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The assessment of the genetic structuring of biodiversity is crucial for management and conservation. This is particularly critical for widely distributed and highly mobile deep‐water teleosts, such as hoki (Macruronus novaezelandiae). This species is significant to Māori people and supports the largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge for management. Here, we apply a comprehensive genomic analysis to shed light on the demographic structure of this species by (1) assembling the genome, (2) generating a catalogue of genome‐wide SNPs to infer the stock structure and (3) identifying regions of the genome under selection. The final genome assembly used short and long reads and is near complete, representing 93.8% of BUSCO genes, and consisting of 566 contigs totalling 501 Mb. Whole‐genome re‐sequencing of 510 hoki sampled from 14 locations around New Zealand and Australia, at a read depth greater than 10×, produced 227,490 filtered SNPs. Analyses of these SNPs were able to resolve the stock structure of hoki into two genetically and geographically distinct clusters, one including the Australian and the other one all New Zealand locations, indicating genetic exchange between these regions is limited. Location differences within New Zealand samples were much more subtle (global F ST = 0.0006), and while small and significant differences could be detected, they did not conclusively identify additional substructures. Ten putative adaptive SNPs were detected within the New Zealand samples, but these also did not geographically partition the dataset further. Contemporary and historical N e estimation suggest the current New Zealand population of hoki is large yet declining. Overall, our study provides the first genomic resources for hoki and provides detailed insights into the fine‐scale population genetic structure to inform the management of this species.

Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is nontrivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye (Sander vitreus), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We then performed three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (i) inexpensive Chelex extractions performed well for genotyping; (ii) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was probably unnecessary; and (iii) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa.

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage‐based tagging (PBT) may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded‐wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774—individual, 267—population baseline available for assignment. Coho salmon from un‐CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT‐GSI system of identification to individuals in 2017 fisheries and escapements provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian‐origin coho salmon relative to CWTs, and an opportunity for a genetic‐based system to replace the current CWT system for coho salmon assessment.

We investigated the spatial and temporal variability of the fish community and the density, size, and genetic stock composition of juvenile Chinook Salmon Oncorhynchus tshawytscha in shallow tidal freshwater habitats of the Columbia River. We sought to address data gaps related to juvenile Chinook Salmon in this portion of the Columbia River and thereby inform habitat restoration efforts. We examined fish communities, juvenile salmon life history characteristics, and relationships between salmon density and habitat conditions by using beach seine data collected over a 63-month period (2007−2012) from two tidal freshwater areas: the Sandy River delta (river kilometer [rkm] 188–202) and the lower river reach (rkm 110–141). We found few differences in the fish community across the two study areas. Fish community patterns were largely attributable to seasonal changes as opposed to spatial gradients and habitat types. Juvenile Chinook Salmon were the most common salmon species in our catches; this spec...

Juvenile salmon transitioning from freshwater to marine environments experience high variation in growth and survival, yet the specific causes of this variation are poorly understood. Size at and timing of ocean entry may contribute to this variation because they influence both the availability of prey and vulnerability to predators. To explore this issue, we used stock assignments based on genetic stock identification and internal tags to document the stock-specific size and timing of juvenile hatchery and presumed wild Columbia River Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss at ocean entry during 2007–2011. We found that juvenile salmon and steelhead had consistent stock-specific capture dates, with lower-river stocks typically having earlier timing than those originating farther upstream. Mean size also varied among stocks and was related to hatchery practices. Hatchery yearling Chinook Salmon and steelhead were consistently larger than wild fish from the same stocks, alth...

We examined the hypotheses that density and morphometric condition of subyearling juvenile Chinook Salmon Oncorhynchus tshawytscha would decline during periods of high water temperature in the lower Columbia River and estuary. The hypotheses were tested using salmon density measurements and a condition anomaly calculated from residuals of the length–weight linear regression based on 5,536 subyearlings collected from brackish estuarine and tidal freshwater (TFW) habitats. We captured Chinook Salmon at all temperatures encountered (4.2–23.5°C). In the TFW zone, densities were highest at optimal temperatures and lowest at suboptimal and supraoptimal temperatures; in the estuary, density did not differ among temperature regimes. Fish condition was lowest in winter, when temperatures were suboptimal, and highest in summer, when temperatures were supraoptimal. Pairwise comparisons of fish condition between periods of optimal temperature (spring) and supraoptimal or stressful temperature (summer) showed ...

