Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studie

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

Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studie

Das "Frightmotif" : Rekontextualisierung populärkultureller Songs als inzidenzmusikalisches Motiv für das Böse im Horrorfilm

Der Horrorfilm nutzt ein musikalisches Stilmittel, welches in derLiteratur bislang nicht benannt worden ist. Der vom Autorvorgeschlagene Begriff des Frightmotifs steht stellvertretend für dieRekontextualisierung populärkultureller Songs alsinzidenzmusikalisches Motiv für das Böse im Horrorfilm, sowie den ihmeng verwandten Genres bzw. Mischformen mit ähnlicher Wirkästhetik.DasFrightmotif ist ein präexistentes, populärkulturelles und autonomesStück und fungiert als eine Art Beschwörungsformel“ für das Böse, dieals Inzidenzmusik/Source Music ein Teil der Handlung und daher von denAkteuren wahrnehmbar ist. Durch den repetitivenCharakter erhält sie eine übernatürliche Konnotation und wirddekontextualisiert. Für den Zuschauer wird der Song durch den Prozessder Denotation untrennbar mit dem filmischen Objekt verknüpft. Durchdie neu geschaffene Konnotation mit dem Bösen wird seine eigentlichekulturhistorische Bedeutung aufgelöst und der Song rekontextualisiert.There is a stylistic device in modern horror movies that hasn't beennamed yet: the author suggests the term "Frightmotif" for therecontextualization of popular cultural songs as a source music motiffor evil in horror films (or similar genres). The "Frightmotif" is apreexistent, popular cultural and autonomic song that works as somekind of a incantation for evil. This song is always source music sothe protagonists in the movies are able to hear it. It obtains asupernatural connotation through it's repetitive character and it willbe decontextualized. For the audience the Song will be linked with thecinematic object through the process of denotation. The newconnotation with evil dissolves the original historico-culturalmeaning of the song and the song is recontextualized.Abgabedatum: 05.09.2008Paderborn, Univ., Bachelorarb., 200

Next generation characterisation of cereal genomes for marker discovery

Cereal crops form the bulk of the world's food sources and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on faster and more cost effective approaches for genome sequencing and the development of markers for trait association and marker assisted selection (MAS) in crop breeding programs

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