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Hallas JM, Chichvarkhin A, Gosliner TM. Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171095. [PMID: 29134101 PMCID: PMC5666284 DOI: 10.1098/rsos.171095] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
Molecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecular markers (16S, 18S, 28S and cytochrome c oxidase subunit I) for the Nudibranchia using three different methodologies: (i) strict mathematical algorithm; (ii) exclusion of variable or divergent regions and (iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Phylogenetic informativeness (PI) profiles suggest that the molecular markers tested lack the power to resolve relationships at the base of the Doridina, while being more robust at family-level classifications. This supports the lack of consistent resolution between the 19 families within the Doridina across all three alignments. Most of the 19 families were recovered as monophyletic, and instances of non-monophyletic families were consistently recovered between analyses. We conclude that the alignment of variable regions has some effect on phylogenetic estimates of the Doridina, but these effects can vary depending on the size and scope of the phylogenetic query and PI of molecular markers.
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Affiliation(s)
- Joshua M. Hallas
- Department of Biology, University of Nevada, Reno. 1664 N. Virginia St, Reno, NV 89557, USA
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Dr Golden Gate Park, San Francisco, CA 94118, USA
| | - Anton Chichvarkhin
- National Scientific Center of Marine Biology, Far East Branch of Russian Academy of Sciences, Palchevskogo 17, Vladivostok 690041, Russia
- Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia
| | - Terrence M. Gosliner
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Dr Golden Gate Park, San Francisco, CA 94118, USA
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Büsse S, Hörnschemeyer T. The thorax musculature of Anisoptera (Insecta: Odonata) nymphs and its evolutionary relevance. BMC Evol Biol 2013; 13:237. [PMID: 24180622 PMCID: PMC4228402 DOI: 10.1186/1471-2148-13-237] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/29/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Among the winged insects (Pterygota) the Odonata (dragon- and damselflies) are special for several reasons. They are strictly aerial predators showing remarkable flight abilities and their thorax morphology differs significantly from that of other Pterygota in terms of the arrangement and number of muscles. Even within one individual the musculature is significantly different between the nymphal and adult stage. RESULTS Here we present a comparative morphological investigation of the thoracic musculature of dragonfly (Anisoptera) nymphs. We investigated representatives of the Libellulidae, Aeshnidae and Cordulegasteridae and found 71 muscles: 19 muscles in the prothorax, 26 in the mesothorax and 27 in the metathorax. Nine of these muscles were previously unknown in Odonata, and for seven muscles no homologous muscles could be identified in the neopteran thorax. CONCLUSION Our results support and extend the homology hypotheses for the thoracic musculatures of Odonata and Neoptera, thus supplementing our understanding of the evolution of Pterygota and providing additional characters for phylogenetic analyses comprising all subgroups of Pterygota.
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Affiliation(s)
- Sebastian Büsse
- Department of Morphology, Systematic & Evolutionary Biology, J-F-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, Göttingen, Germany
| | - Thomas Hörnschemeyer
- Department of Morphology, Systematic & Evolutionary Biology, J-F-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, Göttingen, Germany
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Mashimo Y, Beutel RG, Dallai R, Lee CY, Machida R. Embryonic development of Zoraptera with special reference to external morphology, and its phylogenetic implications (Insecta). J Morphol 2013; 275:295-312. [DOI: 10.1002/jmor.20215] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/02/2013] [Accepted: 09/06/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Yuta Mashimo
- Sugadaira Montane Research Center; University of Tsukuba; Sugadaira Kogen, Ueda Nagano 386-2204 Japan
| | - Rolf G. Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; Friedrich-Schiller-Universität Jena; Erbertstrasse 1 Jena 07743 Germany
| | - Romano Dallai
- Department of Life Sciences; University of Siena; Via A. Moro 2 Siena I-53100 Italy
| | - Chow-Yang Lee
- School of Biological Sciences; Universiti Sains Malaysia; Penang 11800 Malaysia
| | - Ryuichiro Machida
- Sugadaira Montane Research Center; University of Tsukuba; Sugadaira Kogen, Ueda Nagano 386-2204 Japan
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Kelchner SA. Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers. Mol Phylogenet Evol 2013; 67:404-13. [DOI: 10.1016/j.ympev.2013.02.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 11/14/2012] [Accepted: 02/06/2013] [Indexed: 01/24/2023]
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Wang Y, Engel MS, Rafael JA, Dang K, Wu H, Wang Y, Xie Q, Bu W. A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera. PLoS One 2013; 8:e53679. [PMID: 23301099 PMCID: PMC3536744 DOI: 10.1371/journal.pone.0053679] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/03/2012] [Indexed: 01/30/2023] Open
Abstract
The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.
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Affiliation(s)
- Yanhui Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Michael S. Engel
- Division of Entomology (Paleoentomology), Natural History Museum, London, England
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Jose A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Haoyang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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The utility of indels in population genetics: The Tpi intron for host race genealogy of Acrocercops transecta (Insecta: Lepidoptera). Mol Phylogenet Evol 2011; 59:469-76. [DOI: 10.1016/j.ympev.2011.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/09/2011] [Accepted: 03/04/2011] [Indexed: 11/21/2022]
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