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Whole genome duplication is hypothesized to have played a critical role in the evolution of several major taxa, including vertebrates, and while many lineages have rediploidized, some retain polyploid genomes. Additionally, variation in ploidy can occur naturally or be artificially induced within select plant and animal species. Modern genetic techniques have not been widely applied to polyploid or ploidy-variable species, in part due to the difficulty of obtaining genotype data from polyploids. In this study, we demonstrate a strategy for developing an amplicon sequencing panel of single nucleotide polymorphisms for high-throughput genotyping of polyploid organisms. We then develop a method to infer ploidy of individuals from amplicon sequencing data that is generalized to apply to any ploidy and does not require prior identification of heterozygous genotypes. Combining these two techniques will allow researchers to both infer ploidy and generate ploidy-aware genotypes with the same amplicon sequencing panel. We demonstrate this approach with white sturgeon Acipenser transmontanus, a ploidy-variable (octoploid, decaploid and dodecaploid) imperiled species under conservation management in the Pacific Northwest and obtained a panel of 325 loci. These loci were validated by examining inheritance in known-cross families, and the ploidy inference method was validated with known ploidy samples. We provide scripts that adapt existing pipelines to genotype polyploids and an R package for application of the ploidy inference method. We expect that these techniques will empower studies of genetic variation and inheritance in polyploid organisms that vary in ploidy level, either naturally or as a result of artificial propagation practices.

Sturgeon and paddlefishes (Acipenseriformes) are cultured worldwide for commercial and conservation purposes. Over the past decade, we have learned many sturgeon culture programs experience spontaneous autopolyploidy, or the generation of triploidy without management intervention. Spontaneous autopolyploidy has been shown to negatively impact the physiology, reproductive development and fertility of sturgeon. Given these concerns, it is necessary to understand how it arises, how it affects production, and how it can be managed. The goal of this review is to describe the incidence of spontaneous autopolyploidy in sturgeon relative to other fishes, explain how spontaneous autopolyploids are formed, and report what is known about how triploidy and intermediate ploidy effect sturgeon reproductive development and physiology. We then describe four common methods for detecting spontaneous autopolyploids and their intermediate ploidy progeny and end with recommendations for reducing the incidence of spontaneous autopolyploidy based on the results of recent research. Although spontaneous autopolyploidy may never be completely eliminated from sturgeon culture, following these recommendations may significantly decrease its incidence.

One of the most fundamental aspects of ecological research and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype‐based identification. The CRISPR‐Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR‐Cas13a platform SHERLOCK (Specific High‐sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of “proof of principle” experiments to characterize SHERLOCK’s ability to accurately, sensitively and rapidly distinguish three fish species of management interest co‐occurring in the San Francisco Estuary that are easily misidentified in the field. We improved SHERLOCK’s ease of field deployment by combining the previously demonstrated rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction‐free DNA collection protocol, as well as the option of instrument‐free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.

Triploid salmonids have been shown to underperform in suboptimal environments. It is thought this might be due to having larger cells to accommodate the increased number of chromosomes and therefore effects on aerobic metabolism from having smaller cellular surface area to volume ratios. The goal of this study was to examine the aerobic metabolism of diploid and triploid white sturgeon (Acipenser transmontanus) in ambient (18 °C) and elevated water temperatures (24 °C). Resting and maximum metabolic rates, recovery time from exhaustive exercise, and surface area to volume ratios of erythrocytes and their nuclei in diploid and triploid sturgeon were evaluated. Triploid sturgeon had a reduced aerobic scope and hematological response (hematocrit and hemoglobin) to exhaustive exercise. A reduced surface area to volume ratio of erythrocytes in triploid sturgeon provides evidence that cellular surface area could be one mechanism limiting aerobic metabolism in triploid fishes. A lower aerobic scope found in triploid sturgeon may impact reproductive and somatic growth, yet more research is needed to determine implications for management decisions on farms and hatcheries.

The Green Sturgeon is a long-lived anadromous fish known to spawn in only three locations. Southern Distinct Population Segment (DPS) Green Sturgeon spawn only in the Sacramento drainage, while the Northern DPS spawns in the Klamath and Rogue rivers. In 2011, a young of year (YOY) Green Sturgeon was captured in the Columbia River below Bonneville Dam, providing preliminary evidence of a fourth spawning location. In 2017, four additional Green Sturgeon YOY of similar size were captured in the Columbia River below Bonneville Dam. Genetic analysis of all YOY samples indicates that they belong to the Northern DPS, confirming that the Northern DPS actually spawns in at least three locations. The detection of Green Sturgeon spawning in the Columbia River only in years with relatively high spring flow (2011, 2017), combined with confirmed correlations between flow and spawning for other White and Green Sturgeon populations, suggests that appropriate spawning conditions may only exist above a specific flow threshold. The Columbia River has the potential to play an important role in Green Sturgeon climate change adaptation due to its location at the northernmost end of the species’ reproductive range. We recommend future research to better quantify Green Sturgeon recruitment magnitude, frequency and dynamics in the Columbia River.

