Maximilian J. Telford and D.T.J. Littlewood (eds)
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199549429
- eISBN:
- 9780191721601
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199549429.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics, Developmental Biology
Animal life, now and over the past half billion years, is incredibly diverse. Describing and understanding the evolution of this diversity of body plans — from vertebrates such as humans and fish to ...
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Animal life, now and over the past half billion years, is incredibly diverse. Describing and understanding the evolution of this diversity of body plans — from vertebrates such as humans and fish to the numerous invertebrate groups including sponges, insects, molluscs, and the many groups of worms — is a major goal of evolutionary biology. This book adopts a modern, integrated approach to describe how current molecular genetic techniques and disciplines as diverse as palaeontology, embryology, and genomics have been combined, resulting in a dramatic renaissance in the study of animal evolution. The last decade has seen growing interest in evolutionary biology fuelled by a wealth of data from molecular biology. Modern phylogenies integrating evidence from molecules, embryological data, and morphology of living and fossil taxa provide a wide consensus of the major branching patterns of the tree of life; moreover, the links between phenotype and genotype are increasingly well understood. This has resulted in a reliable tree of relationships that has been widely accepted and has spawned numerous new and exciting questions that require a reassessment of the origins and radiation of animal life. The focus of this volume is at the level of major animal groups, the morphological innovations that define them, and the mechanisms of change to their embryology that have resulted in their evolution. Current research themes and future prospects are highlighted including phylogeny reconstruction, comparative developmental biology, the value of different sources of data and the importance of fossils, homology assessment, character evolution, phylogeny of major groups of animals, and genome evolution. These topics are integrated in the light of a 'new animal phylogeny', to provide fresh insights into the patterns and processes of animal evolution.Less
Animal life, now and over the past half billion years, is incredibly diverse. Describing and understanding the evolution of this diversity of body plans — from vertebrates such as humans and fish to the numerous invertebrate groups including sponges, insects, molluscs, and the many groups of worms — is a major goal of evolutionary biology. This book adopts a modern, integrated approach to describe how current molecular genetic techniques and disciplines as diverse as palaeontology, embryology, and genomics have been combined, resulting in a dramatic renaissance in the study of animal evolution. The last decade has seen growing interest in evolutionary biology fuelled by a wealth of data from molecular biology. Modern phylogenies integrating evidence from molecules, embryological data, and morphology of living and fossil taxa provide a wide consensus of the major branching patterns of the tree of life; moreover, the links between phenotype and genotype are increasingly well understood. This has resulted in a reliable tree of relationships that has been widely accepted and has spawned numerous new and exciting questions that require a reassessment of the origins and radiation of animal life. The focus of this volume is at the level of major animal groups, the morphological innovations that define them, and the mechanisms of change to their embryology that have resulted in their evolution. Current research themes and future prospects are highlighted including phylogeny reconstruction, comparative developmental biology, the value of different sources of data and the importance of fossils, homology assessment, character evolution, phylogeny of major groups of animals, and genome evolution. These topics are integrated in the light of a 'new animal phylogeny', to provide fresh insights into the patterns and processes of animal evolution.
Michael L. Arnold
- Published in print:
- 2008
- Published Online:
- January 2009
- ISBN:
- 9780199539581
- eISBN:
- 9780191716225
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199539581.001.0001
- Subject:
- Biology, Animal Biology, Evolutionary Biology / Genetics
This book is an exploration of how the transfer of genes between divergent lineages — through a diverse array of mechanisms — has affected, and continues to affect, humans. In particular, it is a ...
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This book is an exploration of how the transfer of genes between divergent lineages — through a diverse array of mechanisms — has affected, and continues to affect, humans. In particular, it is a journey into the data that support the hypothesis that Homo sapiens as well as those organisms upon which it depends for survival and battles against for existence are marked by mosaic genomes. This mosaicism reflects the rampant (as reflected by the proportion of organisms that illustrate this process) exchange of genetic material during evolutionary diversification. This is the underlying hypothesis for this book. The book follows in the various chapters that it also reflects the consistent observation made when the genomes of organisms are mined for genetic variation.Less
This book is an exploration of how the transfer of genes between divergent lineages — through a diverse array of mechanisms — has affected, and continues to affect, humans. In particular, it is a journey into the data that support the hypothesis that Homo sapiens as well as those organisms upon which it depends for survival and battles against for existence are marked by mosaic genomes. This mosaicism reflects the rampant (as reflected by the proportion of organisms that illustrate this process) exchange of genetic material during evolutionary diversification. This is the underlying hypothesis for this book. The book follows in the various chapters that it also reflects the consistent observation made when the genomes of organisms are mined for genetic variation.
