Download or read book Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes written by Matthew R. Snyder and published by . This book was released on 2019 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt: Invasive species are one of the top threats to native biodiversity. Their population genetics and genomics can be useful in control and management of invasive species and can be regarded as accidental evolutionary experiments. Here, in a temporal study of the high impact invasive round goby Neogobius melanostomus in the Laurentian Great Lakes, the ability of invasion genetics to track sources and temporal changes in population structure was demonstrated. We tested for three possible alternative temporal patterns in population genetic diversity over time - termed the `genetic stasis', `supplementation', and `replacement' hypotheses. `Genetic stasis' or no change in allelic composition over time could be caused by a large number of introduced propagules that possibly possess all (or most) of the diversity present in the native source, or by a density dependent process circumventing the establishment of later arrivals. Alternatively, there may be `genetic supplementation' in which populations that experienced an initial founder effect then gain diversity over time. Finally, `replacement' of all or some of the initial founding genetic diversity could result when the early arrivals are the best dispersers, followed by those that are better competitors. Results showed that near the site of initial establishment (the invasion core), high genetic diversity due to a large number of introduced individuals precluded significant changes in allelic composition over time. Further from the invasion core, some slight changes in genetic diversity occurred soon after population establishment. Results supported `genetic stasis' and the founder takes all hypothesis. Due to the territoriality of adult round gobies, it is possible that a density dependent process circumvented establishment of later arrivals. Additional introductions from separate native sources were implicated in some areas of the invasion. Detection of newly introduced species before they can become established and characterizing native community composition are top concerns of management agencies. Metabarcode environmental (e)DNA assays are non-invasive sampling tools for detecting species. Targeted and general metabarcode assays and an associated custom library preparation and bioinformatic pipeline that reduce error were designed and tested. This protocol discerned 100% of species present in electrofishing surveys in the Maumee River from just six water samples. Four 1L water samples in the Maumee River were sufficient to identify 88% of species present in concomitant electrofishing surveys and 73% of those in a much larger effort (44 sampling events in 22 sites). Proportions of species-specific high-throughput sequencing reads were weakly correlated with taxa assessed using morphological surveys. Our method identified more invasive species in more samples than did morphological sampling. Haplotypic diversity discerned with metabarcode assays significantly differed from that determined with traditional population genetic data collection. The protocol increased confidence in metabarcode surveys by removing cross-contamination, index-hops (sequence to sample mis-assignment, leading to false positives), and sequencing error and achieved a high detection efficiency. To evaluate the utility of this approach, the protocol was applied to potential retail sources of invasive species in the Great Lakes, including bait and pond stores. Metabarcode assays found a much greater number of stores with illegal native and invasive species compared to morphological sampling. These included juveniles of valuable fishery species, such as walleye Sander vitreus and yellow perch Perca flavescens, and unestablished, potentially high impact invasive species, including the Eurasian ruffe Gymnocephalus cernua, Eurasian ide Leuciscus idus, and silver Hypophthalmichthys molitrix and bighead H. nobilis carps. Presence of illegal species was unrelated to retailer supply chains. Surveys showed that bait dumping is common among anglers in the Great Lakes. There appears to be serious risk of introduction of non-native species via this vector.

Download or read book Molecular Genetics in Fisheries written by Gary R. Carvalho and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: The basic principle of all molecular genetic methods is to employ inherited, discrete and stable markers to identify genotypes that characterize individuals, populations or species. Such genetic data can provide information ori the levels and distribution of genetic variability in relation to mating patterns, life history, population size, migration and environment. Although molecular tools have long been employed to address various questions in fisheries biology and management, their contributions to the field are sometimes unclear, and often controversial. Much of the initial impetus for the deployment of molecular markers arose from the desire to assess fish stock structure based on various interpretations of the stock concept. Although such studies have met with varying success, they continue to provide an impetus for the development of increasingly sensitive population discriminators, yielding information that can be valuable for both sustainable exploitation and the conservation of fish populations. In the last major synthesis of the subject, Ryman and Utter (1987) summarized progress and applications, though this was prior to the wide-scale adoption of DNA methodology. New sources of genetic markers and protocols are now available, in particular those that exploit the widely distributed and highly variable repeat sequences of DNA, and the amplification technique of the polymerase chain reaction.