Conservation-focused reintroduction or supplementation programs using wild-born individuals tend to be more successful than those based on release of captive-born individuals. Negative genetic consequences of captive breeding, such as genetic diversity loss, domestication selection, and inbreeding, may contribute to this lowered success. In this study, we compare genetic consequences of repatriation, or collection of wild-born juveniles for captive rearing and release, and broodstock-based breeding, where wild adults are bred in captivity, in a conservation program for white sturgeon, Acipenser transmontanus. Specifically, we use microsatellite markers to compare the genetic diversity and number of spawners, Ns, represented by each captive breeding strategy. We present a novel method to estimate Ns in which simulated known family configurations of varying complexity are used to identify appropriate inclusive and exclusive probability thresholds in the maximum likelihood-based pedigree reconstruction program Colony. These probability thresholds are then applied to reconstruct progeny arrays and estimate Ns in empirical datasets of two repatriation cohorts and a naturally produced year class. We find that a repatriation approach preserves more genetic diversity and represents more spawners than broodstock-based captive breeding. Furthermore, a repatriation approach represents levels of genetic diversity similar to those found in a wild cohort. These results are the first comparison of Ns between broodstock and repatriation-based methods with respect to a hatchery program, and provide evidence that when possible, repatriation can be a more effective strategy for conserving genetic diversity than broodstock-based breeding for supplementation and reintroduction.

Release of sturgeon with abnormal ploidy into the wild may result in reduced fitness due to lowered fertility in the F2 and subsequent generations. Further, there is evidence that ploidy affects reproductive development and caviar yield. Therefore, the ability to accurately characterize the ploidy of white sturgeon (Acipenser transmontanus) is essential for both commercial and conservation aquaculture. This study compares nuclear volume and whole erythrocyte long-axis lengths obtained using Coulter counter and blood smears, respectively, from captive white sturgeon from populations originating in California and Idaho. We examine which method provides the most accurate, time efficient and cost-effective characterization of ploidy in this species. Results from Coulter counter and blood smears were compared to results from flow cytometry, the gold standard for genome size analysis. Previous work suggests that blood smears can distinguish between 8N (diploid) and 12N (triploid) sturgeon, but further analysis is required to see if this method can also be used to identify 10N fish and to provide robust evidence of its utility in 8N and 12N fish across populations. In this study, we demonstrated that the Coulter counter had 100% agreement with flow cytometry in ploidy assignment, while blood smears vary in their accuracy based on population. Blood smears showed a high degree of overlap in erythrocyte long-axis length between 8N and 10N individuals as well as some overlap between 10N and 12N individuals in the California fish, and a high degree of overlap between 8N and 12N individuals in the Idaho fish. Although blood smears are time-intensive and vary in their ploidy assignment accuracy, they are a low-cost technique and as such may have some utility for caviar farms attempting to identify 12N individuals in a small number of broodstock. By comparing the accuracy, efficiency and cost of these three methods, sturgeon farmers and conservation hatcheries will be able to choose the best method for their needs in determining the ploidy of their fish. We determined that Coulter counter is equally accurate to flow cytometry and is also the most time efficient method for ploidy determination in white sturgeon.

Variation in ploidy occurs naturally in select plant and animal species. Ploidy variation can also occur spontaneously or be induced during artificial propagation of fish and shellfish. Studying species and systems that have variable ploidy requires techniques to infer ploidy of individuals. Massively parallel sequencing of biallelic SNPs has been used to infer ploidy, but existing techniques have several drawbacks. These include being limited to only comparing a fixed number of ploidies (diploidy, triploidy, and tetraploidy) and requiring that heterozygous genotypes in an individual be identified prior to ploidy inference. We describe a method of inferring ploidy from sequencing of biallelic SNPs based on beta-binomial mixture models. This method is generalized to apply to any ploidy and does not require prior identification of heterozygous genotypes. We demonstrate efficacy of this method for comparing ancestral octoploidy, decaploidy, and dodecaploidy (tetraploidy, pentaploidy, and hexaploidy for the sequenced SNPs) in white sturgeon and diploidy and triploidy in Chinook salmon with amplicon sequencing (GT-seq) data. Results indicated that ploidy could be reliably estimated for individuals based on distinct distribution of log-likelihood ratios (LLR) for known ploidy samples of both species that were tested. Confidence in ploidy estimates increased with sequencing depth. We encourage users to explore the sequencing depths and LLR critical values that provide reliable estimates of ploidy for a given organism and set of SNPs. We expect that the R package provided will empower studies of genetic variation and inheritance in organisms that vary in ploidy naturally or as a result of artificial propagation practices.

