Download or read book Genomic and Behavioral Diversity in Rainbow Trout written by Kristen A. Christensen and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In a final study, gene copy number variance was examined in rainbow trout and other organisms. Evidence for previously reported genome duplications in a variety of organisms was found using a new method of transcriptome analysis. This strategy offers advantages in cost and efficiency over existing methods of identifying whole genome duplications.

Download or read book Genomic Analysis of Stress Aggression and Boldness in Rainbow Trout written by Angela Sims and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Behavioural phenotypes are under many influences from external and internal environments. The extent to which genetics affects behaviour has been a focus of recent study. Gradually, evidence demonstrating the influences of genes upon behaviour has mounted in a wide range of studies from family resemblance to gene knockouts to microarrays. A major challenge in behavioural ecology is to investigate the genomic architecture of behaviour, including the numbers, locations and effects of genes associated with behaviour, with the aim of understanding how complex behaviours are influenced by genetic variation. A recent transition in the study of animal behaviour has been in the interest of studying those behaviours that are correlated. When behaviours are correlated, there may be underlying genetic correlations that act as a constraint from performing the most optimal behaviour for the situation. Three traits that are often associated are aggression, boldness and stress responsiveness and it is useful to study these together and separately in order to establish whether genetic correlations exist. Stress, and the related behaviours aggression and boldness, have a significant bearing on the welfare of rainbow trout in aquaculture and are important when considering breeding programmes and rearing conditions for fish farming. These studies aimed to assess the genomic complexity of the evolutionarily important traits, stress responsiveness, aggression and boldness, including the genomic links between behaviours, so as to provide empirical evidence for underlying mechanisms of behavioural syndromes. In addition, this study aimed to identify candidate genes associated with stress and aggression using novel genomic techniques. A combination of genomic approaches was used to understand genomic components of animal behaviour, under the wider context of a behavioural syndrome, where behaviours are correlated across context. The association between heterozygosity and stress responsiveness and the related behaviours was tested to determine genomic influences on behaviour. The number and genomic locations of regions associated with stress responsiveness were determined to understand the level of complexity associated with stress. Using next generation sequencing, the transcriptomes of aggressive and less aggressive fish were characterised, with the aim of identifying the numbers of genes associated with aggressiveness. Crucially, novel candidates for the study of individual and correlated behaviours were identified. Moreover, candidate genes were studied in relation to both stress responsiveness and aggressive behaviour. The results showed that genetic diversity was linked with aggression but not stress responsiveness or boldness. Moreover, genome-wide heterozygosity, rather than heterozygosity at single loci, appeared to be associated with aggressiveness. Similarly, genome regions potentially associated with stress responsiveness were located across the genome. Genomic control of behaviour was complex, where many genes were associated with aggressive behaviour and these effects may interact with the effects of other genes. Furthermore, I showed that novel applications of techniques can yield novel candidates for behaviour, where I identified genome regions that are potentially associated with stress responsiveness and candidate genes associated with aggression using a transcriptome, including unidentified sequences. These results highlighted the complex mechanisms that regulate apparently correlated behaviours. To further the study of behavioural genomics, the impact of environmental conditions and previous experience to investigate non-genomic effects should be considered. Moreover, there may be regulatory systems and pathways that interact both at the genetic and environmental level, which may be studied with the use of next generational genomic tools. These findings may be relevant for better understanding the effects of stress and the related behaviours aggression and boldness in rainbow trout in aquaculture. By determining novel candidates for these traits, it may be possible to use these as biomarkers for the early detection of negative effects or to aid marker-assisted breeding programs.