Determination of run timing is an important component of salmonid fisheries management and was the major focus of the current study. Population structure of Sockeye Salmon Oncorhynchus nerka was examined in the Skeena River, northern British Columbia. Variation at 14 microsatellites was surveyed for 27 populations in the drainage. There were 9,473 individuals sampled in a lower river test fishery during 2000–2011 in order to provide information on relative abundance and time of arrival of specific populations or stocks near the mouth of the river. Within-lake or within-river tributary structuring of populations was the general pattern observed, with 10 populations from Babine Lake clustering together in 91% of dendrograms evaluated, and two populations from Lakelse Lake clustering together in 100% of dendrograms evaluated. The 27 populations sampled were arranged in 12 reporting groups for genetic stock identification applications. The estimated stock composition of known-origin mixtures was withi...

Genetic stock identification (GSI) is widely applied to mixed-stock fisheries for many commercially exploited species. However, the accuracy of GSI depends on the level of differentiation among stocks. To evaluate our ability to estimate contributions in mixed-stock fisheries of Pink Salmon Oncorhynchus gorbuscha, a species with limited population genetic differentiation, we analyzed 46 odd-year Pink Salmon stocks belonging to a baseline of genotypes from southern British Columbia, the Fraser River, and Puget Sound. Samples were obtained without replacement from the baseline (known mixtures), and 16 microsatellite loci were used for analysis with two software packages (cBayes and ONCOR) to evaluate the accuracy of using this marker set to identify the correct region, subregion, and spawning site. The correct subregion was identified for Pink Salmon from southern British Columbia and Puget Sound. However, incorrect assignments were observed for the Fraser River subregions and the stock-specific est...

We present an application of the genetic mark–recapture technique to estimate salmon run size in a large river. Application of this technique requires modifications to estimation methodology. Under a typical Lincoln–Petersen mark–recapture estimation of salmon run size (N = M/p), individual fish are captured and marked (M) in the lower river and are recaptured (m) at escapement (E: the number of fish reached spawning ground) monitoring sites selected upriver where the proportion of marked individuals (p = m/E) is estimated. In this genetic mark–recapture technique, the marked individuals are not captured and recaptured, but rather the naturally distinctive genetic (marked) population is captured and recaptured. Genetically, the lower river population is a mixture of multiple genetic stocks, whereas the upriver escapement population consists of a single genetic stock. Hence, the mark–recapture experiment (N = M/pm) is reversed. The proportion of “marked” genetic stock (pm) is estimated in the lower...

Genetic stock identification (GSI) provides a method of characterizing stock-specific abundance, run timing, and straying as they pertain to the population demographics and behavior of both hatchery and wild fish and thus assists with fisheries management. In this study, tissues were collected and genotyped at 13 microsatellite loci from adult Chinook Salmon Oncorhynchus tshawytscha that passed Bonneville Dam during four consecutive migration years (2004–2007). GSI methods were used to estimate the proportions of stocks in a broad genetic baseline, with high-density coverage of Chinook Salmon across the eastern Pacific Rim. The estimates of abundance for interior Columbia River stocks showed widespread decline consistent with a shift to poor ocean conditions during the years when the fish in this study were at sea, but divergent stock- and age-specific patterns were also observed. For example, the upper Columbia River spring-run stock experienced a unique net gain in abundance during this period, ...

Many Winter Flounder Pseudopleuronectes americanus populations have declined dramatically. In U.S. waters, Winter Flounder are managed as three stocks: Gulf of Maine, southern New England–Mid-Atlantic Bight, and Georges Bank. Historically, it was believed that the spawning of inshore stocks occurs exclusively within natal estuaries. Based on the supposition of estuary-specific spawning, we hypothesized that Winter Flounder exhibit greater stock structure than predicted by the three-stock model and, in fact, that they exhibit genetic differentiation at the level of individual estuaries. We tested this hypothesis by conducting microsatellite DNA analysis at 12 loci and single-nucleotide polymorphism analysis at 4 loci on young-of-the year and adult Winter Flounder collected from 27 estuaries from Newfoundland to Delaware as well as from Georges Bank. We found highly significant coastwide genetic stock structure among Winter Flounder; however, there was little evidence of estuary-specific structure. ...

