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  • 1
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    Phylogenies reveal new interpretation of speciation and the Red Queen (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-17
    Description: The Red Queen describes a view of nature in which species continually evolve but do not become better adapted. It is one of the more distinctive metaphors of evolutionary biology, but no test of its claim that speciation occurs at a constant rate has ever been made against competing models that can predict virtually identical outcomes, nor has any mechanism been proposed that could cause the constant-rate phenomenon. Here we use 101 phylogenies of animal, plant and fungal taxa to test the constant-rate claim against four competing models. Phylogenetic branch lengths record the amount of time or evolutionary change between successive events of speciation. The models predict the distribution of these lengths by specifying how factors combine to bring about speciation, or by describing how rates of speciation vary throughout a tree. We find that the hypotheses that speciation follows the accumulation of many small events that act either multiplicatively or additively found support in 8% and none of the trees, respectively. A further 8% of trees hinted that the probability of speciation changes according to the amount of divergence from the ancestral species, and 6% suggested speciation rates vary among taxa. By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation. This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events that cause reproductive isolation. Attempts to understand species-radiations or why some groups have more or fewer species should look to the size of the catalogue of potential causes of speciation shared by a group of closely related organisms rather than to how those causes combine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venditti, Chris -- Meade, Andrew -- Pagel, Mark -- England -- Nature. 2010 Jan 21;463(7279):349-52. doi: 10.1038/nature08630. Epub 2009 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6BX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010607" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Genetic Speciation ; *Models, Biological ; *Phylogeny ; Selection, Genetic ; Stochastic Processes
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Rise of the digital machine (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pagel, Mark -- England -- Nature. 2008 Apr 10;452(7188):699. doi: 10.1038/452699a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18401394" target="_blank"〉PubMed〈/a〉
    Keywords: Analog-Digital Conversion ; Animals ; *Biological Evolution ; Cooperative Behavior ; Humans ; *Models, Biological ; Phenotype ; Repetitive Sequences, Nucleic Acid/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Genotypic sex determination enabled adaptive radiations of extinct marine reptiles (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-09-18
    Description: Adaptive radiations often follow the evolution of key traits, such as the origin of the amniotic egg and the subsequent radiation of terrestrial vertebrates. The mechanism by which a species determines the sex of its offspring has been linked to critical ecological and life-history traits but not to major adaptive radiations, in part because sex-determining mechanisms do not fossilize. Here we establish a previously unknown coevolutionary relationship in 94 amniote species between sex-determining mechanism and whether a species bears live young or lays eggs. We use that relationship to predict the sex-determining mechanism in three independent lineages of extinct Mesozoic marine reptiles (mosasaurs, sauropterygians and ichthyosaurs), each of which is known from fossils to have evolved live birth. Our results indicate that each lineage evolved genotypic sex determination before acquiring live birth. This enabled their pelagic radiations, where the relatively stable temperatures of the open ocean constrain temperature-dependent sex determination in amniote species. Freed from the need to move and nest on land, extreme physical adaptations to a pelagic lifestyle evolved in each group, such as the fluked tails, dorsal fins and wing-shaped limbs of ichthyosaurs. With the inclusion of ichthyosaurs, mosasaurs and sauropterygians, genotypic sex determination is present in all known fully pelagic amniote groups (sea snakes, sirenians and cetaceans), suggesting that this mode of sex determination and the subsequent evolution of live birth are key traits required for marine adaptive radiations in amniote lineages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Organ, Chris L -- Janes, Daniel E -- Meade, Andrew -- Pagel, Mark -- 1 F32 GM075490-01/GM/NIGMS NIH HHS/ -- 5 F32 GM072494/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Sep 17;461(7262):389-92. doi: 10.1038/nature08350.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA. corgan@oeb.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19759619" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/genetics/physiology ; Algorithms ; Animals ; Bayes Theorem ; *Biological Evolution ; *Extinction, Biological ; Female ; Fossils ; Genotype ; History, Ancient ; Male ; Marine Biology ; Markov Chains ; Monte Carlo Method ; Oviposition/genetics/physiology ; Phylogeny ; Reptiles/classification/*genetics/*physiology ; Sex Chromosomes/*genetics ; *Sex Determination Processes ; Sex Ratio ; Temperature ; Viviparity, Nonmammalian/genetics/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Natural selection 150 years on (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-02-13
    Description: The theory of evolution by natural selection has prospered in its first 150 years and provides a consistent account of species as highly adapted and rare survivors in the struggle for existence. It now faces the challenge of finding order in the evolution of complex systems, including human society.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pagel, Mark -- England -- Nature. 2009 Feb 12;457(7231):808-11. doi: 10.1038/nature07889.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK. m.pagel@reading.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19212397" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biology/*history ; Genetic Speciation ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; Periodicals as Topic ; *Selection, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Large punctuational contribution of speciation to evolutionary divergence at the molecular level (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-10-07
