhibit high levels of phenotypic diversity leading to the recognition of numerous subspecies. A major distinction among Rainbow Trout subspecies exists between Coastal Rainbow Trout (O. m. irideus), which occurs west of the Cascade and Sierra Nevada mountain ranges, and interior Redband Trout (O. mykiss sspp.), largely distributed to the east. Interior Redband Trout are composed of three primary lineages and can share various outward, anatomical or physiological characteristics that are often symplesiomorphies or examples of convergence. We examine high-throughput DNA sequence data from Sacramento Redband Trout O. m. stonei from the Upper Pit and Upper McCloud Rivers along with representatives of Rainbow Trout and Golden Trout lineages to clarify the composition and relationships of the Sacramento Redband Trout. We find O. m. stonei to be polyphyletic, divided between populations in the Pit River and the Upper McCloud River. Redband Trout obtained from the Pit River are most-closely related to Great Basin Redband Trout O. m. newberrii and to fish of the Warner Lakes Basin and Surprise Valley within the O. m. newberrii lineage. The type specimen of O. m. stonei, collected from the Lower McCloud River, is phenotypically similar to Great Basin Redband Trout. We find as well that the isolated populations of trout in the Upper McCloud River Basin represent a lineage of Rainbow Trout now restricted to that region, are monophyletic and are not most closely related to the interior Redband Trout lineages of O. m. newberrii or O. m. gairdnerii. Furthermore, they are not represented by the type specimens of O. m. stonei or O. m. shasta. Consequently, we formally describe the McCloud River Redband Trout O. mykiss calisulat, new subspecies.

Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon.

Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large-scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single-nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. We show that 80 well-chosen loci, drawn from a pool of over 11,500 SNPs developed from restriction site-associated DNA sequencing, can accurately identify Chinook salmon runs and select populations within run. No other SNP panel for Central Valley Chinook salmon has been able to achieve the high accuracy of assignment we show here. This panel will greatly improve our ability to study and manage this ecologically, economically, and socially important species and demonstrates the great utility of using genomics to study migratory species.

Genetic structure of the tick Ornithodoros coriaceus (Acari: Argasidae) in California, Nevada, and Oregon.

The argasid tick Ornithodoros coriaceus (Koch) is the only confirmed vector of epizootic bovine abortion (EBA) in the United States. The disease and its tick vector have historically been reported in the foothills of the Sierra Nevada Mountains and coast ranges of California. In the past two decades, the range of EBA has apparently expanded into southern Oregon and northern Nevada. Possible explanations for this expansion include 1) increased recognition and reporting of EBA in these regions; 2) widespread movement of tick-infested and EBA-infected hosts with subsequent colonization of these regions by infected ticks; and 3) widespread movement of the EBA agent, independent of tick movements, into extant tick populations in these new regions. The current study was performed to evaluate these hypotheses by examining patterns of variability in a 420-bp segment of the 16S mitochondrial rDNA gene sequence among 210 O. coriaceus individuals from 14 sites in California, Oregon, and Nevada. Sixty-three unique haplotypes were identified in the ticks tested, with 84% of the sequence variation attributable to among-population variation and 16% to within-population variation. A majority of the haplotypes were unique to their particular collection site, whereas only four collection sites shared haplotypes. Overall, very little evidence of gene flow among tick populations was detected, making it unlikely that widespread tick movement had introduced O. coriaceus and the EBA agent into new regions.

Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq.

Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon.

Subspecies-informative SNP assays for evaluating introgression between native golden trout and introduced rainbow trout.

We characterize 20 single nucleotide polymorphism assays for evaluating hybridization between native golden trout subspecies (Oncorhynchus mykiss aguabonita and O. m. whitei) and introduced rainbow trout strains. These assays utilize the 5'-nuclease reaction, facilitating high-throughput genotyping of many individuals and making them useful in quantifying and monitoring introgression and potentially applicable to studies of other O. mykiss groups. Minor allele frequency differentials (δq) among native and introduced rainbow groups ranged from 0 to 1, with an average differential of 0.75 for both subspecies aguabonita and whitei relative to the hatchery rainbow trout strain.

Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts.

Ten primer pairs were screened to develop single nucleotide polymorphism (SNP) TaqMan assays that will distinguish California golden trout and some rainbow trouts (Oncorhynchus mykiss sspp., O. m. aguabonita) from the Paiute and Lahontan cutthroat trouts (Oncorhynchus clarkii seleniris, O. c. henshawi). From these 10 primer pairs, one mitochondrial and five nuclear fixed SNP differences were discovered and developed into TaqMan assays. These six assays will be useful for characterizing and monitoring hybridization between these groups. Additional Oncorhynchus clarkii sspp. and Oncorhynchus mykiss sspp. were assayed to determine if these assays are useful in closely related species.