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Part, PART 1 The Genetic Modification and Invention of Human Beings -- chapter Foreword: Are Genes Us? -- chapter 1 Introduction: New Genetics: the Ethical Background -- chapter 2 Genetic Possibilities -- chapter 3 Is There a Cost in the Choice of Genetic Enhancement? -- chapter 4 The Child's Right to an Open Future and Modern Genetics -- chapter 5 The Fear of Playing God -- chapter 6 Deeply Felt Disgust -- a Devlinian Objection to Cloning Humans -- chapter 7 Genetic Intervention and Personal Identity -- part, PART 2 Genetics, Determinism and Personal Identity -- chapter 8 Genetic Reductionism and the Concepts of Health and Disease -- chapter 9 From Catch-Phrase to Catechism: the Central Dogma in Molecular Biology -- chapter 10 Gene Manipulation, Psychology and Molecular Biology -- chapter 11 Patenting Human DNA -- chapter 12 Personal Identity and the Protection of Mankind: Genetics and Legal Philosophy -- part, PART 3 Genes and the Non-Human World -- chapter 13 Commodifying Animals: Ethical Issues in Genetic Engineering of Animals -- chapter 14 Genetically Modified Crops and the Precautionary Principle: Is There a Case for a Moratorium? -- chapter 15 Everyday Risk and the Deliberate Release of Genetically Modified Crops -- chapter 16 Public Deliberation and Private Choice in Human Genetics.

This interdisciplinary thesis questions the issue of globalization through living organisms involved in industrial sociotechnical organizations. The cow, an animal that has evolved alongside humans since Neolithic times, embodies numerous economic, political, cultural and technological issues. The Holstein breed, the incarnation of 'modern' animal as a mix of nature, culture and technoscience, has become symbolic of globalization in the animal world. Present in 130 countries and adopted by many cultural imaginaries, it nevertheless challenges the biological limits of industrial and commercial globalization. By following the actors of cattle breeding at the international level, the thesis brings an original perspective on this question from both STS (Science and Technology Studies) and the discipline of animal genetics. Represented by geneticists, bovine genes fully appear as actors of the globalizing processes of our techno-scientific 'modernity'. Their circulations (re)arrange invisible but constructive links of the global world. The interactions between genes and their environment produce effects that go far beyond the physical boundaries of the animal body and shape the global landscape of animal breeding and production. The growing tensions between scientific and commercial actors, between theories and practices, and between developed and developing countries call for a different view of industrial activities involving living organisms. A holistic approach is adopted here through the unity between the animal and its environment beyond the production system narrowly defined. The notion of 'genotype by environment interaction' issued from statistical genetics and put into politics within the globalization of bovine breeding helps to understand the intrinsic and complex link between biological and social life ; Cette thèse interdisciplinaire traite la question de la globalisation au travers des organismes vivants impliqués dans les organisations sociotechniques industrielles. La vache, animal qui évolue aux ...

Plant genetic diversity is crucial to the breeding of food crops and is therefore a central precondition for food security. This important book contributes to our understanding of how international regimes affect the management of plant genetic resources for food and agriculture in developing countries.