C. Neal Stewart
- Published in print:
- 2004
- Published Online:
- September 2007
- ISBN:
- 9780195157451
- eISBN:
- 9780199790388
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195157451.003.0002
- Subject:
- Biology, Biotechnology
There is a trend towards embracing nature and the acceptance of natural products, even though humans have altered virtually everything. A case in point is food and food crops. No natural human food ...
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There is a trend towards embracing nature and the acceptance of natural products, even though humans have altered virtually everything. A case in point is food and food crops. No natural human food exists except wild game and a few undomesticated plants. There has never been natural corn or wheat, and many vegetable crops such as carrots and Brussel sprouts are recent inventions of crop domestication. Transgenic crops seem transformative since they possess one or two genes from a different species. The process of gene introduction takes place in the lab using biotechnology, but traditional breeding and domestication drastically alter genomes of plants relative to biotechnology, since hundreds to thousands of genes are manipulated in hybridization. Like those of crops, genomes of weeds are also selected and adapted for growth in farmer’s fields. Human and natural selection are powerful forces.Less
There is a trend towards embracing nature and the acceptance of natural products, even though humans have altered virtually everything. A case in point is food and food crops. No natural human food exists except wild game and a few undomesticated plants. There has never been natural corn or wheat, and many vegetable crops such as carrots and Brussel sprouts are recent inventions of crop domestication. Transgenic crops seem transformative since they possess one or two genes from a different species. The process of gene introduction takes place in the lab using biotechnology, but traditional breeding and domestication drastically alter genomes of plants relative to biotechnology, since hundreds to thousands of genes are manipulated in hybridization. Like those of crops, genomes of weeds are also selected and adapted for growth in farmer’s fields. Human and natural selection are powerful forces.
Jan Sapp
- Published in print:
- 2003
- Published Online:
- September 2007
- ISBN:
- 9780195156195
- eISBN:
- 9780199790340
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195156195.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics
This book presents a history of the last two centuries of biology. It covers early evolutionary biology — Lamarck, Cuvier, Darwin, and Wallace through to Mayr and the neodarwinian synthesis — and ...
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This book presents a history of the last two centuries of biology. It covers early evolutionary biology — Lamarck, Cuvier, Darwin, and Wallace through to Mayr and the neodarwinian synthesis — and also discusses social implications, the struggles with our religious understanding, and the interweaving of genetics into evolutionary theory. The book's account is an integration of the cytological tradition and the new understanding of the diversification of life coming from comparative analyses of complete microbial genomes. The book includes the history of research and theories about symbiosis in evolution, research on microbial evolution, bacterial evolution, and symbiosis in evolution.Less
This book presents a history of the last two centuries of biology. It covers early evolutionary biology — Lamarck, Cuvier, Darwin, and Wallace through to Mayr and the neodarwinian synthesis — and also discusses social implications, the struggles with our religious understanding, and the interweaving of genetics into evolutionary theory. The book's account is an integration of the cytological tradition and the new understanding of the diversification of life coming from comparative analyses of complete microbial genomes. The book includes the history of research and theories about symbiosis in evolution, research on microbial evolution, bacterial evolution, and symbiosis in evolution.
Joshua S. Weitz
- Published in print:
- 2016
- Published Online:
- October 2017
- ISBN:
- 9780691161549
- eISBN:
- 9781400873968
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691161549.003.0001
- Subject:
- Biology, Disease Ecology / Epidemiology
This chapter discusses the definition of a virus followed by the dimensions of viral biodiversity. Viruses vary in size from genomes of a few thousand to more than a million nucleotides. Viral ...