Managing weak stocks in mixed-stock fisheries often relies on proxies derived from data-rich indicator stocks, although there have been limited tests of the appropriateness of such proxies. For example, full cohort reconstruction of tagged Klamath River fall-run Chinook Salmon Oncorhynchus tshawytscha of northern California enables the use of detailed models to inform management. Information gained from this stock is also used in the management of the untagged, threatened California Coastal Chinook Salmon (CCC) stock, where it is assumed that a cap on Klamath harvest rates effectively constrains impacts on CCC to acceptable levels. To evaluate use of this proxy, we used a novel approach based on genetic stock identification (GSI) data to compare the two stocks’ size at age and ocean distribution (as inferred from spatial variation in CPUE), two key factors influencing fishery exposure. We developed broadly applicable methods to account for both sampling and genetic assignment uncertainty in estima...

Deer mice (Peromyscus) are the most common native North American mammals, and exhibit great natural genetic variation. Wild-derived stocks from a number of populations are available from the Peromyscus Genetic Stock Center (PGSC). The PGSC also houses a number of natural variants and mutants (many of which appear to differ from Mus). These include metabolic, coat-color/pattern, neurological, and other morphological variants/mutants. Nearly all these mutants are on a common genetic background, the Peromyscus maniculatus BW stock. Peromyscus are also superior behavior models in areas such as repetitive behavior and pair-bonding effects, as multiple species are monogamous. While Peromyscus development generally resembles that of Mus and Rattus, prenatal stages have not been as thoroughly studied, and there appear to be intriguing differences (e.g., longer time spent at the two-cell stage). Development is greatly perturbed in crosses between P. maniculatus (BW) and Peromyscus polionotus (PO). BW females crossed to PO males produce growth-restricted, but otherwise healthy, fertile offspring which allows for genetic analyses of the many traits that differ between these two species. PO females crossed to BW males produce overgrown but severely dysmorphic conceptuses that rarely survive to late gestation. There are likely many more uses for these animals as developmental models than we have described here. Peromyscus models can now be more fully exploited due to the emerging genetic (full linkage map), genomic (genomes of four stocks have been sequenced) and reproductive resources.

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed-stock fishery to an almost exclusively single-stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.

All rights reserved. No part of this periodical may be reproduced or trans mitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. ABSTRACT Genetic stock collections have played an important role in shaping breeding strategies in many crops. With the advance in genomics, they are now essential tools for identifying genes underlying important agronomic traits. The objective of this work is to formally register and document the release of historical sorghum [Sorghum bicolor (L.) Moench] genetic stocks originally collected and curated by the late USDA-ARS sorghum geneticist Keith Schertz. The seeds from the original collection were revitalized at the USDA-ARS Experiment Station at Lubbock, TX in 2004 and 2006, and evaluated for phenotypic variations in 2009. The collection consists of 507 lines and accessions (Reg. No. GS-144, PI 663217 through Reg. No. GS-650, PI 663723). This collection displays signifi cant variation in growth, developmental, and agronomic traits, such as seedling vigor, leaf/vegetative organs, reproduction, maturity, height, and grain quality. Combined with advanced genomic tools, these genetic stocks are vital resources for elucidating the fundamental pathways that make sorghum and other related grasses unusually tolerant to drought and heat stress, have moderate to low requirements for fertilizer, and highly productive under diverse environmental conditions.