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 Environmental DNA in Lake Sediment Reveals Biogeography of Native Genetic Diversity written by Hedin T. Nelson-Chorney and published by . This book was released on 2019 with total page 6 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the historical distributions of species is vital to the conservation and restoration of native species, yet such information is often qualitative. We show that the paleolimnological history of threatened freshwater fishes can be reconstructed using species-diagnostic markers amplified from environmental DNA deposited in lake sediments (lake sedDNA). This method was validated through the detection of lake sedDNA from non-native trout (Yellowstone cutthroat trout, Oncorhynchus clarkii bouvieri), which corroborated historical records of human-mediated introductions. We also discovered native trout (westslope cutthroat trout, Oncorhynchus clarkii lewisi) lake sedDNA that predated human-mediated introductions of freshwater fishes in a watershed with high topographical relief. This unexpected result revealed that the westslope population was of native origin and requires immediate conservation protection. Our findings demonstrate that lake sedDNA can be used to determine the colonization history of freshwater fishes and the structure of ecosystems, aiding in the identification of native ranges, novel native diversity, and introductions of non-native species.

Download or read book Environmental DNA for Assessinging Species Richness Genetic Diversity and Species Abundance written by Kara Andres and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Environmental DNA (eDNA) approaches, which involve the sampling and analysis of DNA directly from environmental samples, have revolutionized the ability to detect species and monitor biodiversity efficiently and noninvasively. Recent work has demonstrated the potential for eDNA to detect intraspecific genetic variation and conduct population genetic assessments; however, the field of eDNA has thus far been limited to the assessment of short mitochondrial markers that may lack the resolution required for detailed population genetic assessments. In this body of work, I explore the potential for eDNA approaches to assess fish species richness, provide population genetic information, and estimate absolute species abundance. I first combine estimates of species richness using eDNA metabarcoding and multiple capture-based sampling methods to determine the allocation of effort and cost that provides the optimal approach for lake-wide species inventories. Moving beyond species detections, I then review the important considerations and types of analyses that are possible when analyzing intraspecific genetic variation from eDNA samples and conduct a simulation experiment to understand the limitations of estimating species abundance with different genetic markers and levels of genetic variation. I then demonstrate successful amplification of nuclear microsatellite markers from eDNA samples in a mesocosm experiment, providing accurate estimates of allele frequencies and abundance of an aquatic invasive fish species, the Round Goby (Neogobius melanostomus). Next, I use these approaches to conduct a field-based population genetics experiment, showing agreement between tissue-based and eDNA-based estimates of allele frequencies and population genetic parameters. Last, I assess the potential for eDNA approaches to estimate Round Goby abundance in natural environments and compare these estimates to benthic images obtained with an autonomous underwater vehicle (AUV). Collectively, these studies indicate that intraspecific genetic variation from nuclear genetic markers can be detected from eDNA samples in both natural and controlled environments and used to estimate population allele frequencies, genetic parameters, and species abundance. However, careful consideration of the challenges and limitations of these approaches are required for eDNA to be reliably used for population monitoring and assessments.

Download or read book Population Genetics written by Eric M. Hallerman and published by . This book was released on 2003 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: "List of Fish Taxa -- Preface -- Introduction -- An Overview of Classical and Molecular Genetics -- Measurement of Genetic Variation -- Allozyme Variation -- Chromosomal Variation -- Mitochondrial DNA -- Nuclear DNA -- Population GeneticProcesses -- Natural Selection -- Random Genetic Drift -- Inbreeding -- Coadaptation and Outbreeding Depression -- Quantitative Genetics -- Practical Applications of Population Genetics -- Genetic Stock Identification and Risk Assessment -- Genetic Guidelines for Hatchery Supplementation Programs --Genetic Impacts of Fish Introductions --Genetic Marking -- Forensics -- Population Viability Analysis --Glossary - Index"--P. v.