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This chapter discusses the definition of a virus followed by the dimensions of viral biodiversity. Viruses vary in size from genomes of a few thousand to more than a million nucleotides. Viral capsids vary in linear dimensions from approximately 20 nm to more than 400 nm in diameter. Virus particles are relatively nutrient rich compared with their hosts. Viral genomes are compact, with the number of putative genes scaling linearly with genome size. The functional diversity of viruses includes many canonical viral genes, such as those that code for capsid proteins and transcriptional regulators. The functional diversity of viruses includes many noncanonical genes, such as those that code for proteins that are part of photosystem pathways or cell-wall pathways.Less
This chapter discusses the definition of a virus followed by the dimensions of viral biodiversity. Viruses vary in size from genomes of a few thousand to more than a million nucleotides. Viral capsids vary in linear dimensions from approximately 20 nm to more than 400 nm in diameter. Virus particles are relatively nutrient rich compared with their hosts. Viral genomes are compact, with the number of putative genes scaling linearly with genome size. The functional diversity of viruses includes many canonical viral genes, such as those that code for capsid proteins and transcriptional regulators. The functional diversity of viruses includes many noncanonical genes, such as those that code for proteins that are part of photosystem pathways or cell-wall pathways.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.003.0011
- Subject:
- Mathematics, Mathematical Biology
This chapter begins by providing a model for multichromosomal circular genomes. It then presents a generalization to signed genomes and some results.
This chapter begins by providing a model for multichromosomal circular genomes. It then presents a generalization to signed genomes and some results.
Joel T. Dudley and Konrad J. Karczewski
- Published in print:
- 2013
- Published Online:
- December 2013
- ISBN:
- 9780199644483
- eISBN:
- 9780191774577
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199644483.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics
This book provides a novel, inquiry-based approach to the understanding and interpretation of the practical, medical, physiological, and societal aspects of personal genomic information. The material ...
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This book provides a novel, inquiry-based approach to the understanding and interpretation of the practical, medical, physiological, and societal aspects of personal genomic information. The material is presented in two parts: the first provides readers of all backgrounds with a fundamental understanding of the biology of human genomes, information on how to obtain and understand digital representations of personal genomic data, tools and techniques for exploring the personal genomics of ancestry and genealogy, discovery and interpretation of genetic trait associations, and the role of personal genomics in drug response. The second part offers more advanced readers an understanding of the science, tools, and techniques for investigating interactions between a personal genome and the environment, connecting DNA to physiology, and assessing rare variants and structural variation.Less
This book provides a novel, inquiry-based approach to the understanding and interpretation of the practical, medical, physiological, and societal aspects of personal genomic information. The material is presented in two parts: the first provides readers of all backgrounds with a fundamental understanding of the biology of human genomes, information on how to obtain and understand digital representations of personal genomic data, tools and techniques for exploring the personal genomics of ancestry and genealogy, discovery and interpretation of genetic trait associations, and the role of personal genomics in drug response. The second part offers more advanced readers an understanding of the science, tools, and techniques for investigating interactions between a personal genome and the environment, connecting DNA to physiology, and assessing rare variants and structural variation.
Barry Barnes and John Dupre
- Published in print:
- 2008
- Published Online:
- March 2013
- ISBN:
- 9780226172958
- eISBN:
- 9780226172965
- Item type:
- book
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226172965.001.0001
- Subject:
- Philosophy, Philosophy of Science
The announcement in 2003 that the Human Genome Project had completed its map of the entire human genome was heralded as a stunning scientific breakthrough. Since then, boasts about the benefits—and ...