    Description: A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pagel, Mark -- Venditti, Chris -- Meade, Andrew -- New York, N.Y. -- Science. 2006 Oct 6;314(5796):119-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK. m.pagel@rdg.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17023657" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Bayes Theorem ; DNA/*genetics ; DNA, Fungal/genetics ; DNA, Plant/genetics ; *Evolution, Molecular ; Founder Effect ; Fungi/classification/genetics ; *Genetic Speciation ; Genetic Variation ; Likelihood Functions ; Mathematics ; Models, Statistical ; Mutation ; Phylogeny ; Plants/classification/genetics ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Molecular phylogenies link rates of evolution and speciation (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-07-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Webster, Andrea J -- Payne, Robert J H -- Pagel, Mark -- New York, N.Y. -- Science. 2003 Jul 25;301(5632):478.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Animal and Microbial Sciences, University of Reading, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12881561" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; *Evolution, Molecular ; *Genes ; Likelihood Functions ; Mathematics ; Models, Statistical ; *Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    On the regulation of populations of mammals, birds, fish, and insects (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-07-26
    Description: A key unresolved question in population ecology concerns the relationship between a population's size and its growth rate. We estimated this relationship for 1780 time series of mammals, birds, fish, and insects. We found that rates of population growth are high at low population densities but, contrary to previous predictions, decline rapidly with increasing population size and then flatten out, for all four taxa. This produces a strongly concave relationship between a population's growth rate and its size. These findings have fundamental implications for our understanding of animals' lives, suggesting in particular that many animals in these taxa will be found living at densities above the carrying capacity of their environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sibly, Richard M -- Barker, Daniel -- Denham, Michael C -- Hone, Jim -- Pagel, Mark -- New York, N.Y. -- Science. 2005 Jul 22;309(5734):607-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK. r.m.sibly@reading.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16040705" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Wild ; *Birds ; Conservation of Natural Resources ; Databases, Factual ; *Ecosystem ; Environment ; *Fishes ; *Insects ; Logistic Models ; *Mammals ; Mathematics ; Models, Biological ; Phylogeny ; Population Density ; Population Dynamics ; Population Growth ; Regression Analysis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Multiple routes to mammalian diversity (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-10-21
    Description: The radiation of the mammals provides a 165-million-year test case for evolutionary theories of how species occupy and then fill ecological niches. It is widely assumed that species often diverge rapidly early in their evolution, and that this is followed by a longer, drawn-out period of slower evolutionary fine-tuning as natural selection fits organisms into an increasingly occupied niche space. But recent studies have hinted that the process may not be so simple. Here we apply statistical methods that automatically detect temporal shifts in the rate of evolution through time to a comprehensive mammalian phylogeny and data set of body sizes of 3,185 extant species. Unexpectedly, the majority of mammal species, including two of the most speciose orders (Rodentia and Chiroptera), have no history of substantial and sustained increases in the rates of evolution. Instead, a subset of the mammals has experienced an explosive increase (between 10- and 52-fold) in the rate of evolution along the single branch leading to the common ancestor of their monophyletic group (for example Chiroptera), followed by a quick return to lower or background levels. The remaining species are a taxonomically diverse assemblage showing a significant, sustained increase or decrease in their rates of evolution. These results necessarily decouple morphological diversification from speciation and suggest that the processes that give rise to the morphological diversity of a class of animals are far more free to vary than previously considered. Niches do not seem to fill up, and diversity seems to arise whenever, wherever and at whatever rate it is advantageous.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venditti, Chris -- Meade, Andrew -- Pagel, Mark -- England -- Nature. 2011 Oct 19;479(7373):393-6. doi: 10.1038/nature10516.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK. c.venditti@hull.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22012260" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Biological Evolution ; Body Size ; Genetic Speciation ; Mammals/anatomy & histology/classification/*physiology ; Models, Biological ; Phylogeny ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Evolutionary biology: Birds of a feather (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-11-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ricklefs, Robert E -- Pagel, Mark -- England -- Nature. 2012 Nov 15;491(7424):336-7. doi: 10.1038/nature11642. Epub 2012 Oct 31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23123856" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Birds/*classification ; *Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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    Evolution: Adapted to culture (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-02-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pagel, Mark -- England -- Nature. 2012 Feb 15;482(7385):297-9. doi: 10.1038/482297a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Reading, UK. m.pagel@reading.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22337031" target="_blank"〉PubMed〈/a〉
    Keywords: Altruism ; Animals ; *Communication/history ; *Cultural Evolution/history ; History, Ancient ; Humans ; Knowledge ; *Language/history ; Learning ; *Social Behavior/history ; Social Justice/psychology ; Survival
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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