Fin Clips Research Articles

Polymorphism of insulin-like growth factor binding protein-3 (IGFBP-3) gene associated with growth traits in Cyprinus carpio

The genetic polymorphism of insulin-like growth factor binding protein ( IGFBP-3 ) and its association with the growth traits namely condition factor, body weight, and total length were investigated in common carp Cyprinus carpio using PCR- single strand conformation polymorphism (SSCP) technique. Caudal fin clips from 120 C. carpio , aging 5 months, were used in this study and a 330 bp DNA fragment was amplified from 5'-UTR of carp IGFBP-3 . SSCP genotyping yielded seven different banding patterns namely A, B, C, D, E, F, and G with frequencies of 14.16, 12.5, 21.67, 9.17, 11.67, 10.0, and 20.84, respectively. The obtained results showed a relatively high polymorphic behavior of 5'-UTR regulatory region of studied locus; therefore it shows the importance of this region in regulation of transcription of IGFBP-3 gene in carp. Marker-trait association showed significant relationships between the detected genotypes and condition factor (CF). IGFBP-3 gene polymorphism in joint with CF signifies relatively high genetic diversity and significant potential for marker-assisted selection in this species.

Experimental Determination of the Limits of Using Stable Isotopes to Distinguish Steelhead and Rainbow Trout Offspring

AbstractSalmonid ecology and conservation projects often necessitate distinguishing the offspring from anadromous or nonanadromous mothers, but the forms are often physically and genetically similar. We reared Oncorhynchus mykiss fry produced by anadromous mothers on one of two diets: one rich in and the other depleted in marine nutrients. We then sampled and analyzed fin and muscle tissues from fish fed both diets for nitrogen stable isotopes over time. Tissue nitrogen values from fish on the marine‐nutrient‐depleted diet indicated the size and time cutoffs at which offspring of anadromous O. mykiss no longer reflected a marine origin (muscle tissue cutoff: 0.81 g, 50.8 mm, and 29.4 d postfeeding; fin tissue cutoff: 0.65 g, 45.9 mm, and 35.3 d). Salmonids smaller than 50 mm cannot provide a sufficiently large fin sample for isotopic analysis without significant risk of mortality. Therefore, our experiment did not reveal a period when fish were large enough to provide a nonlethal fin clip but still maintain their maternal nitrogen isotope signature. However, fish growing slower than those we examined would likely be distinguishable for a longer period of time than our data indicated.Received December 21, 2014; accepted May 2, 2015

Similarities and differences in 13 C and 15 N stable isotope ratios in two non-lethal tissue types from shovelnose sturgeon Scaphirhynchus platorynchus (Rafinesque, 1820)

We tested the hypothesis that δ13C and δ15N signatures of pectoral spines would provide measures of δ13C and δ15N similar to those obtained from fin clips for adult shovelnose sturgeon Scaphirhynchus platorynchus. Thirty-two shovelnose sturgeon (fork length [FL] = 500–724 mm) were sampled from the lower Mississippi River, USA on 23 February 2013. Isotopic relationships between the two tissue types were analyzed using mixed model analysis of covariance. Tissue types differed significantly for both δ13C (P < 0.01; spine: mean = −23.83, SD = 0.62; fin clip: mean = −25.74, SD = 0.97) and δ15N (P = 0.01; spine: mean = 17.01, SD = 0.51; fin clip: mean = 17.19, SD = 0.62). Neither FL nor the FL × tissue type interaction had significant (P > 0.05) effects on δ13C. Fin clip δ13C values were highly variable and weakly correlated (r = 0.16, P = 0.40) with those from pectoral spines. We found a significant FL-tissue type interaction for δ15N, reflecting increasing δ15N with FL for spines and decreasing δ15N with FL for fin clips. These results indicate that spines are not a substitute for fin clip tissue for measuring δ13C and δ15N for shovelnose sturgeon in the lower Mississippi River, but the two tissues have different turnover rates they may provide complementary information for assessing trophic position at different time scales.

Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh.