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The announcement in 2003 that the Human Genome Project had completed its map of the entire human genome was heralded as a stunning scientific breakthrough. Since then, boasts about the benefits—and warnings of the dangers—of genomics have remained front-page news, with everyone agreeing that genomics has the potential to radically alter life as we know it. For the nonscientist, the claims and counterclaims are dizzying—what does it really mean to understand the genome? This book offers an answer to that question and much more with a clear and lively account of the genomic revolution and its promise. The book opens with a brief history of the science of genetics and genomics, from Mendel to Watson and Crick and all the way up to Craig Venter; from there the chapters delve into the use of genomics in determining evolutionary paths—and what it can tell us, for example, about how far we really have come from our ape ancestors. It then considers both the power and risks of genetics, from the economic potential of plant genomes to overblown claims that certain human genes can be directly tied to such traits as intelligence or homosexuality. Ultimately, the chapters in this book argue, we are now living with a new knowledge as powerful in its way as nuclear physics, and the stark choices that face us—between biological warfare and gene therapy, a new eugenics or a new agricultural revolution—will demand the full engagement of both scientists and citizens.Less
The announcement in 2003 that the Human Genome Project had completed its map of the entire human genome was heralded as a stunning scientific breakthrough. Since then, boasts about the benefits—and warnings of the dangers—of genomics have remained front-page news, with everyone agreeing that genomics has the potential to radically alter life as we know it. For the nonscientist, the claims and counterclaims are dizzying—what does it really mean to understand the genome? This book offers an answer to that question and much more with a clear and lively account of the genomic revolution and its promise. The book opens with a brief history of the science of genetics and genomics, from Mendel to Watson and Crick and all the way up to Craig Venter; from there the chapters delve into the use of genomics in determining evolutionary paths—and what it can tell us, for example, about how far we really have come from our ape ancestors. It then considers both the power and risks of genetics, from the economic potential of plant genomes to overblown claims that certain human genes can be directly tied to such traits as intelligence or homosexuality. Ultimately, the chapters in this book argue, we are now living with a new knowledge as powerful in its way as nuclear physics, and the stark choices that face us—between biological warfare and gene therapy, a new eugenics or a new agricultural revolution—will demand the full engagement of both scientists and citizens.
Jeffrey J. Tabor, Matthew Levy, Zachary Booth Simpson, and Andrew D. Ellington
- Published in print:
- 2008
- Published Online:
- August 2013
- ISBN:
- 9780262182683
- eISBN:
- 9780262282093
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262182683.003.0017
- Subject:
- Biology, Microbiology
This chapter describes the top-down approach of simplifying small or minimal genomes to construct an artificial cell. First, it discusses the concept of minimal genomes. This is followed by an ...
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This chapter describes the top-down approach of simplifying small or minimal genomes to construct an artificial cell. First, it discusses the concept of minimal genomes. This is followed by an overview of the past and current efforts in comparative and evolutionary genomics. The metabolic capacities of minimal and natural reduced genomes are also discussed. Finally, the chapter outlines possible implications for the assembly of top-down protocells.Less
This chapter describes the top-down approach of simplifying small or minimal genomes to construct an artificial cell. First, it discusses the concept of minimal genomes. This is followed by an overview of the past and current efforts in comparative and evolutionary genomics. The metabolic capacities of minimal and natural reduced genomes are also discussed. Finally, the chapter outlines possible implications for the assembly of top-down protocells.
Laura I. Walker and Sergio V. Flores
- Published in print:
- 2007
- Published Online:
- March 2012
- ISBN:
- 9780520098596
- eISBN:
- 9780520916159
- Item type:
- chapter
- Publisher:
- University of California Press
- DOI:
- 10.1525/california/9780520098596.003.0027
- Subject:
- Biology, Animal Biology
This chapter studies the expression of nucleolar organizer regions (NORs), distinguished through silver staining procedures, and the distribution of ribosomal genes, detected by fluorescent in situ ...
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This chapter studies the expression of nucleolar organizer regions (NORs), distinguished through silver staining procedures, and the distribution of ribosomal genes, detected by fluorescent in situ hybridization with a ribosomal DNA probe, in Phyllotis rodent species and their laboratory generated hybrids. It notes that in the hybrids between the more genetically distant species, the NORs of one parental genome were preferentially expressed. The chapter explains that this result differs from the codominant rDNA expression previously detected in hybrids between the two more genetically similar of the three species, and suggests that nucleolar dominance is related to the compatibility of parental genomes.Less
This chapter studies the expression of nucleolar organizer regions (NORs), distinguished through silver staining procedures, and the distribution of ribosomal genes, detected by fluorescent in situ hybridization with a ribosomal DNA probe, in Phyllotis rodent species and their laboratory generated hybrids. It notes that in the hybrids between the more genetically distant species, the NORs of one parental genome were preferentially expressed. The chapter explains that this result differs from the codominant rDNA expression previously detected in hybrids between the two more genetically similar of the three species, and suggests that nucleolar dominance is related to the compatibility of parental genomes.
