Michael L. Arnold
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780199229031
- eISBN:
- 9780191728266
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199229031.001.0001
- Subject:
- Biology, Evolutionary Biology / Genetics
Even before the publication of Darwin's Origin of Species, the perception of evolutionary change has been a tree-like pattern of diversification — with divergent branches spreading further and ...
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Even before the publication of Darwin's Origin of Species, the perception of evolutionary change has been a tree-like pattern of diversification — with divergent branches spreading further and further from the trunk. In the only illustration of Darwin's treatise, branches large and small never reconnect. However, it is now evident that this view does not adequately encompass the richness of evolutionary pattern and process. Instead, the evolution of species from microbes to mammals builds like a web that crosses and re-crosses through genetic exchange, even as it grows outward from a point of origin. Some of the avenues for genetic exchange, for example introgression through sexual recombination versus lateral gene transfer mediated by transposable elements, are based on definably different molecular mechanisms. However, even such widely different genetic processes may result in similar effects on adaptations (either new or transferred), genome evolution, population genetics, and the evolutionary/ecological trajectory of organisms. For example, the evolution of novel adaptations (resulting from lateral gene transfer) leading to the flea-borne, deadly, causative agent of plague from a rarely-fatal, orally-transmitted, bacterial species is quite similar to the adaptations accrued from natural hybridization between annual sunflower species resulting in the formation of several new species. Thus, more and more data indicate that evolution has resulted in lineages consisting of mosaics of genes derived from different ancestors. It is therefore becoming increasingly clear that the tree is an inadequate metaphor of evolutionary change. In this book, the author promotes the ‘web-of-life’ metaphor as a more appropriate representation of evolutionary change in all life-forms.Less
Even before the publication of Darwin's Origin of Species, the perception of evolutionary change has been a tree-like pattern of diversification — with divergent branches spreading further and further from the trunk. In the only illustration of Darwin's treatise, branches large and small never reconnect. However, it is now evident that this view does not adequately encompass the richness of evolutionary pattern and process. Instead, the evolution of species from microbes to mammals builds like a web that crosses and re-crosses through genetic exchange, even as it grows outward from a point of origin. Some of the avenues for genetic exchange, for example introgression through sexual recombination versus lateral gene transfer mediated by transposable elements, are based on definably different molecular mechanisms. However, even such widely different genetic processes may result in similar effects on adaptations (either new or transferred), genome evolution, population genetics, and the evolutionary/ecological trajectory of organisms. For example, the evolution of novel adaptations (resulting from lateral gene transfer) leading to the flea-borne, deadly, causative agent of plague from a rarely-fatal, orally-transmitted, bacterial species is quite similar to the adaptations accrued from natural hybridization between annual sunflower species resulting in the formation of several new species. Thus, more and more data indicate that evolution has resulted in lineages consisting of mosaics of genes derived from different ancestors. It is therefore becoming increasingly clear that the tree is an inadequate metaphor of evolutionary change. In this book, the author promotes the ‘web-of-life’ metaphor as a more appropriate representation of evolutionary change in all life-forms.
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.
Maureen A. O'Malley
- Published in print:
- 2012
- Published Online:
- May 2012
- ISBN:
- 9780199691982
- eISBN:
- 9780191738111
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199691982.003.0011
- Subject:
- Philosophy, Philosophy of Science
This chapter provides a manifesto for the importance of taking proper account of microbes, from many perspectives the dominant form of life certainly in the past and arguably even today, in the ...
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This chapter provides a manifesto for the importance of taking proper account of microbes, from many perspectives the dominant form of life certainly in the past and arguably even today, in the philosophy of biology. It is argued that this will transform ideas on ontology, evolution, taxonomy, and biodiversity. A number of recent developments in microbiology—including biofilm formation, chemotaxis, quorum sensing, and gene transfer—highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms.Less
This chapter provides a manifesto for the importance of taking proper account of microbes, from many perspectives the dominant form of life certainly in the past and arguably even today, in the philosophy of biology. It is argued that this will transform ideas on ontology, evolution, taxonomy, and biodiversity. A number of recent developments in microbiology—including biofilm formation, chemotaxis, quorum sensing, and gene transfer—highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms.
Franklin M. Harold
- Published in print:
- 2014
- Published Online:
- May 2015
- ISBN:
- 9780226174143
- eISBN:
- 9780226174310
- Item type:
- chapter
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226174310.003.0002
- Subject:
- Biology, Biochemistry / Molecular Biology
The idea that all living things arose from their progenitors by descent with modification, and that this history can be depicted as a great tree, goes back to Darwin and beyond. Construction of a ...
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The idea that all living things arose from their progenitors by descent with modification, and that this history can be depicted as a great tree, goes back to Darwin and beyond. Construction of a universal tree became possible after Carl Woese introduced ribosomal RNA sequences as a molecular chronometer. The tree consists of three great stems, or domains, designated Bacteria, Archaea and Eukarya, and this tripartite division is now generally accepted. But soon a serious complication arose: lateral transfer of genes between species, genera and even domains is common, particularly among prokaryotes. Lateral gene transfer erodes the phylogenetic trace, and has led some to question the very principle of a tree of life, but the division of all living things into three domains has held up. It is not easy to assign absolute dates to their emergence. The prokaryotes, Bacteria and Archaea, clearly go back more than 3 billion years. Modern Eukarya are much more recent, a billion years or so, but the eukaryotic lineage appears to be very ancient, possibly comparable to the prokaryotic ones.Less
The idea that all living things arose from their progenitors by descent with modification, and that this history can be depicted as a great tree, goes back to Darwin and beyond. Construction of a universal tree became possible after Carl Woese introduced ribosomal RNA sequences as a molecular chronometer. The tree consists of three great stems, or domains, designated Bacteria, Archaea and Eukarya, and this tripartite division is now generally accepted. But soon a serious complication arose: lateral transfer of genes between species, genera and even domains is common, particularly among prokaryotes. Lateral gene transfer erodes the phylogenetic trace, and has led some to question the very principle of a tree of life, but the division of all living things into three domains has held up. It is not easy to assign absolute dates to their emergence. The prokaryotes, Bacteria and Archaea, clearly go back more than 3 billion years. Modern Eukarya are much more recent, a billion years or so, but the eukaryotic lineage appears to be very ancient, possibly comparable to the prokaryotic ones.
