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We present the novel reference genome of the Versatile Fairy Shrimp, Branchinecta lindahli. The Versatile Fairy Shrimp is a freshwater anostracan crustacean found across the western United States from Iowa to Oregon and from Alberta to Baja California. It is an ephemeral pool specialist, living in prairie potholes, irrigation ditches, tire treads, vernal pools, and other temporary freshwater wetlands. Anostracan fairy shrimp are facing global declines with 3 species in California on the Endangered Species list. This species was included in the California Conservation Genomics Project to provide an easily accessible reference genome, and to provide whole-genome resources for a generalist species, which may lead to new insights into Anostracan resiliency in the face of climate change. The final gapped genome comprises 15 chromosome-length scaffolds covering 98.63% of the 384.8 Mb sequence length, and an additional 55 unscaffolded contigs. [ABSTRACT FROM AUTHOR]

We present the reference genome of the Vernal Pool Fairy Shrimp Branchinecta lynchi. This branchiopod crustacean is endemic to California's freshwater ephemeral ponds. It faces enormous habitat loss and fragmentation as urbanization and agriculture have fundamentally changed the vernal pool landscape over the past 3 centuries. The assembled genome consists of 22 chromosome-length scaffolds that account for 96.85% of the total sequence. One hundred and ninety-five unscaffolded contigs comprise the rest of the genome's 575.6 Mb length. The genome is substantially complete with a BUSCO score of 90.0%. There is no immediately identifiable sex chromosome, typical for this class of organism. This new resource will permit researchers to better understand the adaptive capacity of this imperiled species, as well as answer lingering questions about anostracan physiology, sex determination, and development. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 data set from a natural population of octoploid white sturgeon ( Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.6. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Abuse by adults has been reported as a potent predictor of borderline personality disorder (BPD). Unclear is whether victimisation by peers increases the risk of borderline personality symptoms. Method: The Avon Longitudinal Study of Parents and Children (ALSPAC) prospective, longitudinal observation study of 6050 mothers and their children. Child bullying was measured by self-report and mother and teacher report between 4 and 10 years. Family adversity was assessed from pregnancy to 4 years; parenting behaviours from 2 to 7 years, sexual abuse from 1.5 to 9 years, and IQ and DSM-IV axis I diagnoses at 7 to 8 years. Trained psychologists interviewed children at 11.8 years to ascertain DSM-IV BPD symptoms (five or more). Results: Accounting for known confounders, victims of peer bullying had an increased risk of BPD symptoms according to self-report (OR, 2.82; 95% CI, 2.13-3.72); mother report (OR, 2.43; 95% CI, 1.86-3.16); and teacher report (OR, 1.95; 95% CI, 1.34-2.83). Children who reported being chronically bullied (OR, 5.44; 95% CI, 3.86-7.66) or experienced combined relational and overt victimisation (OR, 7.10; 95% CI, 4.79-10.51) had highly increased odds of developing BPD symptoms. Children exposed to chronic victimisation according to mother report were also at heightened risk of developing BPD symptoms (OR, 3.24; 95% CI, 2.24-4.68). Conclusions: Intentional harm inflicted by peers is a precursor or marker on the trajectory towards the development of BPD symptoms in childhood. Clinicians should be adequately trained to deal with, and ask users of mental health services routinely about, adverse experiences with peers. [ABSTRACT FROM AUTHOR]

Abstract: The familial aggregation of Major Depressive Disorder (MDD) has been repeatedly demonstrated. Several studies have investigated associations between various clinical characteristics of MDD in probands and overall rates of MDD in relatives. Few studies, however, have considered the familial aggregation of clinical characteristics of MDD. The aim of the present report is to examine mother–offspring associations of a variety of clinical characteristics of MDD in a general population sample. Data were derived from baseline and 4-year-follow-up data of 933 adolescents and their biological mothers of the Early Developmental Stages of Psychopathology (EDSP) study, a prospective-longitudinal community study. MDD and its characteristics were assessed with the Munich-Composite International Diagnostic Interview. We found that children of mothers who had a lifetime history of severe MDD and high number of symptoms, high impairment and/or melancholia, revealed elevated odds of MDD regarding the same characteristics as their mothers (ORs between 5.2 and 13.9). The observed associations did not differ by the children’s sex. DSM-IV melancholia and severity as well as impairment were found to aggregate within families. This finding can be interpreted as a validation of the DSM-IV MDD severity subtypes as well as of the melancholic specifier. Severe and melancholic MDD reveal a considerable high degree of familiar aggregation making the search for mechanisms involved in the familiar transmission of these forms of MDD particularly promising. [Copyright &y& Elsevier]