Mucus of fish skin harbors complex bacterial communities that likely contribute to fish homeostasis. When the equilibrium between the host and its external bacterial symbionts is disrupted, bacterial diversity decreases while opportunistic pathogen prevalence increases, making the onset of pathogenic bacterial infection more likely. Because of that relationship, documenting temporal and spatial microbial community changes may be predictive of fish health status. The 2010 Deepwater Horizon oil spill was a potential stressor to the Gulf of Mexico's coastal ecosystem. Ribosomal intergenic spacer analysis (RISA) and pyrosequencing were used to analyze the bacterial communities (microbiome) associated with the skin and mucus of Gulf killifish (Fundulus grandis) that were collected from oiled and non-oiled salt marsh sites in Barataria Bay, LA. Water samples and fin clips were collected to examine microbiome structure. The microbiome of Gulf killifish was significantly different from that of the surrounding water, mainly attributable to shifts in abundances of Cyanobacteria and Proteobacteria. The Gulf killifish's microbiome was dominated by Gammaproteobacteria, specifically members of Pseudomonas. No significant difference was found between microbiomes of fish collected from oiled and non-oiled sites suggesting little impact of oil contamination on fish bacterial assemblages. Conversely, seasonality significantly influenced microbiome structure. Overall, the high similarity observed between the microbiomes of individual fish observed during this study posits that skin and mucus of Gulf killifish have a resilient core microbiome.

Important sources of variation to be considered when using fin clips as a surrogate for muscle in trophic studies using stable isotopes

White muscle is the prevalent tissue for C and N stable isotope analysis in fish, requiring the death of the fish or biopsy procedures that could lead to infections or severe damage. Given that caudal fin-clipping does not seriously affect growth or condition, the present study assessed the suitability of caudal fin tissue as replacement for muscle tissue in trophic studies. Clips of caudal fin were a useful non-lethal surrogate of muscle samples in four studied reef-fish (Diplodus argenteus, Pagrus pagrus, Acanthistius patachonicus and Pinguipes brasilianus). Fin clips were easy to collect in quantities adequate for mass spectrometry analyses and had C:N ratios similar to those of white muscle with low lipid content. However, results showed that fin-muscle correction models should be specific and sampling design should be conducted to reduce spatial and temporal variation. Moreover, species-specific correction factors may not be valid for other populations of the same species if the presumed range of δX values differ from the population used to estimate the correction models. Results also showed that the fin-muscle relationship could vary with size. Thus, unless a non-ecological meaningful fin-muscle correlation with body size was previously identified, correction models should be estimated sampling a representative size range and fin samples should be used with caution to study size-related trophodynamics.

Cryptic Ponto-Caspian Bighead Gobies (genus Ponticola, Gobiidae, Perciformes)

Cryptic Ponto-Caspian Bighead Gobies (genus Ponticola, Gobiidae, Perciformes)

Life+ Trout Project (LIFE12 NAT/IT/0000940) for the recovery and conservation of Mediterranean trout (Salmo trutta complex) in the central Apennines (Italy).

Life+ Trout Project (LIFE12 NAT/IT/0000940) for the recovery and conservation of Mediterranean trout (Salmo trutta complex) in the central Apennines (Italy).

Testing of candidate non-lethal sampling methods for detection of Renibacterium salmoninarum in juvenile Chinook salmon Oncorhynchus tshawytscha.

