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      Phylogeny and biogeography of the amphi-Pacific genus Aphananthe

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          Abstract

          Aphananthe is a small genus of five species showing an intriguing amphi-Pacific distribution in eastern, southern and southeastern Asia, Australia, and Mexico, also with one species in Madagascar. The phylogenetic relationships of Aphananthe were reconstructed with two nuclear (ITS & ETS) and two plastid ( psbA- trnH & trnL- trnF) regions. Clade divergence times were estimated with a Bayesian approach, and the ancestral areas were inferred using the dispersal-extinction-cladogenesis and Bayesian Binary MCMC analyses. Aphananthe was supported to be monophyletic, with the eastern Asian A. aspera resolved as sister to a clade of the remaining four species. Aphananthe was inferred to have originated in the Late Cretaceous (71.5 mya, with 95% HPD: 66.6–81.3 mya), and the crown age of the genus was dated to be in the early Miocene (19.1 mya, with 95% HPD: 12.4–28.9 mya). The fossil record indicates that Aphananthe was present in the high latitude thermophilic forests in the early Tertiary, and experienced extinctions from the middle Tertiary onwards. Aphananthe originated in Europe based on the inference that included fossil and extant species, but eastern Asia was estimated to be the ancestral area of the clade of the extant species of Aphananthe. Both the West Gondwanan vicariance hypothesis and the boreotropics hypothesis could be excluded as explanation for its amphi-Pacific distribution. Long-distance dispersals out of eastern Asia into North America, southern and southeastern Asia and Australia, and Madagascar during the Miocene account for its wide intercontinental disjunct distribution.

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          Trends, rhythms, and aberrations in global climate 65 Ma to present.

          Since 65 million years ago (Ma), Earth's climate has undergone a significant and complex evolution, the finer details of which are now coming to light through investigations of deep-sea sediment cores. This evolution includes gradual trends of warming and cooling driven by tectonic processes on time scales of 10(5) to 10(7) years, rhythmic or periodic cycles driven by orbital processes with 10(4)- to 10(6)-year cyclicity, and rare rapid aberrant shifts and extreme climate transients with durations of 10(3) to 10(5) years. Here, recent progress in defining the evolution of global climate over the Cenozoic Era is reviewed. We focus primarily on the periodic and anomalous components of variability over the early portion of this era, as constrained by the latest generation of deep-sea isotope records. We also consider how this improved perspective has led to the recognition of previously unforeseen mechanisms for altering climate.
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            Chronology of fluctuating sea levels since the triassic.

            Advances in sequence stratigraphy and the development of depositional models have helped explain the origin of genetically related sedimentary packages during sea level cycles. These concepts have provided the basis for the recognition of sea level events in subsurface data and in outcrops of marine sediments around the world. Knowledge of these events has led to a new generation of Mesozoic and Cenozoic global cycle charts that chronicle the history of sea level fluctuations during the past 250 million years in greater detail than was possible from seismic-stratigraphic data alone. An effort has been made to develop a realistic and accurate time scale and widely applicable chronostratigraphy and to integrate depositional sequences documented in public domain outcrop sections from various basins with this chronostratigraphic framework. A description of this approach and an account of the results, illustrated by sea level cycle charts of the Cenozoic, Cretaceous, Jurassic, and Triassic intervals, are presented.
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              The Phanerozoic record of global sea-level change.

              K. Miller (2005)
              We review Phanerozoic sea-level changes [543 million years ago (Ma) to the present] on various time scales and present a new sea-level record for the past 100 million years (My). Long-term sea level peaked at 100 +/- 50 meters during the Cretaceous, implying that ocean-crust production rates were much lower than previously inferred. Sea level mirrors oxygen isotope variations, reflecting ice-volume change on the 10(4)- to 10(6)-year scale, but a link between oxygen isotope and sea level on the 10(7)-year scale must be due to temperature changes that we attribute to tectonically controlled carbon dioxide variations. Sea-level change has influenced phytoplankton evolution, ocean chemistry, and the loci of carbonate, organic carbon, and siliciclastic sediment burial. Over the past 100 My, sea-level changes reflect global climate evolution from a time of ephemeral Antarctic ice sheets (100 to 33 Ma), through a time of large ice sheets primarily in Antarctica (33 to 2.5 Ma), to a world with large Antarctic and large, variable Northern Hemisphere ice sheets (2.5 Ma to the present).
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 February 2017
                2017
                : 12
                : 2
                : e0171405
                Affiliations
                [1 ]Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
                [2 ]Baotou Medical College, Baotou, Inner Mongolia, China
                [3 ]Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC, United States of America
                Institute of Botany, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Data curation: MY.

                • Formal analysis: MY.

                • Funding acquisition: TY DL.

                • Investigation: MY TY.

                • Methodology: MY TY JW.

                • Project administration: TY JW.

                • Resources: TY DL.

                • Software: MY.

                • Supervision: TY JW DL.

                • Validation: MY.

                • Visualization: MY.

                • Writing – original draft: MY TY.

                • Writing – review & editing: MY TY DL.

                Article
                PONE-D-15-39359
                10.1371/journal.pone.0171405
                5295712
                28170425
                e9d19e8f-d2fd-4452-8ecf-ee0e60a9863c
                © 2017 Yang 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 September 2015
                : 27 December 2016
                Page count
                Figures: 3, Tables: 2, Pages: 18
                Funding
                Funded by: National Key Basic Research Program of China
                Award ID: 2014CB954100-01
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31129001
                Award Recipient :
                Funded by: Talent Project of Yunnan Province
                Award ID: 2011C1042
                Award Recipient :
                Funded by: National Natural Science Foundation of China (CN)
                Award ID: 31500181
                Award Recipient :
                This study was supported by grants from the National Key Basic Research Program of China (Grant No. 2014CB954100-01), the National Natural Science Foundation (Project No. 31129001), the Talent Project of Yunnan Province (Project No. 2011CI042), and National Natural Science Foundation (Project No. 31500181).
                Categories
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                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
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                Phylogenetic Analysis
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Phylogenetic Analysis
                Biology and Life Sciences
                Biogeography
                Ecology and Environmental Sciences
                Biogeography
                Earth Sciences
                Geography
                Biogeography
                Biology and Life Sciences
                Paleontology
                Fossils
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                Fossils
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                Geologic Time
                Cenozoic Era
                Neogene Period
                Miocene Epoch
                Biology and Life Sciences
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                Africa
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                Custom metadata
                All sequences produced from this study are available at NCBI (NCBI accession numbers in Table 1) and the data matrix could be found at Data Dryad ( http://dx.doi.org/10.5061/dryad.9082p).

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