Gregory P. Cheplick and Stanley H. Faeth
- Published in print:
- 2009
- Published Online:
- January 2009
- ISBN:
- 9780195308082
- eISBN:
- 9780199867462
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195308082.003.0004
- Subject:
- Biology, Ecology
For ongoing coevolution of the grass-endophyte symbiosis through the agents of natural selection, there must be genetic variation within populations for both host and endophyte. The breeding systems ...
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For ongoing coevolution of the grass-endophyte symbiosis through the agents of natural selection, there must be genetic variation within populations for both host and endophyte. The breeding systems of both symbiotic partners influence the distribution and level of genetic variation within populations. Traditional reaction norms and symbiotic interaction norms can be useful in depicting host genotype interactions with environment and infection. Examples are provided for both agronomic and native grass-endophyte symbioses. Endophytes can also modulate phenotypic plasticity of their grass hosts in relation to environmental variation. There is evidence that endophyte genotypes (haplotypes) can differ significantly in their impact on host growth and physiology. Genetic diversity of endophyte isolates has been quantified using isozymes and DNA markers. Host-endophyte compatibility can vary among endophytes and their host grasses as revealed by reciprocal inoculation experiments using fungal isolates from different host populations or species. Multistrain infections of single grass hosts and fungal hybridization within individual hosts have been determined for some symbioses. Genetic variation in both host and endophyte will expedite the continued coevolution of the symbiosis.Less
For ongoing coevolution of the grass-endophyte symbiosis through the agents of natural selection, there must be genetic variation within populations for both host and endophyte. The breeding systems of both symbiotic partners influence the distribution and level of genetic variation within populations. Traditional reaction norms and symbiotic interaction norms can be useful in depicting host genotype interactions with environment and infection. Examples are provided for both agronomic and native grass-endophyte symbioses. Endophytes can also modulate phenotypic plasticity of their grass hosts in relation to environmental variation. There is evidence that endophyte genotypes (haplotypes) can differ significantly in their impact on host growth and physiology. Genetic diversity of endophyte isolates has been quantified using isozymes and DNA markers. Host-endophyte compatibility can vary among endophytes and their host grasses as revealed by reciprocal inoculation experiments using fungal isolates from different host populations or species. Multistrain infections of single grass hosts and fungal hybridization within individual hosts have been determined for some symbioses. Genetic variation in both host and endophyte will expedite the continued coevolution of the symbiosis.
Graham Bell
- Published in print:
- 2007
- Published Online:
- May 2008
- ISBN:
- 9780198569725
- eISBN:
- 9780191717741
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198569725.003.0008
- Subject:
- Biology, Evolutionary Biology / Genetics
Selection in complex and structured environments is likely to cause the divergence of differently adapted lines. This will lead to a diverse array of specialized types, or to one or a few broad ...
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Selection in complex and structured environments is likely to cause the divergence of differently adapted lines. This will lead to a diverse array of specialized types, or to one or a few broad generalists, or to some intermediate situation. The first section in this chapter is called GxE and details the ecogenetic landscape; the magnitude of GxE; inconsistency and responsiveness; the genetic correlation in relation to environmental variance; the outcome of selection in different environments; stability and responsiveness; and the evolution of stability and responsiveness. The second section is about specialization and generalization, and details niche separation; the cost of adaptation; divergent specialization; sources of antagonism: functional interference; sources of antagonism: mutational degradation; and the consequences of interference and degradation. It also gives an experimental adaptive radiation regarding pseudomonas and an historical adaptive radiation concerning anolis. The third section called Opportunities in space, obligations in time, explains simple environments; complex environments; the cost of adaptation in complex environments; structured environments; the outcome of selection in structured environments; fluctuating fitness; and the outcome of selection in variable environments. The final section is called Local adaptation and details the precision of local adaptation and gives reciprocal transplant experiments.Less
Selection in complex and structured environments is likely to cause the divergence of differently adapted lines. This will lead to a diverse array of specialized types, or to one or a few broad generalists, or to some intermediate situation. The first section in this chapter is called GxE and details the ecogenetic landscape; the magnitude of GxE; inconsistency and responsiveness; the genetic correlation in relation to environmental variance; the outcome of selection in different environments; stability and responsiveness; and the evolution of stability and responsiveness. The second section is about specialization and generalization, and details niche separation; the cost of adaptation; divergent specialization; sources of antagonism: functional interference; sources of antagonism: mutational degradation; and the consequences of interference and degradation. It also gives an experimental adaptive radiation regarding pseudomonas and an historical adaptive radiation concerning anolis. The third section called Opportunities in space, obligations in time, explains simple environments; complex environments; the cost of adaptation in complex environments; structured environments; the outcome of selection in structured environments; fluctuating fitness; and the outcome of selection in variable environments. The final section is called Local adaptation and details the precision of local adaptation and gives reciprocal transplant experiments.