Non-lethal pathogen testing can be a useful tool for fish disease research and management. Our research objectives were to determine if (1) fin clips, gill snips, surface mucus scrapings, blood draws, or kidney biopsies could be obtained non-lethally from 3 to 15 g Chinook salmon Oncorhynchus tshawytscha, (2) non-lethal samples could accurately discriminate between fish exposed to the bacterial kidney disease agent Renibacterium salmoninarum and non-exposed fish, and (3) non-lethal samples could serve as proxies for lethal kidney samples to assess infection intensity. Blood draws and kidney biopsies caused ≥5% post-sampling mortality (Objective 1) and may be appropriate only for larger fish, but the other sample types were non-lethal. Sampling was performed over 21 wk following R. salmoninarum immersion challenge of fish from 2 stocks (Objectives 2 and 3), and nested PCR (nPCR) and real-time quantitative PCR (qPCR) results from candidate non-lethal samples were compared with kidney tissue analysis by nPCR, qPCR, bacteriological culture, enzyme-linked immunosorbent assay (ELISA), fluorescent antibody test (FAT) and histopathology/immunohistochemistry. R. salmoninarum was detected by PCR in >50% of fin, gill, and mucus samples from challenged fish. Mucus qPCR was the only non-lethal assay exhibiting both diagnostic sensitivity and specificity estimates>90% for distinguishing between R. salmoninarum-exposed and non-exposed fish and was the best candidate for use as an alternative to lethal kidney sample testing. Mucus qPCR R. salmoninarum quantity estimates reflected changes in kidney bacterial load estimates, as evidenced by significant positive correlations with kidney R. salmoninarum infection intensity scores at all sample times and in both fish stocks, and were not significantly impacted by environmental R. salmoninarum concentrations.

Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers

Event Abstract Back to Event Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers Ágnes Ősz1* 1 Szent István University, Department of Aquaculture, Hungary Ősz Á 1, Kovács B 1, Kánainé Sipos D 1, Hoitsy Gy 2, Snoj A 3, Keszte Sz 1, Sáfrány AJ 1, Herzinyák Z 1, Kaczkó D 1, Palkó Cs 4, Urbányi B 1, Horváth Á 1 1 Department of Aquaculture, Szent István University, Páter K. 1, 2100 Gödöllő, Hungary 2 Hoitsy & Rieger Kft., Erzsébet 55, 3517 Lillafüred, Hungary 3 Department of Animal Science, University of Ljubljana, Groblje 3, 1230 Domzale, Slovenia 4 University of West Hungary, Mosonmagyaróvár Vár 2., 9200 Mosonmagyaróvár, Hungary Based on the analyses of the mitochondrial DNA of several European brown trout populations, five evolutionary lineages of brown trout were indentified (Atlantic, Danubian, Mediterranean, Adriatic, Marble). The species is bred primarily for stock enhancement of natural waters, however the most hatchery-maintained broodstocks originate from the Atlantic lineage. Due to the hydrogeography of Hungary our stocks should theoretically belong to the Danubian lineage; however, this has not been investigated earlier by genetic studies. For our genetic analysis, 702 fin clips were collected from two brown trout broodstocks (Lillafüred and Szilvásvárad) as well as populations of natural streams (Bán, Jósva, Kemence, Apátkút, Bittva and Kölöntés) in Hungary. Sequencing of the control region in mitochondrial DNA, three PCR-RFLP (mitochondrial DNA control region, lactate dehydrogenase and somatolactin genes) and five microsatellite markers were used to distinguish between Danubian and Atlantic lineages of brown trout. The proportion of the mitochondrial haplotype of the Danubian lineage was low, with the exception of the Apátkúti, Kölöntés streams and Szilvásvárad broodstock. Analyses of nuclear PCR-RFLP and microsatellites markers showed various distributions of alleles characteristic of the Atlantic or Danubian lineages, although the Atlantic genotype has dominated in all population. In case of the analyses of microsatellites the polymorphism varied greatly at all locations. In addition we found several alleles that were not described earlier in other populations. Those alleles probably would be typical of Hungarian brown trout populations. Overall the populations were effectively in Hardy-Weinberg equilibrium for both PCR-RFLP and microsatellite markers. The remarkably high proportion of allochthonous Atlantic alleles in the analyzed sites is a clear indicator of the import and stocking of non-native individuals. According to these findings, further stocking of brown trout in Hungary should be conducted in more controlled conditions. Acknowledgements This work was supported by 8526-5/2014/TUDPOL and GOP-1.1.1-09/1-2010-0141 projects. Keywords: salmo trutta, PCR-RFLP, microsatellites, lineage, Mitochondrial DNA (mtDNA) Conference: XV European Congress of Ichthyology, Porto, Portugal, 7 Sep - 11 Sep, 2015. Presentation Type: Oral Presentation Topic: Phylogeny, Systematics and Genetics Citation: Ősz Á (2015). Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers. Front. Mar. Sci. Conference Abstract: XV European Congress of Ichthyology. doi: 10.3389/conf.FMARS.2015.03.00240 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 17 Dec 2015; Published Online: 21 Dec 2015. * Correspondence: Miss. Ágnes Ősz, Szent István University, Department of Aquaculture, Gödöllő, 2100, Hungary, sengazso@gmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Ágnes Ősz Google Ágnes Ősz Google Scholar Ágnes Ősz PubMed Ágnes Ősz Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Non-lethal sampling of lake sturgeon for stable isotope analysis: Comparing pectoral fin-clip and dorsal muscle for use in trophic studies

