Comparative genomics of rainbow trout (Oncorhynchus mykiss): Is the genetic architecture of migratory behavior conserved among populations?

Rainbow trout (Oncorhynchus mykiss) are a partially migratory species wherein some individuals undergo long-distance anadromous migrations, and others stay as residents in their native freshwater streams. The decision to migrate is known to be highly heritable, and yet, the underlying genes and alleles associated with migration are not fully characterized. Here we used a pooled approach of whole-genome sequence data from migratory and resident trout of two native populations-Sashin Creek, Alaska and Little Sheep Creek, Oregon-to obtain a genome-wide perspective of the genetic architecture of resident and migratory life history. We calculated estimates of genetic differentiation, genetic diversity, and selection between the two phenotypes to locate regions of interest and then compared these associations between populations. We identified numerous genes and alleles associated with life history development in the Sashin Creek population with a notable area on chromosome 8 that may play a critical role in the development of the migratory phenotype. However, very few alleles appeared to be associated with life history development in the Little Sheep Creek system, suggesting population-specific genetic effects are likely important in the development of anadromy. Our results indicate that a migratory life history is not controlled by a singular gene or region but supports the idea that there are many independent ways for a migratory phenotype to emerge in a population. Therefore, conserving and promoting genetic diversity in migratory individuals is paramount to conserving these populations. Ultimately, our data add to a growing body of literature that suggests that population-specific genetic effects, likely mediated through environmental variation, contribute to life history development in rainbow trout.

Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments

Biomonitoring surveys make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species level resolution. Here, we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different strategies using long fragment sequencing with Oxford Nanopore technology coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion ("mitoenrichment"). A second enrichment approach takes advantage of the CRISPR Cas9 targeted scission on previously dephosphorylated DNA ("targeted mitosequencing"). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17%-12.33% of sequences on target and a mean coverage ranging from 74.9 to 805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83%-55% of sequences on target and a 38 to 2123-fold mean coverage. These produced complete mitogenomes of species with homopolymeric regions, tandem repeats, and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA can be achieved with low computational resources in a cost-effective manner, opening the discovery of mitogenomes of nonmodel or understudied fish taxa to a broad range of laboratories worldwide.

Correction: Fraik et al. The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead (Oncorhynchus mykiss) Populations across the Elwha River Watershed. Genes 2021, 12, 89

In the original publication [...]

Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean

All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km² to depths of 500 m) to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.

Genome-wide markers reveal differentiation between and within the cryptic sister species, sunset and vermilion rockfish

The vermilion rockfish complex, which consists of the cryptic sister species vermilion and sunset rockfish, is one of the most valuable recreational fisheries on the U.S. West Coast. These species are currently managed as a single complex, and because of uncertainty surrounding the relative contribution of each species within existing data sources, the stock status of each species is not fully known. A reliable and cost-effective method is needed to disentangle these species that will allow for the development of abundance indices, life history profiles, and catch histories that may potentially support species-specific stock assessments. Using restriction-site associated DNA sequence (RADseq) markers we generated 10,003 polymorphic loci to characterize the vermilion rockfish complex. PCA and Bayesian clustering approaches based on these loci clearly distinguished between sunset and vermilion rockfishes and identified hybrid individuals. These loci included 203 highly differentiated (FST ≥ 0.99) single nucleotide polymorphisms, which we consider candidates in the planned development of a diagnostic assay capable of distinguishing between these cryptic species. In addition to clearly delineating to species, subsets of the interspecific markers allowed for insight into intraspecific differentiation in both species. Population genetic analyses for sunset rockfish identified two weakly divergent genetic groups with similar levels of genetic diversity. Vermilion rockfish, however, were characterized by three distinct genetic groups with much stronger signals of differentiation and significantly different genetic diversities. Collectively, these data will contribute to well-informed, species-specific management strategies to protect this valuable species complex.

Differential gene expression associated with behavioral variation in ecotypes of Lake Superior brook trout (Salvelinus fontinalis)

Associations between behaviors and the development of different life history tactics have been documented in several species of salmon, trout, and charr. While it is well known that such behaviors are heritable the genes and molecular pathways connected to these behaviors remain unknown. We used an RNA-seq approach to identify genes and molecular pathways differentially regulated in brain tissue between "shy" and "bold" brook trout (Salvelinus fontinalis). A small number of genes were differentially expressed between the behavioral types at several months after hatching and two years of age. Pathway analysis revealed that EIF2 signaling differed consistently between shy and bold individuals suggesting large-scale differences in protein synthesis between behavioral types in the brain. Additionally, the RNA-seq data were used to find polymorphisms within the brook trout genome and a GWAS approach was used to test for statistical associations between genetic variants and behavior type. One allele located in a transcription factor (TSHZ3) contained a protein-coding non-synonymous SNP suggesting that functional variation within TSHZ3 is connected to the development of different behaviors. These results suggest that the molecular basis of behavioral development is complex and due to the differential expression of many genes involved in a wide-range of different molecular pathways.

Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish

Concepts of evolutionary biology suggest that morphological change may occur by rare punctual but rather large changes, or by more steady and gradual transformations. It can therefore be asked whether genetic changes underlying morphological, physiological, and/or behavioral innovations during evolution occur in a punctual manner, whereby a single mutational event has prominent phenotypic consequences, or if many consecutive alterations in the DNA over longer time periods lead to phenotypic divergence. In the marine teleost, sablefish (Anoplopoma fimbria), complementary genomic and genetic studies led to the identification of a sex locus on the Y Chromosome. Further characterization of this locus resulted in identification of the transforming growth factor, beta receptor 1a (tgfbr1a) gene, gonadal somatic cell derived factor (gsdf), as the main candidate for fulfilling the master sex determining (MSD) function. The presence of different X and Y Chromosome copies of this gene indicated that the male heterogametic (XY) system of sex determination in sablefish arose by allelic diversification. The gsdfY gene has a spatio-temporal expression profile characteristic of a male MSD gene. We provide experimental evidence demonstrating a pivotal role of a transposable element (TE) for the divergent function of gsdfY. By insertion within the gsdfY promoter region, this TE generated allelic diversification by bringing cis-regulatory modules that led to transcriptional rewiring and thus creation of a new MSD gene. This points out, for the first time in the scenario of MSD gene evolution by allelic diversification, a single, punctual molecular event in the appearance of a new trigger for male development.

The rise and fall of the ancient northern pike master sex-determining gene

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome

Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod (Ophiodon elongatus), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site-associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F-statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low FST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome-level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management.

A mobile sex-determining region, male-specific haplotypes and rearing environment influence age at maturity in Chinook salmon

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males influenced by large (up to 20 Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex determination in this species and Pacific salmon in general.

A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska

In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes.

Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae

Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10-15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout (Oncorhynchus mykiss) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific "dangerous duplicates", that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns.

Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead (Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment

Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout (Oncorhynchus mykiss) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.

Rainbow trout personality: individual behavioural variation in juvenile Oncorhynchus mykiss

We evaluated the variation in dispersal, exploration, and aggression across time in juvenile progeny produced from wild caught rainbow trout (Oncorhynchus mykiss) at a critical developmental shift associated with the highest mortality in fish. By testing multiple ecologically relevant behaviours repeatedly in the same individuals, we simultaneously tested multiple hypotheses regarding personality, plasticity, and behavioural syndromes to better understand the innate behavioural variation in a population containing both migratory and resident life histories. There were consistent behavioural differences, or personality, between individuals across time, for dispersal, aggression, and exploration, unrelated to size or sex. The significant repeatabilities (0.10–0.46) indicate that these traits are potentially heritable. Also, we found both habituation in all behaviours and significant differences between individuals in the rate of that habituation, despite no evidence of a behavioural syndrome. The identification of this individual level variation is a step towards understanding which heritable traits selection could influence.

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Genomic signatures among Oncorhynchus nerka ecotypes to inform conservation and management of endangered Sockeye Salmon

Conservation of life history variation is an important consideration for many species with trade-offs in migratory characteristics. Many salmonid species exhibit both resident and migratory strategies that capitalize on benefits in freshwater and marine environments. In this study, we investigated genomic signatures for migratory life history in collections of resident and anadromous Oncorhynchus nerka (Kokanee and Sockeye Salmon, respectively) from two lake systems, using ~2,600 SNPs from restriction-site-associated DNA sequencing (RAD-seq). Differing demographic histories were evident in the two systems where one pair was significantly differentiated (Redfish Lake, F_ST = 0.091 [95% confidence interval: 0.087 to 0.095]) but the other pair was not (Alturas Lake, F_ST = -0.007 [-0.008 to -0.006]). Outlier and association analyses identified several candidate markers in each population pair, but there was limited evidence for parallel signatures of genomic variation associated with migration. Despite lack of evidence for consistent markers associated with migratory life history in this species, candidate markers were mapped to functional genes and provide evidence for adaptive genetic variation within each lake system. Life history variation has been maintained in these nearly extirpated populations of O. nerka, and conservation efforts to preserve this diversity are important for long-term resiliency of this species.

MicroRNAs are involved in cadmium tolerance in Daphnia pulex

Daphnia can develop tolerance to cadmium (Cd) after multi-generational exposures. Until now, Cd tolerance in this crustacean was thought to be mainly due to its sequestration via induction of metallothioneins (MTs). Our research supports other studies showing microRNAs (miRNAs) also play a role in this enhanced tolerance. We induced Cd tolerance in Daphnia pulex after exposing them for 25 generations and examined the maintenance of enhanced Cd tolerance under a Cd-free environment for an additional three generations. Acute Cd tolerance as well as long-term effects on population dynamics were measured in selected generations via 48h LC50 tests and 21 d reproductive tests, respectively. Cd tolerance was associated with differential expression of 10 miRNAs (miR-2, miR-33, miR-92, miR-96, miR-153, miR-252, miR-279, miR-283, miR-305 and miR-615). Pathway analysis revealed these miRNAs might increase Cd tolerance by suppressing cellular growth and proliferation by GTPase and cuticle protein pathways, which switch cellular energy allocation to detoxification processes. Moreover, we found increased Cd tolerance is related with induction of MT3 and MT4 and a subsequent downregulation of MT1 and MT3 expression when animals are moved to a Cd-free environment. This is the first study linking aquatic invertebrate miRNAs with induced tolerance to environmental stressors.