Author(s): Mahardja, Brian; Goodman, Andrew; Goodbla, Alisha; Schreier, Andrea D.; Johnston, Catherine; Fuller, Rebecca C.; Contreras, Dave; McMartin, Louanne | Abstract: Biological invasion by non-native species has been identified as one of the major threats to native fish communities worldwide. The fish community of San Francisco Estuary is no exception, as the estuary has been recognized as one of the most invaded on the planet and the system has been impacted significantly by these invasions. Here, we summarize the introduction and probable establishment of a new species in the Sacramento–San Joaquin Delta, the Bluefin Killifish (Lucania goodei), as discovered by the US Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP). The DJFMP has conducted a large-scale beach seine survey since 1976, and it is the longest-running monitoring program in the San Francisco Estuary that extensively monitors the shallow-water nearshore habitat. Possibly introduced as discarded aquarium fish within the vicinity of the Delta Cross Channel, Bluefin Killifish is a close relative of the Rainwater Killifish (Lucania parva), another non-native fish species that has been present in the San Francisco Estuary system for decades. Studies in their native range suggest that Bluefin Killifish will fill a similar niche to Rainwater Killifish, albeit with a more freshwater distribution. The potential ecological impact of Bluefin Killifish remains unclear in the absence of additional studies. However, we have been able to track the spread of the species within the Sacramento–San Joaquin Delta through the existence of long-term monitoring programs. Our findings demonstrate the value of monitoring across various habitats for the early detection and proactive management of invasive species.

The valley elderberry longhorn beetle (VELB), Desmocerus californicus dimorphus (Coleoptera: Cerambycidae), is a federally threatened subspecies endemic to the Central Valley of California. The VELB range partially overlaps with that of its morphologically similar sister taxon, the California elderberry longhorn beetle (CELB), Desmocerus californicus californicus (Coleoptera: Cerambycidae). Current surveying methods are limited to visual identification of larval exit holes in the VELB/CELB host plant, elderberry (Sambucus spp.), into which larvae bore and excavate feeding galleries. Unbiased genetic approaches could provide a much-needed complementary approach that has more precision than relying on visual inspection of exit holes. In this study we developed a DNA sequencing-based method for indirect detection of VELB/CELB from frass (insect fecal matter), which can be easily and non-invasively collected from exit holes. Frass samples were collected from 37 locations and the 12S and 16S mitochondrial genes were partially sequenced using nested PCR amplification. Three frass-derived sequences showed 100% sequence identity to VELB/CELB barcode references from museum specimens sequenced for this study. Database queries of frass-derived sequences also revealed high similarity to common occupants of old VELB feeding galleries, including earwigs, flies, and other beetles. Overall, this non-invasive approach is a first step towards a genetic assay that could augment existing VELB monitoring and accurately discriminate between VELB, CELB, and other insects. Furthermore, a phylogenetic analysis of 12S and 16S data from museum specimens revealed evidence for the existence of a previously unrecognized, genetically distinct CELB subpopulation in southern California.

