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Author: Ellen Leffler
Publisher:
ISBN: 9781303423123
Category :
Languages : en
Pages : 225
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Book Description
Genetic variation within a population reflects a balance of evolutionary forces, with variation introduced by mutation or gene flow, eliminated by genetic drift or by positive/purifying selection and, potentially, maintained by balancing selection. In addition, the fates of variants are tied to those of nearby sites via linkage, to an extent determined by the recombination rate. Patterns of diversity throughout the genome thus hold a very rich, albeit convoluted and partial, record of evolutionary processes. It has become common to gather variation information across multiple individuals, increasingly genome-wide, providing the data with which to describe and test the influence of these various forces globally and at particular loci. In my dissertation, I use large-scale genetic variation data to address several evolutionary questions: First, I ask what are the important determinants of overall intraspecific genetic diversity levels by compiling and analyzing genetic diversity estimates from the literature for eukaryotic species. I find some intriguing patterns, but mainly highlight how much is still unresolved. Next, I use the genetic variation within two species, chimpanzees and humans, to look for evidence of loci under long-term balancing selection, a mode of selection for which conclusive signatures have been difficult to find and whose prevalence in nature is long debated. I find at least six loci with strong evidence that balancing selection has acted since before the species split, suggesting that long-term balancing selection may be more common than currently believed. Finally, using recombination events inferred from human pedigrees, I estimate the heritability of recombination phenotypes and conduct a genome-wide association study to identify genetic variation contributing to differences in recombination rates and patterns between individuals. These studies demonstrate how population patterns of genetic variation can provide insight into the action of selection and the genetic basis of recombination.
Author: Ellen Leffler
Publisher:
ISBN: 9781303423123
Category :
Languages : en
Pages : 225
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Book Description
Genetic variation within a population reflects a balance of evolutionary forces, with variation introduced by mutation or gene flow, eliminated by genetic drift or by positive/purifying selection and, potentially, maintained by balancing selection. In addition, the fates of variants are tied to those of nearby sites via linkage, to an extent determined by the recombination rate. Patterns of diversity throughout the genome thus hold a very rich, albeit convoluted and partial, record of evolutionary processes. It has become common to gather variation information across multiple individuals, increasingly genome-wide, providing the data with which to describe and test the influence of these various forces globally and at particular loci. In my dissertation, I use large-scale genetic variation data to address several evolutionary questions: First, I ask what are the important determinants of overall intraspecific genetic diversity levels by compiling and analyzing genetic diversity estimates from the literature for eukaryotic species. I find some intriguing patterns, but mainly highlight how much is still unresolved. Next, I use the genetic variation within two species, chimpanzees and humans, to look for evidence of loci under long-term balancing selection, a mode of selection for which conclusive signatures have been difficult to find and whose prevalence in nature is long debated. I find at least six loci with strong evidence that balancing selection has acted since before the species split, suggesting that long-term balancing selection may be more common than currently believed. Finally, using recombination events inferred from human pedigrees, I estimate the heritability of recombination phenotypes and conduct a genome-wide association study to identify genetic variation contributing to differences in recombination rates and patterns between individuals. These studies demonstrate how population patterns of genetic variation can provide insight into the action of selection and the genetic basis of recombination.
Author: Tanya Ngoc Phung
Publisher:
ISBN:
Category :
Languages : en
Pages : 213
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Book Description
Understanding how different evolutionary processes shape genetic variation within and between species is an important question in population genetics. The advent of next generation sequencing has allowed for many theories and hypotheses to be tested explicitly with data. However, questions such as what evolutionary processes affect neutral divergence (DNA differences between species) or genetic variation in different regions of the genome (such as on autosomes versus sex chromosomes) or how many genetic variants contribute to complex traits are still outstanding. In this dissertation, I utilized different large-scale genomic datasets and developed statistical methods to determine the role of natural selection on genetic variation between species, sex-biased evolutionary processes on shaping patterns of genetic variation on the X chromosome and autosomes, and how population history, mutation, and natural selection interact to control complex traits. First, I used genome-wide divergence data between multiple pairs of species ranging in divergence time to show that natural selection has reduced divergence at neutral sites that are linked to those under direct selection. To determine explicitly whether and to what extent linked selection and/or mutagenic recombination could account for the pattern of neutral divergence across the genome, I developed a statistical method and applied it to human-chimp neutral divergence dataset. I showed that a model including both linked selection and mutagenic recombination resulted in the best fit to the empirical data. However, the signal of mutagenic recombination could be coming from biased gene conversion. Comparing genetic diversity between the X chromosome and the autosomes could provide insights into whether and how sex-biased processes have affected genetic variation between different genomic regions. For example, X/A diversity ratio greater than neutral expectation could be due to more X chromosomes than expected and could be a result of mating practices such as polygamy where there are more reproducing females than males. I next utilized whole-genome sequences from dogs and wolves and found that X/A diversity is lower than neutral expectation in both dogs and wolves in ancient time-scales, arguing for evolutionary processes resulting in more males reproducing compared to females. However, within breed dogs, patterns of population differentiation suggest that there have been more reproducing females, highlighting effects from breeding practices such as popular sire effect where one male can father many offspring with multiple females. In medical genetics, a complete understanding of the genetic architecture is essential to unravel the genetic basis of complex traits. While genome wide association studies (GWAS) have discovered thousands of trait-associated variants and thus have furthered our understanding of the genetic architecture, key parameters such as the number of causal variants and the mutational target size are still under-studied. Further, the role of natural selection in shaping the genetic architecture is still not entirely understood. In the last chapter, I developed a computational method called InGeAr to infer the mutational target size and explore the role of natural selection on affecting the variant's effect on the trait. I found that the mutational target size differs from trait to trait and can be large, up to tens of megabases. In addition, purifying selection is coupled with the variant's effect on the trait. I discussed how these results support the omnigenic model of complex traits. In summary, in this dissertation, I utilized different types of large genomic dataset, from genome-wide divergence data to whole genome sequence data to GWAS data to develop models and statistical methods to study how different evolutionary processes have shaped patterns of genetic variation across the genome.
