The first mitochondrial genome of Creophilus Leach and Platydracus Thomson (Coleoptera: Staphylinidae: Staphylinini) and phylogenetic implications

Author:

ZHAO TIAN-YOUORCID,HE LIANGORCID,XU XIN,CHEN ZHEN-NING,GAO YA-YUEORCID,LÜ LIANGORCID

Abstract

Creophilus Leach and Platydracus Thomson are two genera whose members were formerly included in a poorly defined Staphylinus. Both include large-sized rove beetles that can be frequently found in carrion, faeces, and other such rotting materials worldwide. But there are not yet mitochondrial genomes in public databases, which deters scientists from further studies that involve species of these two genera. Here we present the first complete mitochondrial genomes of two typical Palaearctic species, Creophilus maxillosus and Platydracus impotens, which are also the first for the two genera. Additionally, we included the new mitogenomic data in a phylogenetic context using maximum likelihood phylogenetic analyses. Our results confirm the results of previous studies but show that the position of Creophilus, and therefore the monophyly of Staphylinina, could be affected by dataset constitution and model selection.  

Publisher

Magnolia Press

Subject

Animal Science and Zoology,Ecology, Evolution, Behavior and Systematics

Reference2 articles.

1.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. & Stadler, P.F. (2013) MITOS: Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69, 313–319. https://doi.org/10.1016/j.ympev.2012.08.023
Brunke, A.J., Chatzimanolis, S., Schillhammer, H. & Solodovnikov, A. (2016) Early evolution of the hyperdiverse rove beetle tribe Staphylinini (Coleoptera: Staphylinidae: Staphylininae) and a revision of its higher classification. Cladistics, 32, 427–451. https://doi.org/10.1111/cla.12139
Brunke, A.J. & Smetana, A. (2019) A new genus of Staphylinina and a review of major lineages (Staphylinidae: Staphylininae: Staphylinini). Systematics and Biodiversity, 17, 745–758. https://doi.org/10.1080/14772000.2019.1691082
Chani-Posse, M.R., Brunke, A.J., Chatzimanolis, S., Schillhammer, H. & Solodovnikov, A. (2018) Phylogeny of the hyper-diverse rove beetle subtribe Philonthina with implications for classification of the tribe Staphylinini (Coleoptera: Staphylinidae). Cladistics 34, 1–40. https://doi.org/10.1111/cla.12188
Chatzimanolis, S., Cohen, I.M., Schomann, A. & Solodovnikov, A.Yu. (2010) Molecular phylogeny of the mega-diverse rove beetle tribe Staphylinini (Insecta, Coleoptera, Staphylinidae). Zoologica Scripta, 39, 436–449. https://doi.org/10.1111/j.1463-6409.2010.00438.x
Chernomor, O., von Haeseler, A. & Minh, B.Q. (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Systematic Biology, 65, 997–1008. https://doi.org/10.1093/sysbio/syw037
Clarke, D.J. (2011) Testing the phylogenetic utility of morphological character systems, with a revision of Creophilus Leach (Coleoptera: Staphylinidae). Zoological Journal of the Linnean Society, 163, 723–812. https://doi.org/10.1111/j.1096-3642.2011.00725.x
Coiffait, H. (1974) Coléoptères Staphylinides de la région paléarctique occidentale II. Sous famille Staphilininae, Tribus Philonthini et Staphylinini. Nouvelle Revue d’Entomologie, Supplément 1974 (4), 1–593.
Criscuolo, A. & Gribaldo, S. (2010) BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10, 210. https://doi.org/10.1186/1471-2148-10-210
Crotty, S.M., Minh, B.Q., Bean, N.G., Holland, B.R., Tuke, J., Jermiin, L.S. & Haeseler, A.V. (2020) GHOST: recovering historical signal from heterotachously evolved sequence alignments. Systematic Biology, 69, 249–264. https://doi.org/10.1093/sysbio/syz051
Erichson, W.F. (1839) Genera et Species Staphylinorum Insectorum Coleopterorum Familiae. F. H. Morin, Berlin, 400 pp.
Gruber, A.R., Bernhart, S.H. & Lorenz, R. (2015) The ViennaRNA Web Services. In: Picardi, E. (Ed.), RNA Bioinformatics. Methods in Molecular Biology. Springer, New York, New York, pp. 307–326.
Herman, L.H. (2001) Catalog of the Staphylinidae (Insecta, Coleoptera): 1758 to the end of the second millennium. Bulletin of the American Museum of Natural History, 265, 1–4218.
Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q. & Vinh, L.S. (2018) UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35, 518–522. https://doi.org/10.1093/molbev/msx281
Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A. & Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14, 587–589. https://doi.org/10.1038/nmeth.4285
Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780. https://doi.org/10.1093/molbev/mst010
Lacordaire, J.T. (1835) s.n. In: Boisduval, J. & Lacordaire, T. (Eds.), Faune entomologique des environs de Paris; ou species généralde s insectes qui se trouvent dans un rayon de quinze à vingt lieues aux alentours de Paris. Vol. 1 (only). Méquignon-Marvis, Paris, pp. 1–696.
Le, S.Q., Dang, C.C. & Gascuel, O. (2012) Modeling protein evolution with several amino acid replacement matrices depending on site rates. Molecular Biology and Evolution, 29, 2921–2936. https://doi.org/10.1093/molbev/mss112
Le, S.Q., Gascuel, O. & Lartillot, N. (2008a) Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics, 24, 2317–2323. https://doi.org/10.1093/bioinformatics/btn445