Gregory P. Cheplick and Stanley H. Faeth
- Published in print:
- 2009
- Published Online:
- January 2009
- ISBN:
- 9780195308082
- eISBN:
- 9780199867462
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195308082.003.0007
- Subject:
- Biology, Ecology
Systemic endophytes of grasses provide ideal systems for testing ecological and evolutionary theory, as well as providing an important research platform for developing and improving pasture and turf ...
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Systemic endophytes of grasses provide ideal systems for testing ecological and evolutionary theory, as well as providing an important research platform for developing and improving pasture and turf grasses. Presently, most basic and applied research has been directed towards Neotyphodium-infected agronomic grasses. There is an urgent need to expand basic ecological and, especially, evolutionary studies to native grass systems and other systemic endophytes and the more ubiquitous, non-systemic endophytes. Little is understood about the effects of endophytes on host biology and reproduction, and even less about the complex effects of endophytes that change with host and endophyte genotype, host ontogeny, environment, and the presence of other interacting species. Long-term cost-benefit analyses across an array of varying biotic and abiotic factors seems like a prudent path of investigation. Studies of the coevolutionary dynamics of endophyte-host interactions are still in their infancy, yet endophyte-host interactions are ideal systems in which to test contemporary theories. There is still a lack of detailed knowledge of how the genetics of endophytes and their hosts alter interaction outcomes, especially in complex natural communities. Grass-endophyte symbioses offer tractable systems for addressing societal problems such as global environmental change, invasive species and emerging infectious diseases, restoration of degraded ecosystems, and food, fuel, and forage shortages.Less
Systemic endophytes of grasses provide ideal systems for testing ecological and evolutionary theory, as well as providing an important research platform for developing and improving pasture and turf grasses. Presently, most basic and applied research has been directed towards Neotyphodium-infected agronomic grasses. There is an urgent need to expand basic ecological and, especially, evolutionary studies to native grass systems and other systemic endophytes and the more ubiquitous, non-systemic endophytes. Little is understood about the effects of endophytes on host biology and reproduction, and even less about the complex effects of endophytes that change with host and endophyte genotype, host ontogeny, environment, and the presence of other interacting species. Long-term cost-benefit analyses across an array of varying biotic and abiotic factors seems like a prudent path of investigation. Studies of the coevolutionary dynamics of endophyte-host interactions are still in their infancy, yet endophyte-host interactions are ideal systems in which to test contemporary theories. There is still a lack of detailed knowledge of how the genetics of endophytes and their hosts alter interaction outcomes, especially in complex natural communities. Grass-endophyte symbioses offer tractable systems for addressing societal problems such as global environmental change, invasive species and emerging infectious diseases, restoration of degraded ecosystems, and food, fuel, and forage shortages.
Roger Cousens, Calvin Dytham, and Richard Law
- Published in print:
- 2008
- Published Online:
- May 2008
- ISBN:
- 9780199299126
- eISBN:
- 9780191715006
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299126.003.0006
- Subject:
- Biology, Ecology, Plant Sciences and Forestry
This chapter explores the spatial dynamics of invading species, paying particular attention to the patterns formed as they spread, i.e., the rate of increase of the area invaded and the rate at which ...
