The Experts below are selected from a list of 321 Experts worldwide ranked by ideXlab platform
Douglas L. Theobald - One of the best experts on this subject based on the ideXlab platform.
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On universal Common Ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
Biology direct, 2011Co-Authors: Douglas L. TheobaldAbstract:Background The universal Common Ancestry (UCA) of all known life is a fundamental component of modern evolutionary theory, supported by a wide range of qualitative molecular evidence. Nevertheless, recently both the status and nature of UCA has been questioned. In earlier work I presented a formal, quantitative test of UCA in which model selection criteria overwhelmingly choose Common Ancestry over independent Ancestry, based on a dataset of universally conserved proteins. These model-based tests are founded in likelihoodist and Bayesian probability theory, in opposition to classical frequentist null hypothesis tests such as Karlin-Altschul E-values for sequence similarity. In a recent comment, Koonin and Wolf (K&W) claim that the model preference for UCA is "a trivial consequence of significant sequence similarity". They support this claim with a computational simulation, derived from universally conserved proteins, which produces similar sequences lacking phylogenetic structure. The model selection tests prefer Common Ancestry for this artificial data set.
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A formal test of the theory of universal Common Ancestry
Nature, 2010Co-Authors: Douglas L. TheobaldAbstract:Universal Common Ancestry (UCA), the idea that all terrestrial life is genetically related, from some warm little pond as Darwin put it, has become central to modern evolutionary theory. The classic evidence for UCA is extensive, but largely qualitative, and the theory is rarely subjected to a formal, quantitative test. And the UCA view has been called into question by the existence of extensive horizontal gene transfer in many organisms. Douglas Theobald has framed the UCA view as a formal hypothesis and put it to the test using Bayesian statistical analysis of the sequences of universally conserved proteins and contrasting the results with alternative models where genetic similarity is not assumed to reflect phylogenetic relatedness. The UCA view wins out: a single origin of life is overwhelmingly more likely than any competing hypothesis.
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A formal test of the theory of universal Common Ancestry
Nature, 2010Co-Authors: Douglas L. TheobaldAbstract:Universal Common Ancestry (UCA), the idea that all terrestrial life is genetically related, from some “warm little pond” as Darwin put it, has become central to modern evolutionary theory. The classic evidence for UCA is extensive, but largely qualitative, and the theory is rarely subjected to a formal, quantitative test. And the UCA view has been called into question by the existence of extensive horizontal gene transfer in many organisms. Douglas Theobald has framed the UCA view as a formal hypothesis and put it to the test using Bayesian statistical analysis of the sequences of universally conserved proteins and contrasting the results with alternative models where genetic similarity is not assumed to reflect phylogenetic relatedness. The UCA view wins out: a single origin of life is overwhelmingly more likely than any competing hypothesis. It is generally assumed that life had a single origin — or, at least, that all extant life descended from a 'universal Common ancestor' (UCA) — although this view has been called into question by evidence for extensive horizontal gene transfer. Here, the UCA view is framed as a formal hypothesis and tested (crucially, without assuming that genetic similarity reflects genetic kinship). The UCA view triumphs: a single origin of life is overwhelmingly more likely than any competing hypothesis. Universal Common Ancestry (UCA) is a central pillar of modern evolutionary theory^ 1 . As first suggested by Darwin^ 2 , the theory of UCA posits that all extant terrestrial organisms share a Common genetic heritage, each being the genealogical descendant of a single species from the distant past^ 3 , 4 , 5 , 6 . The classic evidence for UCA, although massive, is largely restricted to ‘local’ Common Ancestry—for example, of specific phyla rather than the entirety of life—and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing^ 7 , 8 , 9 , 10 , and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope^ 1 , 5 , 8 , 9 , 11 , 12 , 13 , 14 , 15 . Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life^ 11 , 14 , 15 . Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory^ 5 , 16 , 17 to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent Ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.
Elliott Sober - One of the best experts on this subject based on the ideXlab platform.