The associations between maternal smoking and nicotine dependence and patterns of smoking and nicotine dependence in offspring were examined in a large community-based sample of adolescents. Data were derived from baseline and 4-year follow-up assessments of 938 respondents aged 14-17 years at the outset of the Early Developmental Stages of Psychopathology (EDSP) study, a prospective-longitudinal community study of adolescents and young adults and their parents respectively. Smoking and nicotine dependence in respondents were assessed using the Munich Composite International Diagnostic Interview (DSM-IV algorithms). Diagnostic information about smoking behavior in mothers was collected by independent direct diagnostic interviews with the mothers. In comparison to children of non- or occasionally smoking mothers, children of regularly smoking and nicotine-dependent mothers had higher probabilities of using tobacco as well as of developing nicotine dependence. For all ages under consideration, survival analyses revealed a higher cumulative lifetime risk of regular smoking and nicotine dependence among these children. Maternal smoking during pregnancy seems to represent an additional risk for these outcomes in children, specifically with regard to the risk of developing nicotine dependence. Associations were comparable for sons and daughters. Our findings show that maternal smoking predicts escalation of smoking, development of nicotine dependence, and stability of smoking behavior in children. Implications for specific intervention and prevention efforts are discussed. [ABSTRACT FROM AUTHOR]

White sturgeon (Acipenser transmontanus) are the largest freshwater fish in North America, with reproducing populations in the Sacramento-San Joaquin, Fraser, and Columbia River Basins. Of these, the Columbia River is the largest, but it is also highly fragmented by hydroelectric dams, and many segments are characterized by declining abundance and persistent recruitment failure. Efforts to conserve and supplement these fish requires an understanding of their spatial genetic structure. Here, we assembled a large set of samples from throughout the Columbia River Basin, along with representative collections from adjacent basins, and genotyped them using a panel of 325 single-nucleotide markers. Results from individual- and group-based analyses of these data indicate that white sturgeon in the uppermost Columbia River Basin, in the Kootenai and upper Snake Rivers, are the most distinct, while the remaining populations downstream in the basin can be described as a genetic gradient consistent with an isolation-by-distance effect. Notably, the population in the lowest reaches of the Columbia River is more distinct from the middle or upper reaches than from outside basins, and suggests historically a higher or more recent gene exchange through coastal routes than with populations in the interior Columbia Basin. Nonetheless, proximal reaches were generally only marginally or non-significantly divergent, suggesting that transplanting larvae or juveniles from nearby sources poses relatively little risk of outbreeding depression. Indeed, we inferred examples of dispersal between reaches via close-kin mark-recapture and genetic mark-recapture that indicate movement between nearby reaches is not unusual. Samples from the Kootenai and upper Snake Rivers exhibited notably lower genetic diversity than the remaining samples as a result of population bottlenecks, genetic drift, and/or historical divergence. Conservation actions, such as supplementation, are underway to maintain population viability and will require balanced efforts to increase demographic abundance while maintaining genetic diversity. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract 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. [ABSTRACT FROM AUTHOR]

Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real‐time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR‐based genetic tools can fill an unoccupied niche between real‐time, inexpensive, but error‐prone visual identification and more expensive or time‐consuming, but accurate genetic identification for taxonomic units that are difficult or impossible to visually identify. Herein, we use genomic data to develop CRISPR‐based SHERLOCK assays capable of rapidly (<1 h), accurately (94%–98% concordance between phenotypic and genotypic assignments), and sensitively (detects 1–10 DNA copies/reaction) distinguishing ESA‐listed Chinook salmon runs (winter‐ and spring‐run) from each other and from unlisted runs (fall‐ and late fall‐run) in California's Central Valley. The assays can be field deployable with minimally invasive mucus swabbing negating the need for DNA extraction (decreasing costs and labour), minimal and inexpensive equipment needs, and minimal training to conduct following assay development. This study provides a powerful genetic approach for a species of conservation concern that benefits from near real‐time management decision‐making but also serves as a precedent for transforming how conservation scientists and managers view genetic identification going forward. Once developed, CRISPR‐based tools can provide accurate, sensitive, and rapid results, potentially without the prohibitive need for expensive specialty equipment or extensive molecular training. Further adoption of this technology will have widespread value for the monitoring and protection of our natural resources. [ABSTRACT FROM AUTHOR]

After centuries of overexploitation and habitat loss, many of the world's sturgeon (Acipenseridae) populations are at the brink of extinction. Although significant resources are invested into the conservation and restoration of imperiled sturgeons, the burgeoning commercial culture industry poses an imminent threat to the persistence of many populations. In the past decade, the number and distribution of captive sturgeon facilities has grown exponentially and now encompasses diverse interest groups ranging from hobby aquarists to industrial‐scale commercial facilities. Expansion of sturgeon captive culture has largely fallen outside the purview of existing regulatory frameworks, raising concerns that continued growth of this industry has real potential to jeopardize conservation of global sturgeon populations. Here, we highlight some of the most significant threats commercial culture poses to wild populations, with particular emphasis on how releases can accelerate wild population declines through mechanisms such as hybridization, introgression, competition, and disease transmission. We also note that in some circumstances, commercial captive culture has continued to motivate harvest of wild populations, potentially accelerating species' declines. Given the prevalence and trajectory of sturgeon captive culture programs, we comment on modifications to regulatory frameworks that could improve the ability of captive culture to support wild sturgeon conservation. [ABSTRACT FROM AUTHOR]