Spontaneous autopolyploidy, a 1.5x increase in genome size resulting from second polar body retention after fertilization, has been documented in cultured sturgeons, with the proportion of spontaneous autopolyploid progeny ranging widely among maternal families. Sturgeon farms wish to reduce the number of spontaneous autopolyploids because their progeny, when crossed with a normal ploidy parent, exhibit intermediate ploidies, resulting in reproductive abnormalities. However, there is limited knowledge of the causes of the second polar body retention in sturgeon culture. In this study, we report the results of experiments performed from 2015 to 2019 aimed at identifying the sources of spontaneous autopolyploidy in white sturgeon (Acipenser transmontanus) culture. In collaboration with several sturgeon farms, we tested whether post-ovulatory ageing, mechanical shock during egg de-adhesion, and the combined effects of both factors increased spontaneous autopolyploidy. To test the effect of post-ovulatory ageing, eggs were collected from females and either fertilized at the industry normative time (2–5 h post-oviposition) or stored in ovarian fluid at 15 °C for 6–8 h before fertilization. To test the effect of mechanical shock, eggs were collected, fertilized 2–5 h post-oviposition and exposed to either gentle or vigorous mixing during the 60 min de-adhesion treatment. Results from this work reveal that post-ovulatory ageing does increase the incidence of spontaneous autopolyploidy in some females, but overall the proportions produced were low (range 0–15%). Proportions of spontaneous autopolyploids in eggs exposed to vigorous mixing were also variable (1–92%) but significantly higher in 75% of the females when compared to their respective controls or gentle mixing treatments, indicating that mechanical shock during egg de-adhesion is likely the primary cause of spontaneous autopolyploidy. To our knowledge this is the first study to document mechanical shock to eggs during de-adhesion as a cause of abnormal ploidy in cultured fishes. We observed high variability in egg quality among females and a significant relationship between embryo mortality and the incidence of spontaneous autopolyploidy when eggs were exposed to mechanical shock. Repeated spawning of a female that produced a high proportion of spontaneous autopolyploids provided preliminary evidence that genetic background may influence the likelihood that a female's eggs will be prone to second polar body retention when subjected to mechanical shock. Although spontaneous autopolyploidy in sturgeon culture will likely never be eliminated entirely, we provide practical recommendations to sturgeon producers to reduce its incidence in a production setting.

Environmental DNA (eDNA) analysis has gained traction as a precise and cost-effective method for species and waterways management. To date, publications on eDNA protocol optimization have focused primarily on DNA yield. Therefore, it has not been possible to evaluate the cost and speed of specific components of the eDNA protocol, such as water filtration and DNA extraction method when designing or choosing an eDNA protocol. At the same time, these two parameters are essential for the experimental design of a project. Here we evaluate and rank 27 different eDNA protocols in the context of Chinook salmon (Oncorhynchus tshawytscha) eDNA detection in an estuarine environment. We present a comprehensive evaluation of multiple eDNA protocol parameters, balancing time, cost and DNA yield. We collected samples composed of 500 mL estuarine water from Deverton Slough (38°11'16.7"N 121°58'34.5"W) and 500 mL from tank water containing 1.3 juvenile Chinook Salmon per liter. Then, we compared extraction methods, filter types, use of inhibitor removal kit for DNA yield, processing time, and protocol cost. Lastly, we used an MCMC algorithm together with machine learning to understand the DNA yield of each step of the protocol as well as the interactions between those steps. Glass fiber filtration was to be the most resilient to high turbidites, filtering the samples in 2.32 ± 0.08 min instead of 14.16 ± 1.86 min and 6.72 ± 1.99 min for nitrocellulose and paper filter N1, respectively. The filtration DNA yield percentages for paper filter N1, glass fiber, and nitrocellulose were 0.00045 ± 0.00013, 0.00107 ± 0.00013, 0.00172 ± 0.00013. The DNA extraction yield percentage for QIagen, dipstick, NaOH, magnetic beads, and direct dipstick ranged from 0.047 ± 0.0388 to 0.475 ± 0.0357. For estuarine waters, which are challenging for eDNA studies due to high turbidity, variable salinity, and the presence of PCR inhibitors, we found that a protocol combining glass filters, magnetic beads, and an extra step for PCR inhibitor removal, is the method that best balances time, cost, and yield. In addition, we provide a generalized decision tree for determining the optimal eDNA protocol for other studies in aquatic systems. Our findings should be applicable to most aquatic environments and provide a clear guide for determining which eDNA protocol should be used under different study constraints.

Exotic species have been implicated as a major threat to native freshwater fish communities in the Unites States. The San Francisco Estuary watershed has been recognized as one of the most invaded systems where exotics often dominate the fish community. On October 6, 2014, members of the U.S. Fish and Wildlife Service detected a previously unknown exotic fish in a disconnected pool immediately upstream from the Chowchilla Bifurcation Structure in the San Joaquin River, a major tributary of the San Francisco Estuary. A member of the U.S. Fish and Wildlife Service initially identified the fish as an Oriental Weatherfish Misgurnus anguillicaudatus using external morphological characteristics. We conducted additional fish sampling near the Chowchilla Bifurcation Structure in November 2014 and collected a total of six additional specimens in disconnected pool habitats. Unexpectedly, genetic and meristic techniques revealed that these specimens were Large-Scale Loach Paramisgurnus dabryanus. To our knowledge this is the first confirmed occurrence of Large-Scale Loach in the United States and the suspected pathway of introduction is release from aquaria. Very little is known about the population in the San Joaquin River. We recommend further evaluation of the ecology, distribution, and abundance of Large-Scale Loach to better understand their potential impact on the fish communities of the San Joaquin River and the likelihood of establishment throughout the United States.