Assessments of threatened wild Snake River steelhead Oncorhynchus mykiss have historically been limited due to a lack of stock-specific information and difficulties in field sampling efforts. We used genetic stock identification (GSI) to estimate the composition of wild adult steelhead migrating past Lower Granite Dam on the Snake River between August 24 and November 25, 2008. Further, we combined genetic data with information on sex, length, age, and run timing to examine for differences in life history or demography among stocks. In total, 1,087 samples collected at the dam were genotyped with 13 standardized steelhead microsatellite loci and a new modified Y-chromosome-specific assay that differentiates sex. A genetic baseline of 66 populations was used to complete GSI of unknown-origin samples from Lower Granite Dam. Large differences in reporting group (stock) contributions were observed for the run as a whole; the Snake River–lower Clearwater River reporting group had the largest single con...

The following questions were addressed in this study: (1) If a suite of 12–15 microsatellites were used in the genetic stock identification (GSI) of Chinook salmon Oncorhynchus tshawytscha, which microsatellites should be in the suite? (2) How many microsatellites are required to provide stock identification resolution equivalent to that of 72 single-nucleotide polymorphisms (SNPs)? (3) How many SNPs are required to replace the current microsatellite baselines used in GSI applications? (4) If additional GSI power is required for microsatellite baselines, what is the incremental increase provided by SNPs and microsatellites? The variation at 29 microsatellite loci and 73 SNP loci was surveyed in 60 populations of Chinook salmon in 16 regions in British Columbia. Microsatellites with more observed alleles provided more accurate estimates of stock composition than those with fewer alleles. The options available for improving the accuracy and precision of stock composition estimates for a 12-locus Fi...

The ocean feeding grounds of juvenile Pacific salmon Oncorhynchus spp. range over several thousand kilometers in which ocean conditions, prey quality and abundance, and predator assemblages vary greatly. Therefore, the fate of individual stocks may depend on where they migrate and how much time they spend in different regions. Juvenile (n = 6,266) and immature (n = 659) Chinook salmon Oncorhynchus tshawytscha were collected from coastal Washington to Southeast Alaska in coastal trawl surveys from February to November 1998–2008, which allowed us to reconstruct changes in stock composition for seasons and regions by means of DNA stock identification techniques. Individuals were allocated to 12 regional stocks. The genetic stock assignments were directly validated by showing that 96% of the 339 known-origin, coded-wire-tagged fish were accurately allocated to their region of origin. Overall, the analyses performed in this study support the main findings of previous work based on tagging. However, gi...

Yukon River Chinook salmon Oncorhynchus tshawytscha are described as having a “stream-type” life history strategy. After emergence from river gravel, juveniles typically feed and grow in tributary streams of the Yukon River throughout their first summer, overwinter in freshwater, and usually leave their rearing areas for marine waters during the second spring or summer. Nonnatal rearing has been described in the upper Canadian portion of the drainage, but information is lacking for downstream U.S. waters. In 2006–2007, a study was conducted to document nonnatal rearing and the genetic origin of Chinook salmon in U.S. tributary streams of the Yukon River. Eight nonspawning streams were selected for study, seven located in a 260-km segment between the U.S.–Canada border and Circle, Alaska, and one located 742 km downstream from the border. Age-0 juveniles were captured in all eight streams. Genetic stock composition analyses using 13 standardized microsatellite loci assigned the fish to Canadian so...

There is extensive evidence that fishing is often selective for specific phenotypic characteristics, and that selective harvest can thus result in genotypic change. To date, however, there are no studies that evaluate whether fishing is selective for certain physiological or energetic characteristics that may influence fish behaviour and thus vulnerability to capture. Here, adult sockeye salmon (Oncorhynchus nerka) were used as a model to test the null hypothesis that fishing is not selective for specific physiological or energetic traits. Fish were intercepted during their spawning migrations, implanted with a gastric radio transmitter, and biopsied (i.e., non-lethally sampled for blood, gill tissue and quantification of energetic status). In both 2003 and 2006, we tagged and biopsied 301 and 770 sockeye salmon, respectively, in the marine environment en route to their natal river system to spawn. In 2006 an additional 378 individuals were tagged and biopsied in freshwater. We found that 23 (7.6%) of the marine fish tagged in 2003, 78 (10.1%) of the marine fish tagged in 2006 and 57 (15.1%) of the freshwater fish tagged in 2006 were harvested by one of three fisheries sectors that operate in the coastal marine environment and the Fraser River (i.e. commercial, recreational or First Nations fisheries between the site of release and Hell's Gate in the Fraser River, approximately 250 km upriver and 465 km from the ocean tagging site). However, fisheries were not open continually or consistently in different locations and for different fisheries sectors necessitating a paired analytical approach. As such, for statistical analyses we paired individual fish that were harvested with another fish of the same genetic stock that was released on the same date and exhibited similar migration behaviour, except that they successfully evaded capture and reached natal spawning grounds. Using two-tailed Wilcoxon matched pairs signed-rank tests, we revealed that the physiological and energetic characteristics of harvested fish did not differ from those of the successful migrants despite evaluating a number of biochemical (e.g. plasma metabolites, cortisol, plasma ions, gill Na+/K+-ATPase) and energetic (e.g. gross somatic energy density) variables (P's all >0.10). However, for some analyses we suffered low statistical power and the study design had several shortcomings that could have made detection of differences difficult. We suggest that additional research explore the concept of fishing-induced selection for physiological characteristics because physiology is closely linked to three traits where fisheries-induced selection does occur (i.e. life-history, behaviour and morphology).