When used to study the feeding ecology of fish, stable isotope analyses generally require sacrificing animals to collect tissue samples. Lethal sampling can be undesirable when studying a species at risk such as lake sturgeon (Acipenser fulvescens). We evaluated the feasibility of using pectoral fin clips as an alternative to dorsal muscle tissue in stable isotope studies for adult lake sturgeon. Because lipid content can affect stable isotope ratios, we also determined whether lipid extraction and mathematical normalization affected the relationship between fin-clip and muscle tissue signatures. Dorsal muscle plugs and fin clips were collected from adult lake sturgeon and analyzed for stable isotopes of carbon and nitrogen. Significant, positive relationships were observed between fin and muscle tissues for both δ15N (r2=0.43) and δ13C (r2=0.32). Lipid extraction significantly reduced the among-individual variation, and improved the δ13C relationship significantly (r2=0.74). While general non-linear mathematical lipid normalization did effectively reduce the among-individual variation, a consistent enrichment relative to chemical extraction was observed. An alternative mass balance correction method, however, yielded lake sturgeon specific parameter estimates that facilitated accurate lipid correction. The strong relationships between fin-clip and muscle tissue signatures demonstrate that fin-clips should be considered as good surrogates for muscle tissue, will allow trophic studies to accurately adjust for the effect of differential lipid accumulation and can effectively limit the need for invasive sampling for adult lake sturgeon.

The utility of near infrared spectroscopy for age estimation of deepwater sharks

Reliable age information is vital for effective fisheries management, yet age determinations are absent for many deepwater sharks as they cannot be aged using traditional methods of growth bands counts. An alternative approach to ageing using near infrared spectroscopy (NIRS) was investigated using dorsal fin spines, vertebrae and fin clips of three species of deepwater sharks. Ages were successfully estimated for the two dogfish, Squalus megalops and Squalus montalbani, and NIRS spectra were correlated with body size in the catshark, Asymbolus pallidus. Correlations between estimated-ages of the dogfish dorsal fin spines and their NIRS spectra were good, with S. megalops R2=0.82 and S. montalbani R2=0.73. NIRS spectra from S. megalops vertebrae and fin clips that have no visible growth bands were correlated with estimated-ages, with R2=0.89 and 0.76, respectively. NIRS has the capacity to non-lethally estimate ages from fin spines and fin clips, and thus could significantly reduce the numbers of sharks that need to be lethally sampled for ageing studies. The detection of ageing materials by NIRS in poorly calcified deepwater shark vertebrae could potentially enable ageing of this group of sharks that are vulnerable to exploitation.

Improving the efficiency for generation of genome-edited zebrafish by labeling primordial germ cells

Although CRISPR/Cas, a new versatile genome-editing tool, has been widely used in a variety of species including zebrafish, an important vertebrate model animal for biomedical research, the low efficiency of germline transmission of induced mutations and particularly knockin alleles made subsequent screening for heritable offspring tedious, time-consuming, expensive and at times impossible. In this study, we reported a method for improving the efficiency of germline transmission screening for generation of genome-edited zebrafish mutants. Co-microinjecting yfp-nanos3 mRNA with Cas9 mRNA, sgRNA and single strand DNA donor to label the distribution of microinjected nucleotides in PGCs (primordial germ cells), we demonstrated that founders carrying labeled PGCs produced much higher numbers of knockin and knockout progeny. In comparison with the common practice of selecting founders by genotyping fin clips, our new strategy of selecting founders with tentatively fluorescent-labeled PGCs significantly increase the ease and speed of generating heritable knocking and knockout animals with CRISPR/Cas9.