1 Introduction -- 1.1 The ethological approach to the study of behaviour -- 1.2 A brief outline of classical ethological theory -- 1.3 The modern study of animal behaviour -- 1.4 An outline of the book -- 2 The description and measurement of behaviour -- 2.1 Describing behaviour by its function -- 2.2 Describing behaviour by its form -- 2.3 Describing and measuring the relationship between an animal and its environment -- 2.4 What is the point of all this sophisticated analysis? -- 3 The study of the causes of behavioural change -- 3.1 What constitutes a causal explanation of behaviour? -- 3.2 The different kinds of causal explanation -- 3.3 Motivational models -- 3.4 Studying external influences on behaviour -- 3.5 Studying internal influences on behaviour -- 3.6 What is the nature of the mechanisms which cause behavioural change? -- 3.7 Studying the physiological bases of behavioural change -- 4 The development of behaviour -- 4.1 Problems with the instinct-learning dichotomy -- 4.2 Why is the term innate still used? -- 4.3 Describing the ontogeny of behaviour -- 4.4 Characterizing the factors which influence the development of behaviour -- 4.5 Classifying the factors which influence the development of behaviour -- 4.6 Some general features of behavioural development -- 5 The adaptive significance of behaviour -- 5.1 Sources of evidence about the adaptive significance of behaviour -- 5.2 Difficulties in studying the adaptive significance of behaviour -- 5.3 The state of the art -- 5.4 The adaptive significance of the way animals pattern their behavior in time -- 5.5 The adaptive significance of the way animals use space -- 5.6 The adaptive significance of an animal's aggressive responses -- 5.7 The adaptive significance of an animal's breeding habits; mating systems -- 5.8 Adaptive significance of behaviour accompanying mating -- 5.9 The adaptive significance of parental care -- 5.10 The adaptive significance of living in groups -- 5.11 Behaviour which cannot be explained by classic natural selection theory -- 5.12 Overview; sociobiology and behavioural ecology -- 6 The phylogeny of behaviour -- 6.1 Sources of evidence about the phylogeny of behaviour -- 6.2 Some representative behavioural phylogenies -- 6.3 Deriving general principles of behavioural evolution -- 7 The role of behaviour in the evolutionary process -- 7.1 The behaviour of other animals as a major selective force -- 7.2 Behaviour dictates the selection pressures to which an animal is exposed -- 7.3 The impact of behaviour on population structure -- 8 Behavioural genetics -- 8.1 The objectives of research into the inheritance of behaviour -- 8.2 Potential contributions of genetics to the study of animal behaviour -- 8.3 Quantitative genetics -- 8.5 Screening known genetic variants for behavioural differences -- 8.6 Characterizing the precise behavioural effects of genetic differences -- 8.7 The mechanisms whereby genes influence behaviour -- 8.8 Genetic mosaics -- 8.9 Animal behaviour and behavioural genetics -- 9 Applied ethology -- 9.1 Clarification of terms; what is applied ethology? -- 9.2 Ways in which etiological research can be applied to practical problems -- 9.3 Pest control -- 9.4 Increasing the productivity of commercially important species -- 9.5 Animal welfare -- 9.6 Conservation -- 9.7 Human behaviour -- References -- Author index -- Species index.

Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation

Infection of livestock with Mycobacterium bovis, is the causing agent of bovine tuberculosis and is of major economic and health concern globally, with the cost of livestock loss estimated at ?2 billion globally. In developed nations the majority of the cost involved with bovine tuberculosis is due to controlling the disease, while in developing nations, infection is endemic leading to reduced productivity and loss of livestock. Zoonotic infection of bovine tuberculosis also constitutes a major human health risk in developing nations. In Ireland approximately 15,000-20,000 cattle are infected with bovine tuberculosis each year, with control of bovine tuberculosis in Ireland incurring a cost of ?63 million to the Irish government. While an extensive eradication program has been in place in Ireland since the 1960s, eradication of the disease from the island has remained elusive. This is in part due to the presence of a natural wildlife reservoir for the disease in the form of Eurasian badgers (Melese meles). Ireland has had a successful nation-wide breeding strategy, carried out by the Irish Cattle breeding federation, in place for cattle since the early 2000s. This breeding strategy has been based around developing accurate genetic evaluations for all breeding sires for economically important traits (i.e. milk yield, fertility etc.), using both progeny records and genotype information. This thesis delves into the underlying genetics of Mycobacterium bovis infection in Irish dairy and beef cattle, utilizing a wealth of phenotypic, genetic and pedigree information supplied by national databases operated by Teagasc, the Department of Agriculture, Food and the Marine, the Irish Cattle Breeding Federation and the Centre for Veterinary Epidemiology and Risk Analysis. Variance components and heritability of Mycobacterium bovis susceptibility in Irish Dairy and beef cattle was estimated using a of 105,914 cow, 56,904 heifer and 21,872 steer single intra-dermal comparative tuberculin test records. A heritability of 0.11 was estimated for all animals analyzed (with a variation of 0.08 to 0.19 for each group separately). The genetic correlation between dairy and beef animals (and all groups) were all positive. This work indicated a much higher heritability for Mycobacterium bovis infection than other documented disease traits (~0.03). Moreover the positive genetic correlation between all animal groups and the correlation between increased prevalence of the disease in sire daughters and estimated breeding value, indicates that implementing a national breeding strategy for increased Mycobacterium bovis infection could be possible. As Mycobacterium bovis infection has been documented to be an elusive polygenic traits, several of GWAS methods were implemented in this thesis to elucidate the underlying genes involved in host susceptibility. A total of 841 dairy sire genotypes with estimated breeding values for Mycobacterium bovis susceptibility were available. One quantitative trait locus on chromosome 23 was common to all three genome-wide analyses for association to Mycobacterium bovis susceptibility. Imputation to whole genome sequence of this QTL region revealed the gene FKBP5 which encodes a protein from the immunophillin protein family, a family of proteins often targeted by immunosuppressant drugs. Finally a search for signatures of selection and ancestry mapping was performed on two anciently admixed cattle groups, East African zebu cattle breeds and cattle originating from the Near Eastern Anatolian peninsula. These breeds provide an interesting intersection of the two domestic lines of cattle, Bos indicus and Bos taurus. Moreover mapping signatures of selection and ancestral haplotypes can often have a higher power of analysis that traditional GWAS methods. A number of key identifiers of selection were identified in both breed groups, which East African Zebu breeds having suggestive signatures of selection for innate immunity and signatures of selection in Anatolian breeds indicating selection towards beef and dairy production traits. The work presented in this thesis has helped the development of a national breeding strategy towards improved resistance to Mycobacterium bovis infection in Irish cattle herds which is expected to be implemented within the next two years. Furthermore it has identified a novel QTL region associated with Mycobacterium bovis infection. Infection of livestock with Mycobacterium bovis, is the causing agent of bovine tuberculosis and is of major economic and health concern globally, with the cost of livestock loss estimated at ?2 billion globally. In developed nations the majority of the cost involved with bovine tuberculosis is due to controlling the disease, while in developing nations, infection is endemic leading to reduced productivity and loss of livestock. Zoonotic infection of bovine tuberculosis also constitutes a major human health risk in developing nations. In Ireland approximately 15,000-20,000 cattle are infected with bovine tuberculosis each year, with control of bovine tuberculosis in Ireland incurring a cost of ?63 million to the Irish government. While an extensive eradication program has been in place in Ireland since the 1960s, eradication of the disease from the island has remained elusive. This is in part due to the presence of a natural wildlife reservoir for the disease in the form of Eurasian badgers (Melese meles). Ireland has had a successful nation-wide breeding strategy, carried out by the Irish Cattle breeding federation, in place for cattle since the early 2000s. This breeding strategy has been based around developing accurate genetic evaluations for all breeding sires for economically important traits (i.e. milk yield, fertility etc.), using both progeny records and genotype information. This thesis delves into the underlying genetics of Mycobacterium bovis infection in Irish dairy and beef cattle, utilizing a wealth of phenotypic, genetic and pedigree information supplied by national databases operated by Teagasc, the Department of Agriculture, Food and the Marine, the Irish Cattle Breeding Federation and the Centre for Veterinary Epidemiology and Risk Analysis. Variance components and heritability of Mycobacterium bovis susceptibility in Irish Dairy and beef cattle was estimated using a of 105,914 cow, 56,904 heifer and 21,872 steer single intra-dermal comparative tuberculin test records. A heritability of 0.11 was estimated for all animals analyzed (with a variation of 0.08 to 0.19 for each group separately). The genetic correlation between dairy and beef animals (and all groups) were all positive. This work indicated a much higher heritability for Mycobacterium bovis infection than other documented disease traits (~0.03). Moreover the positive genetic correlation between all animal groups and the correlation between increased prevalence of the disease in sire daughters and estimated breeding value, indicates that implementing a national breeding strategy for increased Mycobacterium bovis infection could be possible. As Mycobacterium bovis infection has been documented to be an elusive polygenic traits, several of GWAS methods were implemented in this thesis to elucidate the underlying genes involved in host susceptibility. A total of 841 dairy sire genotypes with estimated breeding values for Mycobacterium bovis susceptibility were available. One quantitative trait locus on chromosome 23 was common to all three genome-wide analyses for association to Mycobacterium bovis susceptibility. Imputation to whole genome sequence of this QTL region revealed the gene FKBP5 which encodes a protein from the immunophillin protein family, a family of proteins often targeted by immunosuppressant drugs. Finally a search for signatures of selection and ancestry mapping was performed on two anciently admixed cattle groups, East African zebu cattle breeds and cattle originating from the Near Eastern Anatolian peninsula. These breeds provide an interesting intersection of the two domestic lines of cattle, Bos indicus and Bos taurus. Moreover mapping signatures of selection and ancestral haplotypes can often have a higher power of analysis that traditional GWAS methods. A number of key identifiers of selection were identified in both breed groups, which East African Zebu breeds having suggestive signatures of selection for innate immunity and signatures of selection in Anatolian breeds indicating selection towards beef and dairy production traits. The work presented in this thesis has helped the development of a national breeding strategy towards improved resistance to Mycobacterium bovis infection in Irish cattle herds which is expected to be implemented within the next two years. Furthermore it has identified a novel QTL region associated with Mycobacterium bovis infection. ; TARA (Trinity?s Access to Research Archive) has a robust takedown policy. 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Studies on the determinants of physical activity have traditionally focused on social factors and environmental barriers, but recent research has shown the additional importance of biological factors, including genetic variation. Here we review the major tenets of this research to arrive at three major conclusions: First, individual differences in physical activity traits are significantly influenced by genetic factors, but genetic contribution varies strongly over age, with heritability of leisure time exercise behavior ranging from 27% to 84% and heritability of sedentary behaviors ranging from 9% to 48%. Second, candidate gene approaches based on animal or human QTLs or on biological relevance (e.g., dopaminergic or cannabinoid activity in the brain, or exercise performance influencing muscle physiology) have not yet yielded the necessary evidence to specify the genetic mechanisms underlying the heritability of physical activity traits. Third, there is significant genetic modulation of the beneficial effects of daily physical activity patterns on strength and endurance improvements and on health-related parameters like body mass index. Further increases in our understanding of the genetic determinants of sedentary and exercise behaviors as well as the genetic modulation of their effects on fitness and health will be key to meaningful future intervention on these behaviors.