Complete sequencing of the mtDNA control region (CR) from five specimens of brown trout Salmo trutta from the Amu Darya River identified two novel haplotypes belonging to the Danubian lineage. This finding supports the long-standing hypothesis that brown trout in the Aral Sea represent a distinct genetic stock and also illustrates the benefits that complete sequencing of the CR can provide for elucidating phylogeographic relationships.

Results of a pilot study designed to estimate the variance of growth rates within and between full sibling families of the lobster Homarus americanus are presented. Progenies raised simultaneously for 100 days under optimal temperature (˜21 C) and diet (live, adult brine shrimp fed ad libitum) grow at significantly different rates. Pronounced environmental effects on growth are inferred from an inverse rank correlation (rS = -0.91) between progeny mean growth rates and the temporal sequence with which progenies were introduced into the experimental space. Differences in growth rates between siblings grown in two independent, experimental seawater tables are also significant in some cases. Family x table interaction is observed indicating that growth may not always be predictable from knowledge of genetic stock and quality of the rearing system alone. Implications for selective breeding of faster growing lobsters are discussed.

We used genetic identification methods to examine the stock composition of subyearling Chinook salmon Oncorhynchus tshawytscha in floodplain wetland and main-stem habitats of the lower Willamette River, Oregon. Using a microsatellite DNA baseline of 13 standardized loci and 30 Columbia River basin populations, we analyzed 280 subyearlings collected in winter and spring 2005-2006 from wetland and main-stem river sites. Genetic stock identification analysis indicated that spring Chinook salmon originating from the Willamette River made up a substantial proportion of the samples and contributed 16-71% to sample mixtures representing the wetland habitat sites. Fall Chinook salmon from lower Columbia River sources were also present and contributed 58% of winter samples. Spring Chinook salmon from lower Columbia River populations were present in both wetland (17%) and river (16%) samples in spring 2005, and subyearlings from summer-fall-run populations in the middle and upper Columbia River contributed...

An international multi-laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha ). This project was in response to the needs of the Chinook Technical Committee of the Pacific Salmon Commission to identify stock composition of Chinook salmon caught in fisheries during their oceanic migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed in each of the laboratories. To test that the loci were reproducible among laboratories, blind tests were conducted to verify scoring consistency for the nearly 500 total alleles. Once standardized, a dataset of over 16,000 Chinook salmon representing 110 putative populations was constructed ranging throughout the area of interest of the Pacific Salmon Commission from Southeast Alaska to the Sacramento River in California. The dataset differentiates the major known genetic lineages of Chinook salmon and provides a tool for genetic stock identification of ...

The Atlantic sturgeon Acipenser oxyrinchus oxyrinchus is a highly migratory anadromous acipenserid that is distributed along the Atlantic coast of North America. The abundance of Atlantic sturgeon has not increased appreciably in recent years despite the imposition of a moratorium on its harvest in U.S. waters in 1998. Two measures being considered to restore depleted or extirpated populations are designation of Atlantic sturgeon as federally endangered under the U.S. Endangered Species Act and the use of hatchery-reared fish to supplement natural reproduction. Implementation of these approaches requires detailed knowledge of this species' population structure. Previous genetic stock identification studies failed to address the discreteness of Atlantic sturgeon populations along the U.S. mid-Atlantic coast that historically supported two of the largest fisheries for the species. We used mitochondrial DNA (mtDNA) control region sequence data to elucidate the population structure of Atlantic sturge...