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Similarities as Evidence for Common Ancestry{A Likelihood Epistemology
The British Journal for the Philosophy of Science, 2017Co-Authors: Elliott Sober, Mike SteelAbstract:AbstractDarwin claims in the Origin that similarity is evidence for Common ances-try, but that adaptive similarities are \almost valueless" as evidence. Thisclaim seems reasonable for some adaptive similarities but not for others.Here we clarify and evaluate these and related matters by using the lawof likelihood as an analytic tool and by considering mathematical modelsof three evolutionary processes { directional selection, stabilizing selection,and drift. Our results apply both to Darwin’s theory of evolution and tomodern evolutionary biology. Keywords: Common Ancestry, Darwin, drift, likelihood, natural selection. 1 Introduction In the last paragraph of the Origin, Darwin (1859, p. 490) says that, in the begin-ning, life was breathed \into a few forms, or into one." The caution embodied in\one or a few" is not to be found in present-day biology, which embraces the ideaof universal Common Ancestry. Darwin tentatively reaches towards that strongerthesis a few pages earlier:... I believe that animals have descended from at most only four or ve progenitors, and plants from an equal or lesser number. Analogywould lead me one step further, namely to the belief that all animalsand plants have descended from some one prototype. But analogymay be a deceitful guide. Nevertheless all living things have much inCommon, in their chemical composition, their germinal vesicles, theircellular structure, and their laws of growth and reproduction. We seethis even in so triing a circumstance as that the same poison oftensimilarly a ects plants and animals; or that the poison secreted bythe gall-y produces monstrous growths on the wild rose or oak-tree.Therefore I should infer from analogy that probably all organic beingswhich have ever lived on this earth have descended from some oneprimordial form, into which life was rst breathed. (Darwin 1859, p.484)Darwin’s idea that universal Common Ancestry is supported by the fact that \allliving things have much in Common" is an instance of a broader principle: whentwo or more taxa have trait X, this similarity favors the hypothesis of CommonAncestry over the hypothesis of separate Ancestry.2
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similarities as evidence for Common Ancestry a likelihood epistemology
The British Journal for the Philosophy of Science, 2017Co-Authors: Elliott Sober, Mike SteelAbstract:AbstractDarwin claims in the Origin that similarity is evidence for Common ances-try, but that adaptive similarities are \almost valueless" as evidence. Thisclaim seems reasonable for some adaptive similarities but not for others.Here we clarify and evaluate these and related matters by using the lawof likelihood as an analytic tool and by considering mathematical modelsof three evolutionary processes { directional selection, stabilizing selection,and drift. Our results apply both to Darwin’s theory of evolution and tomodern evolutionary biology. Keywords: Common Ancestry, Darwin, drift, likelihood, natural selection. 1 Introduction In the last paragraph of the Origin, Darwin (1859, p. 490) says that, in the begin-ning, life was breathed \into a few forms, or into one." The caution embodied in\one or a few" is not to be found in present-day biology, which embraces the ideaof universal Common Ancestry. Darwin tentatively reaches towards that strongerthesis a few pages earlier:... I believe that animals have descended from at most only four or ve progenitors, and plants from an equal or lesser number. Analogywould lead me one step further, namely to the belief that all animalsand plants have descended from some one prototype. But analogymay be a deceitful guide. Nevertheless all living things have much inCommon, in their chemical composition, their germinal vesicles, theircellular structure, and their laws of growth and reproduction. We seethis even in so triing a circumstance as that the same poison oftensimilarly a ects plants and animals; or that the poison secreted bythe gall-y produces monstrous growths on the wild rose or oak-tree.Therefore I should infer from analogy that probably all organic beingswhich have ever lived on this earth have descended from some oneprimordial form, into which life was rst breathed. (Darwin 1859, p.484)Darwin’s idea that universal Common Ancestry is supported by the fact that \allliving things have much in Common" is an instance of a broader principle: whentwo or more taxa have trait X, this similarity favors the hypothesis of CommonAncestry over the hypothesis of separate Ancestry.2
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How probable is Common Ancestry according to different evolutionary processes
Journal of theoretical biology, 2015Co-Authors: Elliott Sober, Mike SteelAbstract:Darwin and contemporary biologists argue that all present-day life traces back to one or a few Common ancestors. Here we investigate the relationship of different evolutionary processes to this hypothesis of Common Ancestry. We identify the property of an evolutionary process that determines what its probabilistic impact on the Common Ancestry thesis will be. The point of this exercise is to understand how the parts of Darwin׳s powerful theory fit together, not to call into question Common Ancestry or natural selection, since these two pillars of Darwin׳s theory enjoy strong support.