Download or read book Inland Fishes of the Greater Southwest written by W. L. Minckley and published by University of Arizona Press. This book was released on 2009 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive new book replaces and substantially expands upon the landmark Fishes of Arizona, which has been the authoritative source since it was first published in 1973. Inland Fishes of the Greater Southwest is a one-volume guide to native and non-native fishes of the lower Colorado River basin, downstream from the Grand Canyon, and of the northern tributaries of the Sea of Cortez in the United States and Mexico. In all, there are in-depth accounts of more than 165 species representing 30 families. The book is not limited to the fish. It provides insights into their aquatic world with information on topography, drainage relations, climate, geology, vegetational history, aquatic habitats, human-made water systems, and conservation. A section of the book is devoted to fish identification, with keys to native and non-native families as well as family keys to species. The book is illustrated with more than 120 black-and-white illustrations, 47 full-color plates of native fishes, and nearly 40 maps and figures. Many native fish species are unique to the Southwest. They possess interesting and unusual adaptations to the challenges of the region, able to survive silt-laden floods as well as extreme water temperatures and highly fluctuating water flows ranging from very low levels to flash floods. However, in spite of being well-adapted, many of the fish described here are threatened or endangered, often due to the acts of humans who have altered the natural habitat. For that reason, Inland Fishes of the Greater Southwest presents a vast amount of information about the ecological relationships between the fishes it describes and their environments, paying particular attention to the ways in which human interactions have modified aquatic ecosystemsÑand to how humans might work to ensure the survival of rapidly disappearing native species.

Download or read book Bioeconomics of Invasive Species written by Reuben P. Keller and published by Oxford University Press. This book was released on 2009-04-22 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological invasions are one of the strongest drivers of global environmental change, and invasive species are now often in the public discourse. At the same time, economists have begun to take a real interest in determining how invasive species interact with economic systems, and how invaders should be controlled to optimize societal wealth. Although the work from ecologists and economists have both greatly expanded our understanding of the drivers and impacts of invasions, little integration between the fields has occurred that would allow managers and policy-makers to identify the optical expenditures on, for example, prevention and control of invasive species. Because the level of effort expended on invasive species management is intricately linked to the costs and projected benefits of that management, there is an urgent need for greater synthesis between ecology and economics. This book brings ecology and economics together in new ways to address how we deal with the dynamics and impacts of invasive species, and is the outcome fo many years of collaborative research between a small group of economists and ecologists. The outcome is clear demonstration of the utility of combining ecological and economic models for addressing critical questions in the management of invasive species.

Download or read book Bigheaded Carps written by Cindy S. Kolar and published by . This book was released on 2007 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a detailed risk assessment and biological synopsis of the bigheaded carps of the genus Hypophthalmichthys, which includes the bighead, silver, and largescale silver carps. It summarizes the scientific literature describing their biology, ecology, uses, ecological effects, and risks to the environment. -- Publisher's description.

Download or read book Invasive Asian Carps in North America written by Duane C. Chapman and published by . This book was released on 2011 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Proceedings of the Symposium, 'Invasive Asian Carps in North America: a Forum to Understand the Biology and Manage the Problem,' held in Peoria, Illinois, USA, August 22-23, 2006