In this paper, we report on the scaffold-level assembled genome for the federally endangered, California endemic crustacean Lepidurus packardi (the Vernal Pool Tadpole Shrimp). L. packardi is a key food source for other conserved California species including the California Tiger Salamander Ambystoma californiense. It faces significant habitat loss and fragmentation as vernal pools are threatened by urbanization, agricultural conversion, and climate change. This resource represents the first scaffold-level genome of any Lepidurus species. The assembled genome spans 108.6 Mbps, with 6 chromosome-length scaffolds comprising 71% of total genomic length and 444 total contigs. The BUSCO score for this genome is 97.3%, suggesting a high level of completeness. We produced a predicted gene set for this species trained on the Daphnia magna set of genes and predicted 17,650 genes. These tools can aid researchers in understanding the evolution and adaptive potential of alternative reproductive modes within this species. [ABSTRACT FROM AUTHOR]

Using a system optimized for propagating human keratinocytes, culture of skin samples from white and green sturgeons generated epithelial cells capable of making cross-linked protein envelopes. Two distinct forms of TGM1-like mRNA were molecularly cloned from the cells of white sturgeon and detected in green sturgeon cells, accounting for their cellular envelope forming ability. The protein translated from each displayed a cluster of cysteine residues resembling the membrane anchorage region expressed in epidermal cells of teleosts and tetrapods. One of the two mRNA forms (called A) was present at considerably higher levels than the other (called B) in both species. Continuous lines of white sturgeon epidermal cells were established and characterized. Size measurements indicated that a substantial fraction of the cells became enlarged, appearing similar to squames in human epidermal keratinocyte cultures. The cultures also expressed CYP1A, a cytochrome P450 enzyme inducible by activation of aryl hydrocarbon receptor 2 in fish. The cells gradually improved in growth rate over a dozen passages while retaining envelope forming ability, TGM1 expression and CYP1A inducibility. These cell lines are thus potential models for studying evolution of fish epidermis leading to terrestrial adaptation and for testing sturgeon sensitivity to environmental stresses such as pollution. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. • Triploid white sturgeon exhibited reduced growth from weeks 9 to 15. • Aerobic scope was lower in triploid white sturgeon at week 15 but not weeks 1 or 6. • Diploid and triploid white sturgeon exhibited similar swimming activities and condition factors. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Release of sturgeon with abnormal ploidy into the wild may result in reduced fitness due to lowered fertility in the F 2 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. • Comparing ploidy assignment in A. transmontanus reveals Coulter counter to be the most accurate and efficient method tested. • Examining erythrocyte size of three ploidy classes demonstrates overlap between cell long-axes lengths between ploidies. • Accuracy of blood smears in ploidy assignment must be validated in each new population where it is utilized. • We recommend that blood smears only be used for identifying 12N individuals in a limited number of broodstock. • Efficient and accurate ploidy assignment in A. transmontanus using Coulter counter will improve ploidy management in culture. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 ( h 2 = 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Objective: This study evaluated the associations between suicidal ideation and suicide attempts in mothers and various aspects of suicidality in their offspring in a representative community sample. Method: Baseline and 4-year follow-up data were used from the Early Developmental Stages of Psychopathology study, a prospective, longitudinal community study of adolescents and young adults. Results are based on 933 adolescents who completed follow-up and for whom direct diagnostic information for the biological mother was available. Suicidal ideation and suicide attempts were assessed in adolescents and mothers with the Munich-Composite international Diagnostic Interview. Results: Compared to offspring of mothers without suicidality, offspring of mothers reporting suicide attempts showed a remarkably higher risk for suicidal thoughts and suicide attempts and a tendency toward suicide attempts at an earlier age. Associations were comparable for male and female offspring. Transmission of maternal suicidality was roughly stable with control for maternal comorbid psychopathology. Conclusions: The offspring of mothers with suicide attempts are at a markedly increased risk for suicidality themselves and tend to manifest suicide attempts earlier than offspring of mothers without suicidality. Suicidality seems to run in families, independent of depression and other psychopathology. [ABSTRACT FROM AUTHOR]

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. • Mechanical shock to eggs during de-adhesion is the main cause of spontaneous autopolyploidy in cultured white sturgeon. • Post-ovulatory ageing can also contribute to spontaneous autopolyploidy. • We found a significant relationship between egg quality, as measured by embryo mortality, and the incidence of spontaneous autopolyploidy. [ABSTRACT FROM AUTHOR]