Many states have established special harvest seasons and hunting zones to target overabundant populations of temperate-nesting Canada geese (Branta canadensis) and protect less abundant northern-nesting populations of Canada geese and cackling geese (B. hutchinsii). To meet management needs for spatially and temporally explicit harvest estimates, we utilized established methods of genetic stock identification and standardized harvest sample collections to estimate proportional contributions of cackling (B. h. hutchinsii) and Canada geese (B. c. maxima and B. c. interior) to 5 consecutive annual harvests (1998–2002) in Michigan, USA. Harvest samples (n = 2,272) were analyzed for several seasons at statewide, regional, and local spatial scales. We expanded upon previous studies that used genetic methods to monitor cackling goose and Canada goose harvests by analyzing harvests within regional and local goose management areas. Likelihood ratio tests were also employed to compare harvest composition a...

In all, 472 lingcod Ophiodon elongatus from six areas of Puget Sound, the Strait of Juan de Fuca, and the outer coast of Washington were assayed for 44 allozyme and 9 microsatellite DNA loci to investigate possible population subdivision. Levels of genetic variation at many of the allozyme loci and all of the microsatellite DNA loci were reasonably high, and there was no evidence of significant Hardy–Weinberg or linkage disequilibrium. Pairwise genotypic tests of population differentiation showed no evidence of genetic structuring among the 23 variable allozyme loci, the 9 microsatellite loci, or all 32 variable loci combined. The results of this investigation are consistent with the existence of a single genetic stock of lingcod throughout the greater Puget Sound region, including the Strait of Juan de Fuca and San Juan Islands. Despite the fact that most of the collections we analyzed did not consist of spawning fish from the spawning grounds, we believe that the combined absence of significant...

Inference that more than one genetic stock of walleyes Sander vitreus was present in Claytor Lake, Virginia, and its main influent, the New River, raised questions concerning the spawning movements, locations of spawning grounds, and home range of resident stocks. We conducted a radiotelemetry study of 52 walleyes in Claytor Lake and the upper New River over a period of 2 years. Our findings support the hypothesis that two populations coexist within the system, exhibiting different home ranges, spawning movements, and spawning grounds, even though there is no physical barrier to movement between the spatially disjunct populations. Walleyes living within Claytor Lake mostly spawn at the first riffle area above the reservoir, whereas those living in the New River mostly spawn at two riffle areas well upstream. Coexistence of distinct populations in the system justifies different management strategies. Management of the walleye population in Claytor Lake should focus on increasing the exploitation o...

Forty-nine white-flowered sweet clover (Melilotus alba) genetic stocks and a yellow-flowered sweet clover (Melilotus officinalis) genetic stock (N56) were developed jointly by the USDA-ARS and the Agricultural Research Division, Institute of Agriculture and Natural Resources, University of Nebraska-Lincoln and were jointly released in May 2004. The genetic stocks, which contain unique combinations of genes and traits, were developed over more than 3 decades of cooperative sweet clover research. The 49 sweet clover genetic stocks include a set of 16 lines (N30-N45), which represent all possible homozygous combinations of 4 allelic pairs, Y/y, C/c, Cu/cu and B/b. The Y/y alleles affect seed colour and the C/c alleles are concerned with both seed and seedling colour. The Cu/cu and B/b genes affect coumarin (more accurately o-hydroxycinnamic acid β-D-glucoside) content and β-glucosidase activity, respectively. The other genetic stocks were N46-N53, N54-N55, N741, N743, N745, N747, U362, U363, U367, U369-U374, U389-U394, U396-U398 and U500. Registration of these genetic stocks supplements 3 previously released and registered biennial, yellow-flowered sweet clover germplasms (N27, N28 and N29).