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This chapter explores the spatial dynamics of invading species, paying particular attention to the patterns formed as they spread, i.e., the rate of increase of the area invaded and the rate at which their boundaries move. The development of models for population expansion — comprising a range of structures and assumptions both simple and complex — is reviewed. Rare long distance dispersal events are shown to dictate the rate of spread, the pattern in population margins, and the distribution of genotypes. Movement through heterogeneous landscapes is shown to be further affected by the connectivity and distribution of suitable patches.Less
This chapter explores the spatial dynamics of invading species, paying particular attention to the patterns formed as they spread, i.e., the rate of increase of the area invaded and the rate at which their boundaries move. The development of models for population expansion — comprising a range of structures and assumptions both simple and complex — is reviewed. Rare long distance dispersal events are shown to dictate the rate of spread, the pattern in population margins, and the distribution of genotypes. Movement through heterogeneous landscapes is shown to be further affected by the connectivity and distribution of suitable patches.
Kim Cornish and John Wilding
- Published in print:
- 2010
- Published Online:
- September 2010
- ISBN:
- 9780195179941
- eISBN:
- 9780199864652
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195179941.001.0001
- Subject:
- Neuroscience, Behavioral Neuroscience, Development
What is attention? How does it go wrong? Do attention deficits arise from genes or from the environment? Can we cure it with drugs or training? Are there disorders of attention other than deficit ...
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What is attention? How does it go wrong? Do attention deficits arise from genes or from the environment? Can we cure it with drugs or training? Are there disorders of attention other than deficit disorders? The past decade has seen a burgeoning of research on the subject of attention. This research has been facilitated by advances on several fronts: New methods are now available for viewing brain activity in real time, there is expanding information on the complexities of the biochemistry of neural activity, individual genes can be isolated and their functions identified, analysis of the component processes included under the broad umbrella of “attention” has become increasingly sophisticated, and ingenious methods have been devised for measuring typical and atypical development of these processes, from infancy into childhood, and then into adulthood. This book is concerned with attention and its development, both typical and atypical, particularly in disorders with a known genetic etiology or assumed genetic linkage. Tremendous advances across seemingly diverse disciplines — molecular genetics, pediatric neurology, child psychiatry, developmental cognitive neuroscience, and education s— have culminated in a wealth of new methods for elucidating disorders at multiple levels, possibly paving the way for new treatment options. The book uses three specific-yet-interlinking levels of analysis: genetic blueprint (genotype), the developing brain, and the behavioral-cognitive outcomes (phenotype), as the basis for charting the attention profiles of six well-documented neurodevelopmental disorders: ADHD, autism, fragile X syndrome, Down syndrome, Williams syndrome, and 22q11 deletion syndrome.Less
What is attention? How does it go wrong? Do attention deficits arise from genes or from the environment? Can we cure it with drugs or training? Are there disorders of attention other than deficit disorders? The past decade has seen a burgeoning of research on the subject of attention. This research has been facilitated by advances on several fronts: New methods are now available for viewing brain activity in real time, there is expanding information on the complexities of the biochemistry of neural activity, individual genes can be isolated and their functions identified, analysis of the component processes included under the broad umbrella of “attention” has become increasingly sophisticated, and ingenious methods have been devised for measuring typical and atypical development of these processes, from infancy into childhood, and then into adulthood. This book is concerned with attention and its development, both typical and atypical, particularly in disorders with a known genetic etiology or assumed genetic linkage. Tremendous advances across seemingly diverse disciplines — molecular genetics, pediatric neurology, child psychiatry, developmental cognitive neuroscience, and education s— have culminated in a wealth of new methods for elucidating disorders at multiple levels, possibly paving the way for new treatment options. The book uses three specific-yet-interlinking levels of analysis: genetic blueprint (genotype), the developing brain, and the behavioral-cognitive outcomes (phenotype), as the basis for charting the attention profiles of six well-documented neurodevelopmental disorders: ADHD, autism, fragile X syndrome, Down syndrome, Williams syndrome, and 22q11 deletion syndrome.
F. Nicholas Braun
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.003.0007
- Subject:
- Biology, Evolutionary Biology / Genetics
The extant phylogenetic variability of a given protein contains information about its underlying sequence-fitness landscape, potentially of value to ancestral reconstruction. In extracting such ...
