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      Molecular phylogeny, systematics and generic classification of the butterfly subfamily Trapezitinae (Lepidoptera: Papilionoidea: Hesperiidae)

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      Zoological Journal of the Linnean Society
      Oxford University Press (OUP)

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          Abstract

          Trapezitinae skippers are restricted to Australia and New Guinea. Despite decades of taxonomic work, their systematics and phylogeny remain little understood. To resolve the composition of genera and determine their evolutionary relationships, we inferred a comprehensive multilocus molecular phylogeny of Trapezitinae. Our results recover a monophyletic Trapezitinae as sister to Barcinae, with a poorly resolved backbone possibly indicating an early rapid radiation. We recover two main clades comprising all currently described genera, including the previously contentious Prada Evans, 1949 but excluding Tiacellia Evans, 1949. Several genera are recovered as paraphyletic or polyphyletic, rendering the classification of Trapezitinae incompatible with the new phylogeny. Therefore, we synonymize Motasingha Watson, 1893 syn. nov. and Oreisplanus Waterhouse & Lyell, 1914 syn. nov. with Hesperilla Hewitson, 1868 and Neohesperilla Waterhouse & Lyell, 1914 syn. nov. with Toxidia Mabille, 1891. To reflect the placement of Anisynta dominula outside of Anisynta, we describe the new genus Atkinsia Braby & Toussaint gen. nov., which includes the sole species Atkinsia dominula (Plötz, 1884) comb. nov. Two species of Toxidia and two species of Signeta Waterhouse & Lyell, 1914 are placed into Timoconia Strand, 1909, yielding four new combinations: Timoconia melania (Waterhouse, 1903) comb. nov., Timoconia peron (Latreille, 1824) comb. nov., Timoconia flammeata (Butler, 1882) comb. nov. and Timoconia tymbophora (Meyrick & Lower, 1902) comb. nov. Thus, SignetaWaterhouse & Lyell, 1914 syn. nov. is now regarded as a junior synonym of Timoconia. Overall, our phylogeny has provided the basis for 20 nomenclatural changes at the species and subspecies level, including 14 new combinations.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          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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            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.
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              IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

              Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                August 01 2022
                July 29 2022
                February 06 2022
                August 01 2022
                July 29 2022
                February 06 2022
                : 195
                : 4
                : 1407-1421
                Article
                10.1093/zoolinnean/zlab086
                8c7f0ad3-97be-4161-ac61-4ee6e93a08ba
                © 2022

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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