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      Phylogenetic incongruence in Cymbidium orchids

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          Abstract

          Cymbidium, which includes approximately 80 species, is one of the most ornamental and cultivated orchid genera. However, a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus. In the present study, we reconstructed the phylogenetic relationships by utilizing one nuclear DNA (nrITS) and seven plastid genes ( rbcL, trnS, trnG, matK, trnL, psbA, and atpI) from 70 species (varieties) in Cymbidium. We also examined the occurrence of phylogenetic conflict between nuclear (nrITS) and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus. We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics. Our results do not support previous classification of the subgenera and sections within Cymbidium. Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium. Overall, our study indicates that Cymbidium has undergone a complex evolution.

          Highlights

          • •

            A comprehensive understanding of  Cymbidium phylogeny.

          • •

            Reticulate evolution occurred in the genus  Cymbidium.

          • •

            Cymbidium has a complex evolution.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          R. C. Edgar (2004)
          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

            K Tamura, D. Peterson, N. Peterson … (2011)
            Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
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              Creating the CIPRES Science Gateway for inference of large phylogenetic trees

              Mark A. Miller, Wayne Pfeiffer, Terri Schwartz (2010)
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                Author and article information

                Contributors
                Zhong-Jian Liu
                Si-Ren Lan
                Journal
                Journal ID (nlm-ta): Plant Divers
                Journal ID (iso-abbrev): Plant Divers
                Title: Plant Diversity
                Publisher: Kunming Institute of Botany, Chinese Academy of Sciences
                ISSN (Print): 2096-2703
                ISSN (Electronic): 2468-2659
                Publication date PMC-release: 09 September 2021
                Publication date Collection: December 2021
                Publication date (Electronic): 09 September 2021
                Volume: 43
                Issue: 6
                Pages: 452-461
                Affiliations
                [a ]Forestry College of Fujian Agriculture and Forestry University, Fuzhou, 350002, China
                [b ]Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
                [c ]Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
                Author notes
                [∗ ]Corresponding author. zjliu@ 123456fafu.edu.cn
                [∗∗ ]Corresponding author. Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China lkzx@ 123456fafu.edu.cn
                [1]

                These authors contributed equally to this work.

                Article
                Publisher Item ID: S2468-2659(21)00107-4
                DOI: 10.1016/j.pld.2021.08.002
                PMC ID: 8720702
                PubMed ID: 35024514
                SO-VID: 8d65cd17-6cc3-470f-ae59-926959d22ad7
                Copyright © © 2021 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.
                License:

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                Date received : 10 October 2020
                Date revision received : 11 August 2021
                Date accepted : 13 August 2021
                Categories
                Subject: Research Paper

                Keywords: cymbidium,phylogenetic conflict,nrits,cpdna,reticulate evolution
                Data availability:
                Keywords: cymbidium, phylogenetic conflict, nrits, cpdna, reticulate evolution

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