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Similarities as Evidence for Common Ancestry -- A Likelihood Epistemology
arXiv: Populations and Evolution, 2015Co-Authors: Elliott Sober, Mike SteelAbstract:Darwin claims in the {\em Origin} that similarity is evidence for Common Ancestry, but that adaptive similarities are "almost valueless" as evidence. This claim seems reasonable for some adaptive similarities but not for others. Here we clarify and evaluate these and related matters by using the law of likelihood as an analytic tool and by considering mathematical models of three evolutionary processes -- directional selection, stabilizing selection, and drift. Our results apply both to Darwin's theory of evolution and to modern evolutionary biology.
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Anthropomorphism, Parsimony, and Common Ancestry
Mind & Language, 2012Co-Authors: Elliott SoberAbstract:I consider three theses that are friendly to anthropomorphism. Each makes a claim about what can be inferred about the mental life of chimpanzees from the fact that humans and chimpanzees both have behavioral trait B and humans produce this behavior by having mental trait M. The first thesis asserts that this fact makes it probable that chimpanzees have M. The second says that this fact provides strong evidence that chimpanzees have M. The third claims that the fact is evidence that chimpanzees have M. The third thesis follows from a plausible Reichenbachian model of how a Common ancestor is probabilistically related to its descendants. The first two theses do not, and they have no general evolutionary justification.
Mike Steel - One of the best experts on this subject based on the ideXlab platform.
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Similarities as Evidence for Common Ancestry{A Likelihood Epistemology
The British Journal for the Philosophy of Science, 2017Co-Authors: Elliott Sober, Mike SteelAbstract:AbstractDarwin claims in the Origin that similarity is evidence for Common ances-try, but that adaptive similarities are \almost valueless" as evidence. Thisclaim seems reasonable for some adaptive similarities but not for others.Here we clarify and evaluate these and related matters by using the lawof likelihood as an analytic tool and by considering mathematical modelsof three evolutionary processes { directional selection, stabilizing selection,and drift. Our results apply both to Darwin’s theory of evolution and tomodern evolutionary biology. Keywords: Common Ancestry, Darwin, drift, likelihood, natural selection. 1 Introduction In the last paragraph of the Origin, Darwin (1859, p. 490) says that, in the begin-ning, life was breathed \into a few forms, or into one." The caution embodied in\one or a few" is not to be found in present-day biology, which embraces the ideaof universal Common Ancestry. Darwin tentatively reaches towards that strongerthesis a few pages earlier:... I believe that animals have descended from at most only four or ve progenitors, and plants from an equal or lesser number. Analogywould lead me one step further, namely to the belief that all animalsand plants have descended from some one prototype. But analogymay be a deceitful guide. Nevertheless all living things have much inCommon, in their chemical composition, their germinal vesicles, theircellular structure, and their laws of growth and reproduction. We seethis even in so triing a circumstance as that the same poison oftensimilarly a ects plants and animals; or that the poison secreted bythe gall-y produces monstrous growths on the wild rose or oak-tree.Therefore I should infer from analogy that probably all organic beingswhich have ever lived on this earth have descended from some oneprimordial form, into which life was rst breathed. (Darwin 1859, p.484)Darwin’s idea that universal Common Ancestry is supported by the fact that \allliving things have much in Common" is an instance of a broader principle: whentwo or more taxa have trait X, this similarity favors the hypothesis of CommonAncestry over the hypothesis of separate Ancestry.2
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similarities as evidence for Common Ancestry a likelihood epistemology