Previous studies have provided evidence of a reduced aerobic metabolic capacity, both at the cellular (metabolic enzyme activity) and the whole organism (aerobic scope) level in juvenile triploid white sturgeon, compared to diploid siblings. The downstream costs of this reduced metabolic capacity are still unclear, yet a lower aerobic scope suggests triploid white sturgeon likely have less energy to allocate to biological processes like growth and development. We conducted a 15-week growth trial to assess energy allocation to somatic growth in 2-month-old diploid and triploid white sturgeon. Spontaneous swimming activity, hepatosomatic index, condition factor, and deformities were also measured throughout the growth trial as indices of energy allocation to activity and fish condition. In general, our results indicate that triploid white sturgeon may have less energy available for processes beyond basal maintenance. This could be linked to a reduced overall performance as evidenced by lower weights and more deformities when compared with their diploid counterparts. However, many indices were still mostly unaffected by triploidy (condition factor, hepatosomatic index, and swimming activity). Whether this lower growth performance seen in juvenile triploid white sturgeon continues through sub-adulthood, puberty and final maturation requires further long-term studies.

The on-going and precipitous decline in sturgeon abundance and increased demand for caviar have promoted the development of sustainable sturgeon aquaculture. One common problem that confounds caviar farming efficiency is highly variable roe yield associated with the proliferation of ovarian fat: sturgeon females with fatty ovaries tend to produce a smaller yield of inferior quality roe compared to those with lean ovaries. Here, we evaluated the effects of finishing diet, farm origin, age at maturity, tank, and genotype on ovarian adiposity and caviar yield in cultured white sturgeon (Acipenser transmontanus). We conducted a feeding trial in which fish aged 5 + years at two different commercial farms were either maintained on a high fat production diet or received a low fat finishing diet for 19 and 33 months before caviar harvest; at this time fish were aged 7 or 8 years, respectively. Measurements of ovarian fattiness, caviar yield, and morphology were collected at the time of harvest. Microsatellite genotyping was performed to estimate relatedness among experimental fish and subsequent heritability of these traits. Mean caviar yield normalized by body weight increased from 7.6–8.6% to 8.0–9.2% and mean caviar yield scaled by ovary weight increased from 55.5–59.8% to 61.3–64.6% in white sturgeon fed the high and low fat diets, respectively. All females were classified post hoc according to degree of ovarian fattiness: low, medium, or high. Regardless of diet, farm, or age, females in the high ovarian adiposity group had larger body size, higher condition factor, but lower caviar yields than those in the low fattiness group because of the presence of large ovarian fat lobes and adipocytes surrounding individual oocytes. Furthermore, only 11.8–17.2% of female white sturgeon given the low fat finishing diet displayed a high degree of ovarian fattiness compared to 18.0–33.2% of those on the high fat diet. Robust negative correlations were found between measurements of ovarian adiposity and caviar yield further illustrating this inverse relationship observed by caviar farmers. The fixed effects of diet, farm, age, and tank all significantly influenced ovarian adiposity and caviar yield except farm origin did not significantly impact ovarian fat lobe weight. Heritability values for measurements of ovarian adiposity and caviar yield were moderate and ranged from 0.20–0.39, however heritability of ovarian tissue weight was slightly lower (h2 = 0.11). Our study demonstrates that finishing diet, farm origin, age at maturity, tank and genotype significantly affect and may be manipulated to increase caviar yield in cultured white sturgeon. Statement of relevance Study findings will increase sturgeon aquaculture profits.

