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       Hedysarumqilianshanense sp. nov. (Fabaceae, Hedysareae), a new species from the Qilianshan Mountains in Gansu, China

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          Abstract

          Hedysarum qilianshanense sp. nov. ( Fabaceae , Hedysareae) is described and illustrated from the Qilianshan Mountains in Gansu, China. This new species is similar to H. przewalskii , but can be distinguished by its corolla being light purple to purple, standard 15–19 mm long, wings 14–16 mm long, keels 16–19 mm long, and the ovary and legume being glabrous. The new species can be easily distinguished from H. neglectum Ledeb. by its bract being shorter than the pedicel, and the ovary and legume being glabrous. Phylogenetic tree based on the nuclear ITS and ETS sequences shows that H. qilianshanense is sister to H. przewalskii , while the tree based on the plastid psbA-trnH, trnC-petN, trnL-F, trnS-G and petN-psbM sequences shows H. qilianshanense as sister to a clade consisting of H. hedysaroides , H. inundatum , H. americanum and H. neglectum . The new species is a diploid with the chromosome number 2n = 14. Based on morphological, phylogenetic and karyotypic evidence, the new species may originate from an ancient homoploid hybrid speciation event.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Alexandros Stamatakis (2014)
          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)
              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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                Author and article information

                Contributors
                Pei-Liang Liu:
                ORCID: https://orcid.org/0000-0001-6566-7824
                Role: ConceptualizationRole: Writing - original draftRole: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: Visualization
                Qian-Xi Guo:
                ORCID: https://orcid.org/0009-0002-9144-5752
                Role: Writing - original draftRole: Data curationRole: MethodologyRole: Visualization
                Jian-Qi Zhang: Role: Writing - review and editingRole: InvestigationRole: Resources
                Lu-Lu Xun:
                ORCID: https://orcid.org/0000-0002-6861-5883
                Role: Writing - review and editingRole: Investigation
                Yuan Lu:
                ORCID: https://orcid.org/0000-0002-0329-0803
                Role: Writing - review and editingRole: Investigation
                Ming Yue:
                ORCID: https://orcid.org/0000-0002-8618-1126
                Role: ConceptualizationRole: Writing - review and editingRole: Funding acquisitionRole: Project administrationRole: Supervision
                Journal
                Journal ID (nlm-ta): PhytoKeys
                Journal ID (iso-abbrev): PhytoKeys
                Journal ID (publisher-id): 3
                Journal ID (index): urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:66878968-5FA3-48E4-A0CA-743FBBB0315D
                Title: PhytoKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-2011
                ISSN (Electronic): 1314-2003
                Publication date Collection: 2024
                Publication date (Electronic): 22 January 2024
                Volume: 237
                Pages: 103-116
                Affiliations
                [1 ] Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, Shaanxi 710069, China Northwest University Xi’an China
                [2 ] Linhai City Natural Resources and Planning Bureau of Zhejiang Province, Linhai, Zhejiang 317099, China Linhai City Natural Resources and Planning Bureau of Zhejiang Province Linhai China
                [3 ] Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, Shaanxi 710061, China Xi’an Botanical Garden of Shaanxi Province Xi’an China
                Author notes
                Corresponding author: Ming Yue ( yueming@ 123456nwu.edu.cn)

                Academic editor: Clifford Morden

                Author information
                https://orcid.org/0000-0001-6566-7824
                https://orcid.org/0009-0002-9144-5752
                https://orcid.org/0000-0002-6861-5883
                https://orcid.org/0000-0002-0329-0803
                https://orcid.org/0000-0002-8618-1126
                Article
                Publisher ID: 116236
                DOI: 10.3897/phytokeys.237.116236
                PMC ID: 10825973
                PubMed ID: 38292074
                SO-VID: a8947dfc-febe-4bce-8166-af5284b3f3ae
                Copyright © Pei-Liang Liu, Qian-Xi Guo, Jian-Qi Zhang, Lu-Lu Xun, Yuan Lu, Ming Yue
                License:

                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
                Date received : 24 November 2023
                Date accepted : 22 December 2023
                Funding
                Funded by: National Natural Science Foundation of China 501100001809 http://doi.org/10.13039/501100001809
                Basic Research Program of the Shaanxi Academy of Sciences
                Categories
                Subject: Research Article
                Subject: Fabaceae
                Subject: Nomenclature
                Subject: Phylogeny
                Subject: Taxonomy
                Subject: Cenozoic
                Subject: China

                ScienceOpen disciplines: Plant science & Botany
                Keywords: karyotype,phylogeny,qinghai-tibetan plateau,taxonomy
                Data availability:
                ScienceOpen disciplines: Plant science & Botany
                Keywords: karyotype, phylogeny, qinghai-tibetan plateau, taxonomy

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