Novel Cadmium Responsive MicroRNAs in Daphnia pulex

Daphnia pulex is a widely used toxicological model and is known for its sensitivity to cadmium (Cd). Recent research suggests that microRNAs (miRNAs) play a critical role in animal responses to heavy metals. To investigate the functions of D. pulex miRNAs under Cd exposure, we analyzed the miRNA profiles of D. pulex after 48 h using miRNA microarrays and validated our findings by q-PCR. miRNA dpu-let-7 was identified as a stably expressed gene and used as a reference. We identified 22 and 21 differentially expressed miRNAs under low (20 μg/L CdCl2) and high-exposure (40 μg/L CdCl2) concentrations compared to controls, respectively. Cellular functions of predicted miRNA target Cd-responsive genes included oxidative stress, ion transport, mitochondrial damage, and DNA repair. An insulin-related network was also identified in relation to several Cd-responsive miRNAs. The expression of three predicted target genes for miR-71 and miR-210 were evaluated, and expression of two of them (SCN2A and SLC31A1) was negatively correlated with the expression of their regulator miRNAs. We show miR-210 is hypoxia-responsive in D. pulex and propose Cd and hypoxia induce miR-210 via a same HIF1α modulated pathway. Collectively, this research advances our understanding on the role of miRNAs in response to heavy-metal exposure.

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi

The Opisthokonta are a eukaryotic supergroup divided in two main lineages: animals and related protistan taxa, and fungi and their allies [1, 2]. There is a great diversity of lifestyles and morphologies among unicellular opisthokonts, from free-living phagotrophic flagellated bacterivores and filopodiated amoebas to cell-walled osmotrophic parasites and saprotrophs. However, these characteristics do not group into monophyletic assemblages, suggesting rampant convergent evolution within Opisthokonta. To test this hypothesis, we assembled a new phylogenomic dataset via sequencing 12 new strains of protists. Phylogenetic relationships among opisthokonts revealed independent origins of filopodiated amoebas in two lineages, one related to fungi and the other to animals. Moreover, we observed that specialized osmotrophic lifestyles evolved independently in fungi and protistan relatives of animals, indicating convergent evolution. We therefore analyzed the evolution of two key fungal characters in Opisthokonta, the flagellum and chitin synthases. Comparative analyses of the flagellar toolkit showed a previously unnoticed flagellar apparatus in two close relatives of animals, the filasterean Ministeria vibrans and Corallochytrium limacisporum. This implies that at least four different opisthokont lineages secondarily underwent flagellar simplification. Analysis of the evolutionary history of chitin synthases revealed significant expansions in both animals and fungi, and also in the Ichthyosporea and C. limacisporum, a group of cell-walled animal relatives. This indicates that the last opisthokont common ancestor had a complex toolkit of chitin synthases that was differentially retained in extant lineages. Thus, our data provide evidence for convergent evolution of specialized lifestyles in close relatives of animals and fungi from a generalist ancestor.

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

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

Genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis commonly stocked in Lake Superior

Fitness related traits often show spatial variation across populations of widely distributed species. Comparisons of genetic variation among populations in putatively neutral DNA markers and in phenotypic traits susceptible to selection (Q_ST F_ST analysis) can be used to determine to what degree differentiation among populations can be attributed to selection or genetic drift. Traditionally, Q_ST F_ST analyses require a large number of populations to achieve sufficient statistical power; however, new methods have been developed that allow Q_ST F_ST comparisons to be conducted on as few as two populations if their pedigrees are informative. This study compared genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis that were historically or currently used for stocking in the Lake Superior Basin. Herein we examined if morphological divergence among populations showed temporal variation, and if divergence could be attributed to selection or was indistinguishable from genetic drift. Multivariate Q_ST F_ST analysis showed evidence for divergent selection between populations. Univariate analyses suggests that the pattern observed in the multivariate analyses was largely driven by divergent selection for length and weight, and moreover by divergence between the Assinica strain and each of the Iron River and Siskiwit strains rather than divergent selection between each population pair. While it could not be determined if divergence was due to natural selection or inadvertent artificial selection in hatcheries, selected differences were consistent with patterns of domestication commonly found in salmonids.

Divergence in expression of candidate genes for the smoltification process between juvenile resident rainbow and anadromous steelhead trout

Rainbow and steelhead trout (Oncorhynchus mykiss), among other salmonid fishes, exhibit tremendous life history diversity, foremost of which is variation in migratory propensity. While some individuals possess the ability to undertake an anadromous marine migration, others remain resident in freshwater throughout their life cycle. Those that will migrate undergo tremendous physiological, morphological, and behavioral transformations in a process called smoltification which transitions freshwater-adapted parr to marine-adapted smolts. While the behavior, ecology, and physiology of smoltification are well described, our understanding of the proximate genetic mechanisms that trigger the process are not well known. Quantitative genetic analyses have identified several genomic regions associated with smoltification and migration-related traits within this species. Here we investigate the divergence in gene expression of 18 functional and positional candidate genes for the smoltification process in the brain, gill, and liver tissues of migratory smolts, resident parr, and precocious mature male trout at the developmental stage of out-migration. Our analysis reveals several genes differentially expressed between life history classes and validates the candidate nature of several genes in the parr-smolt transformation including Clock1α, FSHβ, GR, GH2, GHR1, GHR2, NDK7, p53, SC6a7, Taldo1, THRα, THRβ, and Vdac2.

Mapping and Expression of Candidate Genes for Development Rate in Rainbow Trout (Oncorhynchus mykiss)

Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life-history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a quantitative trait locus for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression, and quantitative genetic methods to further identify the genetic basis of embryonic developmental rate in O. mykiss Among the genes located in the region of the major development rate quantitative trait locus (GHR1, Clock1a, Myd118-1, and their paralogs), all were expressed early in embryonic development (fertilization through hatch), but none were differentially expressed between individuals with the fast- or slow-developing alleles for a major embryonic development rate quantitative trait locus. In a follow-up study of migratory and resident rainbow trout from natural populations in Alaska, we found significant additive variation in development rate and, moreover, found associations between development rate and allelic variation in all 3 candidate genes within the quantitative trait locus for embryonic development. The mapping of these genes to this region and associations in multiple populations provide positional candidates for further study of their roles in growth, development, and life-history diversity in this model salmonid.