Green sturgeon (Acipenser medirostris) is a highly migratory, marine oriented species that congregates in non-natal estuaries during summer and early fall. Individuals from the threatened Southern Distinct Population Segment (SDPS) and non-listed Northern Distinct Population Segment (NDPS) regularly co-occur in non-natal estuaries including the Columbia River estuary, Willapa Bay, and Grays Harbor in relative proportions not explained by abundance or distance from natal river. We used genetic markers to assign green sturgeon sampled in these estuaries from 2010 to 2012 to distinct population segments (DPS). We then examined interannual differences in DPS composition among estuaries. Fork length distributions were compared between SDPS and NDPS green sturgeon to determine whether size varied within and among DPSs and estuaries. The majority of green sturgeon sampled in the Columbia River estuary and Willapa Bay were assigned to the SDPS, while we assigned nearly even DPS proportions to our Grays Harbor samples. NDPS green sturgeon were significantly smaller than those originating from the SDPS within and among estuaries. We used these findings to develop several hypotheses about the mechanisms that may lead to specific patterns of non-natal estuary use. Genetic markers also assigned a single age-0 green sturgeon sampled in the Columbia River to the NDPS, although our analyses suggest that this individual’s parents may not have originated from known NDPS spawning populations. Because the Columbia River may serve as alternative spawning habitat for green sturgeon as climate change occurs, we recommend monitoring the Columbia River more closely for further evidence of green sturgeon spawning.

Prior to the Deepwater Horizon oil spill, we lacked a comprehensive baseline of oil contamination in the Gulf of Mexico's sediments, water column, and biota. Gaps in prespill knowledge limit our ability to determine the aftereffects of the Deepwater Horizon blowout or prepare to mitigate similar impacts during future oil spill disasters. We examined spatiotemporal differences in exposure to and metabolism of polycyclic aromatic hydrocarbons (PAHs) in 2 hake species (Urophycis spp.) to establish a current baseline for these ecologically important, abundant, and at‐risk demersal fishes. Gulf hake (Urophycis cirrata) and southern hake (Urophycis floridana) were collected throughout the Gulf of Mexico during extensive longline surveys from 2012 to 2015. Analyses of biliary PAH metabolites and liver PAH concentrations provided evidence of exposures to di‐ and tricyclic compounds, with the highest concentrations measured in the northern Gulf of Mexico. Species‐specific differences were not detected, but temporal trends observed in biliary PAHs suggest a decrease in acute exposures, whereas increasing liver PAHs suggest chronic exposures marked by greater assimilation than metabolism rates. To our knowledge, the present study provides the first multitissue contaminant analyses, as well as the most exhaustive biometric analyses, for both gulf and southern hakes. Though sources of exposure are complex because of multiple natural and anthropogenic PAH inputs, these results will facilitate the development of much needed health metrics for Gulf of Mexico benthos. Environ Toxicol Chem 2019;38:2740–2749. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC., Analyses of biliary polycyclic aromatic hydrocarbon (PAH) metabolites and liver PAH concentrations provide evidence of recent and chronic exposure to di‐ and tricyclic compounds, with the highest concentrations measured in the northern Gulf of Mexico. DWH = Deepwater Horizon; NC = north central; SW = southwest; WFS = west Florida shelf.

© 2018 Elsevier Inc. Previous studies have demonstrated reduced performance in triploid fish when reared under suboptimal conditions, which may be the result of a higher susceptibility to stressors when compared to diploids. The goal of this project was to investigate differences in the capacity of diploid (8 N) and triploid (12 N) white sturgeon, Acipenser transmontanus, to respond to both warm acclimation (6-weeks of acclimation to either 18 or 22 °C) and a subsequent acute stress (10-min low water stress). Following the 6-week acclimation, fish were sampled either before or following an acute low water stress. Bioindices of the primary and secondary stress response, hematology and cellular metabolic status were measured. We also sought to determine if time to peak cortisol levels were similar between diploid and triploid sturgeon after exposure to a severe acute stressor (netting stress). While both ploidies had similar primary and secondary responses to acute stress, both with and without warm acclimation, warm acclimation impacted the ability of diploid and triploid white sturgeon to mount a typical stress response to an acute stressor. In response to warm acclimation, triploids exhibited little change in branchial lactate dehydrogenase activity, while diploids increased activity. After exposure to an acute water reduction stress, diploids increased citrate synthase activity, yet triploids showed a decrease in activity. Differences in metabolic enzyme activity in response to warm acclimation and acute stress suggest triploid white sturgeon may have a reduced cellular metabolic capacity under chronic and acute stress, which may impact performance of triploid sturgeon in suboptimal conditions.