The populations of sockeye salmon Oncorhynchus nerka of the south-central coast of British Columbia are in decline. To assist in recovery planning, we determined the population structure of sockeye salmon in the region by assaying the genetic variability of 10 microsatellite DNA loci in samples of sockeye salmon from 22 sites associated with 15 rearing lakes. Samples of sockeye salmon from the watersheds with the largest historical runs in the region were studied. Special emphasis was given to investigating genetic divergence among sockeye salmon spawning in seven rivers of the Owikeno Lake watershed, which once supported the largest sockeye salmon run in south-central British Columbia. Across the region, a mosaic of genetic divergence was evident. Reproductive isolation among watersheds was pronounced in all but one case, making transfer of fish between watersheds inadvisable. Genetic stock identification simulations demonstrated that fish from different watersheds could be accurately distinguis...

Differential performance of genetic strains of largemouth bass Micropterus salmoides is an important management consideration. In Puerto Rico, largemouth bass are widely stocked without attention to which stock is the superior genetic stock for island reservoirs. We simultaneously stocked fingerling Florida largemouth bass M. s. floridanus and intergrade (hybrids of Florida and northern largemouth bass M. s. salmoides) largemouth bass at four sites within Lucchetti Reservoir, Puerto Rico. Recapture efforts 24–26 d following stocking revealed no differences in initial growth or survival. Dispersion from stocking sites varied among sites and between groups at two sites and for all sites pooled; Florida largemouth bass were significantly more mobile after stocking. Relative abundance of each group was similar at age 1, but Florida largemouth bass accounted for 76% of the catch at age 2 and 100% at ages 3 and 4. Initial growth rate was rapid for both groups (1.25 mm/d) until about 275 mm total length...

The feasibility of using genetic stock identification to analyse seasonal changes in stock compositions of Atlantic salmon catches in the Baltic Sea was examined. The analysis employed seven variable allozyme loci from most of the potentially contributing stocks (16) from Finland and Sweden. Catch samples were collected from Finnish salmon fisheries in the eastern Bothnian Sea during the 1992 fishing season. Simulation studies were used to evaluate the feasibility of identifying Baltic salmon stocks with allozyme data. Special attention was paid to analysing the wild production of salmon stocks. Clear seasonal diVerences in stock composition were found. The estimates were compared with smolt production and Carlin-tag data. The proportions of the Neva and Oulujoki river stocks could be estimated as individual stocks, whereas the contributions of the remaining stocks were estimated as four composite stock groups. One of the groups consisted of wild stocks from the rivers Kalixalven and Simojoki. Identification of this group, which could be used as an index of wild production in the catches, requires catch sample sizes >300 salmon if

We report the development of seven polymorphic microsatellite loci in muskellunge ( Esoxmasquinongy ) using an unenriched subgenomic library. Polymorphic loci exhibited 2–11alleles with observed heterozygosities ranging from 0.190 to 0.917 ( n = 24). All seven lociamplified by their respective primer pairs resulted in monomorphic products in northernpike ( E. lucius ) whereas three loci amplified monomorphic products in grass pickerel( E. americanus americanus ); these results imply conservation of flanking sequence butloss of polymorphism between these closely related species. Only one of six microsatelliteprimers developed in a previous study in northern pike amplified polymorphic productsin muskellunge. Keywords : Esox , grass pickerel, microsatellite, muskellunge, northern pike Received 17 February 2003; revision received 14 May 2003; accepted 14 May 2003 The muskellunge ( Esox masquinongy ) is a large predatoryfish common to lakes and large rivers in northern USand Canada. Despite the important ecological role that themuskellunge plays as the apex predator in many fresh-water ecosystems and the value of the species to recre-ational fisheries there has been very little investigationof the genetic population structure of this species. In theonly published study of muskellunge genetic variationKoppleman & Philipp (1986) found significant variation atseveral allozyme markers between muskellunge fromwidespread localities within North America. The potentialfor genetic stock structure may be of particular importanceconsidering the widespread stocking of muskellungethroughout North America. Microsatellites have beenisolated for the northern pike (

A microsatellite-enriched genomic library was obtained from black-bellied angler Lophius budegassa and six polymorphic dinucleotide markers were successfully optimized. These markers showed levels of polymorphism ranging from 0.363 to 0.662 and allele numbers ranging from three to seven. These markers were also found to successfully amplify in the closely related Lophius piscatorius (angler) and thus appear to be useful for genetic stock structure analysis in both species.

