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      Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics

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          Abstract

          Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                14 March 2023
                2023
                : 14
                : 1089165
                Affiliations
                [1] 1 Department of Islands and Coast Biodiversity, Division of Botany, Honam National Institute of Biological Resources , Mokpo, Republic of Korea
                [2] 2 Department of Botany, Graduate School of Science, Kyoto University , Kyoto, Japan
                [3] 3 Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University , Daegu, Republic of Korea
                [4] 4 Department of Biological Sciences, Sungkyunkwan University , Suwon, Republic of Korea
                [5] 5 Botanical Garden-Institute, Far Eastern Branch of the Russian Academy of Sciences , Vladivostok, Russia
                [6] 6 Botanical Gardens, Tohoku University , Sendai, Japan
                Author notes

                Edited by: Mi-Jeong Yoo, Clarkson University, United States

                Reviewed by: Shih-Hui Liu, National Sun Yat-sen University, Taiwan; Zelong Nie, Jishou University, China

                †These authors have contributed equally to this work and share first authorship

                This article was submitted to Plant Systematics and Evolution, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2023.1089165
                10043388
                36998693
                f9863251-08c2-45ba-8d88-f7d481866e33
                Copyright © 2023 Kim, Kim, Yang, Cho, Koldaeva, Ito, Maki and Kim

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 04 November 2022
                : 23 February 2023
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 73, Pages: 15, Words: 9215
                Funding
                Funded by: National Institute of Biological Resources , doi 10.13039/501100005880;
                Award ID: 2020NIBR202005201
                This research was funded in part by the National Institute of Biological Resources (NIBR, grant number 2020NIBR202005201), under the program of “A Study on Plant Resources on DNA Sequences Utilizing Next Generation Sequencing Technique (3rd year).”
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                aizopsis,aneuploid series,phedimus,polyploid,subgenus aizoon ,plastome,nrdna its
                Plant science & Botany
                aizopsis, aneuploid series, phedimus, polyploid, subgenus aizoon , plastome, nrdna its

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