Identification of Two Channel Catfish Stocks, Ictalurus punctatus, Cultivated in Northeast Mexico

AbstractThe channel catfish farming in Mexico began in the 1970s. One of the most important areas of production is its northeastern region. Traditionally, the channel catfish farmers have attempted to preserve their original genetic stock. After more than 30 yr of production, the genetic relationship between stocks has not been assessed. The goal of this study was to evaluate the genetic differentiation between five channel catfish farm populations, using 13 microsatellite markers. A total of 154 fin clip samples were collected from five channel catfish farms in Tamaulipas. We also included 31 individuals of the commercial strain NWAC103. In each population, we calculated parameter of genetic variability: inbreeding coefficient (FIS), pairwise differentiation (FST), and genetic distance (DC). For the inference of populations and individual assignment two Bayesian methods were used. Genetic variability parameters were NA = 9.54–11.08 and AE = 5.40–6.67. Hardy–Weinberg equilibrium deviations were observed for all farm populations examined, and a deficit of heterozygotes was found. Signals of inbreeding were observed, particularly for the ACU (Acuamex) hatchery. Populations EKA (Empresas Karol) and ACU showed higher genetic differentiation values with respect to the commercial strain (FST = 0.107; FST = 0.082, respectively). Moderated genetic differences (FST = 0.067; DC = 0.080) were observed between the EKA and ACU. Clustering analysis revealed a well‐defined group between EKA and TPA (El Tiron Parejo). In the Bayesian analysis three groups were defined. The first group was formed by EKA and TPA, the second group included ACU, LAJ (La Lajilla), and PRO (Prodatec). In the third group was the commercial strain. In the assignment of individuals, EKA and ACU were represented by exclusive genotypes. Identification of two genetic stocks, one located in the EKA and the other in the ACU population, will be relevant for future management of these hatcheries. Additionally, the information from microsatellites and the statistical procedures presented will be important tools for genetic monitoring of these farm populations.

Impacts of External and Surgery‐Based Tagging Techniques on Small Northern Pike Under Field Conditions

AbstractIn Northern Pike Esox lucius negligible effects of external tags on growth and survival have commonly been reported, but no studies exist for age‐0 fish. We tested the impacts of fin clipping, PIT tags, and three external tags (T‐bar anchor, opercular, and streamer tags) on age‐0 Northern Pike in a pond. We also examined the impacts of surgically implanted transmitters on small adult Northern Pike in a natural lake. The loss of PIT tags was lowest among all tags and close to 0%. Of the external tags, T‐bar anchor tags performed best. Loss of these tags was initially low (on average 5.7% after 195 d) increasing to about 20.0% by 520 d posttagging. Tagging‐induced mortality of a few percent was present in all tags tested within the first 195 d posttagging in the pond environment but not present afterwards. The PIT tags, fin clips, and external tags did not affect the growth or condition of surviving fish. Surgically implanted transmitters reduced the growth of small adult Northern Pike with total lengths &lt;480 mm, but no effects were found for larger individuals. We conclude that PIT tagging is the most suitable marking technique for age‐0 Northern Pike. If external visibility is required, T‐bar anchor tags are also useful, as long as tagging‐induced mortality and tag loss rates are accounted for at the analysis stage. Our study raises a cautionary note about surgically implanted transmitters in small adult Northern Pike, as they may negatively affect behavior and fitness.Received March 27, 2013; accepted November 26, 2013

Variation in Telomere Length of the Common Carp,Cyprinus carpio(Cyprinidae), in Relation to Body Length