The British Journal for the Philosophy of Science, 2017Co-Authors: Elliott Sober, Mike SteelAbstract:AbstractDarwin claims in the Origin that similarity is evidence for Common ances-try, but that adaptive similarities are \almost valueless" as evidence. Thisclaim seems reasonable for some adaptive similarities but not for others.Here we clarify and evaluate these and related matters by using the lawof likelihood as an analytic tool and by considering mathematical modelsof three evolutionary processes { directional selection, stabilizing selection,and drift. Our results apply both to Darwin’s theory of evolution and tomodern evolutionary biology. Keywords: Common Ancestry, Darwin, drift, likelihood, natural selection. 1 Introduction In the last paragraph of the Origin, Darwin (1859, p. 490) says that, in the begin-ning, life was breathed \into a few forms, or into one." The caution embodied in\one or a few" is not to be found in present-day biology, which embraces the ideaof universal Common Ancestry. Darwin tentatively reaches towards that strongerthesis a few pages earlier:... I believe that animals have descended from at most only four or ve progenitors, and plants from an equal or lesser number. Analogywould lead me one step further, namely to the belief that all animalsand plants have descended from some one prototype. But analogymay be a deceitful guide. Nevertheless all living things have much inCommon, in their chemical composition, their germinal vesicles, theircellular structure, and their laws of growth and reproduction. We seethis even in so triing a circumstance as that the same poison oftensimilarly a ects plants and animals; or that the poison secreted bythe gall-y produces monstrous growths on the wild rose or oak-tree.Therefore I should infer from analogy that probably all organic beingswhich have ever lived on this earth have descended from some oneprimordial form, into which life was rst breathed. (Darwin 1859, p.484)Darwin’s idea that universal Common Ancestry is supported by the fact that \allliving things have much in Common" is an instance of a broader principle: whentwo or more taxa have trait X, this similarity favors the hypothesis of CommonAncestry over the hypothesis of separate Ancestry.2
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How probable is Common Ancestry according to different evolutionary processes
Journal of theoretical biology, 2015Co-Authors: Elliott Sober, Mike SteelAbstract:Darwin and contemporary biologists argue that all present-day life traces back to one or a few Common ancestors. Here we investigate the relationship of different evolutionary processes to this hypothesis of Common Ancestry. We identify the property of an evolutionary process that determines what its probabilistic impact on the Common Ancestry thesis will be. The point of this exercise is to understand how the parts of Darwin׳s powerful theory fit together, not to call into question Common Ancestry or natural selection, since these two pillars of Darwin׳s theory enjoy strong support.
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Similarities as Evidence for Common Ancestry -- A Likelihood Epistemology
arXiv: Populations and Evolution, 2015Co-Authors: Elliott Sober, Mike SteelAbstract:Darwin claims in the {\em Origin} that similarity is evidence for Common Ancestry, but that adaptive similarities are "almost valueless" as evidence. This claim seems reasonable for some adaptive similarities but not for others. Here we clarify and evaluate these and related matters by using the law of likelihood as an analytic tool and by considering mathematical models of three evolutionary processes -- directional selection, stabilizing selection, and drift. Our results apply both to Darwin's theory of evolution and to modern evolutionary biology.
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Origins of life: Common Ancestry put to the test.
Nature, 2010Co-Authors: Mike Steel, David PennyAbstract:The question of whether or not all life on Earth has an ultimate Common origin is a subtle one, complicated by the phenomenon of lateral gene transfer. It has now been tackled with a formal statistical analysis. Universal Common Ancestry (UCA), the idea that all terrestrial life is genetically related, from some “warm little pond” as Darwin put it, has become central to modern evolutionary theory. The classic evidence for UCA is extensive, but largely qualitative, and the theory is rarely subjected to a formal, quantitative test. And the UCA view has been called into question by the existence of extensive horizontal gene transfer in many organisms. Douglas Theobald has framed the UCA view as a formal hypothesis and put it to the test using Bayesian statistical analysis of the sequences of universally conserved proteins and contrasting the results with alternative models where genetic similarity is not assumed to reflect phylogenetic relatedness. The UCA view wins out: a single origin of life is overwhelmingly more likely than any competing hypothesis.