Fitness consequences of dispersal: is leaving home the best of a bad lot?

Using 20 years of demographic and genetic data from four populations of banner-tailed kangaroo rats (Dipodomys spectabilis), we asked whether dispersing individuals gain benefits during adulthood that might compensate for the substantial survival costs they experience as juveniles. Compared to philopatric animals, within- and between-population dispersers gained no measureable advantages in adult survival, fecundity, or probability of recruiting offspring to adulthood. Restricting analyses to members of two central populations living more than 15 times the median dispersal distance from the study site edge, and using peripheral populations only to detect dispersal or offspring recruitment "offsite," did not change this result. Population density during year of birth had small negative effects on adult survival and fecundity, but there were no interactions with dispersal phenotype. We found no evidence that dispersers gained access to superior habitat or that their offspring suffered less inbreeding depression. Our results are consistent with fitness advantages being indirect; by leaving, dispersers release their kin from competition. Our results are also consistent with the possibility that dispersal is the "best of a bad lot." If dispersal is a conditional strategy, then the benefits may be obscured in observational data that compare dispersing individuals to philopatric individuals rather than to individuals whose dispersal phenotype is experimentally manipulated.

Mapping rainbow trout immune genes involved in inflammation reveals conserved blocks of immune genes in teleosts

We report the genetic map location of 14 genes involved in the inflammatory response to salmonid bacterial and viral pathogens, which brings the total number of immune genes mapped in rainbow trout (RT, Oncorhynchus mykiss) to 61. These genes were mapped as candidate genes that may be involved in resistance to bacterial kidney disease, as well as candidates for known QTL for resistance to infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus and Ceratomyxa shasta. These QTL map to one or more of the linkage groups containing immune genes. The combined analysis of these linkage results and those of previously mapped immune genes in RT shows that many immune genes are found in syntenic blocks of genes that have been retained in teleosts despite species divergence and genome duplication events.

Genetic architecture of migration-related traits in rainbow and steelhead trout, Oncorhynchus mykiss

Although migration plays a critical role in the evolution and diversification of species, relatively little is known of the genetic architecture underlying this life history in any species. Rainbow and steelhead trout (Oncorhynchus mykiss) naturally segregate for both resident and migratory life-history types, respectively, as do other members of the salmonid family of fishes. Using an experimental cross derived from wild resident rainbow and wild migratory steelhead trout from Southeast Alaska and high throughput restriction-site associated DNA (RAD) tag sequencing, we perform a quantitative trait locus (QTL) analysis to identify the number, position, and relative contribution of genetic effects on a suite of 27 physiological and morphological traits associated with the migratory life history in this species. In total, 37 QTL are localized to 19 unique QTL positions, explaining 4-13.63% of the variation for 19 of the 27 migration-related traits measured. Two chromosomal positions, one on chromosome Omy12 and the other on Omy14 each harbor 7 QTL for migration-related traits, suggesting that these regions could harbor master genetic controls for the migratory life-history tactic in this species. Another QTL region on Omy5 has been implicated in several studies of adaptive life histories within this species and could represent another important locus underlying the migratory life history. We also evaluate whether loci identified in this out-crossed QTL study colocalize to genomic positions previously identified for associations with migration-related traits in a doubled haploid mapping family.

Differential gene expression in male and female rainbow trout embryos prior to the onset of gross morphological differentiation of the gonads

BACKGROUND

There are large differences between the sexes at the genetic level; these differences include heterogametic sex chromosomes and/or differences in expression of genes between the sexes. In rainbow trout (Oncorhynchus mykiss) qRT-PCR studies have found significant differences in expression of several candidate sex determining genes. However, these genes represent a very small fraction of the genome and research in other species suggests there are large portions of the transcriptome that are differentially expressed between the sexes. These differences are especially noticeable once gonad differentiation and maturation has occurred, but less is known at earlier stages of development. Here we use data from a microarray and qRT-PCR to identify genes differentially expressed between the sexes at three time points in pre-hatch embryos, prior to the known timing of sexual differentiation in this species.

RESULTS

The microarray study revealed 883 differentially expressed features between the sexes with roughly equal numbers of male and female upregulated features across time points. Most of the differentially expressed genes on the microarray were not related to sex function, suggesting large scale differences in gene expression between the sexes are present early in development. Candidate gene analysis revealed sox9, DMRT1, Nr5a1 and wt1 were upregulated in males at some time points and foxl2, ovol1, fst and cyp19a1a were upregulated in females at some time points.

CONCLUSION

This is the first study to identify sexual dimorphism in expression of the genome during embryogenesis in any fish and demonstrates that transcriptional differences are present before the completion of gonadogenesis.