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/9780199229031.003.0002
- Subject:
- Biology, Evolutionary Biology / Genetics
This chapter introduces the topic of species concepts and the study of genetic exchange. It uses only four (biological, phylogenetic, cohesion, and prokaryotic) of the many definitions to illustrate ...
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This chapter introduces the topic of species concepts and the study of genetic exchange. It uses only four (biological, phylogenetic, cohesion, and prokaryotic) of the many definitions to illustrate how our concept of (i) what a species is and (ii) how it originates influences what evolutionary importance (or lack there of) we ascribe to genetic exchange. The chapter concludes by suggesting how we might use species concepts — often the bane of evolutionists interested in gene exchange — to afford a clearer understanding of the importance of natural hybridization and lateral gene transfer.Less
This chapter introduces the topic of species concepts and the study of genetic exchange. It uses only four (biological, phylogenetic, cohesion, and prokaryotic) of the many definitions to illustrate how our concept of (i) what a species is and (ii) how it originates influences what evolutionary importance (or lack there of) we ascribe to genetic exchange. The chapter concludes by suggesting how we might use species concepts — often the bane of evolutionists interested in gene exchange — to afford a clearer understanding of the importance of natural hybridization and lateral gene transfer.
Eric Bapteste and Gemma Anderson
- Published in print:
- 2018
- Published Online:
- July 2018
- ISBN:
- 9780198779636
- eISBN:
- 9780191824685
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198779636.003.0014
- Subject:
- Philosophy, Philosophy of Science, Metaphysics/Epistemology
Processes are ubiquitous in biology and play a key explanatory role in evolutionary biology, where they are frequently depicted by patterns. In particular, phylogenetic trees represent divergence ...
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Processes are ubiquitous in biology and play a key explanatory role in evolutionary biology, where they are frequently depicted by patterns. In particular, phylogenetic trees represent divergence from a last common ancestor with a branching pattern. However, the increasingly recognized underdetermination of phylogenetic trees limits the accuracy of tree-based retrodiction. Even phylogenetic networks, which include additional processes intersecting with vertical descent, still provide incomplete descriptions of evolutionary processes, as they usually miss processes that impact unrelated lineages. Interaction networks highlight the intersection of processes that sustain biological diversity. The complex topology of all these networks further challenges retrodiction. Remarkably, when intersecting processes are involved in evolutionary transitions, they introduce new biological processes on Earth. Processes, and hence the explanantia of evolutionary biology, evolve, which challenges uniformitarian approaches to retrodiction. Despite these difficulties, a yet to be introduced typology of processes would help to analyse the (big) processual picture of life.Less
Processes are ubiquitous in biology and play a key explanatory role in evolutionary biology, where they are frequently depicted by patterns. In particular, phylogenetic trees represent divergence from a last common ancestor with a branching pattern. However, the increasingly recognized underdetermination of phylogenetic trees limits the accuracy of tree-based retrodiction. Even phylogenetic networks, which include additional processes intersecting with vertical descent, still provide incomplete descriptions of evolutionary processes, as they usually miss processes that impact unrelated lineages. Interaction networks highlight the intersection of processes that sustain biological diversity. The complex topology of all these networks further challenges retrodiction. Remarkably, when intersecting processes are involved in evolutionary transitions, they introduce new biological processes on Earth. Processes, and hence the explanantia of evolutionary biology, evolve, which challenges uniformitarian approaches to retrodiction. Despite these difficulties, a yet to be introduced typology of processes would help to analyse the (big) processual picture of life.
Maureen A. O’malley
- Published in print:
- 2018
- Published Online:
- January 2019
- ISBN:
- 9780226569871
- eISBN:
- 9780226570075
- Item type:
- chapter
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226570075.003.0008
- Subject:
- History, History of Science, Technology, and Medicine
W. Ford Doolittle is well known as an iconoclastic and visionary microbial evolutionist. As well as challenging orthodoxies about the tree of life, he has made major contributions to empirically ...
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W. Ford Doolittle is well known as an iconoclastic and visionary microbial evolutionist. As well as challenging orthodoxies about the tree of life, he has made major contributions to empirically grounded evolutionary theory. His ideas about selfish DNA, introns, Gaia, and non-adaptive evolution have made a significant impact on how evolutionary biologists think about evolution. But how did these fundamental challenges to orthodoxy come about, and how did they succeed in gaining footing within mainstream biology? This chapter will address all these aspects of Doolittle’s long career, and also his recent more explicitly philosophical turn, in which he brings each of these revolutionary moments together under an emerging advocacy for explanatory and conceptual pluralism.Less
W. Ford Doolittle is well known as an iconoclastic and visionary microbial evolutionist. As well as challenging orthodoxies about the tree of life, he has made major contributions to empirically grounded evolutionary theory. His ideas about selfish DNA, introns, Gaia, and non-adaptive evolution have made a significant impact on how evolutionary biologists think about evolution. But how did these fundamental challenges to orthodoxy come about, and how did they succeed in gaining footing within mainstream biology? This chapter will address all these aspects of Doolittle’s long career, and also his recent more explicitly philosophical turn, in which he brings each of these revolutionary moments together under an emerging advocacy for explanatory and conceptual pluralism.