Determinations of the age structure of wild teleost populations are vital for sustainable management and conservation efforts. Yet the commonly applied increment-based ageing techniques are limited in some teleost species due to the subjectivity and interpretation of increment patterning, and destructive sampling. Here the application of telomere length as an alternate age determinate was assessed in wild caught specimens of the common carp (Cyprinus carpio). Telomere lengths were measured from muscle biopsies and fin clips using the absolute quantitative PCR method and correlated to specimen fork lengths. Measures of telomere lengths did not differ between sexes or states of sexual maturity. However, tissue type influenced telomere lengths, with telomere lengths measured in muscle biopsies significantly increasing with increased fork lengths of C. carpio. No discernable trend was seen for fin clip derived telomeres. High levels of variability in telomere length within and among size cohorts suggest that ...

First Records of the Night Smelt,Spirinchus starksi, in the Salish Sea, Washington

Ten species of smelts (Osmeridae), including 1 introduced species, have been found in the eastern North Pacific (Love and others 2005). Of these 10 species, 5 have been recorded from the inland marine waters of the Salish Sea, including Puget Sound and the Straits of Juan de Fuca and Georgia (Hart 1973): Whitebait Smelt (Allosmerus elongatus), Surf Smelt (Hypomesus pretiosus), Capelin (Mallotus villosus), Longfin Smelt (Spirinchus thaleichthys), and Eulachon (Thaleichthys pacificus). Results from a study using molecular markers to distinguish smelt remains found in the stomach contents of fishes (Paquin and others 2014) indicated that a specimen collected from Discovery Bay, Washington, an embayment at the eastern terminus of the Strait of Juan de Fuca, was misidentified as S. thaleichthys in the online Barcode of Life Database (BOLD; Ratnasingham and Hebert 2007). Subsequent examination of the preserved specimen has confirmed its identity as Night Smelt (Spirinchus starksi) and constitutes a new record for this species in the Salish Sea. Since this discovery, additional specimens of S. starksi have been collected in the area for inclusion in this study. To confirm the identification of the Discovery Bay specimen, both morphological and nucleotide sequence data from S. starksi were compared with data from the closely related species S. thaleichthys. Whole specimens and tissue samples (frozen or preserved in ethanol) from 11 S. starksi and 5 S. thaleichthys were obtained from the Northwest Fisheries Science Center (NWFSC) and the University of Washington Fish Collection (UW). Specimens of S. starksi were collected from Discovery Bay, Washington (n 5 1), Green Point, Washington (n 5 5), and north of Monterey Bay off the California coast (n 5 5). Specimens of S. thaleichthys were collected from the Gulf of Alaska (n 5 1), San Juan Islands (n 5 1), and Puget Sound (n 5 3) (Table 1). DNA extractions were performed on fin clips using a QIAGEN DNeasy kit (QIAGEN, Valencia, CA) and the manufacturer’s animal tissue protocol. A 750 base-pair region of the mitochondrial genome, cytochrome c oxidase I (COI), was amplified using PCR with universal fish primer cocktail C_FishF1t1-C_FishR1t1 (Ivanova and others 2007). The COI gene region has been used as the barcode for biodiversity to distinguish among species, whether they are distantly related species such as mammals and insects, or closely related congenerics (Ward and others 2005, 2009; Holloway 2006; Ward and others 2009). Nucleotide sequence data were collected for 16 samples (including the misidentified specimen of S. starksi from Discovery Bay) in both forward and reverse directions with Big Dye chemistry using EXOSAP purified PCR products. Sequences were read using an ABI 3730 automated sequencer

GENETIC VARIABILITY OF GIANT GOURAMY STRAINS REVEALED BY RANDOM AMPLIFIED POLYMORPHISM DNA

Genetic variability of giant gouramy strains has been observed using RAPD Marker. Genomic DNA was extracted from giant gouramy fin clip, and amplified using primers OPA 1-20. There was no significant difference among three strains of giant gouramy analyzed. Based on two primers of RAPD (OPA 4 and 7), the highest variability was observed in Bluesafir with heterogeneity value of 0.3050 and followed by Paris (0.2832) and Soang (0.2360) respectively. The average of Nei’s genetic distance is 0.118, and the smallest on is between Paris and Bluesafir.