Transcriptome profiling of embryonic development rate in rainbow trout advanced backcross introgression lines

In rainbow trout (Oncorhynchus mykiss) and other fishes, embryonic development rate is an ecologically and evolutionarily important trait that is closely associated with survival and physiological performance later in life. To identify genes differentially regulated in fast and slow-developing embryos of rainbow trout, we examined gene expression across developmental time points in rainbow trout embryos possessing alleles linked to a major quantitative trait loci (QTL) for fast versus slow embryonic development rate. Whole genome expression microarray analyses were conducted using embryos from a fourth generation backcross family, whereby each backcross generation involved the introgression of the fast-developing alleles for a major development rate QTL into a slow-developing clonal line of rainbow trout. Embryos were collected at 15, 19, and 28 days post-fertilization; sex and QTL genotype were determined using molecular markers, and cDNA from 48 embryos were used for microarray analysis. A total of 183 features were identified with significant differences between embryonic development rate genotypes. Genes associated with cell cycle growth, muscle contraction and protein synthesis were expressed significantly higher in embryos with the fast-developing allele (Clearwater) than those with the slow-developing allele (Oregon State University), which may associate with fast growth and early body mass construction in embryo development. Across time points, individuals with the fast-developing QTL allele appeared to have earlier onset of these developmental processes when compared to individuals with the slow development alleles, even as early as 15 days post-fertilization. Differentially expressed candidate genes chosen for linkage mapping were localized primarily to regions outside of the major embryonic development rate QTL, with the exception of a single gene (very low-density lipoprotein receptor precursor).

Heritability of morphology in brook trout with variable life histories

Distinct morphological variation is often associated with variation in life histories within and among populations of both plants and animals. In this study, we examined the heritability of morphology in three hatchery strains of brook trout (Salvelinus fontinalis), which were historically or are currently used for stocking and supplementation of both migratory and resident ecotypes in the upper Great Lakes region. In a common garden experiment, significant variation in body morphology was observed within and across populations sampled at three time periods. The most notable differences among strains were differences in dorso-ventral body depth and the shape of the caudal peduncle, with some differences in the anterior-posterior placement of the dorsal and ventral fins. Variation with and among 70 half-sib families indicates that heritabilities of morphology and body size were significant at most developmental time points both within and across strains. Heritabilities for morphological characters within strains ranged from 0 to 0.95 across time points. Significant within-strain heritabilities for length ranged from 0 to 0.93 across time points and for weight ranged from 0 to 0.88. Significant additive genetic variation exists within and across hatchery brook trout strains for morphology and size, indicating that these traits are capable of responding to natural or artificial selection.

Recombination is suppressed over a large region of the rainbow trout Y chromosome

The previous genetic mapping data have suggested that most of the rainbow trout sex chromosome pair is pseudoautosomal, with very small X-specific and Y-specific regions. We have prepared an updated genetic and cytogenetic map of the male rainbow trout sex linkage group. Selected sex-linked markers spanning the X chromosome of the female genetic map have been mapped cytogenetically in normal males and genetically in crosses between the OSU female clonal line and four different male clonal lines as well as in outcrosses involving outbred OSU and hybrids between the OSU line and the male clonal lines. The cytogenetic maps of the X and Y chromosomes were very similar to the female genetic map for the X chromosome. Five markers on the male maps are genetically very close to the sex determination locus (SEX), but more widely spaced on the female genetic map and on the cytogenetic map, indicating a large region of suppressed recombination on the Y chromosome surrounding the SEX locus. The male map is greatly extended at the telomere. A BAC clone containing the SCAR (sequence characterized amplified region) Omy-163 marker, which maps close to SEX, was subjected to shotgun sequencing. Two carbonyl reductase genes and a gene homologous to the vertebrate skeletal ryanodine receptor were identified. Carbonyl reductase is a key enzyme involved in production of trout ovarian maturation hormone. This brings the number of type I genes mapped to the sex chromosome to six and has allowed us to identify a region on zebrafish chromosome 10 and medaka chromosome 13 which may be homologous to the distal portion of the long arm of the rainbow trout Y chromosome.

Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss

Effects of maternal cytoplasmic environment (MCE) on development rate in rainbow trout were evaluated within a quantitative trait loci (QTL) analysis framework. Previous research had identified QTL for development rate in doubled haploid (DH) progeny produced from a cross between the Oregon State University (OSU) and the Swanson (SW) River rainbow trout clonal lines. In this study, progeny for QTL mapping were produced from a cross between the OSU and Clearwater (CW) River clonal lines. Doubled haploids were produced from the OSU x CW F1 by androgenesis using eggs from different females (or MCEs); with androgenesis, the maternal nuclear genome was destroyed by irradiation and diploidy was restored by blocking the first embryonic cleavage by heat shock. All embryos were incubated at the same temperature and development rate quantified as time to hatch. Using a linkage map constructed primarily with AFLP markers, QTL mapping was performed, including MCE covariates and QTL x MCE effects in models for testing. The major QTL for development rate in the OSU x SW cross overlaps with the major QTL found in this OSU x CW cross; effects at this locus were the same across MCEs. Both MCE and QTL x MCE effects contribute to variability in development rate, but QTL x MCE were minor and detected only at small-effect QTL.

Assignment of rainbow trout linkage groups to specific chromosomes

The rainbow trout genetic linkage groups have been assigned to specific chromosomes in the OSU (2N=60) strain using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group. There was a rough correlation between chromosome size and size of the genetic linkage map in centimorgans for the genetic maps based on recombination from the female parent. Chromosome size and structure have a major impact on the female:male recombination ratio, which is much higher (up to 10:1 near the centromeres) on the larger metacentric chromosomes compared to smaller acrocentric chromosomes. Eighty percent of the BAC clones containing duplicate genes mapped to a single chromosomal location, suggesting that diploidization resulted in substantial divergence of intergenic regions. The BAC clones that hybridized to both duplicate loci were usually located in the distal portion of the chromosome. Duplicate genes were almost always found at a similar location on the chromosome arm of two different chromosome pairs, suggesting that most of the chromosome rearrangements following tetraploidization were centric fusions and did not involve homeologous chromosomes. The set of BACs compiled for this research will be especially useful in construction of genome maps and identification of QTL for important traits in other salmonid fishes.

