23
views
0
recommends
+1 Recommend
2 collections
    0
    shares

      Publish your biodiversity research with us!

      Submit your article here.

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

      Evaluating the significance of wing shapes in inferring phylogenetic proximity among the generic taxa: an example of Cantharinae (Coleoptera, Cantharidae)

      , , ,
      Arthropod Systematics & Phylogeny
      Pensoft Publishers

      Read this article at

      ScienceOpenPublisher
      Bookmark
          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 resolution of phylogenetic relationship among animals is still one of the most challenging problems in systematic zoology. Insect wing is a highly valued morphological character in the systematics, but few studies have been conducted to quantify wing shape variations for phylogenetic reconstruction. In this study, with Cantharinae as the subject, we conducted the GM analyses from hindwings of 16 representative genera. Further, we conducted the UPGMA based on Procrustes distance and Euclidean similarity measure of Mahalanobis distance, respectively, and NJ analysis of the Mahalanobis distance, as well as MP analysis using merged landmark dataset. In the meantime, we constructed the phylogenetic relationships among these genera based on the mitochondrial genomes, with a total of 41 sequences novel to Cantharinae, by BI and ML analyses. As a result, the CVA analysis demonstrated that the hindwing shapes of the cantharid genera are significantly different from one another. All the topologies produced by the GM data partially correspond with that of mitogenomic data. The close relationships of some genera are frequently recovered, including Cyrebion + Themus, Cantharis + Taiwanocantharis + Taocantharis, Stenothemus + Falsopodabrus + Habronychus. These results prove the importance and potential application of the hindwing shapes in recovering the relationships among the sibling genera.

          Related collections

          Most cited references77

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

            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.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
                Bookmark

                Author and article information

                Contributors
                Journal
                Arthropod Systematics & Phylogeny
                ASP
                Pensoft Publishers
                1864-8312
                1863-7221
                March 17 2023
                March 17 2023
                : 81
                : 303-316
                Article
                10.3897/asp.81.e101411
                b0eb4876-ebf1-4f98-80dc-a039aee1a09a
                © 2023

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

                History

                Comments

                Comment on this article