Author(s): Lessard, JoAnna; Cavallo, Brad; Anders, Paul; Sommer, Ted; Schreier, Brian; Gille, Daphne; Schreier, Andrea; Finger, Amanda; Hung, Tien-Chieh; Hobbs, James; May, Bernie; Schultz, Andrew; Burgess, Oliver; Clarke, Robert | Abstract: An extreme decline in Delta Smelt (Hypomesus transpacificus) abundance has led to a number of management actions to support this endangered species, including the development and refinement of culture techniques and the creation of a refuge population. The wild Delta Smelt population has diminished to the point that many in the scientific community believe population supplementation using cultured fish needs to be experimentally evaluated as a possible management tool. Concerns about supplementation include the effectiveness of this action, and its potential to divert attention and funding from other needed management actions such as habitat restoration. Here, we describe the outcomes of a 2-day workshop that described the current refuge population, and identified key issues for potential future use of cultured Delta Smelt for research and management. Expanded use of cultured Delta Smelt is controversial and requires consideration for complexities that include legal constraints and permitting requirements. Developing policies that allow for in situ experiments using cultured Delta Smelt appears to be a precursor for advancing policies that might allow supplementation actions. Releases of cultured fish, either experimentally or as a management action, clearly need to be conducted within an adaptive management program that is integrated with other strategies, including habitat restoration. We describe a general framework for evaluating the potential risks of supplementation and include suggestions for how to reduce risks and uncertainty. Overall, we conclude there is sufficient baseline information about Delta Smelt and the existing culture program to proceed with targeted field research that utilizes cultured fish. Finally, given the dire status of this species, we conclude that rapid progress toward the development of a viable and testable supplementation program must be a priority for Delta Smelt conservation.

© 2018 Elsevier Inc. Previous studies suggest fish with additional copies of their genome (polyploids) underperform in suboptimal conditions and may be more susceptible to stress and disease. The objective of this study was to determine the role ploidy plays in the physiological response of white sturgeon to chronically elevated water temperatures. White sturgeon of two ploidies (8 N and 10 N) were acclimated to ambient (18 °C) and warm (22 °C) water. Bioindices of stress (plasma cortisol, glucose and lactate, total erythrocyte count, hematocrit, hemoglobin, mean erythrocyte volume, mean erythrocyte hemoglobin, and mean erythrocyte hemoglobin concentration), immunity (respiratory burst, plasma lysozyme, and total leukocyte count), and cellular metabolic capacity (lactate dehydrogenase and citrate synthase activity) were measured before and after a 6-week acclimation period. Both ploidies appear comparable in their constitutive immune and stress parameters and respond similarly to warming. Hematological indices suggest 8 N and 10 N sturgeon are similar in oxygen carrying capacity; however, differences in enzyme activity between ploidies indicate that 10 N sturgeon may have a lower cellular aerobic capacity. Our results have implications for the screening and management of ploidy on white sturgeon farms and hatcheries, as the differences between ploidies may affect 10 N sturgeon performance at elevated water temperatures. Further research is needed to elucidate the differences in inducible stress and immune responses and metabolism of white sturgeon of different ploidies.

The success of captive and supportive breeding programs is often determined by abundance criteria but it is also necessary to consider genetic characteristics of reintroduced or supplemented populations as genetic diversity loss can reduce population viability. Genetic analysis of the parent pools is often used to determine whether captive or supportive breeding programs conserve adequate levels of genetic diversity and maximize the effective population size (Ne). This practice assumes that released cohorts reflect the genetic characteristics of parents. Here we provide a case study of how post-release mortality can alter the genetic composition of released cohorts in a supportive breeding program for an endangered population of white sturgeon. Data from ongoing genetic monitoring of wild broodstock in the Kootenai River white sturgeon conservation aquaculture program are combined with multi-year post-release abundance monitoring of captive bred juveniles to reveal high variability in recapture among families. We found that genetic monitoring of broodstock used in supportive breeding overestimates genetic diversity conservation in most year classes due to differential post-release mortality among families. Ne was reduced in most year classes when post-release mortality was considered due to reduced parental representation in released cohorts. Although rarely performed, our results indicate that post-release genetic monitoring is necessary to accurately characterize the genetic composition of released cohorts altered by post-release mortality and should be considered when designing a captive or supportive breeding program.