Comprehensive gene expression profiling following DNA vaccination of rainbow trout against infectious hematopoietic necrosis virus

The DNA vaccine based on the glycoprotein gene of Infectious hematopoietic necrosis virus induces a non-specific anti-viral immune response and long-term specific immunity against IHNV. This study characterized gene expression responses associated with the early anti-viral response. Homozygous rainbow trout were injected intra-muscularly (I.M.) with vector DNA or the IHNV DNA vaccine. Gene expression in muscle tissue (I.M. site) was evaluated using a 16,008 feature salmon cDNA microarray. Eighty different genes were significantly modulated in the vector DNA group while 910 genes were modulated in the IHNV DNA vaccinate group relative to control group. Quantitative reverse-transcriptase PCR was used to examine expression of selected immune genes at the I.M. site and in other secondary tissues. In the localized response (I.M. site), the magnitudes of gene expression changes were much greater in the vaccinate group relative to the vector DNA group for the majority of genes analyzed. At secondary systemic sites (e.g. gill, kidney and spleen), type I IFN-related genes were up-regulated in only the IHNV DNA vaccinated group. The results presented here suggest that the IHNV DNA vaccine induces up-regulation of the type I IFN system across multiple tissues, which is the functional basis of early anti-viral immunity.

Model selection in binary trait locus mapping

Quantitative trait locus (QTL) mapping methodology for continuous normally distributed traits is the subject of much attention in the literature. Binary trait locus (BTL) mapping in experimental populations has received much less attention. A binary trait by definition has only two possible values, and the penetrance parameter is restricted to values between zero and one. Due to this restriction, the infinitesimal model appears to come into play even when only a few loci are involved, making selection of an appropriate genetic model in BTL mapping challenging. We present a probability model for an arbitrary number of BTL and demonstrate that, given adequate sample sizes, the power for detecting loci is high under a wide range of genetic models, including most epistatic models. A novel model selection strategy based upon the underlying genetic map is employed for choosing the genetic model. We propose selecting the "best" marker from each linkage group, regardless of significance. This reduces the model space so that an efficient search for epistatic loci can be conducted without invoking stepwise model selection. This procedure can identify unlinked epistatic BTL, demonstrated by our simulations and the reanalysis of Oncorhynchus mykiss experimental data.

Examination of reproductive endpoints in goldfish (Carassius auratus) exposed in situ to municipal sewage treatment plant effluent discharges in Michigan, USA

Effects of representative mid-Michigan (USA) wastewater treatment plant (WWTP) effluents on the reproductive physiology of common goldfish (Carassius auratus) were assessed in situ by measuring plasma concentrations of vitellogenin (VTG), 17 beta-estradiol (E2), and testosterone (T), and evaluating gonad histology. Caged adult male and female goldfish were exposed for six weeks to WWTP effluents. One riverine site and one lacustrine site were included as references for comparison to WWTP sites. There was differential growth and gonadal development among locations, which confounded the interpretation of biomarker responses. A linear contrast model was developed by analysis of covariance, and adjusted values were developed for concentrations of VTG, E2, and T in the plasma of both male and female fish. In general, VTG concentrations were significantly less in male than in female goldfish. Most concentrations of VTG in male goldfish were less than the method detection limit. There were no significant differences in plasma VTG of either male or female goldfish among locations or between sites at WWTPs and reference sites. Concentrations of E2 in the plasma of female goldfish were similar among WWTP sites, all of which were less than in females at a pond reference location. Concentrations of E2 in the plasma of male goldfish were similar at all WWTP locations, except for one, where they were greater. No consistent trends in hormone concentrations or gonadal histology could be attributed to putative endocrine disrupter exposure in WWTP effluents. The results indicate that the risk for estrogen agonist exposure below these mid-Michigan WWTPs is small.

Mapping multiple genetic loci associated with Ceratomyxa shasta resistance in Oncorhynchus mykiss

Ceratomyxa shasta is enzootic to some rivers of the Pacific Northwest and California, and has caused extensive mortalities of salmonids, the only known host of the actinosporean stage of the pathogen. Mortalities from C. shasta are induced by severe inflammation and necrosis of the intestinal tract, and no therapeutants have been discovered for the treatment of ceratomyxosis. Inheritance studies by previous investigators suggested that C. shasta resistance is genetically controlled, but none have revealed the number and locations of gene regions associated with resistance. Here, we characterized differences in resistance among clonal lines, and used line crosses between clonal lines with resistance differences for a genetic analysis of C. shasta resistance in Oncorhynchus mykiss, following a short term in situ exposure to the pathogen. We found that Oregon State University (OSU) x Arlee (ARL) clonal hybrids were highly susceptible, while OSU x Clearwater (CW) hybrids were highly resistant to C. shasta. Doubled haploids, produced by androgenesis from an F1 hybrid between the OSU and CW lines, were evaluated for the co-segregation of molecular markers and resistance phenotype. Amplified fragment length polymorphic (AFLP) markers, used to construct a genetic linkage map in this cross, were tested for associations with resistance expressed as absolute survival (binary trait) and days to death (survival analysis). Segregation of the resistance phenotype suggested that the resistance was inherited as a single Mendelian locus, but the binary trait failed to map to a single genomic location. Markers identified in single-marker analyses were used in multiple-regression model selection, within both the linear regression and Cox proportional-hazards survival analysis frameworks, to determine the number and potential location of loci simultaneously contributing to variation in the survival phenotypes of doubled-haploid progeny. We found multiple genomic loci associated with C. shasta resistance through these models, confirming studies by previous investigators that suggested C. shasta resistance is polygenic.