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The extant phylogenetic variability of a given protein contains information about its underlying sequence-fitness landscape, potentially of value to ancestral reconstruction. In extracting such information, it is pertinent to focus on coarse-grained traits of sequence with strong physicochemical bearing on the protein's phenotype. This chapter uses phylogenetic data to stake out roughly the landscape for a protein component of spider silk.Less
The extant phylogenetic variability of a given protein contains information about its underlying sequence-fitness landscape, potentially of value to ancestral reconstruction. In extracting such information, it is pertinent to focus on coarse-grained traits of sequence with strong physicochemical bearing on the protein's phenotype. This chapter uses phylogenetic data to stake out roughly the landscape for a protein component of spider silk.
Jesus Gonzalez-Bosquet and Stephen J. Chanock
- Published in print:
- 2009
- Published Online:
- May 2010
- ISBN:
- 9780195398441
- eISBN:
- 9780199776023
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195398441.003.0002
- Subject:
- Public Health and Epidemiology, Public Health, Epidemiology
This chapter presents an overview of the development and progress in applications of genomic technologies, with a focus on genomic sequence variation. Topics discussed include genetic variation, ...
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This chapter presents an overview of the development and progress in applications of genomic technologies, with a focus on genomic sequence variation. Topics discussed include genetic variation, genotype analysis, genome-wide association studies, genotyping issues, quality control in the laboratory, and bioinformatics.Less
This chapter presents an overview of the development and progress in applications of genomic technologies, with a focus on genomic sequence variation. Topics discussed include genetic variation, genotype analysis, genome-wide association studies, genotyping issues, quality control in the laboratory, and bioinformatics.
D. Dudley Williams
- Published in print:
- 2005
- Published Online:
- September 2007
- ISBN:
- 9780198528128
- eISBN:
- 9780191713538
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198528128.003.0010
- Subject:
- Biology, Aquatic Biology
This chapter underlines the importance of temporary water habitats as repositories for rare species and genotypes, at a time when such wetland habitats are being destroyed or altered at a rapid rate. ...
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This chapter underlines the importance of temporary water habitats as repositories for rare species and genotypes, at a time when such wetland habitats are being destroyed or altered at a rapid rate. The problems encountered in trying to protect these habitats and their biodiversity are examined, particularly those associated with protective legislation. Existing management practices are evaluated.Less
This chapter underlines the importance of temporary water habitats as repositories for rare species and genotypes, at a time when such wetland habitats are being destroyed or altered at a rapid rate. The problems encountered in trying to protect these habitats and their biodiversity are examined, particularly those associated with protective legislation. Existing management practices are evaluated.
D. Dudley Williams
- Published in print:
- 2005
- Published Online:
- September 2007
- ISBN:
- 9780198528128
- eISBN:
- 9780191713538
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198528128.003.0005
- Subject:
- Biology, Aquatic Biology
This chapter highlights the seasonality of temporary waters and how this relates to variability in the life cycles of their inhabitants, leading to discussion of phenotypic and genotypic solutions. ...
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This chapter highlights the seasonality of temporary waters and how this relates to variability in the life cycles of their inhabitants, leading to discussion of phenotypic and genotypic solutions. The physiology of desiccation a major stressor in these habitats is reviewed, as are other adaptations of the biota such as cyclical dispersal and colonization. The differences between active and passive strategies of the latter are emphasized.Less
This chapter highlights the seasonality of temporary waters and how this relates to variability in the life cycles of their inhabitants, leading to discussion of phenotypic and genotypic solutions. The physiology of desiccation a major stressor in these habitats is reviewed, as are other adaptations of the biota such as cyclical dispersal and colonization. The differences between active and passive strategies of the latter are emphasized.
Carsten Wiuf, Philippe Lamy, and Claus L. Andersen
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199532872
- eISBN:
- 9780191714467
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199532872.003.0003
- Subject:
- Mathematics, Probability / Statistics, Biostatistics
This chapter discusses statistical methods to derive loss-of-heterozygosity (LOH) and allele specific copy numbers in cancer cells. SNP arrays enable simultaneous information about thousands of DNA ...