Coded-Wire Tag Expansion Factors for Chinook Salmon Carcass Surveys in California: Estimating the Numbers and Proportions of Hatchery-Origin Fish

Recovery of fish with adipose fin clips (adc) and coded-wire tags (cwt) in escapement surveys allows calculation of expansion factors used in estimation of the total number of fish from each adc,cwt release group, allowing escapement to be resolved by age and stock of origin. Expanded recoveries are used to derive important estimates such as the total number and proportion of hatchery-origin fish present. The standard estimation scheme assumes accurate visual classification of adc status, which can be problematic for decomposing carcasses. Failure to account for this potential misclassification can lead to significant estimation bias. We reviewed sample expansion factors used for the California Central Valley Chinook salmon 2010 carcass surveys in this context. For upper Sacramento River fall-run and late fall-run carcass surveys, the estimated proportions of adc,cwt fish for fresh and non-fresh carcasses differed substantially, likely from the under-recognition of adc fish in non-fresh carcasses. The resulting estimated proportions of hatchery-origin fish in the upper Sacramento River fall-run and late fall-run carcass surveys were 2.33 to 2.89 times higher if only fresh carcasses are considered. Similar biases can be avoided by consideration of only fresh carcasses for which determination of adc status is relatively straightforward; however, restricting the analysis entirely to fresh carcasses may limit precision because of reduced sample size, and is only possible if protocols for sampling and recording data ensure that the sample data and results for fresh carcasses can be extracted. Thus we recommend sampling protocols that are clearly documented and separately track fresh versus non-fresh carcasses, either collecting only definitively adc fish or that carefully track non-fresh carcasses that are definitively adc versus those that are possibly adc. This would allow judicious use of non-fresh carcass data when sample sizes are otherwise inadequate.

Genomic Consequences of Ecological Speciation in Astyanax Cavefish

The cave environment is consistently radically different than the surface environment because it lacks light, and animals adapting to cave life are subject to strong selective forces much different than those experienced by their ancestors who evolved in the presence of light. As such, their divergence from surface ancestors and eventual speciation is likely to be driven by the shift in ecology. We report here that hybrids between cave and surface Astyanax mexicanus fishes produce offspring with allelic frequencies that differ significantly from Mendelian expectations both for transmission ratios and for independent assortment of unlinked markers. Comparison of allelic content of DNA from fin clips and sperm pools show that the transmission ratio distortion likely occurs during spermatogenesis. Departures from expectations of independent assortment are essentially epistatic phenomena generating linkage disequilibrium. A novel analysis of the epistatic interactions reveals an apparent network of interactions among genes known or suspected to be involved in cave adaptation, implying that the epistasis arose as a “by product” of the divergence due to cave adaptation.

Artificial Marker Selection and Subsequent Tagging Evaluations with Juvenile Burbot

AbstractA conservation program developed by regional stakeholders incorporates stock enhancement as one of several approaches to restore an imperiled Burbot Lota lota population native to Idaho and British Columbia. Tagging juvenile fish is pivotal to stock enhancement monitoring; however, limited information is currently available on marks or tags applied to Burbot. We identified six criteria to guide artificial marker selection that are specific to imperiled juvenile fish. A short‐term experiment with age‐0 Burbot (65–92 mm TL) tested fin clips, freeze brands, visible implant elastomer, passive integrated transponders, and an unmarked control group. At 4 weeks posttagging, no significant differences were found between marking treatments with respect to fish survival (100%), absolute growth rate (0.15 ± 0.06 mm/d), specific growth rate (0.55 ± 0.32 g·g−1·d−1), or condition factor (0.64 ± 0.05). Mean tag retention ranged from 88% to 100%, and no significant differences were detected between treatments. Recognition of dorsal freeze brands differed significantly between two independent tag assessments. Overall, we found no adverse short‐term effects and high tag retention in this preliminary trial of seven artificial marks applied to hatchery‐reared Burbot.