A consolidated linkage map for rainbow trout (Oncorhynchus mykiss)

Androgenetic doubled haploid progeny produced from a cross between the Oregon State University and Arlee clonal rainbow trout (Oncorhynchus mykiss) lines, used for a previous published rainbow trout map, were used to update the map with the addition of more amplified fragment length polymorphic (AFLP) markers, microsatellites, type I and allozyme markers. We have added more than 900 markers, bringing the total number to 1359 genetic markers and the sex phenotype including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR, 38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four allozymes. Thirty major linkage groups were identified. Synteny of linkage groups in our map with the outcrossed microsatellite map has been established for all except one linkage group in this doubled haploid cross. Putative homeologous relationships among linkage groups, resulting from the autotetraploid nature of the salmonid genome, have been revealed based on the placement of duplicated microsatellites and type I loci.

Cloning novel immune-type inhibitory receptors from the rainbow trout, Oncorhynchus mykiss

Novel immune-type receptor ( NITR) genes that encode two extracellular immunoglobulin domains and cytoplasmic immunoreceptor tyrosine-based inhibition motifs (ITIMs) have been described previously in three lineages of bony fish. In the current study, four ITIM-containing NITR cDNAs are identified in the rainbow trout ( Oncorhynchus mykiss), and their expression patterns and genomic complexity are characterized. The ITIM-containing NITR2 gene maps 1.3 cM from an ITIM-containing C-type lectin receptor ( TCL-2) on linkage group XXI. A comprehensive, phylogenetic analysis of NITRs from rainbow trout and three other major lineages of bony fish defines conserved families of NITRs and suggests an ancient lineage of distinct groups of genes. Several probable scenarios that explain the origins of variant forms of NITRs are described.

Effects of nonylphenol ethoxylate exposure on reproductive output and bioindicators of environmental estrogen exposure in fathead minnows Pimephales promelas

Nonylphenol ethoxylates (NPEOs) were evaluated in the laboratory for potential effects on the reproductive physiology and fecundity of fathead minnows (Pimephales promelas). Groups of three adult male and three female fathead minnows were exposed in a continuous flow-through system to 0, 0.21, 0.65, 2.1, or 7.9 microg NPEO/L for 42 d. Rabbit anti-goldfish vitellogenin (VTG) antiserum was prepared and a competitive enzyme-linked immunosorbent assay (ELISA) was adapted for measurement of plasma VTG in fish following exposure. Plasma 17beta-estradiol (E2) and testosterone (T) were also quantified by ELISA at the end of the exposure. Neither survival nor fecundity of fathead minnows exhibited a concentration-dependent response to NPEOs. No significant differences were observed in plasma VTG concentrations among treatments for males or females. Mean plasma VTG concentrations in females ranged from 291.7 to 895.1 microg VTG/ml among treatments and did not overlap with mean concentrations measured in the plasma of males, which ranged from less than the method detection limit (0.27 microg VTG/ml) to 3.2 microg VTG/ml. Plasma E2 concentrations exhibited a significant difference between males and females within all NPEO treatments, but no differences were observed among treatments. Similarly, plasma T concentrations did not exhibit a concentration-dependent response to NPEOs.

In vitro vitellogenin production by carp (Cyprinus carpio) hepatocytes as a screening method for determining (anti)estrogenic activity of xenobiotics

The yolk protein precursor vitellogenin (Vtg) is secreted by the liver of female as well as male fish, in response to estrogenic compounds. In this study, an in vitro assay was developed for measuring Vtg induction, using cultured primary hepatocytes from genetically uniform strains of carp (Cyprinus carpio). Vtg production was measured by indirect competitive ELISA, using a polyclonal antiserum against goldfish Vtg that cross-reacts with carp Vtg. Vtg was dose-dependently induced by 17beta-estradiol (E2) in hepatocytes of both sexes. E2 had a lowest observed effect concentration (LOEC) for Vtg induction of 2 nM, an EC50 between 50 and 150 nM, and a maximum response at 2 microM. The plasticizer and xenoestrogen bisphenol-A induced Vtg secretion by hepatocytes of both sexes at 50 and 100 microM. This carp hepatocyte (CARP-HEP) assay can also be used to detect antiestrogenic activity, which was measured as the reduction of E2-stimulated Vtg synthesis. Two well-known antiestrogenic compounds, tamoxifen and 2,3,7, 8-tetrachlorodibenzo-p-dioxin (TCDD), were tested. TCDD caused a reduction in Vtg synthesis in female hepatocytes at concentrations <0.1 nM, making it approximately 10,000-fold more potent than tamoxifen. Carp hepatocytes were also sensitive to induction of cytochrome P4501A (CYP1A) activity, measured as ethoxyresorufin O-deethylase (EROD). Depending on the exposure time, 18 or 96 h, EROD EC50 values for TCDD were 27 or 6 pM, respectively. The CARP-HEP assay, using the 96-well plate format, offers good possibilities to screen large numbers of compounds for (anti)estrogenic properties. In addition, it can simultaneously determine aryl hydrocarbon receptor agonist properties, measured as CYP1A induction.