Download or read book Nonanadromous Life History Diversity of Rainbow Trout Oncorhynchus Mykiss written by Martin C. Arostegui and published by . This book was released on 2019 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Rainbow trout (Oncorhynchus mykiss) is a salmonid species, native to Pacific Ocean drainages in North America and eastern Russia, which exhibits fluvial (stream-resident), adfluvial (lake-migrant), and anadromous (ocean-migrant) ecotypes. The differentiation of fluvial and anadromous individuals in sympatry is well-studied, whereas comparatively little research has focused on the adfluvial form and its distinction from fluvial individuals in sympatry. Thus, the purpose of this dissertation was to investigate the ecological, genetic, and phenotypic diversity of nonanadromous rainbow trout in a natural stream-lake system to better understand the differentiation of fluvial and adfluvial individuals in sympatry, the basis of residency versus migration in this species, and the role of lakes in salmonid diversification. Rainbow trout were sampled in the lake (thus, by definition, adfluvial) and in several tributary streams (where adfluvial and fluvial individuals may co-occur), and were examined for a variety of features to develop a holistic understanding of the behavior, ecology, and evolution of these life history pathways. Stomach contents and stable isotopes revealed disparate trophic ecology among rainbow trout in connected stream and lake habitats, suggesting both an ontogenetic shift in the diet of adfluvial fish as well as divergence in diet between adfluvial and fluvial ecotypes. Rainbow trout in streams fed primarily on aquatic insects, while those in the lake largely consumed snails and amphipods; however, partial trophic convergence among trout in these two habitats occurred when they incorporated the marine nutrient subsidy of spawning sockeye salmon eggs. Stable isotope data suggested that the minimum size of migration from stream to lake habitat by adfluvial fish was ~150 mm fork length, suggesting a juvenile stream-rearing period of a year or more prior to lake entry. Dietary niche comparisons with sympatric Salvelinus species suggested a greater degree of dietary overlap between rainbow trout and Dolly Varden (S. malma) in streams than between rainbow trout and Arctic char (S. alpinus) in the lake, which may increase the relative fitness benefits of migration over residency for rainbow trout. Restriction site-associated DNA sequencing revealed an association between habitat type (stream or lake) and a chromosomal inversion in the rainbow trout genome as well as numerous single nucleotide polymorphisms, supporting the genetic divergence of adfluvial and fluvial ecotypes in sympatry. Rainbow trout in streams were nearly fixed for the rearranged haplotype of the Omy05 inversion, whereas trout in the lake exhibited a markedly higher frequency of the ancestral, anadromy-associated haplotype. The functions of outlier genes with nonsynonymous mutations among stream- and lake-caught trout paralleled those documented in studies of fluvial and anadromous O. mykiss, highlighting the migratory nature of the adfluvial ecotype even though it is nonanadromous. Structure was present at both non-outlier and outlier loci among and within streams supporting populations nearly fixed for the rearranged Omy05 haplotype (i.e., with a genetic predisposition for stream-residency), highlighting the roles of local adaptation and genetic drift via spatial isolation in population divergence. Assessment of lateral coloration patterns and multivariate analyses of body shape of rainbow trout from stream and lake habitats over a range of body sizes revealed ontogenetic and ecotypic variation in coloration and morphology. Color differences among trout of different size classes and habitats indicated ecotype-specific pathways resulting in different terminal coloration patterns; banded parr in streams transitioned to either a silver coloration suited to pelagic waters in the lake (when adfluvial) or bronze coloration suited to confined cover in streams (when fluvial). The morphology of lake-caught rainbow trout was distinct from that of stream-caught trout, and their morphological differentiation exhibited many shared but some unique patterns compared to sympatric Dolly Varden in streams and Arctic char in the lake. Patterns of morphological variation in rainbow trout among and within habitats suggested the presence of partial migration, in which both fluvial and adfluvial individuals are produced from the same population. A review of the spawning behaviors, rearing strategies, and trophic polymorphisms in lakes among 16 species of salmonids from the genera Oncorhynchus, Salmo, and Salvelinus identified a negative association between the extent of reliance on lakes and the degree of anadromy. Oncorhynchus exhibits the least lake reliance, Salmo an intermediate level, and Salvelinus the greatest; opposite of the anadromy spectrum identified in previous studies. Lakes support life history forms, reproductive ecotypes, and trophic morphs unique to lacustrine habitat, and also support anadromous and fluvial salmonids by providing spawning, rearing, overwintering, and/or summer refuge habitat. Adfluvial and anadromous salmonids exhibit similar migration-associated traits and behaviors including the parr-smolt transformation, sex-biased partial migration, and the presence of precocious 'jack' males.