Apparently at some stage in early evolution DNA evolved to complement RNA for information storage. In this paper we investigate under which circumstances the amount of accessible information is enhanced by using long-lived molecules for information storage. We show that pattern formation is essential for the exploitation of information stored in long-lived molecules.

General (GVA) and specific (SVA) varietal ability quantify the value of genetic stocks as components for synthetic varieties. Additionally, these parameters can be used to predict the performance of the synthetics. The concept of varietal ability is known for completely allogamous crops. It has not yet been worked out for partial allogamy with a genotype-dependent degree of cross-fertilization. We have developed formulae to calculate GVA and SVA referring to generation Syn 1 in this general situation. The concept of varietal ability considers the influence of the components' per se performance on the resulting synthetic variety. This influence increases with decreasing degree of cross-fertilization. Thus, our formulae should be of special benefit to partially allogamous crops. The formulae are illustrated by a numerical example taken from our research on Vicia faba L. To estimate the relevant parameters for Vicia fabe L., we propose to use two morphological markers (flowers and seed colour) simultaneously.

Restriction fragment length polymorphism (RFLP) analysis was performed on the mitochondria) DNA (mtDNA) of 33 lake whitefish Coregonus clupeaformis from four spawning populations in north-central Minnesota. Diagnostic differences between the RFLP patterns of mtDNA from lake whitefish and cisco C. artedi were useful in the identification of fresh fillets and fresh or frozen carcasses. However, mtDNA analysis was of little use for identification of lake whitefish populations because of the low diversity documented among study populations.

We used electrophoresis to determine the number and characteristics of genetically distinct stocks of odd-year pink salmon in Washington and southern British Columbia. We analysed 5128 fish from 52 collections (taken in 1985, 1987 and 1989). We observed genetic variation at 53 enzyme-coding loci, 19 of which were polymorphic at the Po-95 level in at least one stock. Genotypic proportions conformed to Hardy-Weinberg expectations in nearly all cases. The genetic profiles of individual populations were generally stable over the three cycle years studied. Significant differences in allele frequencies at sAAT-3*, PEP-LT* and PGDH* for several stocks were, however, noted between this study and previously reported data for pink salmon. We used G-tests and cluster analysis of genetic distances to evaluate genetic interrelationships among collections and to define genetically distinct stocks. Differentiation among stocks exhibited a clear geographic pattern with three major clusters of stocks recognizable: (1) Hood Canal and Washington Strait of Juan de Fuca stocks, (2) Puget Sound, Fraser River, and southern Canada South Coast stocks, and (3) northern Canada South Coast stocks and Canada North Coast stocks. Computer simulations using 14 and 28 loci, and sample sizes of 15C600, demonstrated that accurate estimates of stock-group composition could be obtained for pink salmon fisheries having a considerable range of stock compositions. The simulations revealed that approximately 50% fewer fish were required to obtain a given level of precision of stock group composition estimates with 28 loci as with the set of 14 loci used in previous investigations.

Stocks of northern largemouth bass Micropterus salmoides salmoides, Florida largemouth bass M. s. floridanus, and both reciprocal F1 hybrids were produced in Champaign, Illinois, with natural spawning techniques. The genetic composition of each of these stocks was confirmed electrophoretically. Overwinter survival of northern largemouth bass in central Illinois was significantly greater than that of Florida largemouth bass; the two reciprocal F1 hybrids had intermediate survival. The absolute survival rate of all stocks decreased as the severity of the winter increased; however, the effects were most dramatic for the Florida subspecies. The northern largemouth bass also exhibited-greater second- and third-year growth than the Florida largemouth bass; again, the reciprocal F1 hybrids were intermediate. Results of this study indicate the potential negative effects that may arise when Florida largemouth bass or hybrids between it and the northern subspecies are introduced into waters of the USA and ...