Le, S.Q., Lartillot, N. & Gascuel, O. (2008b) Phylogenetic mixture models for proteins. Philosophical Transactions of the Royal Society B: Biological Sciences, 363, 3965–3976. https://doi.org/10.1098/rstb.2008.0180
Leach, W.E. (1819) [New genera]. In: Samouelle, G. (Ed.), The Entomologist’s useful compendium; or an introduction to the knowledge of British insects, comprising the best means of obtaining and preserving them, and a description of the apparatus generally used; together with the genera of Linné, and the modern method of arranging the classes Crustacea, Myriapoda, spiders, mites, and insects from their affinities and structure, according to the views of Dr. Leach. Also an explanation of the terms used in entomology; a calendar of the times of appearance, and usual situations of near 3000 species of British insects; with instructions for collecting and fitting up objects for the microscope. Thomas Boys, London, 496 pp.
Lee, B.D. (2018) Python implementation of codon adaptation index. Journal of Open Source Software, 3, 905. https://doi.org/10.21105/joss.00905
Letunic, I. & Bork, P. (2021) Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research 49, W293–W296. https://doi.org/10.1093/nar/gkab301
Liu, H.-L., Chen, Q.-D., Chen, S., Pu, D.-Q., Chen, Z.-T., Liu, Y.-Y. & Liu, X. (2020) The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha). PeerJ, 8, e9932. https://doi.org/10.7717/peerj.9932
Löbl, I. & Löbl, D. (2015) Catalogue of Palaearctic Coleoptera. Volume 2: Hydrophiloidea—Staphylinoidea. Revised and Updated Edition. Koninklijke Brill NV, Leiden, xxvi + 1702 pp.
Lü, L., Cai, C.-Y., Zhang, X., Newton, A.F., Thayer, M.K. & Zhou, H.-Z. (2020) Linking evolutionary mode to palaeoclimate change reveals rapid radiations of staphylinoid beetles in low-energy conditions. Current Zoology, 66, 435–444. https://doi.org/10.1093/cz/zoz053
McKenna, D.D., Farrell, B.D., Caterino, M.S., Farnum, C.W., Hawks, D.C., Maddison, D.R., Seago, A.E., Short, A.E.Z., Newton, A.F. & Thayer, M.K. (2015) Phylogeny and evolution of Staphyliniformia and Scarabaeiformia: Forest litter as a stepping stone for diversification of nonphytophagous beetles. Systematic Entomology, 40, 35–60. https://doi.org/10.1111/syen.12093
Meng, G., Li, Y., Yang, C. & Liu, S. (2019) MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, 47, e63. https://doi.org/10.1093/nar/gkz173
Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., von Haeseler, A. & Lanfear, R. (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37, 1530–1534. https://doi.org/10.1093/molbev/msaa015
Nie, R., Andújar, C., Gómez-Rodríguez, C., Bai, M., Xue, H.-J., Tang, M., Yang, C.-T., Tang, P., Yang, X.-K. & Vogler, A.P. (2020) The phylogeny of leaf beetles (Chrysomelidae) inferred from mitochondrial genomes. Systematic Entomology, 45, 188–204. https://doi.org/10.1111/syen.12387
Nie, R.-E., Breeschoten, T., Timmermans, M.J.T.N., Nadein, K., Xue, H.-J., Bai, M., Huang, Y., Yang, X.-K. & Vogler, A.P. (2018) The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes. Cladistics, 34, 113–130. https://doi.org/10.1111/cla.12196
Perna, N.T. & Kocher, T.D. (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution, 41, 353–358. https://doi.org/10.1007/BF01215182
Smetana, A. & Davies, A. (2000) Reclassification of the north temperate taxa associated with Staphylinus sensu lato, including comments on relevant subtribes of Staphylinini (Coleoptera: Staphylinidae). American Museum Novitates, No. 3287, 1–88.
Solodovnikov, A. & Brunke, A. (2016) Cafioquedus gularis Sharp, 1886 and other poorly understood Staphylinini: a review of the New Zealand fauna of the tribe with discussion of its potential for biogeography (Insecta: Coleoptera: Staphylinidae). New Zealand Entomologist, 39, 40–61. https://doi.org/10.1080/00779962.2015.1076595
Solodovnikov, A. & Schomann, A. (2009) Revised systematics and biogeography of “Quediina” of sub-Saharan Africa: new phylogenetic insights into the rove beetle tribe Staphylinini (Coleoptera: Staphylinidae). Systematic Entomology, 34, 443–466. https://doi.org/10.1111/j.1365-3113.2008.00468.x
Thomson, C.G. (1858) Försök till uppställning af Sveriges Staphyliner. Öfversigt af Kongl. Vetenskaps-Akademiens Förhandlingar, 15, 27–40.
Wang, L.-F. & Lü, L. (2021) Review of the Chinese species of Deleaster Erichson, 1839 (Coleoptera, Staphylinidae, Oxytelinae) with a mitogenome of Deleaster bactrianus Semenov, 1900. Zootaxa, 5027 (3), 301–331. https://doi.org/10.11646/zootaxa.5027.3.1
Zhang, D., Gao, F., Jakovlić, I., Zou, H., Zhang, J., Li, W.X. & Wang, G.T. (2020) PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 20, 348–355. https://doi.org/10.1111/1755-0998.13096
Zhao, T.-Y., Zhang, C.-J. & Lü, L. (2021) Comparative description of the mitochondrial genome of Scaphidium formosanum Pic, 1915 (Coleoptera: Staphylinidae: Scaphidiinae). Zootaxa, 4941 (4), 487–510. https://doi.org/10.11646/zootaxa.4941.4.2
Żyła, D. & Solodovnikov, A. (2019) Multilocus phylogeny defines a new classification of Staphylininae (Coleoptera, Staphylinidae), a rove beetle group with high lineage diversity. Systematic Entomology. [published online] https://doi.org/10.1111/syen.12382

2.

 

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3