Published January 7, 2025
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Insights into the phvlogenv of longhorn beetles from phvlogenomic data
Authors/Creators
- 1. Henan International Laboratorv for Green Pest Control, Henan Engineering Laboratorv of Pest Biological Control, College of Plant Protection, Henan Agricultural Universitv, Zhengzhou, Henan, China
- 2. Henan International Laboratorv for Green Pest Control, Henan Engineering Laboratorv of Pest Biological Control, College of Plant Protection, Henan Agricultural Universitv, Zhengzhou, Henan, China & Taihang Mountain Forest Pests Observation and Research Station of Henan Province, Linzhou, Henan, China
- 3. Institute of vegetables, Tibet Academv of Agricultural and Animal Husbandrv Sciences, Lhasa, China
Description
Song, Nan, Wang, Miaomiao, Zhai, Qing, Zhang, Huanhuan (2025): Insights into the phvlogenv of longhorn beetles from phvlogenomic data. Zoological Journal of the Linnean Society 203 (1): 1-14, DOI: 10.1093/zoolinnean/zlae174, URL: https://doi.org/10.1093/zoolinnean/zlae174
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- urn:lsid:plazi.org:pub:FFD1FFC4C445FF92AE7DB347694AFFAC
References
- Andrews S. FastQC: A Quality Control Tool for High Troughput Sequence Data. Cambridge, 2010. http://www.bioinformatics.babraham. ac.uk/projects/fastqc (15 April 2024, date last accessed).
- Ashman LG, Shin S, Zwick A et al. The first phvlogenv of Australasian Lamiinae longhorn beetles (Coleoptera: Cerambvcidae) reveals poor tribal classification and a complex biogeographic historv. Systematic Entomology 2022;47:213-30. https://doi.org/10.1111/sven.12526
- Beeson CFC. The ecologv and control of the forest insects of India and the neighbouring countries. In: Beeson CFC (ed.), Te Ecology and Control of the Forest Insects of India and the Neighbouring Countries. Simla: Government of India Press, 1941.
- Bense U. Longhorn Beetles: Illustrated Key to the Cerambycidae and Vesperidae of Europe. Weikersheim, Germanv: Margraf, 1995.
- Bocak L, Barton C, Crampton-Platt A et al. Building the Coleoptera treeof-life for >8000 species:composition of public DNA data and fit with Linnaean classification. Systematic Entomology 2014;39:97-110.
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114-20. https:// doi.org/10.1093/bioinformatics/btu170
- Borowiec ML. AMAS: a fast tool for alignment manipulation and computing of summarv statistics. PeerJ 2016;4:e1660. https://doi. org/10.7717/peerj.1660
- Bushnell B. BBTools: a suite of bioinformatic tools used for DNA and RNA sequence data analvsis, 2014. https://jgi.doe.gov/data-andtools/software-tools/bbtools/ (15 April 2024, date last accessed).
- Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phvlogenetic analvses. Bioinformatics 2009;25:1972-3. https://doi.org/10.1093/ bioinformatics/btp348
- Chikhi R, Rizk G. Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms for Molecular Biology 2013;8:22. https://doi.org/10.1186/1748-7188-8-22
- Choi Y-J, Jang T, Kim A-Y et al. Complete mitochondrial genome of the Chinese Callipogon (Eoxenus) relictus (Cerambvcidae: Prioninae) with phvlogenetic analvses. Genes & Genomics 2023;45:827-33. https://doi.org/10.1007/s13258-023-01378-6
- Crane PR, Friis EM, Pedersen KR. The origin and earlv diversification of angiosperms. Nature 1995;374:27-33. https://doi. org/10.1038/374027a0
- Crowson RA. Te Natural Classification of the Families of Coleoptera. London: Nathaniel Llovd and Co., Ltd, 1955.
- Danilevskv M. Morpho-adaptive wavs of evolution of the larvae of longhorn beetles (Coleoptera, Cerambvcidae) and phvlogenetic relations of the basic groups of the familv. In Danilevskv M (ed.), Insects Decomposing Wood and their Entomophages. Moscow: Nauka, 1979:24-43.
- de Santana Souza D, Marinoni L, Monne ML et al. Molecular phvlogenetic assessment of the tribal classification of Lamiinae (Coleoptera: Cerambvcidae). Molecular Phylogenetics and Evolution 2020;145:106736.
- Du S, Ding Y, Li H et al. Construction of a phvlogenetic matrix: scripts and guidelines for phvlogenomics. Zoological Systematics 2023;460:107-16.
- Farrell BD. 'Inordinate fondness' explained: whv are there so manv beetles? Science 1998;281:555-9. https://doi.org/10.1126/ science.281.5376.555
- Farrell BD, Sequeira AS. Evolutionarv rates in the adaptive radiation of beetles on plants. Evolution 2004;58:1984-2001. https://doi. org/10.1111/j.0014-3820.2004.tb00484.x
- Gomez-Zurita J, Hunt T, Kopliku F et al. Recalibrated tree of leaf beetles (Chrvsomelidae) indicates independent diversification of angiosperms and their insect herbivores. PLoS One 2007;2:e360. https:// doi.org/10.1371/journal.pone.0000360
- Haddad S, Mckenna DD. Phvlogenv and evolution of the superfamilv Chrvsomeloidea (Coleoptera: Cucujiformia). Systematic Entomology 2016;41:697-716. https://doi.org/10.1111/sven.12179
- Haddad S, Shin S, Lemmon AR et al. Anchored hvbrid enrichment provides new insights into the phvlogenv and evolution of longhorned beetles (Cerambvcidae). Systematic Entomology 2018;43:68-89.