The book introduces the basic concepts and methods that are useful in the statistical analysis and modeling of DNA-based marker and phenotypic data that arise in agriculture, forrestry, experimental biology, and other fields. It concentrates on the linkage analysis of markers, map construction and quantitative trait locus (QTL) mapping and assumes a background in regression analysis and maximum likelihood approaches. The strengths of this book lie in the construction of general models and algorithms for linkage analysis and QTL mapping in any kind of crossed pedigrees initiated with inbred lines of crops and plant and animal model systems or outbred lines in forest trees and wildlife species. The book includes a detailed description of each approach and the step-by-step demonstration of live-example analyses designed to explain the utilization and usefulness of statistical methods. The book also includes exercise sets and computer codes for all the analyses used. This book can serve as a textbook for graduates and senior undergraduates in genetics, agronomy, forest biology, plant breeding and animal sciences. It will also be useful to researchers and other professionals in the areas of statistics, biology and agriculture. Rongling Wu is Associate Professor of Statistics at the University of Florida, Gainesville. He currently serves as Associate Editor for six genetics and bioinformatics journals. Chang-Xing Ma is Assistant Professor of Biostatistics at the State University of New York at Buffalo. George Casella is Distinguished Professor of Statistics and Distinguished Member of the Genetics Institute at the University of Florida, Gainesville. He is a fellow of the American Statistical Association and the Institute of Mathematical Sciences, and the author of four other statistics books.