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This chapter discusses statistical methods to derive loss-of-heterozygosity (LOH) and allele specific copy numbers in cancer cells. SNP arrays enable simultaneous information about thousands of DNA markers and their allele specific copy numbers, but to extract the information advanced statistical tools are required. The chapter shows how Hidden Markov Models (HMM) can be applied to infer LOH from genotype data and how the allele intensities are informative about allelic copy number. The methods are illustrated by examples.Less
This chapter discusses statistical methods to derive loss-of-heterozygosity (LOH) and allele specific copy numbers in cancer cells. SNP arrays enable simultaneous information about thousands of DNA markers and their allele specific copy numbers, but to extract the information advanced statistical tools are required. The chapter shows how Hidden Markov Models (HMM) can be applied to infer LOH from genotype data and how the allele intensities are informative about allelic copy number. The methods are illustrated by examples.
Dale Walters
- Published in print:
- 2021
- Published Online:
- September 2021
- ISBN:
- 9781683401674
- eISBN:
- 9781683402343
- Item type:
- chapter
- Publisher:
- University Press of Florida
- DOI:
- 10.5744/florida/9781683401674.003.0014
- Subject:
- Environmental Science, Environmental Studies
Earth’s climate is changing, with consequences for all life on the planet. The changing climate is already affecting some of the world’s cacao-growing regions and projections suggest that cultivating ...
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Earth’s climate is changing, with consequences for all life on the planet. The changing climate is already affecting some of the world’s cacao-growing regions and projections suggest that cultivating cacao in some parts of West Africa, for example, might become impossible. This chapter examines the causes of climate change, how we know the Earth’s climate is changing, and what can be done to mitigate its effects, including adopting policies to protect against deforestation. The implications for cacao growers are discussed, along with the approaches they might adopt to mitigate the effects of climate change. These approaches include developing new cacao genotypes better adapted to deal with the heat and drought stress associated with a warming climate.Less
Earth’s climate is changing, with consequences for all life on the planet. The changing climate is already affecting some of the world’s cacao-growing regions and projections suggest that cultivating cacao in some parts of West Africa, for example, might become impossible. This chapter examines the causes of climate change, how we know the Earth’s climate is changing, and what can be done to mitigate its effects, including adopting policies to protect against deforestation. The implications for cacao growers are discussed, along with the approaches they might adopt to mitigate the effects of climate change. These approaches include developing new cacao genotypes better adapted to deal with the heat and drought stress associated with a warming climate.
William Bernet and Anas Alkhatib
- Published in print:
- 2009
- Published Online:
- May 2009
- ISBN:
- 9780195340525
- eISBN:
- 9780199867219
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195340525.003.0009
- Subject:
- Law, Criminal Law and Criminology
This chapter describes how testimony regarding behavioral genomics is currently used in legal settings and how it may be used in the future. It focuses on three ways in which a specific individual's ...
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This chapter describes how testimony regarding behavioral genomics is currently used in legal settings and how it may be used in the future. It focuses on three ways in which a specific individual's genetic makeup may be relevant to his or her behavior. First, the person's genotype may exactly designate a psychiatric or medical diagnosis that clearly explains the person's abnormal behavior. Second, the person's genotype may support a psychiatric diagnosis that has been made on clinical grounds. Third, the person's genotype may help to explain his or her violent or criminal behavior.Less
This chapter describes how testimony regarding behavioral genomics is currently used in legal settings and how it may be used in the future. It focuses on three ways in which a specific individual's genetic makeup may be relevant to his or her behavior. First, the person's genotype may exactly designate a psychiatric or medical diagnosis that clearly explains the person's abnormal behavior. Second, the person's genotype may support a psychiatric diagnosis that has been made on clinical grounds. Third, the person's genotype may help to explain his or her violent or criminal behavior.
Diana Kuh and Yoav Ben-Shlomo
- Published in print:
- 2004
- Published Online:
- September 2009
- ISBN:
- 9780198578154
- eISBN:
- 9780191724039
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198578154.003.0015
- Subject:
- Public Health and Epidemiology, Public Health, Epidemiology
This chapter examines the sources of variation in fetal growth, in particular nutrition in the context of the fetal nutritional programming hypothesis. The influence of fetal and maternal genotype on ...