Author: Jud G. Isebrands
Publisher: CABI
ISBN: 1780641087
Category : Technology & Engineering
Languages : en
Pages : 700
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Book Description
Poplars and willows form an important component of forestry and agricultural systems, providing a wide range of wood and non-wood products. This book synthesizes research on poplars and willows, providing a practical worldwide overview and guide to their basic characteristics, cultivation and use, issues, problems and trends. Prominence is given to environmental benefits and the importance of poplar and willow cultivation in meeting the needs of people and communities, sustainable livelihoods, land use and development.
Author: Om P. Rajora
Publisher: Springer
ISBN: 3030045897
Category : Science
Languages : en
Pages : 824
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Book Description
Population genomics has revolutionized various disciplines of biology including population, evolutionary, ecological and conservation genetics, plant and animal breeding, human health, medicine and pharmacology by allowing to address novel and long-standing questions with unprecedented power and accuracy. It employs large-scale or genome-wide genetic information and bioinformatics to address various fundamental and applied aspects in biology and related disciplines, and provides a comprehensive genome-wide perspective and new insights that were not possible before. These advances have become possible due to the development of new and low-cost sequencing and genotyping technologies and novel statistical approaches and software, bioinformatics tools, and models. Population genomics is tremendously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome and populations; improving the assessment of population genetic parameters or processes such as adaptive evolution, effective population size, gene flow, admixture, inbreeding and outbreeding depression, demography, and biogeography; resolving evolutionary histories and phylogenetic relationships of extant, ancient and extinct species; understanding the genomic basis of fitness, adaptation, speciation, complex ecological and economically important traits, and disease and insect resistance; facilitating forensics, genetic medicine and pharmacology; delineating conservation genetic units; and understanding the genetic effects of resource management practices, and assisting conservation and sustainable management of genetic resources. This Population Genomics book discusses the concepts, approaches, applications and promises of population genomics in addressing most of the above fundamental and applied crucial aspects in a variety of organisms from microorganisms to humans. The book provides insights into a range of emerging population genomics topics including population epigenomics, landscape genomics, seascape genomics, paleogenomics, ecological and evolutionary genomics, biogeography, demography, speciation, admixture, colonization and invasion, genomic selection, and plant and animal domestication. This book fills a vacuum in the field and is expected to become a primary reference in Population Genomics world-wide.
Author: Paul Schmid-Hempel
Publisher: Princeton University Press
ISBN: 9780691059242
Category : Science
Languages : en
Pages : 436
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Book Description
In addition, the author develops new insights, especially in his examination of the intricate relationships between parasites and their social hosts through the rigorous use of evolutionary and ecological concepts.".
Author: Hugo de Vries
Publisher: Good Press
ISBN:
Category : Science
Languages : en
Pages : 502
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Book Description
In 'Species and Varieties, Their Origin by Mutation,' Hugo de Vries offers a groundbreaking exploration of the concept of mutation and its role in the development of new species. Written in a clear and concise style, De Vries delves into the mechanisms of genetic variation and how it contributes to the diversity of life forms. Drawing on his extensive research and experiments with plant breeding, the author presents a comprehensive analysis of evolution through mutation in both plants and animals, challenging established theories of natural selection. This influential work is a key text in the study of genetics and evolutionary biology, providing valuable insights into the mechanisms of biological diversity. Hugo de Vries' meticulous approach and innovative ideas have left a lasting impact on the field of biology, shaping our understanding of the origins of species and the process of adaptation. His work continues to inspire further research and exploration into the mechanisms of genetic variation and evolutionary change. 'Species and Varieties, Their Origin by Mutation' is a must-read for anyone interested in the fascinating world of evolutionary biology and the complex processes that drive the diversity of life on Earth.