Download or read book Occupancy Estimation and Modeling written by Darryl I. MacKenzie and published by Elsevier. This book was released on 2017-11-17 with total page 668 pages. Available in PDF, EPUB and Kindle. Book excerpt: Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition, provides a synthesis of model-based approaches for analyzing presence-absence data, allowing for imperfect detection. Beginning from the relatively simple case of estimating the proportion of area or sampling units occupied at the time of surveying, the authors describe a wide variety of extensions that have been developed since the early 2000s. This provides an improved insight about species and community ecology, including, detection heterogeneity; correlated detections; spatial autocorrelation; multiple states or classes of occupancy; changes in occupancy over time; species co-occurrence; community-level modeling, and more. Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition has been greatly expanded and detail is provided regarding the estimation methods and examples of their application are given. Important study design recommendations are also covered to give a well rounded view of modeling. - Provides authoritative insights into the latest in occupancy modeling - Examines the latest methods in analyzing detection/no detection data surveys - Addresses critical issues of imperfect detectability and its effects on species occurrence estimation - Discusses important study design considerations such as defining sample units, sample size determination and optimal effort allocation

Download or read book Nonindigenous Fishes Introduced Into Inland Waters of the United States written by Pam L. Fuller and published by . This book was released on 1999 with total page 636 pages. Available in PDF, EPUB and Kindle. Book excerpt: This report provides species accounts for all known nonindigenous fishes in inland, open waters of the United States on record at the U.S. Geological Survey, Biological Resources Division's laboratory in Gainesville, Florida (USGS/BRD-G). Online access to the dataset is available on the Internet at http://nas.er.usgs.gov.

Download or read book Marine Algae of California written by Isabella A. Abbott and published by Stanford University Press. This book was released on 1992-08-01 with total page 856 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a complete, systematic treatment of the marine algae (seaweeds) flora of California. The 726 species treated are each illustrated by a detailed line drawing made from an actual specimen. The two authors have drawn upon their phycological research to offer a definitive representation of benthic marine algae from the Californian coast. The floristic treatment in this first paperback edition should aid accurate and speedy identification of flora due to the improved keys, descriptions, illustrations and more detailed coverage of taxa, and should enhance the reader's knowledge of Californian macro-algae.

Download or read book Freshwater Crayfish written by Tadashi Kawai and published by CRC Press. This book was released on 2015-08-05 with total page 666 pages. Available in PDF, EPUB and Kindle. Book excerpt: For their great commercial importance as a human food delicacy, crayfish are now becoming of wider interest to molecular biologists, and also to conservationists due to the fact that in some countries many of the native crayfish species are under threat from human activity, disease, and competition from other introduced crayfish species. Helmed by

Download or read book Physical Processes in a Large Lake written by Setsuo Okuda and published by American Geophysical Union. This book was released on 1995-01-09 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published by the American Geophysical Union as part of the Coastal and Estuarine Studies, Volume 48. Lake Biwa is very important in a social context. It is the largest lake in Japan and presently supplies some 15 million people in four prefectures, Shiga, Kyoto, Osaka and Hyogo with drinking water, making it the single most important source of water in Japan. It is also important from a geographical perspective. It is a natural lake born some five million years ago and is therefore geologically one of the oldest lakes in the world.

Download or read book Biology and Ecology of Crayfish written by Matt Longshaw and published by CRC Press. This book was released on 2016-06-22 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by world experts in astacology, this book covers a range of aspects of the biology and ecology of freshwater crayfish. With a strong focus on wild crayfish, the book studies the taxonomy and genetics of this interesting group of animals. Under examination also are crayfish growth and reproduction, with detailed illustrations; behavior and c

Download or read book Hierarchical Modeling and Inference in Ecology written by J. Andrew Royle and published by Elsevier. This book was released on 2008-10-15 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods.This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures.The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution* abundance models based on many sampling protocols, including distance sampling* capture-recapture models with individual effects* spatial capture-recapture models based on camera trapping and related methods* population and metapopulation dynamic models* models of biodiversity, community structure and dynamics - Wide variety of examples involving many taxa (birds, amphibians, mammals, insects, plants) - Development of classical, likelihood-based procedures for inference, as well as Bayesian methods of analysis - Detailed explanations describing the implementation of hierarchical models using freely available software such as R and WinBUGS - Computing support in technical appendices in an online companion web site