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This chapter examines the sources of variation in fetal growth, in particular nutrition in the context of the fetal nutritional programming hypothesis. The influence of fetal and maternal genotype on fetal growth is considered and set in the context of non-genetic intergenerational influences on birthweight, such as the mother's height and her own birthweight. The concept of programming is considered both with reference to nutritional programming and the wider view of programming, with particular reference to the hormonal, metabolic, and circulatory milieu to which the fetus is exposed.Less
This chapter examines the sources of variation in fetal growth, in particular nutrition in the context of the fetal nutritional programming hypothesis. The influence of fetal and maternal genotype on fetal growth is considered and set in the context of non-genetic intergenerational influences on birthweight, such as the mother's height and her own birthweight. The concept of programming is considered both with reference to nutritional programming and the wider view of programming, with particular reference to the hormonal, metabolic, and circulatory milieu to which the fetus is exposed.
Michael L. Arnold
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780199229031
- eISBN:
- 9780191728266
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199229031.003.0005
- Subject:
- Biology, Evolutionary Biology / Genetics
This chapter illustrates the fact that hybrid genotypes, like any other set of genotypes, demonstrate a range of fitness estimates. It demonstrates this point with examples involving natural ...
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This chapter illustrates the fact that hybrid genotypes, like any other set of genotypes, demonstrate a range of fitness estimates. It demonstrates this point with examples involving natural hybridization, viral recombination, and lateral gene transfer. For all classes the conclusion is the same, some hybrid/recombinant genotypes have lower, some the same, and others higher fitness estimates relative to their progenitors.Less
This chapter illustrates the fact that hybrid genotypes, like any other set of genotypes, demonstrate a range of fitness estimates. It demonstrates this point with examples involving natural hybridization, viral recombination, and lateral gene transfer. For all classes the conclusion is the same, some hybrid/recombinant genotypes have lower, some the same, and others higher fitness estimates relative to their progenitors.
Thomas A. Louis, Benilton S. Carvalho, M. Daniele Fallin, Rafael A. Irizarryi, Qing Li, and Ingo Ruczinski
- Published in print:
- 2011
- Published Online:
- January 2012
- ISBN:
- 9780199694587
- eISBN:
- 9780191731921
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199694587.003.0013
- Subject:
- Mathematics, Probability / Statistics
High‐throughput single nucleotide polymorphism (SNP) arrays, typically used in genome‐wide association studies with a trait of interest, provide estimates of genotypes for up to several million loci. ...
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High‐throughput single nucleotide polymorphism (SNP) arrays, typically used in genome‐wide association studies with a trait of interest, provide estimates of genotypes for up to several million loci. Most genotype estimates are very accurate, but genotyping errors do occur and can influence test statistics, p‐values and ranks. Some SNPs are harder to call than others due to probe properties and other technical/biological factors; uncertainties can be associated with features of interest. SNP‐ and case‐specific genotype posterior probabilities are available, but they are typically not used or used only informally, for example by setting aside the most uncertain calls. To improve on these approaches we take full advantage of Bayesian structuring and develop an analytic framework that accommodates genotype uncertainties. We show that the power of a score test (and statistical information more generally) is directly a function of the correlation of the genotype probabilities with the true genotypes. We demonstrate that compared to picking a single AA, AB or BB genotype or to setting aside difficult calls, Bayesian structuring can substantially increase statistical information for detecting a true association and for ranking SNPs, whether the ranking be frequentist or optimal Bayes. This improvement is primarily associated with genotypes that are difficult to call.Less
High‐throughput single nucleotide polymorphism (SNP) arrays, typically used in genome‐wide association studies with a trait of interest, provide estimates of genotypes for up to several million loci. Most genotype estimates are very accurate, but genotyping errors do occur and can influence test statistics, p‐values and ranks. Some SNPs are harder to call than others due to probe properties and other technical/biological factors; uncertainties can be associated with features of interest. SNP‐ and case‐specific genotype posterior probabilities are available, but they are typically not used or used only informally, for example by setting aside the most uncertain calls. To improve on these approaches we take full advantage of Bayesian structuring and develop an analytic framework that accommodates genotype uncertainties. We show that the power of a score test (and statistical information more generally) is directly a function of the correlation of the genotype probabilities with the true genotypes. We demonstrate that compared to picking a single AA, AB or BB genotype or to setting aside difficult calls, Bayesian structuring can substantially increase statistical information for detecting a true association and for ranking SNPs, whether the ranking be frequentist or optimal Bayes. This improvement is primarily associated with genotypes that are difficult to call.