Andrei V. Polyakov, Alex Beharav, Tamar Krugman, Aaron Avivi, and Eviatar Nevo
- Published in print:
- 2007
- Published Online:
- March 2012
- ISBN:
- 9780520098596
- eISBN:
- 9780520916159
- Item type:
- chapter
- Publisher:
- University of California Press
- DOI:
- 10.1525/california/9780520098596.003.0028
- Subject:
- Biology, Animal Biology
This chapter examines 426 loci of Amplified Fragment Length Polymorphisms (AFLP) in Israeli Spalax, across coding and noncoding regions of genomes, along a gradient of increasing aridity. It compares ...
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This chapter examines 426 loci of Amplified Fragment Length Polymorphisms (AFLP) in Israeli Spalax, across coding and noncoding regions of genomes, along a gradient of increasing aridity. It compares and contrasts AFLP diversity with previous phylogenetic and ecological conclusions, based on other protein and DNA molecular markers in 114 subterranean blind mole rats representing four species of the Spalax ehrenbergi superspecies in Israel: S. galili (2n=52), S. golani (2n=54), S. carmeli (2n=58), and S. judaei (2n=60), and indicates results hereof. The chapter concludes that AFLP diversity, spreading across coding and noncoding genomic regions, is subject to natural selection like other molecular markers and displays molecular ecological adaptive radiation caused by interacting biotic and abiotic environmental stresses.Less
This chapter examines 426 loci of Amplified Fragment Length Polymorphisms (AFLP) in Israeli Spalax, across coding and noncoding regions of genomes, along a gradient of increasing aridity. It compares and contrasts AFLP diversity with previous phylogenetic and ecological conclusions, based on other protein and DNA molecular markers in 114 subterranean blind mole rats representing four species of the Spalax ehrenbergi superspecies in Israel: S. galili (2n=52), S. golani (2n=54), S. carmeli (2n=58), and S. judaei (2n=60), and indicates results hereof. The chapter concludes that AFLP diversity, spreading across coding and noncoding genomic regions, is subject to natural selection like other molecular markers and displays molecular ecological adaptive radiation caused by interacting biotic and abiotic environmental stresses.
David L. Kirchman
- Published in print:
- 2018
- Published Online:
- August 2018
- ISBN:
- 9780198789406
- eISBN:
- 9780191831256
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198789406.003.0005
- Subject:
- Biology, Ecology, Aquatic Biology
The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated ...
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The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.Less
The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.003.0003
- Subject:
- Mathematics, Mathematical Biology
Unsigned permutations were the first combinatorial model of genomes for the study of rearrangements, and are still used when the orientation of the markers is not known. This chapter discusses ...
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Unsigned permutations were the first combinatorial model of genomes for the study of rearrangements, and are still used when the orientation of the markers is not known. This chapter discusses transposition distance; prefix transposition distance; reversal distance; prefix reversal distance (pancake-flipping); variants; and relations between distances on unsigned permutations.Less
Unsigned permutations were the first combinatorial model of genomes for the study of rearrangements, and are still used when the orientation of the markers is not known. This chapter discusses transposition distance; prefix transposition distance; reversal distance; prefix reversal distance (pancake-flipping); variants; and relations between distances on unsigned permutations.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.003.0004
- Subject:
- Mathematics, Mathematical Biology
Signed permutations allow the relative orientation of homologous markers to be taken into account and constitute a more biologically relevant model for genomes. Reversals, for instance, always change ...
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Signed permutations allow the relative orientation of homologous markers to be taken into account and constitute a more biologically relevant model for genomes. Reversals, for instance, always change the strand of the reversed segment, so that the orientation of a gene inside the segment is also changed. Thus, whenever the orientation of genes is known and mutations that affect orientations are considered, it is better to use signed permutations as a model. This chapter discusses conserved interval distance; signed reversal distance; variants of sorting by reversals; combined operations; and double cut-and-joins.Less
Signed permutations allow the relative orientation of homologous markers to be taken into account and constitute a more biologically relevant model for genomes. Reversals, for instance, always change the strand of the reversed segment, so that the orientation of a gene inside the segment is also changed. Thus, whenever the orientation of genes is known and mutations that affect orientations are considered, it is better to use signed permutations as a model. This chapter discusses conserved interval distance; signed reversal distance; variants of sorting by reversals; combined operations; and double cut-and-joins.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.003.0010
- Subject:
- Mathematics, Mathematical Biology
This chapter discusses the modeling of a genome with several chromosomes by a set of paths and cycles. The model captures all the information about the order of the genes and their partition into ...
