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      Zehneria grandibracteata (Cucurbitaceae), an overlooked new species from western Kenyan forests

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          Abstract

          Zehneria grandibracteata , a new species of Cucurbitaceae from western Kenya, is described here, based on morphological and molecular data. It has long been misidentified as the widely-distributed species Z. scabra . However, it differs by its ovate leafy probract at the base of the inflorescences, subglabrous condition of the entire plant, shorter receptacle-tube and filaments, as well as denser and sessile inflorescences. Furthermore, the molecular phylogenetic analysis of Zehneria , based on nrITS sequences, further supports the argument that Z. grandibracteata should be segregated from Z. scabra .

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          Most cited references 31

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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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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Contributors
                Journal
                PhytoKeys
                PhytoKeys
                3
                urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2020
                28 October 2020
                : 165
                : 85-98
                Affiliations
                [1 ] CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, CN-430074, China
                [2 ] Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, CN-430074, China
                [3 ] University of Chinese Academy of Sciences, Beijing, CN-100049, China
                [4 ] East Africa Herbarium, National Museums of Kenya, P.O. Box 451660-0100, Nairobi, Kenya
                Author notes
                Corresponding author: Guang-Wan Hu ( guangwanhu@ 123456wbgcas.cn )

                Academic editor: N. Holstein

                Article
                57399
                10.3897/phytokeys.165.57399
                7642130
                Neng Wei, Zhi-Xiang Zhong, David Kimutai Melly, Solomon Kipkoech, Benjamin Muema Watuma, Veronicah Mutele Ngumbau, Peris Kamau, Guang-Wan Hu, Qing-Feng 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.

                Categories
                Research Article
                Cucurbitaceae
                Nomenclature
                Systematics
                Taxonomy
                Vascular Plants
                Africa
                East Africa
                Kenya

                Plant science & Botany

                east africa, flora of kenya, phylogeny, taxonomy, zehneria scabra

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