Wolfgang Jagla, Tanja Breitsprecher, Itala Kucsera, Gyula Kovacs, Bernd Wissinger, Samir S. Deeb, and Lindsay T. Sharpe
- Published in print:
- 2003
- Published Online:
- April 2010
- ISBN:
- 9780198525301
- eISBN:
- 9780191584947
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198525301.003.0032
- Subject:
- Psychology, Cognitive Neuroscience
This chapter determines the variability in genotype among anomalous trichromats and dichromats, and correlates this to their colour vision phenotype. It shows that the severity of anomalous ...
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This chapter determines the variability in genotype among anomalous trichromats and dichromats, and correlates this to their colour vision phenotype. It shows that the severity of anomalous trichromacy roughly correlates with the estimated spectral separation between the normal and the hybrid pigment. However, considerable phenotypic variability is associated with any given phenotype. The variation found with L2M3 or M3L4-hybrid genes is greater than that found with other hybrids, and cannot merely be associated with coding sequence differences in exon 2. These findings underscore an important issue in colour vision: how spectral differences between two photopigments actually translate to colour discrimination performance, and about how other retinal and cortical factors act upon photopigment differences and influence discrimination.Less
This chapter determines the variability in genotype among anomalous trichromats and dichromats, and correlates this to their colour vision phenotype. It shows that the severity of anomalous trichromacy roughly correlates with the estimated spectral separation between the normal and the hybrid pigment. However, considerable phenotypic variability is associated with any given phenotype. The variation found with L2M3 or M3L4-hybrid genes is greater than that found with other hybrids, and cannot merely be associated with coding sequence differences in exon 2. These findings underscore an important issue in colour vision: how spectral differences between two photopigments actually translate to colour discrimination performance, and about how other retinal and cortical factors act upon photopigment differences and influence discrimination.
M. Daniele Fallin and W.H. Linda Kao
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780195187113
- eISBN:
- 9780199864898
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195187113.003.0008
- Subject:
- Public Health and Epidemiology, Public Health, Epidemiology
Genetic epidemiology is one of the most rapidly growing fields of epidemiologic research. Almost every human disease has some genetic component. The main purpose of genetic epidemiology is to ...
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Genetic epidemiology is one of the most rapidly growing fields of epidemiologic research. Almost every human disease has some genetic component. The main purpose of genetic epidemiology is to identify genes that cause, or contribute to risk for human disease. The central paradigm for the identification of genes that contribute to disease risk involves a set of questions and design/analytic strategies to answer those questions. This chapter presents different types of measuring genetic variables. The use of the case-control design in genetic epidemiology is presented through various methods of analysis such as regression models and genetic models. The chapter also describes the various components of the case-parent trio design as well as the case only design, including various approaches of analysis.Less
Genetic epidemiology is one of the most rapidly growing fields of epidemiologic research. Almost every human disease has some genetic component. The main purpose of genetic epidemiology is to identify genes that cause, or contribute to risk for human disease. The central paradigm for the identification of genes that contribute to disease risk involves a set of questions and design/analytic strategies to answer those questions. This chapter presents different types of measuring genetic variables. The use of the case-control design in genetic epidemiology is presented through various methods of analysis such as regression models and genetic models. The chapter also describes the various components of the case-parent trio design as well as the case only design, including various approaches of analysis.