Download or read book Personality in Nonhuman Animals written by Jennifer Vonk and published by Springer. This book was released on 2017-07-26 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: This stimulating and comprehensive collection brings together multiple perspectives on the topic of personality in nonhuman animals—linking historical perspectives, theoretical approaches, methods, and cutting-edge discoveries. Experts from various fields describe their findings on species ranging from dogs, cats, chimpanzees, and dolphins to sharks, snakes, and other reptiles. Chapters not only discuss the evolution of personality, but also describe potential applications within the areas of animal-human interactions, animal ethics and welfare, conservation science, and other areas. A key focus is the role of genetics and the environment in determining animal behavior and personality, including related traits, such as creativity and boredom. These chapters present the study of personality in nonhumans as a means by which we can better understand medical and psychological issues specific to our own species as well. Chapters include: · Exploring factor space (and other adventures) with the Hominoid Personality Questionnaire · The quantitative and molecular genetics of individual differences in animal personality · Personality, temperament and individuality in reptile behavior · What do we want to know about personality in marine mammals? · Individual differences in nonhuman animals: examining boredom, curiosity, and creativity · The interplay between animal personality and foraging ecology Taking significant steps in advancing the study of animal personality, Personality in Nonhuman Animals will engage personality psychologists, comparative psychologists, and behavior ecologists as well as conservationists, zookeepers, livestock managers, and all those interested in the brain and behavior of animals.

Download or read book Evolution s Rainbow written by Joan Roughgarden and published by Univ of California Press. This book was released on 2013-09-14 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this innovative celebration of diversity and affirmation of individuality in animals and humans, Joan Roughgarden challenges accepted wisdom about gender identity and sexual orientation. A distinguished evolutionary biologist, Roughgarden takes on the medical establishment, the Bible, social science—and even Darwin himself. She leads the reader through a fascinating discussion of diversity in gender and sexuality among fish, reptiles, amphibians, birds, and mammals, including primates. Evolution's Rainbow explains how this diversity develops from the action of genes and hormones and how people come to differ from each other in all aspects of body and behavior. Roughgarden reconstructs primary science in light of feminist, gay, and transgender criticism and redefines our understanding of sex, gender, and sexuality. Witty, playful, and daring, this book will revolutionize our understanding of sexuality. Roughgarden argues that principal elements of Darwinian sexual selection theory are false and suggests a new theory that emphasizes social inclusion and control of access to resources and mating opportunity. She disputes a range of scientific and medical concepts, including Wilson's genetic determinism of behavior, evolutionary psychology, the existence of a gay gene, the role of parenting in determining gender identity, and Dawkins's "selfish gene" as the driver of natural selection. She dares social science to respect the agency and rationality of diverse people; shows that many cultures across the world and throughout history accommodate people we label today as lesbian, gay, and transgendered; and calls on the Christian religion to acknowledge the Bible's many passages endorsing diversity in gender and sexuality. Evolution's Rainbow concludes with bold recommendations for improving education in biology, psychology, and medicine; for democratizing genetic engineering and medical practice; and for building a public monument to affirm diversity as one of our nation's defining principles.

Download or read book Maintaining a Species Tapestry written by Eric Burke Taylor and published by B.C. Ministry of Environment, Lands and Parks. This book was released on 1996 with total page 51 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Diversity of Fishes written by Douglas E. Facey and published by John Wiley & Sons. This book was released on 2022-12-05 with total page 724 pages. Available in PDF, EPUB and Kindle. Book excerpt: THE DIVERSITY OF FISHES The third edition of The Diversity of Fishes is a major revision of the widely adopted ichthyology textbook, incorporating the latest advances in the biology of fishes and covering taxonomy, anatomy, physiology, biogeography, ecology, and behavior. Key information on the evolution of various fishes is also presented, providing expansive and conclusive coverage on all key topics pertaining to the field. To aid in reader comprehension, each chapter begins with a summary that provides a broad overview of the content of that chapter, which may be particularly useful for those using the text for a course who don’t intend to address every chapter in detail. Detailed color photographs throughout the book demonstrate just some of the diversity and beauty of fishes that attract many to the field. A companion website provides related videos selected by the authors, instructor resources, and additional references and websites for further reading. Sample topics covered and learning resources included in The Diversity of Fishes are as follows: How molecular genetics has transformed many aspects of ichthyology The close relationship between structure and function, including adaptations to special environments Many physical and behavioral adaptations reflecting the fact that many fishes are both predators and prey Fish interactions with other species within fish assemblages and broader communities, plus their impacts on ecosystems Global maps that more accurately represent the comparative sizes of oceans and land masses than maps used in prior editions For students, instructors, and individuals with an interest in ichthyology, The Diversity of Fishes is an all-in-one introductory resource to the field, presenting vast opportunities for learning, many additional resources to aid in information retention, and helpful recommendations on where to go to explore specific topics further.

Download or read book Molecular Genetic Analysis of Rainbow Trout Populations written by Mark Joseph Bagley and published by . This book was released on 1997 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Behavioral Analyses of Strains of Rainbow Trout with Varying Histories of Domestication written by Megan D. Hines and published by . This book was released on 2001 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Hormones and Reproduction of Vertebrates written by David O. Norris and published by Academic Press. This book was released on 2010-11-25 with total page 1681 pages. Available in PDF, EPUB and Kindle. Book excerpt: This series of volumes represents a comprehensive and integrated treatment of reproduction in vertebrates from fishes of all sorts through mammals. It is designed to provide a readable, coordinated description of reproductive basics in each group of vertebrates as well as an introduction to the latest trends in reproductive research and our understanding of reproductive events. Whereas each chapter and each volume is intended to stand alone as a review of that topic or vertebrate group, respectively, the volumes are prepared so as to provide a thorough topical treatment across the vertebrates. Terminology has been standardized across the volumes to reduce confusion where multiple names exist in the literature, and a comprehensive glossary of these terms and their alternative names is provided. A complete, essential and up to date reference for research scientists working on vertebrate hormones and reproduction - and on animlals as models in human reproductive research Covers the endocrinology, neuroendocrinology, physiology, behaviour and anatomy of vertebrate reproduction Structured coverage of the major themes for all five vertebrate groups allows a consistent treatment for all Special chapters elaborate on features specific to individual vertebrate groups and to comparative aspects, similarities and differences between them

Download or read book Evolutionary Genetics of Fishes written by Bruce Turner and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 651 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is my hope that this collection of reviews can be profitably read by all who are interested in evolutionary biology. However, I would like to specifically target it for two disparate groups of biologists seldom men tioned in the same sentence, classical ichthyologists and molecular biologists. Since classical times, and perhaps even before, ichthyologists have stood in awe at the tremendous diversity of fishes. The bulk of effort in the field has always been directed toward understanding this diversity, i. e. , extracting from it a coherent picture of evolutionary processes and lineages. This effort has, in turn, always been overwhelmingly based upon morphological comparisons. The practical advantages of such compari sons, especially the ease with which morphological data can be had from preserved museum specimens, are manifold. But considered objectively (outside its context of "tradition"), morphological analysis alone is a poor tool for probing evolutionary processes or elucidating relationships. The concepts of "relationship" and of "evolution" are inherently genetic ones, and the genetic bases of morphological traits are seldom known in detail and frequently unknown entirely. Earlier in this century, several workers, notably Gordon, Kosswig, Schmidt, and, in his salad years, Carl Hubbs, pioneered the application of genetic techniques and modes of reasoning to ichthyology. While certain that most contemporary ichth yologists are familiar with this body of work, I am almost equally certain that few of them regard it as pertinent to their own efforts.

Download or read book Mechanisms and Pathways Contributing to the Diversity of Aging across the Tree of Life written by Joris Deelen and published by Frontiers Media SA. This book was released on 2022-03-11 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Genetic Diversity Evolution and Fitness of Infectious Hematopoietic Necrosis Virus Within an Endemic Focus in Rainbow Trout Aquaculture written by Ryan M. Troyer and published by . This book was released on 2002 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Conservation and the Genomics of Populations written by Fred W. Allendorf and published by Oxford University Press. This book was released on 2022-02-10 with total page 785 pages. Available in PDF, EPUB and Kindle. Book excerpt: The relentless loss of biodiversity is among the greatest problems facing the world today. The third edition of this established textbook provides an updated and comprehensive overview of the essential background, concepts, and tools required to understand how genetics can be used to conserve species, reduce threat of extinction, and manage species of ecological or commercial importance. This edition is thoroughly revised to reflect the major contribution of genomics to conservation of populations and species. It includes two new chapters: "Genetic Monitoring" and a final "Conservation Genetics in Practice" chapter that addresses the role of science and policy in conservation genetics. New genomic techniques and statistical analyses are crucial tools for the conservation geneticist. This accessible and authoritative textbook provides an essential toolkit grounded in population genetics theory, coupled with basic and applied research examples from plants, animals, and microbes. The book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, evolutionary response to anthropogenic change, and applications in conservation and management. Conservation and the Genomics of Populations helps demystify genetics and genomics for conservation practitioners and early career scientists, so that population genetic theory and new genomic data can help raise the bar in conserving biodiversity in the most critical 20 year period in the history of life on Earth. It is aimed at a global market of applied population geneticists, conservation practitioners, and natural resource managers working for wildlife and habitat management agencies. It will be of particular relevance and use to upper undergraduate and graduate students taking courses in conservation biology, conservation genetics, and wildlife management.

Download or read book Genomic Consequences of Hybridization Between Rainbow and Cutthroat Trout written by Carl O. Ostberg and published by . This book was released on 2015 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introgressive hybridization creates novel gene combinations that may generate important evolutionary novelty and thus contribute to biological complexity and diversification. On the other hand, hybridization with introduced species can threaten native species, such as cutthroat trout (Oncorhynchus clarkii) following the introduction of rainbow trout (O. mykiss). While rainbow trout introgression in cutthroat trout is well documented, neither the evolutionary consequences nor conservation implications are well understood. Hybridization between rainbow and cutthroat trout occurs in the context of substantial chromosomal rearrangement, as well incompletely re-diploidized genomes. Rainbow and cutthroat trout are descended from an autopolyploid ancestor, and extensive chromosome arm rearrangements have occurred between the species following their divergence from the last common ancestor. Evidence for incomplete re-diploidization includes the occasional formation of multivalents and duplicated loci occasionally exhibit a mixture of disomic and tetrasomic inheritance. Thus, transmission genetics may be complicated by recombination between homeologs. Here, I evaluated the phenotypic and genetic consequences of introgression between rainbow trout and Yellowstone cutthroat trout (O. clarkii bouvieri) to provide insights into genome processes that may help explain how introgression affects hybrid genome evolution. The overall aim of the first part of this dissertation (Chapters 1 and 2) was to evaluate phenotypic variation and gene expression among parental species and hybrids to gain insight into the genetic basis of hybrid and parental morphologies. We constructed seven line crosses: both parental species, both reciprocal F1 hybrids, first-generation backcrosses, and F2 hybrids. In Chapter 1, we aimed to assess the role of introgression on growth (length and weight gain), morphology, and developmental instability among these seven crosses. Growth was related to the proportion of rainbow trout genome contained within crosses. Rainbow and cutthroat trout were morphologically divergent: rainbow trout were generally robust whereas cutthroat trout were typically more slender and their hybrids tended to be morphologically intermediate, although backcrosses were morphologically more similar to their backcrossing parental species. These differences in growth and body morphology may be maintained, in part, through the regulation of muscle growth-related genes. Therefore, in Chapter 2, we aimed to characterize the expression of muscle growth-related genes and to describe relationships between gene expression and growth patterns among parental species and hybrids to gain insight into the underlying genetic basis of the difference in their body shapes. Our findings suggest that rainbow and cutthroat trout exhibit differences in muscle growth regulation, that transcriptional networks may be modified by hybridization, and that hybridization disrupts intrinsic relationships between gene expression and growth patterns that may be functionally important for phenotypic adaptations. The overall aim of the second part of this dissertation (Chapters 3 and 4) was to assess the genetic consequences of introgression to determine how the genomic architecture of hybrids affects allelic inheritance, and thus their subsequent evolution. In Chapter 3, we generated a genetic linkage map for rainbow-Yellowstone cutthroat trout hybrids to evaluate genome process that may influence introgression genome evolution in hybrid populations. Our results suggest that few genomic incompatibilities exist between rainbow and cutthroat trout, allowing their to genomes introgress freely, with the exception that differences in chromosome arrangement between the species may act as barriers to introgression and enable large portions of non-recombined chromosomes to persist within admixed populations. In Chapter 4, we aimed to determine the effect of incomplete re-diploidization on transmission genetics in hybrids, compared to pure species. We used the parental gametic phase from existing genetic linkage maps to identify the homeologs that recombine, to characterize this recombination, and to verify meiotic models of residual tetrasomic inheritance in autotetraploids. Recombination between homeologs occurred frequently in hybrids and results in the non-random segregation of alleles across extended chromosomal regions as well as extensive double-reduction in hybrid parental gametes. Taken together, the results from Chapters 3 and 4 suggested that chromosome rearrangements and recombination of homeologs could influence genome evolution in admixed populations. The research presented in this dissertation indicated that the evolutionary fate of hybrid genomes is unpredictable. Some of our findings suggest that introgressions proceeds in a predictable fashion in admixed populations; rainbow and cutthroat genomes freely introgress, with the exception that chromosome rearrangements may suppress recombination across large chromosomal regions. However, homeologous recombination during meiosis in hybrids results in unpredictable segregation of chromosomes, and the segregation of these chromosomes may depend on the hybrid generation of each parent within an admixed population. Furthermore, phenotype and gene expression are quantitative traits, and expression of these traits may depend on hybrid genotypes across transcriptional networks that are controlled by genes distributed over the entire genome. Consequently, hybridization may alter transcriptional regulation of genes, resulting in unpredictable gene expression patterns, which, in turn, contribute to the high phenotypic variation in hybrids.

Download or read book Genomic and Fitness Consequences of Hybridization Between Cutthroat and Rainbow Trout written by Daniel P. Drinan and published by . This book was released on 2015 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hybridization is an important and common evolutionary process that can contribute to diversification, adaptation, and speciation. When species hybridize, divergent genomes are combined through recombination and may result in phenotypic changes. Such phenotypic changes may be the result of differences in chromosomal structure or adaptive divergence between the parental species and may ultimately affect fitness. Understanding how phenotypes change following hybridization, as well as the genetic mechanisms responsible for changes is critical for understanding divergent selection, speciation, and identifying populations that may be at risk from hybridization. Here, the effect of hybridization between cutthroat (Oncorhynchus clarkii) and rainbow trout (O. mykiss) on fitness was investigated using three techniques. In the first chapter, fitness influencing traits were compared among individuals at various hybridization levels. In the second chapter, genomic changes that could affect fitness were identified in the hybrid relative to rainbow trout. And, in the third chapter, correlations between reproductive success and hybridization were investigated in a wild population, as well as the genomic and ecological mechanisms responsible for those changes. The first chapter of this dissertation aimed to identify how traits potentially involved in fitness (embryonic survival, ova size, ova energy concentration, sperm motility, burst swimming performance, juvenile survival, and juvenile growth) changed with hybridization between cutthroat and rainbow trout and whether those changes could explain previously observed reductions in reproductive success of individuals with increased rainbow trout ancestry. Using progeny from wild caught fish, differences in phenotypes based on hybridization were observed for embryonic survival, ova energy concentration, juvenile weight, and burst swimming based on ancestry. However, the correlations differed from previously observed patterns of reproductive success and likely do not explain declines in reproductive success associated with hybridization. The second chapter of this dissertation aimed to identify how hybridization affects the genome by identifying genomic regions with changes in recombination rates in the hybrid relative to rainbow trout as well as genomic areas with excess species-specific ancestry in the hybrid. Previous studies of hybridization have observed recombination suppression in genomic regions where structural differences, such as inversions or karyotype differences, exist between parental species. Such regions may retain groups of adaptive alleles. Additionally, adaptive divergence between the parental species may result in alleles that are preferentially selected in the hybrid progeny. Identification of regions with suppressed recombination or excess species-specific ancestry would provide insight into markers that may be important to fitness and that have differentially evolved in each of the parental species. In total, eight and seven chromosomes were identified to have changes in recombination rates in the hybrid female and male relative to O. mykiss. Recombination was suppressed in the hybrids on two chromosomes with known structural differences between the parental species. In addition, changes in recombination rates were observed on five chromosomes with high proportions of duplicated markers and may be due to increased homeologous chromosome pairing. Recombination patterns were similar between the sexes which suggests that hybridization affects recombination in the same way in females and males. Regions of excess species-specific ancestry covered 11 and 10% of the mapped genome in the female and male and regions of excess were evenly split between cutthroat trout and O. mykiss. Genetic drift may be responsible for much of the observed patterns of excess species-specific ancestry, but selection may also play a role. The aim of the third chapter of this dissertation was to identify the fitness consequences of hybridization, mechanisms responsible for the retention of hybridization, and genomic regions correlated with changes in reproductive success in a wild population of westslope cutthroat trout hybridized with non-native rainbow trout. Adult samples from a previous study, collected over a five year period, were sequenced at 3027 loci. Increased admixture from non-native rainbow trout had a strong, negative effect on reproductive success. A decline of 53% was observed for individuals with an increased genetic contribution of 0.20 from rainbow trout. Despite apparent strong selection against rainbow trout ancestry, hybridization appears to be maintained largely by the invasion of rainbow trout from outside populations as well as the relatively high fitness of few hybrid individuals. Ten loci correlated with reproductive success were identified in females. Seven of the ten loci were linked to chromosomes and three were positioned on chromosomes. Loci linked to reproductive success were identified on chromosomes with excess species-specific ancestry in hybrid progeny (RYHyb14 and RYHyb18) as well as chromosomes with a high proportion of duplicated markers (RYHyb02) and known Robertsonian polymorphism (RYHyb20). The research presented in this dissertation will elucidate our understanding of the phenotypic and genetic changes correlated with hybridization between rainbow and cutthroat trout as well as identify genetic and ecological mechanisms that may be responsible for those changes. In addition, results from this study provide insight into differences in adaptive divergence and markers that may be involved in the early stages of speciation in the wild. Results could be used by managers to identify populations that are at risk from hybridization.

Download or read book The Search for the Kern River Rainbow written by Peter Bjorn Erickson and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The Kern River rainbow trout (Oncorhynchus mykiss gilberti, "KRRT"), like many freshwater fish, has been heavily impacted by the introduction of non-native species into its native range. Angling interest in the region beginning over a century ago led to rampant transplantation of several different types of trout into lakes and streams throughout KRRT's range, the upper Kern River basin in southern California. These introductions resulted in hybridization and introgression with KRRT, and a dwindling number of purely native fish. In the following chapters I use genetic tools to examine the impact of this history of introductions, to measure current genetic characteristics of wild populations, and to provide guidance for the development of KRRT hatchery broodstock with the hope of helping to preserve one of California's native fish. In Chapter 1, I used SNP (single nucleotide polymorphism) and microsatellite markers to determine if a consistent genetic signature of KRRT within the upper Kern River basin still exists. I then measured introgression between KRRT and non-native trout, including coastal rainbow trout (O. mykiss), Little Kern golden trout (O. m. whitei), and California golden trout (O. m. aguabonita). We found that there is indeed still a genetic signature distinct from the non-native trout that have been introduced, but that introgression with those fish is widespread. Nonetheless, we did find several populations with very little introgression, and discovered that a number of populations in the upper Kern River basin still largely represent the native genotype, despite the lengthy history of stocking. In Chapter 2, I used microsatellites to examine gene flow and genetic diversity, particularly as they related to introgression. I found that those populations that have escaped introgression seem to have done so by being reproductively isolated from other populations. This isolation, however, coincides with reduced genetic diversity and genetic signs of population bottlenecks. In this way, avoidance of the primary threat to KRRT has exposed isolated populations to the threats of small population size and reduced genetic diversity. In Chapter 3, I present a Hatchery Genetic Management Plan for KRRT. This plan details recommendations for the collection of wild KRRT, and the development and maintenance of a hatchery broodstock to be planted back into the Kern River in areas currently planted with non-native trout. I describe the genetic factors germane to maximizing genetic diversity, limiting inbreeding, and limiting adaptation to captivity. I also provide guidelines for planting the resulting fish, and for monitoring both existing wild populations as well as hatchery-origin fish. This plan is an important part of helping to restore KRRT to its native range, while ensuring proper management of KRRT populations that still exist. Although this research focuses on KRRT, the issues addressed are relevant to a broader array of taxa threatened by the introduction of non-native species. In particular, the retention of a KRRT genetic signal despite a long history of introductions indicates some degree of resistance on the part of native taxa, and has implications for invasion biology. In addition, the balance between the competing threats of introgression and low genetic diversity provides an example of the many challenges involved in the attempt to preserve biodiversity in a changing world.