Research on coordination and decision-making in humans and nonhuman primates has increased considerably throughout the last decade. However, terminology has been used inconsistently, hampering the broader integration of results from different studies. In this short article, we provide a glossary containing the central terms of coordination and decision-making research. The glossary is based on previous definitions that have been critically revised and annotated by the participants of the symposium "Where next? Coordination and decision-making in primate groups" at the XXIIIth Congress of the International Primatological Society (IPS) in Kyoto, Japan. We discuss a number of conceptual and methodological issues and highlight consequences for their implementation. In summary, we recommend that future studies on coordination and decision-making in animal groups do not use the terms "combined decision" and "democratic/despotic decision-making." This will avoid ambiguity as well as anthropocentric connotations. Further, we demonstrate the importance of 1) taxon-specific definitions of coordination parameters (initiation, leadership, followership, termination), 2) differentiation between coordination research on individual-level process and group-level outcome, 3) analyses of collective action processes including initiation and termination, and 4) operationalization of successful group movements in the field to collect meaningful and comparable data across different species. ; peerReviewed

Intro -- Contents -- Part I The Animal and Its Environment -- An Introduction to Reproducibility in the Context of Animal Research -- 1 An Introduction to Reproducibility in the Context of Animal Research -- 1.1 Reproducibility -- 2 Part I: The Animal and Its Environment -- 3 Part II: Statistics: Basics and Explanation of Different Designs and Tests -- 4 Part III: Systematic Reviews and Publishing -- References -- Rodent Genetics -- 1 Introduction to Mendelian Genetics and Genomics -- 1.1 Genes, Alleles and Their Interactions -- 1.1.1 Dominance, Recessivity and Co-dominance -- 1.1.2 Epistasis and Pleiotropy -- 1.1.3 Penetrance and Expressivity -- 1.2 Genomes and Genetic Variation -- 1.2.1 Genes, Gene Families and Pseudogenes -- 1.2.2 Repetitive DNA Sequences -- 1.2.3 Copy Number Variations, Indels, Transposable Elements and SNPs -- 1.2.4 Functional Annotation of the Mouse Genome -- 2 Standardized Strains of Laboratory Rodents -- 2.1 Inbred Strains and Substrains -- 2.2 F1 Hybrids -- 2.3 Co-isogenic, Congenic and Consomic Strains -- 2.4 Recombinant Inbred Strains and Recombinant Congenic Strains -- 2.5 The Mouse Collaborative Cross -- 2.6 Outbred Stocks -- 3 Genetically Altered (GA) Rodents -- 3.1 Spontaneous and Chemically Induced Mutants -- 3.2 Classical Transgenesis by Pronuclear Microinjection (Random Insertion) -- 3.3 Targeted Mutagenesis Using ES Cells -- 3.4 Gene Editing Using Nucleases -- 3.4.1 Zinc-Finger Nucleases and TALEN -- 3.4.2 CRISPR-Cas System -- 4 Genetic Quality Control for Mice and Rats -- 4.1 Current Tools for Genetic Quality Control -- 4.1.1 Microsatellite (SSLP) Markers -- 4.1.2 Single Nucleotide Polymorphisms (SNPs) -- 4.2 Genetic Quality Control of Inbred Strains and Outbred Stocks -- 4.2.1 Genetic Monitoring to Confirm Strain Identity -- 4.2.2 Discrimination of Substrains -- 4.2.3 Genetic Monitoring for Outbred Colonies.

While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material—including other animal species, plants, or microorganisms—is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities. ; MA, FP, MO, NP, AML and VG are supported by the Portuguese Foundation for Science and Technology (FCT), European RegionalDevelopment Fund (ERDF) and Programa Operacional Potencial Humano,through the grants IF/00955/2014, IF/01356/2012, SFRH/BPD/66071/2009, SFRH/BPD/97414/2013, IF/01262/2014 and SFRH/BPD/76207/2011, respectively. MA was also supported by the "Ramón y Cajal" grant RYC-2015-18241 from the Spanish Government. IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT. The funders had no role in the preparation of the article.

AbstractThe increase of parental reproductive age is a worldwide trend in modern society in recent decades. In general, older parents have a significant impact on reproductive genetics and the health of offspring. In particular, advanced parental age contributes to the increase in the risk of adverse neurodevelopmental outcomes in offspring. However, it is currently under debate how and to what extent the health of future generations was affected by the parental age. In this review, we aimed to (i) provide an overview of the effects of age on the fertility and biology of the reproductive organs of the parents, (ii) highlight the candidate biological mechanisms underlying reproductive genetic alterations, and (iii) discuss the relevance of the effect of parental age on offspring between animal experiment and clinical observation. In addition, we think that the impact of environmental factors on cognitive and emotional development of older offspring will be an interesting direction.