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      Molecular and morphological evidence support a new species of Rosaceae Prunus subg. Cerasus from Wuyishan National Park, southeast China

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          Abstract

          Prunus tongmuensis , a new species of cherry blossom, is described and illustrated from Wuyishan National Park, southeast China. This species is characterized by its tubular to nearly bottle-shaped receptacles and dark purple drupes. It can be distinguished from other wild cherry trees by its flowers and leaves, reddish brown young leaves, presence of 1–2 glands at the base of leaves, petioles densely covered with yellowish brown villi, longer pedicels (0.6–2.5 cm), villous pistil, and dark purple drupes. In the present study, we conducted a comprehensive morphological study based on specimens of the new species and its morphologically close species, field observations, and examination of pollen morphology. In addition, our phylogenetic analysis based on the complete plastid genome sequences further confirms the status of the new species and indicates that it is closely related to Prunus clarofolia , however, it notably differs in leaf shape, size, petiole villus color, gland location, timing of flower and leaf openings, and reflexed or spread sepals, as well as drupe color.

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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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            MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

            Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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              Phylogeny and classification of Prunus sensu lato (Rosaceae).

              The classification of the economically important genus Prunus L. sensu lato (s.l.) is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.l. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions (atpB-rbcL, matK, ndhF, psbA-trnH, rbcL, rpL16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycf1) and three nuclear genes (ITS, s6pdh and SbeI) to explore their infrageneric relationships. The results of these analyses were used to develop a new, phylogeny-based classification of Prunus s.l. Our phylogenetic reconstructions resolved three main clades of Prunus s.l. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades: subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae (T. T. Yü & L. T. Lu) S. L. Zhou and one new species name, Prunus tianshanica (Pojarkov) S. Shi, were proposed. © 2013 Institute of Botany, Chinese Academy of Sciences.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Writing - review and editing
                Role: ConceptualizationRole: Writing - original draft
                Role: Data curation
                Role: Data curation
                Role: Data curation
                Role: Data curation
                Role: Data curation
                Role: Conceptualization
                Role: Conceptualization
                Journal
                PhytoKeys
                PhytoKeys
                3
                urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                urn:lsid:zoobank.org:pub:66878968-5FA3-48E4-A0CA-743FBBB0315D
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2024
                31 January 2024
                : 237
                : 269-279
                Affiliations
                [1 ] Co-Innovation Center for the Sustainable Forestry in Southern China, College of life sciences, Cerasus Research Center, Nanjing Forestry University, Nanjing 210037, Jiangsu, China Nanjing Forestry University Nanjing China
                Author notes
                Corresponding author: Xiangui Yi ( yixiangui@ 123456njfu.edu.cn)

                Academic editor: Hanno Schaefer

                Author information
                https://orcid.org/0000-0003-3123-9076
                https://orcid.org/0000-0001-5269-4778
                https://orcid.org/0000-0003-2085-3388
                https://orcid.org/0000-0002-7940-909X
                Article
                115098
                10.3897/phytokeys.237.115098
                10851151
                38333591
                8b57ca5e-933f-4849-9c7a-34c8d28b448b
                Xiangui Yi, Jingjing Dong, Jie Chen, Huajin Zhou, Tong Wu, Shucheng Gao, Xiangzhen Chen, Meng LI, Xianrong Wang

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 02 November 2023
                : 19 January 2024
                Categories
                Research Article
                Rosaceae
                Taxonomy
                China

                Plant science & Botany
                molecular phylogeny,morphological comparison rosaceae,subgenus. cerasus,taxonomy

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