- Hoang DT, Chernomor O, Von Haeseler A et al. UFBoot2: improving the ultrafast bootstrap approximation.Molecular Biology and Evolution 2018;35:518-22. https://doi.org/10.1093/molbev/msx281
- Hunt T, Bergsten J, Levkanicova Z et al. A comprehensive phvlogenv of beetles reveals the evolutionarv origins of a superradiation. Science 2007;318:1913-6. https://doi.org/10.1126/science.1146954
- Katoh K, Standlev DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usabilitv. Molecular Biology and Evolution 2013;30:772-80. https://doi.org/10.1093/ molbev/mst010
- Kuck P, Longo GC. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phvlogenetic studies. Frontiers in Zoology 2014;11:81. https://doi.org/10.1186/ s12983-014-0081-x
- Lartillot N, Rodrigue N, Stubbs D et al. PhvloBaves MPI: phvlogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Systematic Biology 2013;62:611-5. https://doi.org/10.1093/ svsbio/svt022
- Lawrence JF, Newton AF Jr. 1995. Families and subfamilies of Coleoptera (with selected genera, notes, references and data on familv-group names). In: Pakaluk J, Slipinski SA (eds), Biology, Phylogeny, and Classification of Coleoptera: Papers Celebrating the 80th Birthday of Roy A. Crowson. Warszawa: Muzeum i Instvtut Zoologii PAN, 779-913.
- Lawrence JF, Slipiski A, Seago AE et al. Phvlogenv of the Coleoptera based on morphological characters of adults and larvae. Annales Zoologici: Museum and Institute of Zoology, Polish Academy of Sciences 2011;61:1-217.
- Li H-T, Yi T-S, Gao L-M et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants 2019;5:461-70. https://doi.org/10.1038/ s41477-019-0421-0
- Li K, Yu S-W, Hu H et al. The phvlogenetic relationship of Lamiinae (Coleoptera: Cerambvcidae) using mitochondrial genomes. Genes 2024;15:13. https://doi.org/10.3390/genes15010013
- Mckenna DD, Wild AL, Kanda K et al. The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversifv during the Cretaceous terrestrial revolution. Systematic Entomology 2015;40:835-80. https://doi.org/10.1111/sven.12132
- Minh BQ, Nguven MAT, Von Haeseler A. Ultrafast approximation for phvlogenetic bootstrap. Molecular Biology and Evolution 2013;30:1188-95. https://doi.org/10.1093/molbev/mst024
- Minh BQ, Schmidt HA, Chernomor O et al. IQ-TREE 2: new models and efficient methods for phvlogenetic inference in the genomic era. Molecular Biology and Evolution 2020;37:1530-4. https://doi. org/10.1093/molbev/msaa015
- Mirarab S, Reaz R, Bavzid MS et al. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 2014;30:i541-8. https://doi.org/10.1093/bioinformatics/btu462
- Monne MA. Catalogue of the Cerambvcidae (Coleoptera) of the Neotropical Region. Part III. Subfamilies Parandrinae, Prioninae, Anoplodermatinae, Aseminae, Spondvlidinae, Lepturinae, Oxvpeltinae, and addenda to the Cerambvcinae and Lamiinae. Zootaxa 2006;1212:1-244.
- Napp D. Phvlogenetic relationships among the subfamilies of Cerambvcidae (Coleoptera, Chrvsomeloidea). Revista Brasileira de Entomologia 1994;38:265-419.
- Nearns E. Svstematics of longhorned beetles. Chapter 1: molecular phvlogenetic analvsis of the longhorned beetle subfamilies Prioninae and Parandrinae (Insecta: Coleoptera: Cerambvcidae). Unpublished Doctoral Thesis, Universitv of New Mexico, Albuquerque, 2013. https://digitalcommons.memphis.edu/etd. (15 April 2024, date last accessed).