Author: Anne Charmantier
Publisher: OUP Oxford
ISBN: 0191655953
Category : Science
Languages : en
Pages : 293
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Book Description
Although the field of quantitative genetics - the study of the genetic basis of variation in quantitative characteristics such as body size, or reproductive success - is almost 100 years old, its application to the study of evolutionary processes in wild populations has expanded greatly over the last few decades. During this time, the use of 'wild quantitative genetics' has provided insights into a range of important questions in evolutionary ecology, ranging from studies conducting research in well-established fields such as life-history theory, behavioural ecology and sexual selection, to others addressing relatively new issues such as populations' responses to climate change or the process of senescence in natural environments. Across these fields, there is increasing appreciation of the need to quantify the genetic - rather than just the phenotypic - basis and diversity of key traits, the genetic basis of the associations between traits, and the interaction between these genetic effects and the environment. This research activity has been fuelled by methodological advances in both molecular genetics and statistics, as well as by exciting results emerging from laboratory studies of evolutionary quantitative genetics, and the increasing availability of suitable long-term datasets collected in natural populations, especially in animals. Quantitative Genetics in the Wild is the first book to synthesize the current level of knowledge in this exciting and rapidly-expanding area. This comprehensive volume also offers exciting perspectives for future studies in emerging areas, including the application of quantitative genetics to plants or arthropods, unraveling the molecular basis of variation in quantitative traits, or estimating non-additive genetic variance. Since this book deals with many fundamental questions in evolutionary ecology, it should be of interest to graduate, post-graduate students, and academics from a wide array of fields such as animal behaviour, ecology, evolution, and genetics.
Author: Ilga M. Porth
Publisher: Springer
ISBN: 9783030210038
Category : Science
Languages : en
Pages : 218
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Book Description
This book offers comprehensive information on the genomics of spruces (Picea spp.), naturally abundant conifer tree species that are widely distributed in the Northern Hemisphere. Due to their tremendous ecological and economic importance, the management of forest genetic resources has chiefly focused on conservation and tree improvement. A draft genome sequence of the 20-gigabase Norway spruce genome was published in the journal Nature in 2013. Continuous efforts to improve the spruce genome assembly are underway, but are hindered by the inherent characteristics of conifer genomes: high amounts of repetitive sequences (introns and transposable elements) in the genome and large gene family expansions with regards to abiotic stress, secondary metabolism and spruces' defense responses to pathogens and herbivory. This book presents the latest information on the status of genome assemblies, provides detailed insights into transposable elements and methylation patterns, and highlights the extensive genomic resources available for inferring population genomics and climate adaptation, as well as emerging genomics tools for tree improvement programs. In addition, this volume features whole-genome comparisons among conifer species, and demonstrates how functional genomics can be used to improve gene function annotations. The book closes with an outlook on emerging fields of research in spruce genomics.
Author: National Research Council
Publisher: National Academies Press
ISBN: 0309184746
Category : Science
Languages : en
Pages : 101
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Book Description
This book assesses the scientific value and merit of research on human genetic differencesâ€"including a collection of DNA samples that represents the whole of human genetic diversityâ€"and the ethical, organizational, and policy issues surrounding such research. Evaluating Human Genetic Diversity discusses the potential uses of such collection, such as providing insight into human evolution and origins and serving as a springboard for important medical research. It also addresses issues of confidentiality and individual privacy for participants in genetic diversity research studies.
Author: Rajeev K. Varshney
Publisher: Springer
ISBN: 3319661175
Category : Science
Languages : en
Pages : 152
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Book Description
This book sheds new light on the chickpea genome sequencing and resequencing of chickpea germplasm lines and provides insights into classical genetics, cytogenetics, and trait mapping. It also offers an overview of the latest advances in genome sequencing and analysis. The growing human population, rapid climate changes and limited amounts of arable land are creating substantial challenges in connection with the availability and affordability of nutritious food for smallholder farmers in developing countries. In this context, climate smart crops are essential to alleviating the hunger of the millions of poor and undernourished people living in developing countries. In addition to cereals, grain legumes are an integral part of the human diet and provide sustainable income for smallholder farmers in the arid and semi-arid regions of the world. Among grain legumes, the chickpea (Cicer arietinum) is the second most important in terms of production and productivity. Besides being a rich source of proteins, it can fix atmospheric nitrogen through symbiosis with rhizobia and increase the input of combined nitrogen. Several abiotic stresses like drought, heat, salinity, together with biotic stresses like Fusarium wilt, Ascochyta blight, and Botrytis grey mould have led to production losses, as the chickpeas is typically grown in the harsh climates of our planet’s semi-arid regions.
