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      On the Origin and Trigger of the Notothenioid Adaptive Radiation

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      1 , 2 , 1 , *
      PLoS ONE
      Public Library of Science

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          Abstract

          Adaptive radiation is usually triggered by ecological opportunity, arising through ( i) the colonization of a new habitat by its progenitor; ( ii) the extinction of competitors; or ( iii) the emergence of an evolutionary key innovation in the ancestral lineage. Support for the key innovation hypothesis is scarce, however, even in textbook examples of adaptive radiation. Antifreeze glycoproteins (AFGPs) have been proposed as putative key innovation for the adaptive radiation of notothenioid fishes in the ice-cold waters of Antarctica. A crucial prerequisite for this assumption is the concurrence of the notothenioid radiation with the onset of Antarctic sea ice conditions. Here, we use a fossil-calibrated multi-marker phylogeny of nothothenioid and related acanthomorph fishes to date AFGP emergence and the notothenioid radiation. All time-constraints are cross-validated to assess their reliability resulting in six powerful calibration points. We find that the notothenioid radiation began near the Oligocene-Miocene transition, which coincides with the increasing presence of Antarctic sea ice. Divergence dates of notothenioids are thus consistent with the key innovation hypothesis of AFGP. Early notothenioid divergences are furthermore congruent with vicariant speciation and the breakup of Gondwana.

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          Rapid Cenozoic glaciation of Antarctica induced by declining atmospheric CO2.

          The sudden, widespread glaciation of Antarctica and the associated shift towards colder temperatures at the Eocene/Oligocene boundary (approximately 34 million years ago) (refs 1-4) is one of the most fundamental reorganizations of global climate known in the geologic record. The glaciation of Antarctica has hitherto been thought to result from the tectonic opening of Southern Ocean gateways, which enabled the formation of the Antarctic Circumpolar Current and the subsequent thermal isolation of the Antarctic continent. Here we simulate the glacial inception and early growth of the East Antarctic Ice Sheet using a general circulation model with coupled components for atmosphere, ocean, ice sheet and sediment, and which incorporates palaeogeography, greenhouse gas, changing orbital parameters, and varying ocean heat transport. In our model, declining Cenozoic CO2 first leads to the formation of small, highly dynamic ice caps on high Antarctic plateaux. At a later time, a CO2 threshold is crossed, initiating ice-sheet height/mass-balance feedbacks that cause the ice caps to expand rapidly with large orbital variations, eventually coalescing into a continental-scale East Antarctic Ice Sheet. According to our simulation the opening of Southern Ocean gateways plays a secondary role in this transition, relative to CO2 concentration.
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            Paleontological evidence to date the tree of life.

            The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.
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              Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.

              Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models. We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model. We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models. The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models. These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                18 April 2011
                : 6
                : 4
                : e18911
                Affiliations
                [1 ]Zoological Institute, University of Basel, Basel, Switzerland
                [2 ]Institute of Fisheries Ecology, Johann Heinrich von Thünen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
                Laboratoire Arago, France
                Author notes

                Conceived and designed the experiments: MM RH WS. Performed the experiments: MM. Analyzed the data: MM WS. Contributed reagents/materials/analysis tools: MM RH WS. Wrote the paper: MM RH WS.

                Article
                PONE-D-11-01227
                10.1371/journal.pone.0018911
                3078932
                21533117
                c2ff21fd-a5c8-4973-aa9b-0d463b255df4
                Matschiner et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 7 January 2011
                : 11 March 2011
                Page count
                Pages: 9
                Categories
                Research Article
                Biology
                Ecology
                Biogeography
                Evolutionary Biology
                Evolutionary Processes
                Adaptation
                Evolutionary Systematics
                Phylogenetics
                Organismal Evolution
                Animal Evolution
                Marine Biology
                Paleontology
                Vertebrate Paleontology

                Uncategorized
                Uncategorized

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