13
views
0
recommends
+1 Recommend
1 collections
    0
    shares

      Publish your biodiversity research with us!

      Submit your article here.

      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Phylogeny and classification of Endromidae (Lepidoptera: Bombycoidea) based on mitochondrial genomes

      , , , , , ,
      Arthropod Systematics & Phylogeny
      Pensoft Publishers

      Read this article at

      ScienceOpenPublisher
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The small, relict-like moth family Endromidae is well-established within the superfamily Bombycoidea, but relationships within the family have remained vague for the last decade, primarily due to very limited taxon sampling. This resulted in the explicit removal of all internal suprageneric classification by Zwick et al. (2011) when they synonymized Mirinidae and the bombycid subfamilies Oberthueriinae and Prismostictinae with Endromidae. Nucleotide and amino acid data sets of the 13 mitochondrial, protein-coding genes from representatives of 13 of the 16 accepted endromid genera were used to estimate phylogenetic relationships based on maximum likelihood and Bayesian inference methods. The results strongly support Endromidae as a monophyletic group and enable the establishment and diagnosis of four subfamilies (Endrominae, Mirininae stat. rev., Oberthueriinae stat. rev. and Prismostictinae stat. rev.). Within subfamily Oberthueriinae, we establish three tribes: Oberthueriini stat. rev., Andracini tribe nov. and Mustiliini tribe nov. We provide morphological diagnoses and a genus-level checklist for the three tribes. Promustilia yajiangensis Wang, X. & Zolotuhin, 2015 is transferred to Mustilizans as M. yajiangensis comb. nov. to establish reciprocal monophyly of the two genera, and Andraca gongshanensis is transferred to Pseudandraca as P. gongshanensis comb. nov. We also synonymize Andraca (Chrypathemola) syn. nov. with Andraca (Andraca), as the latter is deeply nested within the former.

          Related collections

          Most cited references61

          • Record: found
          • Abstract: found
          • Article: not found

          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            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%.
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              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

                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                Arthropod Systematics & Phylogeny
                ASP
                Pensoft Publishers
                1864-8312
                1863-7221
                April 20 2023
                April 20 2023
                : 81
                : 395-408
                Article
                10.3897/asp.81.e90721
                5665bbeb-7f54-4e66-9b64-2240967ddb4f
                © 2023

                http://creativecommons.org/licenses/by/4.0/

                History

                Comments

                Comment on this article

                Related Documents Log