Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery.

A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing the methylation patterns in different generations of hatchery fish (G1, G2, G3) with their wild parents (G0). We discovered a total of 132 significant DMRs (p < .05) between G0 and G1, 132 significant DMRs between G0 and G2, and 201 significant DMRs between G0 and G3. Our results demonstrate substantial differences in methylation patterns emerged between the wild and hatchery-reared fish in the early generations in the hatchery, with a higher proportion of hypermethylated DMRs in hatchery-reared fish. The rearing environment was found to be a stronger predictor of individual clustering based on methylation patterns than family, sex or generation. Our study indicates a reinforcement of the epigenetic status with successive generations in the hatchery environment, as evidenced by an increase in methylation in hypermethylated DMRs and a decrease in methylation in hypomethylated DMRs over time. Lastly, our results demonstrated heterogeneity in inherited methylation pattern in families across generations. These insights highlight the long-term consequences of hatchery practices on the epigenetic landscape, potentially impacting wild fish populations.

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.

Effect of freezing rate for cryopreservation of Persian sturgeon (Acipenser persicus) spermatozoa.

This study examined the effect of freezing rate (-10 °C, -15 °C, -20 °C, -30 °C, and -40 °C/min) on motility parameters, rates of fertilization and hatching, ATP content, and indices of oxidative stress including thiobarbituric acid reactive substances and carbonyl derivatives of proteins in Persian sturgeon (Acipenser persicus) sperm. After sampling, sperm was diluted in an extender composed of 23.4-mM sucrose, 0.25-mM KCl, and 30-mM Tris-HCl, pH 8.0, containing 10% methanol and subsequently frozen in a programmable freezer. For postthaw sperm that were frozen at a rate of -40 °C/min, sperm motile duration (134 ± 27.01 seconds), sperm motile percent (60 ± 4.1%), fertilizability (72 ± 8.36% for fertilization rate and 65 ± 7.58% for hatching rate), and ATP content (4.8 ± 0.57 nmol/10(8) sperm) were significantly higher than for sperm frozen at any of the four slower rates (P < 0.05). Moreover, sperm cryopreserved using the fastest freezing rate had significantly lower levels of thiobarbituric acid reactive substances (0.5 ± 0.05 nmol/10(8) sperm) and carbonyl derivatives of proteins (41.3 ± 4.9 nmol/10(8) sperm) than sperm cryopreserved using all other freezing rates (P < 0.05). In addition, there is a significant difference (P < 0.05) between fresh sperm and the recovery of cryopreserved Persian sturgeon sperm using programmable freezing with -40 °C/min being the optimal freezing rate among those tested.