Linkage mapping reveals strong chiasma interference in Sockeye salmon: Implications for interpreting genomic data

Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies

Nebraska Rainbow Trout

Chapter 1 Lethal and Preferred Temperatures of Lake McConaughy Rainbow Trout Versus Domestic Strain Rainbow Trout By R. Vancil, G. Zuerlein and L. Hesse Chapter 2 A Nitrifying Filter-Cooling Condenser System for Total Water Re-use in Cold-Water Fish Holding or Rearing Applications By L. Hesse, G. Zuerlein and R. Vancil Chapter 3 Biochemical Genetic Analysis of Two Strains of Nebraska Rainbow Trout By J. Seeb and L. Wishard The self-sustaining rainbow trout population living in Lake Mcconaughy and the North Platte River tributaries is unique to the Great Plains region. The population spends most of its adult life in the reservoir, but moves into tributary streams to spawn. Two spawning runs occur. The largest is from September through November followed by a reduced migration. in March and April of the following spring. Rainbow trout fingerlings spend about a year in the stream before smolting and migrating to the reservoir. Fishing for Mcconaughy rainbows in the tributaries and reservoir began in the late 1940\u27s. Concern for the maintenance of this fishery prompted several investigations which were directed at development of a management plan. From these studies it was evident that the McConaughy rainbow possessed a selective advantage over hatchery origin fish stocked in the streams and reservoir. Temperatures, normally too high for successful rainbow survival, were often encountered in the streams and the eutrophying Lake McConaughy. This study was designed to compare the temperature tolerance and preference of Mcconaughy rainbow trout with hatchery origin fish. Chapter 1 describes the results of this study. Chapter 2 describes the laboratory facility developed to hold fish for relatively long periods while conducting the experiments. Chapter 3 contains the results of studies designed to characterize the genetic differences between hatchery fish from Massachusetts and the self-sustaining Mcconaughy rainbow trout. The Pacific Fisheries Research Laboratory in Olympia, Washington, was contracted to perform an electrophoresis characterization of the frequency of biochemical genetic variants among the McConaughy and hatchery rainbow groups

Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing

Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis

Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha)

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (Nb) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high-diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low-diversity natural populations were likely subsequently founded from a reduced number of individuals.Fil: Gomez Uchida, Daniel. Núcleo Milenio Invasal; Chile. Universidad de Concepción; ChileFil: Cañas Rojas, Diego. Núcleo Milenio Invasal; Chile. Universidad de Concepción; ChileFil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Ciancio Blanc, Javier Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Pascual, Miguel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Ernst, Billy. Universidad de Concepción; Chile. Núcleo Milenio Invasal; ChileFil: Aedo, Eduardo. Universidad Austral de Chile; ChileFil: Musleh, Selim S.. Universidad de Concepción; Chile. Núcleo Milenio Invasal; ChileFil: Valenzuela Aguayo, Francisca. Universidad de Concepción; ChileFil: Quinn, Thomas P.. Núcleo Milenio Invasal; Chile. University of Washington; Estados UnidosFil: Seeb, James E.. Núcleo Milenio Invasal; Chile. University of Washington; Estados UnidosFil: Seeb, Lisa W.. Núcleo Milenio Invasal; Chile. University of Washington; Estados Unido

Concordance of Nuclear and Mitochondrial DNA Markers in Detecting a Founder Event in Lake Clark Sockeye Salmon

Genetic bottleneck effects can reduce genetic variation, persistence probability, and evolutionary potential of populations. Previous microsatellite analysis suggested a bottleneck associated with a common founding of sockeye salmon Oncorhynchus nerka populations of Lake Clark, Alaska, about 100 to 400 generations ago. The common founding event occurred after the last glacial recession and resulted in reduced allelic diversity and strong divergence of Lake Clark sockeye salmon relative to neighboring Six Mile Lake and Lake Iliamna populations. Here we used two additional genetic marker types (allozymes and mtDNA) to examine these patterns further. Allozyme and mtDNA results were congruent with the microsatellite data in suggesting a common founder event in Lake Clark sockeye salmon and confirmed the divergence of Lake Clark populations from neighboring Six Mile Lake and Lake Iliamna populations. The use of multiple marker types provided better understanding of the bottleneck in Lake Clark. For example, the Sucker Bay Lake population had an exceptionally severe reduction in allelic diversity at microsatellite loci, but not at mtDNA. This suggests that the reduced microsatellite variation in Sucker Bay Lake fish is due to consistently smaller effective population size than other Lake Clark populations, rather than a more acute or additional bottleneck since founding. Caution is urged in using reduced heterozygosity as a measure of genetic bottleneck effects because stochastic variance among loci resulted in an overall increase in allozyme heterozygosity within bottlenecked Lake Clark populations. However, heterozygosity excess, which assesses heterozygosity relative to allelic variation, detected genetic bottleneck effects in both allozyme and microsatellite loci

So, You Want to Use Next Generation Sequencing In Marine Systems? Insight from the Pan Pacific Advanced Studies Institute

The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled Genomic Applications to Marine Science and Resource Management in Southeast Asia was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions

So, You Want to Use Next-Generation Sequencing in Marine Systems? Insight from the Pan-Pacific Advanced Studies Institute

The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled “Genomic Applications to Marine Science and Resource Management in Southeast Asia” was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions