Download or read book Harnessing the Power of Whole Genome Sequencing for the Conservation and Management of Marine Organisms written by Runyang Lou and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Whole genome sequencing (WGS) has become increasingly affordable, and it is particularly useful for characterizing the distribution of neutral and adaptive genetic variation across space and time in marine systems. In this dissertation, I provide practical resources for a cost-effective WGS strategy and use real and simulated data to demonstrate the utilities of WGS in the population genetics and conservation of marine organisms. Low-coverage WGS (lcWGS) has emerged as a powerful WGS approach. However, it requires specialized analytical tools. It is also unclear what the best practices are when designing a lcWGS experiment. In the first chapter, I provide an overview of software packages for low-coverage data. I assess the accuracy of different population genetic inferences under different sequencing designs. I show that spreading a given amount of sequencing effort across more samples is generally preferable, with a few exceptions. A key strength of lcWGS is that pre-existing datasets can be combined and reused. However, a common concern is that non-biological differences between datasets may confound real biological patterns, a problem known as batch effects. In the second chapter, I combine two lcWGS datasets and show that batch effects are rampant. I demonstrate that they result from multiple technical artifacts, and that they can be detected and mitigated with simple bioinformatic strategies. When combined with an artificial selection experiment, WGS becomes a powerful tool to detect the quantitative trait loci (QTLs) of complex traits. In the third chapter, I use forward genetic simulation to build a more realistic model of an artificial selection experiment. I study the power of QTL detection and show that this power is influenced by different aspects of trait architecture. These findings have important implications in the study of fisheries-induced evolution. The genomic processes accompanying a population collapse are a central topic in conservation genomics. In the fourth chapter, I use time-series WGS data to track an Atlantic cod population before and after its collapse. I find that overexploitation has eroded its genetic diversity. There is a lack of strong genetic signatures of fisheries-induced evolution, suggesting that it is potentially reversible on the genetic level.
Download or read book Evolutionary and Ecological Genomics in Deep sea Organisms written by Santiago Herrera Monroy and published by . This book was released on 2015 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hydrothermal vents and coral ecosystems are conspicuous biological hotspots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species' relatedness, diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomics and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. These tools are then applied to test global- and regional-scale biogeographic hypotheses of vent fauna using barnacles as model. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa. Finally, I explore the adaptive potential of deep-sea corals to environmental changes by examining a case of adaptation to shallow water from the deep sea. Overall, these results constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems.
Download or read book Whole Genome Approaches to Uncover Etiology of Disease in Endangered Animals and Critically Ill Humans written by John Edward Gorzynski and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Identification of disease etiology using whole genome data has the potential to promote the health and wellbeing of both humans and other animals. Historically, the cost to generate genomic data has been restrictive. However, advances in genome sequencing technologies have enabled high throughput data generation at a reduced cost. Now genome data is being generated at an unprecedented scale leading to rapid growth in the field of genomics, and as a result is ready for widespread applications in humans and other animals. The overarching goal of the work presented here is to harness the power of next generation sequencing- combining it with refined analysis pathways and novel applications- to advance precision human medicine and promote the integration of genomic data into veterinary and conservation medicine. In the first section of this dissertation, I demonstrate the utility of whole genome sequencing data in population management of critically endangered ex situ living non-human great apes. Using genomic data from these species, I accurately determine kinship, a measure of relatedness used to select appropriate mating pairs, in effort to promote genetic diversity. Additionally, I investigate genetic determinants of two overrepresented disease phenotypes in ex situ living great apes: interstitial myocardial fibrosis in western lowland gorillas and arrhythmogenic right ventricular cardiomyopathy in bonobos. These data suggest that integration of genomic data into population management has the potential to profoundly impact these endangered species. In the second section of this dissertation, I describe the development of an ultra-rapid whole genome sequencing diagnostic test for use in a critical care setting. This protocol took as little as 7 hours and 18 minutes to complete using highly parallel nanopore sequencing, a high-performance cloud compute system, and a custom scheme for variant prioritization. Rapid genetic diagnosis can impact the early clinical decision-making process, enabling clinicians to provide fast and precise medical care. My thesis research has focused on the utility of whole genome sequencing in a variety of medical settings with the aim to promote the health of animals and humans alike.
Download or read book Population Genomics Marine Organisms written by Marjorie F. Oleksiak and published by Springer Nature. This book was released on 2019-12-31 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics has provided unprecedented opportunities to unravel the mysteries of marine organisms in the oceans' depths. The world's oceans, which make up 70% of our planet, encompass diverse habitats and host numerous unexplored populations and species. Population genomics studies of marine organisms are rapidly emerging and have the potential to transform our understanding of marine populations, species, and ecosystems, providing insights into how these organisms are evolving and how they respond to different stimuli and environments. This knowledge is critical for understanding the fundamental aspects of marine life, how marine organisms will respond to environmental changes, and how we can better protect and preserve marine biodiversity and resources. This book brings together leading experts in the field to address critical aspects of fundamental and applied research in marine species and share their research and insights crucial for understanding marine ecosystem diversity and function. It also discusses the challenges, opportunities and future perspectives of marine population genomics.
Download or read book Prospects and challenges for the implementation of HTS genetic methods in fisheries research surveys and stock assessments written by Fran Saborido-Rey and published by Frontiers Media SA. This book was released on 2023-08-02 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Dragonflies and Damselflies written by Alex Córdoba-Aguilar and published by OUP Oxford. This book was released on 2008-08-28 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dragonflies and Damselflies documents the latest advances in odonate biology and relates these to a broader ecological and evolutionary research agenda. Despite being one of the smallest insect orders, dragonflies offer a number of advantages for both laboratory and field studies. In fact, they have been crucial to the advancement of our understanding of insect ecology and evolution. This book provides a critical summary of the major advances in these fields. Contributions from many of the leading researchers in dragonfly biology offer new perspectives and paradigms as well as additional, unpublished, data. The editor has carefully assembled a mix of theoretical and applied chapters (including those addressing conservation and monitoring) and achieves a balance of emerging and established research topics, providing suggestions for future study in each case. This accessible text is not about dragonflies per se but an essential source of knowledge that describes how different sets of evolutionary and ecological principles/ideas have been tested on a particular taxon. It will therefore be suitable for graduate students and researchers in entomology, evolutionary biology, population and behavioural ecology, and conservation biology. It will of course be of particular interest and use to those working on insects and an indispensable reference text for odonate biologists.
Download or read book Environmental DNA written by Pierre Taberlet and published by Oxford University Press. This book was released on 2018-02-02 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning. There is now a rapidly-growing interest amongst biologists in applying analysis of environmental DNA to their own research. However, good practices and protocols dealing with environmental DNA are currently widely dispersed across numerous papers, with many of them presenting only preliminary results and using a diversity of methods. In this context, the principal objective of this practical handbook is to provide biologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practices and analyses based on environmental DNA.
Download or read book Gene Drives on the Horizon written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2016-08-28 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research on gene drive systems is rapidly advancing. Many proposed applications of gene drive research aim to solve environmental and public health challenges, including the reduction of poverty and the burden of vector-borne diseases, such as malaria and dengue, which disproportionately impact low and middle income countries. However, due to their intrinsic qualities of rapid spread and irreversibility, gene drive systems raise many questions with respect to their safety relative to public and environmental health. Because gene drive systems are designed to alter the environments we share in ways that will be hard to anticipate and impossible to completely roll back, questions about the ethics surrounding use of this research are complex and will require very careful exploration. Gene Drives on the Horizon outlines the state of knowledge relative to the science, ethics, public engagement, and risk assessment as they pertain to research directions of gene drive systems and governance of the research process. This report offers principles for responsible practices of gene drive research and related applications for use by investigators, their institutions, the research funders, and regulators.
Download or read book The State of the World s Aquatic Genetic Resources for Food and Agriculture written by Food and Agriculture Organization of the United Nations and published by Food & Agriculture Org.. This book was released on 2019-07-24 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: The conservation, sustainable use and development of aquatic genetic resources (AqGR) is critical to the future supply of fish. The State of the World’s Aquatic Genetic Resources for Food and Agriculture is the first ever global assessment of these resources, with the scope of this first Report being limited to cultured AqGR and their wild relatives, within national jurisdiction. The Report draws on 92 reports from FAO member countries and five specially commissioned thematic background studies. The reporting countries are responsible for 96 percent of global aquaculture production. The Report sets the context with a review of the state of world’s aquaculture and fisheries and includes overviews of the uses and exchanges of AqGR, the drivers and trends impacting AqGR and the extent of ex situ and in situ conservation efforts. The Report also investigates the roles of stakeholders in AqGR and the levels of activity in research, education, training and extension, and reviews national policies and the levels of regional and international cooperation on AqGR. Finally, needs and challenges are assessed in the context of the findings from the data collected from the countries. The Report represents a snapshot of the present status of AqGR and forms a valuable technical reference document, particularly where it presents standardized key terminology and concepts.
Download or read book The Ocean Economy in 2030 written by OECD and published by OECD Publishing. This book was released on 2016-04-27 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report explores the growth prospects for the ocean economy, its capacity for future employment creation and innovation, and its role in addressing global challenges. Special attention is devoted to the emerging ocean-based industries.
