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      Biogeography of Coptis Salisb. (Ranunculales, Ranunculaceae, Coptidoideae), an Eastern Asian and North American genus

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          Abstract

          Background

          Numerous studies have favored dispersal (colonization) over vicariance (past fragmentation) events to explain eastern Asian-North American distribution patterns. In plants, however the disjunction between eastern Asia and western North America has been rarely examined using the integration of phylogenetic, molecular dating, and biogeographical methods. Meanwhile, the biogeographic patterns within eastern Asia remain poorly understood. The goldthread genus Coptis Salisb. includes 15 species disjunctly distributed in North America, Japan, mainland China, and Taiwan. We present a dated phylogeny for Coptis under the optimal clock model and infer its historical biogeography by comparing different biogeographic models.

          Results

          The split of Coptis and Xanthorhiza Marshall occurred in the middle Miocene (ca. 15.47 Ma). Coptis started their diversification in the early late Miocene (ca. 9.55 Ma). A late Miocene vicariance event resulted in the eastern Asian and western North American disjunction in the genus. Within eastern Asia, dispersals from mainland Asia to Japan and from Japan to Taiwan occurred at ca. 4.85 Ma and at ca. 1.34 Ma, respectively.

          Conclusions

          Our analyses provide evidence that both vicariance and dispersal events have played important roles in shaping the current distribution and endemism of Coptis, likely resulting from eustatic sea-level changes, mountain formation processes and an increasing drier and cooler climate from the middle Miocene onwards.

          Electronic supplementary material

          The online version of this article (10.1186/s12862-018-1195-0) contains supplementary material, which is available to authorized users.

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          Most cited references55

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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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              PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

              PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.
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                Author and article information

                Contributors
                kunlixiang@ibcas.ac.cn
                erst_andrew@yahoo.com
                xiangxg2010@ibcas.ac.cn
                fjabbour@mnhn.fr
                wangwei1127@ibcas.ac.cn
                Journal
                BMC Evol Biol
                BMC Evol. Biol
                BMC Evolutionary Biology
                BioMed Central (London )
                1471-2148
                24 May 2018
                24 May 2018
                2018
                : 18
                : 74
                Affiliations
                [1 ]ISNI 0000 0004 0596 3367, GRID grid.435133.3, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, ; Beijing, 100093 China
                [2 ]ISNI 0000 0004 1797 8419, GRID grid.410726.6, University of Chinese Academy of Sciences, ; Beijing, 100049 China
                [3 ]ISNI 0000 0004 0487 2025, GRID grid.465435.5, Central Siberian Botanical Garden of the Siberian Branch of Russian Academy of Sciences, ; Zolotodolinskaya str. 101, Novosibirsk, 630090 Russia
                [4 ]ISNI 0000 0001 1088 3909, GRID grid.77602.34, Laboratory of Systematics and Phylogeny of Plants, , Tomsk State University, ; Tomsk, 634050 Russia
                [5 ]Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005 Paris, France
                Author information
                http://orcid.org/0000-0001-6901-6375
                Article
                1195
                10.1186/s12862-018-1195-0
                5968522
                29793422
                f29dca9c-b517-4604-909b-e5c666c9c4ab
                © The Author(s). 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 14 September 2017
                : 17 May 2018
                Funding
                Funded by: the Strategic Priority Research Program of the Chinese Academy of Sciences
                Award ID: XDPB0203
                Award Recipient :
                Funded by: the National Basic Research Program of China
                Award ID: 2014CB954100
                Award Recipient :
                Funded by: the National Natural Science Foundation of China
                Award ID: 31270269, 31770231 and 31470315
                Award Recipient :
                Funded by: the Youth Innovation Promotion Association Foundation of CAS
                Funded by: the D.I. Mendeleev Scientific Fund Program of Tomsk State University
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2018

                Evolutionary Biology
                ancestral range evolution,climate change,coptis,eastern asian,taiwan,western north america

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