Effects of waterborne exposure to 4-nonylphenol and nonylphenol ethoxylate on secondary sex characteristics and gonads of fathead minnows (Pimephales promelas)

Fathead minnows were exposed to 4-nonylphenol (NP) or nonylphenol ethoxylate (NPEO) to determine the effects of these weak estrogen agonists on secondary sex characteristics and gonads of sexually mature males and females during 42-day continuous-flow exposures. Neither NP nor NPEO caused statistically significant effects on tubercles or fatpad size at the concentrations tested. Exposure to 1. 1 or 3.4 micrograms NP/L caused changes in the number and size of Sertoli cells and germ cell syncytia. Necrotic aggregates of various stages of germ cells in the spermatogenic sequence were observed in the testes of males exposed to NP. Electron microscopy of the testes of NP-exposed males revealed the presence of phagocytic cells in the lumina of seminiferous tubules. The cytoplasm of some Sertoli cells was distended with myelin figures and necrotic spermatozoa. No significant effects on the stages of follicular development were observed in females exposed to NP. There were no differences in the gonads or secondary sex characteristics of males or females exposed to 5.5 micrograms NPEO/L, the greatest concentration studied. The histologic responses observed are sensitive indicators of waterborne exposure to NP at environmentally relevant concentrations, but not as sensitive as induction of plasma vitellogenin. The secondary sex characteristics were not affected by concentrations of NP or NPEO as great as 3.4 or 5.5 micrograms/L, respectively. Histologic responses occurred at concentrations that were less than the final chronic value based on survival and approximately the same as those required to cause effects on egg production. The histologic effects caused by NP were similar to, but not exactly the same as those caused by exposure of fathead minnows to 17 beta-estradiol.

Effects of waterborne exposure to 4-nonylphenol and nonylphenol ethoxylate on secondary sex characteristics and gonads of fathead minnows (Pimephales promelas)

Fathead minnows were exposed to 4-nonylphenol (NP) or nonylphenol ethoxylate (NPEO) to determine the effects of these weak estrogen agonists on secondary sex characteristics and gonads of sexually mature males and females during 42-day continuous-flow exposures. Neither NP nor NPEO caused statistically significant effects on tubercles or fatpad size at the concentrations tested. Exposure to 1. 1 or 3.4 micrograms NP/L caused changes in the number and size of Sertoli cells and germ cell syncytia. Necrotic aggregates of various stages of germ cells in the spermatogenic sequence were observed in the testes of males exposed to NP. Electron microscopy of the testes of NP-exposed males revealed the presence of phagocytic cells in the lumina of seminiferous tubules. The cytoplasm of some Sertoli cells was distended with myelin figures and necrotic spermatozoa. No significant effects on the stages of follicular development were observed in females exposed to NP. There were no differences in the gonads or secondary sex characteristics of males or females exposed to 5.5 micrograms NPEO/L, the greatest concentration studied. The histologic responses observed are sensitive indicators of waterborne exposure to NP at environmentally relevant concentrations, but not as sensitive as induction of plasma vitellogenin. The secondary sex characteristics were not affected by concentrations of NP or NPEO as great as 3.4 or 5.5 micrograms/L, respectively. Histologic responses occurred at concentrations that were less than the final chronic value based on survival and approximately the same as those required to cause effects on egg production. The histologic effects caused by NP were similar to, but not exactly the same as those caused by exposure of fathead minnows to 17 beta-estradiol.

Clear cell neoplasm

We are reporting four cases of clear cell neoplasm. Local infiltration and destruction was observed in one case while in a second case, originating in the sublingual gland, metastasis to the lymph nodes occurred. The behaviour of these neoplasms has prompted the suggestion that these tumours be designated carcinomas rather that noncommittally tumours or neoplasms (Batsakis and Regezzi, 1977). The histopathological characteristics of our four cases conform to those that have been articulated and believed to be the distinctive features of these tumours (Batsakis and Regezzi, 1977). It is hoped that ours and similar reports will be helpful towards clearing the diagnostic and taxonomic confusion regarding these tumours.

Effects of infrared laser damage to the Euglena photoreceptor on the control of flagellar motility

When the area of the stigma of Euglena was irradiated with an infrared laser beam at a dose too low to cause permanent loss of motility, a reduction in flagellar motility was observed only when the external medium contained less than 1 mM Mg2+. At these low Mg2+ concentrations, the laser caused a decrease in flagellar frequency and a tendency for the flagellar waveform to shift towards that taken during reversed swimming. This suggests that the effect of the laser irradiation was to deplete the cells of Mg2+. After the laser pulse the reversal response remained sensitive to the wavelength of the illuminating light. In white light (420-700 nm) 60% of the Euglena showed a reversed waveform; in orange light (530-700 nm) this increased to 90%. This shows that the photoreceptor was not destroyed by the laser irradiation. These experiments were performed on cells that had been impaled on a microelectrode. If direct electric current was passed into the laser-irradiated cells, the current necessary to cause flagellar arrest was 2 to 4 times less than that for cells not laser irradiated. It is concluded that an internal Mg2+ store is present in the Euglena, localized in the area of the paraflagellar swelling; and that the laser irradiation eliminates this Mg2+ store, but at the power used it does not destroy the ability of the stigma-paraflagella to control the flagellar activity.

Effects of Mg2+ and Ca2+ on photoinduced Euglena flagellar responses

The flagellar frequency and waveform of Euglena were analyzed under full illumination (420-700 nm) and in a restricted wavelength band (530-700 nm) when the cells were in a medium containing Mg2+ or had been microinjected with Mg2+, Mn2+, or Ca2+ in solution. Magnesium abolished the change in flagellar frequency and the reversal in waveform that cells exhibit when illuminated by a 530-700 nm wavelength band. Under this restricted illumination, Ca2+ caused an increase in flagellar waveform reversal and a decrease in beating frequency. The flagellar motility of cells impaled on a microelectrode was examined in cells illuminated with various wavelengths.