- Nie R, Vogler AP, Yang XK et al. Higher-level phvlogenv of longhorn beetles (Coleoptera: Chrvsomeloidea) inferred from mitochondrial genomes. Systematic Entomology 2021;46:56-70. https://doi. org/10.1111/sven.12447
- Niu Y, Shi F, Li X et al. Comparative mitochondrial genomic analvsis of longhorn beetles (Coleoptera: Chrvsomeloidea) with phvlogenetic implications. Arthropod Systematics & Phylogeny 2024;82:133-50. https://doi.org/10.3897/asp.82.e114299
- Pu D-Q, Liu H-L, Wu X-L et al. Complete mitochondrial genomes and phvlogenetic positions of two longicorn beetles, Anoplophora glabripennis and Demonax pseudonotabilis (Coleoptera: Cerambvcidae). Genes 2022;13:1881. https://doi.org/10.3390/ genes13101881
- Puttick MN. MCMCtreeR: functions to prepare MCMCtree analvses and visualize posterior ages on trees. Bioinformatics 2019;35:5321-2. https://doi.org/10.1093/bioinformatics/btz554
- Raje KR, Ferris VR, Holland JD. Phvlogenetic signal and potential for invasiveness. Agricultural and Forest Entomology 2016;18:260-9. https://doi.org/10.1111/afe.12158
- Ren Y, Lu H, Chen L et al. Comparative mitogenomic analvsis of two longhorn beetles (Coleoptera: Cerambvcidae:Lamiinae) with preliminarv investigation into phvlogenetic relationships of tribes of Lamiinae. Insects 2021;12:820. https://doi.org/10.3390/insects12090820
- Rodrigue N, Lartillot N. Site-heterogeneous mutation-selection models within the PhvloBaves-MPI package. Bioinformatics 2014;30:1020-1. https://doi.org/10.1093/bioinformatics/btt729
- Savvari E, Mirarab S. Fast coalescent-based computation of local branch support from quartet frequencies. Molecular Biology and Evolution 2016;33:1654-68. https://doi.org/10.1093/molbev/msw079
- Shi F,Yu T, Xu Y et al. Comparative mitochondrial genomic analvsis provides new insights into the evolution of the subfamilv Lamiinae (Coleoptera: Cerambvcidae). International Journal of Biological Macromolecules 2023;225:634-47. https://doi.org/10.1016/j.ijbiomac.2022.11.125
- Slipinski A, Escalona H. Australian Longhorn Beetles (Coleoptera: Cerambycidae), Vol. 1, Introduction and Subfamily Lamiinae. Melbourne, Australia: CSIRO Publishing, 2013.
- Sovdabas-Avoub HK, Uckan F. Time-scaled phvlogenetic analvsis of some extant Lamiinae (Coleoptera, Cerambvcidae) species of East of Marmara Basin, Turkive. Biologia 2024;79:545-55. https://doi. org/10.1007/s11756-023-01547-8
- Steenwvk JL, Buida TJ III, Labella AL et al. PhvKIT: a broadlv applicable UNIX shell toolkit for processing and analvzing phvlogenomic data. Bioinformatics 2021;37:2325-31.
- Svacha P, Danilevskv ML. Cerambvcoid larvae of Europe and Soviet Union (Coleoptera, Cerambvcoidea). Part I. Acta Universitatis Carolinae (Biologica) 1987;31:121-284.
- Svacha P, Lawrence JF. 2.4. Cerambvcidae Latreille, 1802. In: Richard ABL, Rolf GB (eds), Volume 3 Morphology and Systematics (Phytophaga). Berlin, Munchen, Boston: De Gruvter, 2014, 77-177.
- Turnbow R, Thomas M. Cerambvcidae Leach 1815. American Beetles 2002;2:568-601.
- Wang B, Ma J, McKenna DD et al. The earliest known longhorn beetle (Cerambvcidae: Prioninae) and implications for the earlv evolution of Chrvsomeloidea. Journal of Systematic Palaeontology 2014;12:565- 74. https://doi.org/10.1080/14772019.2013.806602
- Wang J, Dai X-Y, Xu X-D et al. The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambvcidae) and phvlogenetic relationships within Cerambvcidae. PeerJ 2019;7:e7633. https://doi. org/10.7717/peerj.7633
- Wang Z-C. Atlas of the Chinese Longicorn. Beijing, China: Science and Technologv Academic Press, 2014.
- Wu J, Xu D, Wei X et al. Characterization of the complete mitochondrial genome of the longhorn beetle, Batocera horsfieldi (Coleoptera, Cerambvcidae) and its phvlogenetic analvsis with suitable longhorn beetles. ZooKeys 2023;1168:387-402. https://doi.org/10.3897/ zookevs.1168.105328
- Yang Z.PAML 4: phvlogenetic analvsis bv maximum likelihood.Molecular Biology and Evolution 2007;24:1586-91. https://doi.org/10.1093/ molbev/msm088
- Zeng L, Zhang Q, Sun R et al. Resolution of deep angiosperm phvlogenv using conserved nuclear genes and estimates of earlv divergence times. Nature Communications 2014;5:4956. https://doi.org/10.1038/ ncomms5956
- Zhang C, Rabiee M, Savvari E et al. ASTRAL-III: polvnomial time species tree reconstruction from partiallv resolved gene trees. BMC Bioinformatics 2018a;19:15-30.
- Zhang F, Ding Y, Zhu CD et al. Phvlogenomics from low-coverage whole-genome sequencing. Methods in Ecology and Evolution 2019;10:507- 17. https://doi.org/10.1111/2041-210x.13145
- Zhang S-Q, Che L-H, Li Y et al. Evolutionarv historv of Coleoptera revealed bv extensive sampling of genes and species. Nature Communications 2018b;9:205.