Eugene V. Koonin - One of the best experts on this subject based on the ideXlab platform.
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The Common Ancestry of life.
Biology direct, 2010Co-Authors: Eugene V. Koonin, Yuri I. WolfAbstract:Background It is Common belief that all cellular life forms on earth have a Common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide a formal, homology independent test of the Universal Common Ancestry hypothesis by comparing the ability of a Common-Ancestry model and a multiple-Ancestry model to predict sequences of universally conserved proteins.
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Evidence for Common Ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses.
Proceedings of the National Academy of Sciences of the United States of America, 1991Co-Authors: Eugene V. Koonin, Gil H. Choi, Donald L. Nuss, Roni Shapira, James C. CarringtonAbstract:Computer-assisted analysis of the putative polypeptide products encoded by the two open reading frames present in a large virus-like double-stranded RNA, L-dsRNA, associated with hypovirulence of the chestnut blight fungus, Cryphonectria parasitica, revealed five distinct domains with significant sequence similarity to previously described conserved domains within plant potyvirus-encoded polyproteins. These included the putative RNA-dependent RNA polymerase, RNA helicase, two papain-like cysteine proteases related to the potyvirus helper-component protease, and a cysteine-rich domain of unknown function similar to the N-terminal portion of the potyvirus helper-component protein. Phylogenetic trees derived from the alignment of the polymerase domains of L-dsRNA, a subset of positive-stranded RNA viruses, and double-stranded RNA viruses, using three independent algorithms, suggested that the hypovirulence-associated dsRNA and potyvirus genomes share a Common Ancestry. However, comparison of the organization of the conserved domains within the encoded polyproteins of the respective viruses indicated that the proposed subsequent evolution involved extensive genome rearrangement.
Herve Seligmann - One of the best experts on this subject based on the ideXlab platform.
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syntenies between cohosted mitochondrial chloroplast and phycodnavirus genomes functional mimicry and or Common Ancestry
DNA and Cell Biology, 2019Co-Authors: Herve SeligmannAbstract:Recent analyses suggest bacterial and/or mitochondrion-like Ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond Common Ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.
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Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry?
DNA and cell biology, 2019Co-Authors: Herve SeligmannAbstract:Recent analyses suggest bacterial and/or mitochondrion-like Ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond Common Ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.
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Unifying view of stem-loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses
Current Opinion in Microbiology, 2016Co-Authors: Herve SeligmannAbstract:Putatively, stem-loop RNA hairpins explain networks of selfish elements and RNA world remnants. Their genomic density increases with intracellular lifestyle, especially when comparing giant viruses and their virophages. RNA protogenomes presumably templated for mRNAs and self replicating stem-loops, ancestors of modern genes and parasitic sequences, including tRNAs and rRNAs. Primary and secondary structure analyses suggest Common Ancestry for t/rRNAs and parasitic RNAs, parsimoniously link diverse RNA metabolites (replication origins, tRNAs, ribozymes, riboswitches, miRNAs and rRNAs) to parasitic RNAs (ribosomal viroids, Rickettsia repeated palindromic elements (RPE), stem-loop hairpins in giant viruses, their virophages, and transposable retrovirus-derived elements). Results indicate ongoing genesis of small RNA metabolites, and Common Ancestry or similar genesis for rRNA and retroviral sequences. Assuming functional integration of modular duplicated RNA hairpins evolutionarily unifies diverse molecules, postulating stem-loop hairpin RNAs as origins of genetic innovation, ancestors of rRNAs, retro- and Mimivirus sequences, and cells.