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This chapter discusses the modeling of a genome with several chromosomes by a set of paths and cycles. The model captures all the information about the order of the genes and their partition into chromosomes. The discussion covers genomes; breakpoints; intervals; translocation distance; double cut-and-joins (2-break rearrangement); k-break rearrangement; fusions, fissions, translocations, and reversals; and rearrangements with partially ordered chromosomes.Less
This chapter discusses the modeling of a genome with several chromosomes by a set of paths and cycles. The model captures all the information about the order of the genes and their partition into chromosomes. The discussion covers genomes; breakpoints; intervals; translocation distance; double cut-and-joins (2-break rearrangement); k-break rearrangement; fusions, fissions, translocations, and reversals; and rearrangements with partially ordered chromosomes.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.003.0012
- Subject:
- Mathematics, Mathematical Biology
This chapter presents models that deal with the case in which the order of the genes is unknown. While this assumption does not make sense for unichromosomal genomes, a distance between ...
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This chapter presents models that deal with the case in which the order of the genes is unknown. While this assumption does not make sense for unichromosomal genomes, a distance between multichromosomal genomes can be studied, which takes into account only the data about which gene belongs to which chromosome. This distance is known as the syntenic distance. The discussions cover structural properties; lower bounds; diameter; algorithmic results; and conjectures and open problems.Less
This chapter presents models that deal with the case in which the order of the genes is unknown. While this assumption does not make sense for unichromosomal genomes, a distance between multichromosomal genomes can be studied, which takes into account only the data about which gene belongs to which chromosome. This distance is known as the syntenic distance. The discussions cover structural properties; lower bounds; diameter; algorithmic results; and conjectures and open problems.
Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262062824
- eISBN:
- 9780262258753
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062824.003.0013
- Subject:
- Mathematics, Mathematical Biology
This chapter presents models for median and halving problems. It covers the breakpoint median; reversal and DCJ median problems; duplicated genomes; and other variants and generalizations.
This chapter presents models for median and halving problems. It covers the breakpoint median; reversal and DCJ median problems; duplicated genomes; and other variants and generalizations.
Weilong Hao
- Published in print:
- 2012
- Published Online:
- December 2013
- ISBN:
- 9780199642274
- eISBN:
- 9780191774751
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199642274.003.0007
- Subject:
- Biology, Evolutionary Biology / Genetics
Horizontal gene transfer is recognized as a major force in shaping bacterial gene content and has gained incredible attention over the last decade, in part due to the fast growing number of sequenced ...
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Horizontal gene transfer is recognized as a major force in shaping bacterial gene content and has gained incredible attention over the last decade, in part due to the fast growing number of sequenced bacterial genomes. The genomic data have permitted an appreciation that rapid evolution in bacteria is mainly the result of the ability of almost all bacteria to horizontally acquire genes over evolutionary time. Many of these horizontal transfers can occur with multiple genes transferred per event. This chapter discusses some of the features and patterns of rapid evolution via horizontal transfer. In particular, it notes that methods which estimate rates of gene transfers, such as via parsimony or via maximum likelihood, suggest that the estimated levels of horizontal transfer are smaller than the true rates.Less
Horizontal gene transfer is recognized as a major force in shaping bacterial gene content and has gained incredible attention over the last decade, in part due to the fast growing number of sequenced bacterial genomes. The genomic data have permitted an appreciation that rapid evolution in bacteria is mainly the result of the ability of almost all bacteria to horizontally acquire genes over evolutionary time. Many of these horizontal transfers can occur with multiple genes transferred per event. This chapter discusses some of the features and patterns of rapid evolution via horizontal transfer. In particular, it notes that methods which estimate rates of gene transfers, such as via parsimony or via maximum likelihood, suggest that the estimated levels of horizontal transfer are smaller than the true rates.