Christian Braendle, Andreas Heyland, and Thomas Flatt
- Published in print:
- 2011
- Published Online:
- December 2013
- ISBN:
- 9780199568765
- eISBN:
- 9780191774591
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199568765.003.0001
- Subject:
- Biology, Evolutionary Biology / Genetics
This introductory chapter provides a brief overview of life history theory and outlines empirical approaches towards understanding the evolution of life histories. It argues that in order to arrive ...
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This introductory chapter provides a brief overview of life history theory and outlines empirical approaches towards understanding the evolution of life histories. It argues that in order to arrive at a complete understanding of how life history traits are expressed and how they evolve, information on genetic, developmental, and physiological mechanisms needs to be incorporated into the life history framework.Less
This introductory chapter provides a brief overview of life history theory and outlines empirical approaches towards understanding the evolution of life histories. It argues that in order to arrive at a complete understanding of how life history traits are expressed and how they evolve, information on genetic, developmental, and physiological mechanisms needs to be incorporated into the life history framework.
Andreas Wagner
- Published in print:
- 2013
- Published Online:
- December 2013
- ISBN:
- 9780199595372
- eISBN:
- 9780191774799
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199595372.003.0017
- Subject:
- Biology, Evolutionary Biology / Genetics
High-dimensional adaptive landscapes facilitate the origin of evolutionary adaptations and innovations, qualitatively new and beneficial phenotypes. This chapter discusses evidence for this assertion ...
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High-dimensional adaptive landscapes facilitate the origin of evolutionary adaptations and innovations, qualitatively new and beneficial phenotypes. This chapter discusses evidence for this assertion from three classes of systems important for evolutionary innovation, metabolic networks, gene regulation circuits, as well as protein and RNA macromolecules. In all three classes of systems, vast genotype networks — connected sets of genotypes with the same phenotype — exist and extend far through genotype space. These networks are essential for the ability of biological systems to explore many novel phenotypes, and they are a consequence of the high dimensionality of genotype spaces.Less
High-dimensional adaptive landscapes facilitate the origin of evolutionary adaptations and innovations, qualitatively new and beneficial phenotypes. This chapter discusses evidence for this assertion from three classes of systems important for evolutionary innovation, metabolic networks, gene regulation circuits, as well as protein and RNA macromolecules. In all three classes of systems, vast genotype networks — connected sets of genotypes with the same phenotype — exist and extend far through genotype space. These networks are essential for the ability of biological systems to explore many novel phenotypes, and they are a consequence of the high dimensionality of genotype spaces.
David A. Cleveland
- Published in print:
- 2013
- Published Online:
- September 2016
- ISBN:
- 9780520277410
- eISBN:
- 9780520957084
- Item type:
- chapter
- Publisher:
- University of California Press
- DOI:
- 10.1525/california/9780520277410.003.0006
- Subject:
- Society and Culture, Technology and Society
Farmers (beginning in the Neolithic), amateur and professional plant breeders in the last several centuries, and now molecular biologists have greatly increased our ability to genetically manipulate ...
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Farmers (beginning in the Neolithic), amateur and professional plant breeders in the last several centuries, and now molecular biologists have greatly increased our ability to genetically manipulate crop plants to increase desired outputs. The two key steps in plant breeding are the creation of diversity followed by selection of resulting plants with the desired characteristics. Two important relationships determining the outcome of selection are those between plant phenotype and genotype and between heritability of a trait and the selection pressure. Similarities and differences between breeding by farmers and scientists are illustrated by the contrast between yield and yield stability; understanding of basic biological principles, their application and effects; and transgenic varieties. Participatory plant breeding is attempting to reunite farmers and scientists.Less
Farmers (beginning in the Neolithic), amateur and professional plant breeders in the last several centuries, and now molecular biologists have greatly increased our ability to genetically manipulate crop plants to increase desired outputs. The two key steps in plant breeding are the creation of diversity followed by selection of resulting plants with the desired characteristics. Two important relationships determining the outcome of selection are those between plant phenotype and genotype and between heritability of a trait and the selection pressure. Similarities and differences between breeding by farmers and scientists are illustrated by the contrast between yield and yield stability; understanding of basic biological principles, their application and effects; and transgenic varieties. Participatory plant breeding is attempting to reunite farmers and scientists.