Sturgeons (order Acipenseriformes) are members of an ancient evolutionary lineage that has experienced multiple rounds of whole-genome duplication. As a result, most extant species are polyploid and possess more than two complete sets of chromosomes. While interspecific variation in ploidy and overall genome size is common within this order, recent studies have also documented intraspecific variation in some captive bred sturgeon species, most notably in white sturgeon ( Acipenser transmontanus ). The unintentional duplication of one or more complete sets of chromosomes in a single species in the absence of hybridization is known as spontaneous autopolyploidization. The mechanism and the effects on viability and reproductive development of spontaneous autopolyploidy, however, are poorly understood. Sturgeons are valuable aquacultural species for production of boneless meat and caviar, and incidence of spontaneous autopolyploidy could have negative economic implications. In this study, we wished to determine whether there was a maternal or paternal origin of spontaneous autopolyploidy. We used flow cytometry to identify spontaneous autopolyploids and microsatellite genotyping to track the transfer of unique maternal and paternal alleles from broodstock to offspring across multiple full-sibling families in two populations of cultured white sturgeon. In all families, we found that the probability of transfer success of unique maternal alleles was greater than that of unique paternal alleles in spontaneous autopolyploid white sturgeon, indicating a maternal origin of spontaneous autopolyploidy. Secondly, as no spontaneous autopolyploid progeny shared all the same microsatellite alleles as the respective dam as would be expected with premeiotic endomitosis or apomixis, we believe that failure to extrude the second polar body in meiosis II is the most likely cause of spontaneous autopolyploidy in cultured white sturgeon.

Many fish of aquacultural importance including sturgeon and paddlefish have a history of polyploidy in their evolutionary lineages. Spontaneous autopolyploids have been detected in several sturgeon species in culture despite the fact that the induction of triploidy is not a management tool in farming sturgeon for meat and caviar. In 2010, we discovered two female spontaneous autopolyploid white sturgeon (Acipenser transmontanus) on a commercial caviar farm that had successfully produced offspring of intermediate ploidy in crosses with normal males. Here we use flow cytometry and microsatellite genotyping to screen a second aquaculture program for the presence of spontaneous autopolyploids. Flow cytometry of female parents and their progeny in the 2011 year class created by the Kootenai River white sturgeon conservation aquaculture program revealed that wild caught females used as dams possessed normal ploidy (8N). Five of ten families sampled from the 2011 year class contained spontaneous autopolyploids possessing DNA content consistent with dodecaploidy (12N). The percent of autopolyploid individuals sampled ranged from 0 to 33% per family, and the total number of spontaneous autopolyploids in the 2011 year class was 12/150 (8%). Microsatellites were not useful in detecting spontaneous autopolyploids in the conservation aquaculture program due to low levels of genetic diversity in the endangered Kootenai River population. The two families with the highest incidence of spontaneous autopolyploids (33% and 26% of offspring sampled) were sired by a single male, suggesting a paternal effect on the generation of spontaneous autopolyploids in white sturgeon.

The Fraser River system consists of five white sturgeon (Acipenser transmontanus) management units, two of which are listed as endangered populations under Canada's Species at Risk Act. The delineation of these management units was based primarily on population genetic analysis with samples parsed by collection location. We used polysomic microsatellite markers to examine population structure in the Fraser River system with samples parsed by collection location and with a genetic clustering algorithm. Strong levels of genetic divergence were revealed above and below Hells Gate, a narrowing of the Fraser canyon further obstructed by a rockslide in 1913. Additional analyses revealed population substructure on the Fraser River above Hells Gate. The Middle Fraser River (SG-3) and Nechako River were found to be distinct populations, while the Upper Fraser River, although currently listed as an endangered population, represented a mixing area for white sturgeon originating from SG-3 and Nechako. Differences between these results and previous genetic investigations may be attributed to the detection of population mixing when genetic clustering is used to infer population structure. Resume : Le systeme du fleuve Fraser consiste en cinq secteurs de protection de l'esturgeon blanc (Acipenser

A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite dataset from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R packagepolysatversion 1.5.

Worldwide, sturgeons (Acipenseridae) are among the most endangered fishes due to habitat degradation, overfishing, and inherent life history characteristics (long life span, late maturation, and infrequent spawning). As most sturgeons are anadromous, a considerable portion of their life history occurs in estuarine and marine environments where they may encounter unique threats (e.g., interception in non-target fisheries). Of the 16 marine-oriented species, 12 are designated as Critically Endangered by the IUCN, and these include species commercially harvested. We review important research tools and techniques (tagging, electronic tagging, genetics, microchemistry, observatory) and discuss the comparative utility of these techniques to investigate movements, migrations, and life-history characteristics of sturgeons. Examples are provided regarding what the applications have revealed regarding movement and migration and how this information can be used for conservation and management. Through studies that include Gulf (Acipenser oxyrinchus desotoi) and Green Sturgeon (A. medirostris), we illustrate what is known about well-studied species and then explore lesser-studied species. A more complete picture of migration is available for North American sturgeon species, while European and Asian species, which are among the most endangered sturgeons, are less understood. We put forth recommendations that encourage the support of stewardship initiatives to build awareness and provide key information for population assessment and monitoring.