Download or read book Genomics in Aquaculture to Better Understand Species Biology and Accelerate Genetic Progress written by José Manuel Yáñez and published by Frontiers Media SA. This book was released on 2016-09-15 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: From a global perspective aquaculture is an activity related to food production with large potential for growth. Considering a continuously growing population, the efficiency and sustainability of this activity will be crucial to meet the needs of protein for human consumption in the near future. However, for continuous enhancement of the culture of both fish and shellfish there are still challenges to overcome, mostly related to the biology of the cultured species and their interaction with (increasingly changing) environmental factors. Examples of these challenges include early sexual maturation, feed meal replacement, immune response to infectious diseases and parasites, and temperature and salinity tolerance. Moreover, it is estimated that less than 10% of the total aquaculture production in the world is based on populations genetically improved by means of artificial selection. Thus, there is considerable room for implementing breeding schemes aimed at improving productive traits having significant economic impact. By far the most economically relevant trait is growth rate, which can be efficiently improved by conventional genetic selection (i.e. based on breeding values of selection candidates). However, there are other important traits that cannot be measured directly on selection candidates, such as resistance against infectious and parasitic agents and carcass quality traits (e.g. fillet yield and meat color). However, these traits can be more efficiently improved using molecular tools to assist breeding programs by means of marker-assisted selection, using a few markers explaining a high proportion of the trait variation, or genomic selection, using thousands of markers to estimate genomic breeding values. The development and implementation of new technologies applied to molecular biology and genomics, such as next-generation sequencing methods and high-throughput genotyping platforms, are allowing the rapid increase of availability of genomic resources in aquaculture species. These resources will provide powerful tools to the research community and will aid in the determination of the genetic factors involved in several biological aspects of aquaculture species. In this regard, it is important to establish discussion in terms of which strategies will be more efficient to solve the primary challenges that are affecting aquaculture systems around the world. The main objective of this Research Topic is to provide a forum to communicate recent research and implementation strategies in the use of genomics in aquaculture species with emphasis on (1) a better understanding of fish and shellfish biological processes having considerable impact on aquaculture systems; and (2) the efficient incorporation of molecular information into breeding programs to accelerate genetic progress of economically relevant traits.
Download or read book Selective Breeding in Aquaculture an Introduction written by Trygve Gjedrem and published by Springer Science & Business Media. This book was released on 2010-03-17 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: The foundation of quantitative genetics theory was developed during the last century and facilitated many successful breeding programs for cultivated plants and t- restrial livestock. The results have been almost universally impressive, and today nearly all agricultural production utilises genetically improved seed and animals. The aquaculture industry can learn a great deal from these experiences, because the basic theory behind selective breeding is the same for all species. The ?rst published selection experiments in aquaculture started in 1920 s to improve disease resistance in ?sh, but it was not before the 1970 s that the ?rst family based breeding program was initiated for Atlantic salmon in Norway by AKVAFORSK. Unfortunately, the subsequent implementation of selective breeding on a wider scale in aquaculture has been slow, and despite the dramatic gains that have been demonstrated in a number of species, less than 10% of world aquaculture production is currently based on improved stocks. For the long-term sustainability of aquaculture production, there is an urgent need to develop and implement e- cient breeding programs for all species under commercial production. The ability for aquaculture to successfully meet the demands of an ever increasing human p- ulation, will rely on genetically improved stocks that utilise feed, water and land resources in an ef?cient way. Technological advances like genome sequences of aquaculture species, and advanced molecular methods means that there are new and exciting prospects for building on these well-established methods into the future.
Download or read book Insights in evolutionary and population genetics 2022 written by Samuel A. Cushman and published by Frontiers Media SA. This book was released on 2023-07-27 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Barcoding in Marine Perspectives written by Subrata Trivedi and published by Springer. This book was released on 2016-08-31 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: More than two third of the surface area of our planet is covered by oceans and assessment of the marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine recourses for food, energy and other requirements. This puts pressure on the fragile marine environment and needs sustainable conservation efforts. Marine species identification using traditional taxonomical methods are often burdened with taxonomic controversies. Here in this book we will discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be helpful in the assessment of cryptic species which are widespread in marine environment, and can also be used to link the different life cycle stages to the adult which is difficult to accomplish in marine ecosystems. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. DNA barcoding of different marine groups ranging from the microbes to mammals is to be revealed. In conjugation with newer and faster techniques like high throughput sequencing, DNA barcoding is serving as an effective modern tool in marine biodiversity assessment and conservation.
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 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 conservespecies, 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 "ConservationGenetics 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. Thebook 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 historyof 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 coursesin conservation biology, conservation genetics, and wildlife management.
Download or read book Action Before Extinction written by World Fisheries Trust and published by . This book was released on 1998 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Stock Identification Methods written by Steven X. Cadrin and published by Academic Press. This book was released on 2013-10-04 with total page 589 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stock Identification Methods, 2e, continues to provide a comprehensive review of the various disciplines used to study the population structure of fishery resources. It represents the worldwide experience and perspectives of experts on each method, assembled through a working group of the International Council for the Exploration of the Sea. The book is organized to foster interdisciplinary analyses and conclusions about stock structure, a crucial topic for fishery science and management. Technological advances have promoted the development of stock identification methods in many directions, resulting in a confusing variety of approaches. Based on central tenets of population biology and management needs, this valuable resource offers a unified framework for understanding stock structure by promoting an understanding of the relative merits and sensitivities of each approach. - Describes 18 distinct approaches to stock identification grouped into sections on life history traits, environmental signals, genetic analyses, and applied marks - Features experts' reviews of benchmark case studies, general protocols, and the strengths and weaknesses of each identification method - Reviews statistical techniques for exploring stock patterns, testing for differences among putative stocks, stock discrimination, and stock composition analysis - Focuses on the challenges of interpreting data and managing mixed-stock fisheries