Alberto Civetta
- Published in print:
- 2012
- Published Online:
- December 2013
- ISBN:
- 9780199642274
- eISBN:
- 9780191774751
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199642274.003.0017
- Subject:
- Biology, Evolutionary Biology / Genetics
Reproductive genes (RGs) have been shown to evolve rapidly among species, with some being under positive (adaptive) evolution. More recent studies have attempted to decipher the role of sexual ...
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Reproductive genes (RGs) have been shown to evolve rapidly among species, with some being under positive (adaptive) evolution. More recent studies have attempted to decipher the role of sexual selection during the evolution of RGs by using a phylogenetic based approach. Such studies have coupled branch signals of positive selection with phenotypic proxies of sexual selection. The phylogenetic approach, although powerful, suffers the limitation that localized branch-specific bouts of selection would be undetectable and that only coding gene regions are analyzed. This might lead to failure to detect sexual selection at the molecular level. With the rapid accumulation of genome sequence data, it is now possible to test sexual selection by focusing on pairs or trios of species, incorporating a gene’s genomic environment information, and adding polymorphism data. Genomes and gene manipulation technologies should also facilitate our ability to identify associations between genotypes and sexually selected phenotypes.Less
Reproductive genes (RGs) have been shown to evolve rapidly among species, with some being under positive (adaptive) evolution. More recent studies have attempted to decipher the role of sexual selection during the evolution of RGs by using a phylogenetic based approach. Such studies have coupled branch signals of positive selection with phenotypic proxies of sexual selection. The phylogenetic approach, although powerful, suffers the limitation that localized branch-specific bouts of selection would be undetectable and that only coding gene regions are analyzed. This might lead to failure to detect sexual selection at the molecular level. With the rapid accumulation of genome sequence data, it is now possible to test sexual selection by focusing on pairs or trios of species, incorporating a gene’s genomic environment information, and adding polymorphism data. Genomes and gene manipulation technologies should also facilitate our ability to identify associations between genotypes and sexually selected phenotypes.
Sheldon Krimsky
- Published in print:
- 2015
- Published Online:
- November 2015
- ISBN:
- 9780231167482
- eISBN:
- 9780231539401
- Item type:
- chapter
- Publisher:
- Columbia University Press
- DOI:
- 10.7312/columbia/9780231167482.003.0018
- Subject:
- Biology, Bioethics
This dialogue presents a fictional account of a public symposium where the participants explore the ethics of creating human-animal chimeras and hybrids involving the use of stem cells for research ...
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This dialogue presents a fictional account of a public symposium where the participants explore the ethics of creating human-animal chimeras and hybrids involving the use of stem cells for research and therapeutic purposes. Chimeras can be artificially produced in research by transplanting embryonic cells from one organism onto the embryo of another, as in injecting mouse stem cells into mouse blastocysts. There has been great interest among developmental biologists in transplanting human stem cells into the embryos of animals. In stem cell research, human-to-animal chimera experiments typically involve the transfer of multipotent or pluripotent human stem cells into animals in embryonic, fetal, or postnatal stages of development to study stem cell behavior. Here symposium participants discuss some of the reasons for moving human genes into the genomes of other species; commercial applications of chimeras; public opinion on interspecies gene and cell transfer; the distinction between human-animal hybrids and human-animal chimeras; blanket prohibition of transferring human genes into animals; and the moral boundary for managing experiments involving human-animal chimeras.Less
This dialogue presents a fictional account of a public symposium where the participants explore the ethics of creating human-animal chimeras and hybrids involving the use of stem cells for research and therapeutic purposes. Chimeras can be artificially produced in research by transplanting embryonic cells from one organism onto the embryo of another, as in injecting mouse stem cells into mouse blastocysts. There has been great interest among developmental biologists in transplanting human stem cells into the embryos of animals. In stem cell research, human-to-animal chimera experiments typically involve the transfer of multipotent or pluripotent human stem cells into animals in embryonic, fetal, or postnatal stages of development to study stem cell behavior. Here symposium participants discuss some of the reasons for moving human genes into the genomes of other species; commercial applications of chimeras; public opinion on interspecies gene and cell transfer; the distinction between human-animal hybrids and human-animal chimeras; blanket prohibition of transferring human genes into animals; and the moral boundary for managing experiments involving human-animal chimeras.
