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Schmidt R, Dufresnes C, Krištín A, Künzel S, Vences M, Hawlitschek O. Phylogenetic insights into Central European Chorthippus and Pseudochorthippus (Orthoptera: Acrididae) species using ddRADseq data. Mol Phylogenet Evol 2024; 193:108012. [PMID: 38224796 DOI: 10.1016/j.ympev.2024.108012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/09/2023] [Accepted: 01/06/2024] [Indexed: 01/17/2024]
Abstract
The evolution of several orthopteran groups, especially within the grasshopper family Acrididae, remains poorly understood. This is particularly true for the subfamily Gomphocerinae, which comprises cryptic sympatric and syntopic species. Previous mitochondrial studies have highlighted major discrepancies between taxonomic and phylogenetic hypotheses, thereby emphasizing the necessity of genome-wide approaches. In this study, we employ double-digest restriction site-associated DNA sequencing (ddRADseq) to reconstruct the evolution of Central European Chorthippus and Pseudochorthippus species, especially C.smardai, P.tatrae and the C.biguttulus group. Our phylogenomic analyses recovered deep discordance with mitochondrial DNA barcoding, emphasizing its unreliability in Gomphocerinae grasshoppers. Specifically, our data robustly distinguished the C.biguttulus group and confirmed the distinctiveness of C.eisentrauti, also shedding light on its presence in the Berchtesgaden Alps. Moreover, our results support the reclassification of C.smardai to the genus Pseudochorthippus and of P.tatrae to the genus Chorthippus. Our study demonstrates the efficiency of high-throughput genomic methods such as RADseq without prior optimization to elucidate the complex evolution of grasshopper radiations with direct taxonomic implications. While RADseq has predominantly been utilized for population genomics and within-genus phylogenomics, its application extends to resolve relationships between deeply-diverged clades representative of distinct genera.
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Affiliation(s)
- Robin Schmidt
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany.
| | - Christophe Dufresnes
- LASER, College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, People's Republic of China; Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Anton Krištín
- Institute of Forest Ecology SAS, Ľ. Štúra 2, Zvolen, Slovakia
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
| | - Oliver Hawlitschek
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany; Department of Evolutionary Biology and Environmental Studies, Universität Zürich, Zürich, Switzerland
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Wang L, Chen J, Xue X, Qin G, Gao Y, Li K, Zhang Y, Li XJ. Comparative analysis of mitogenomes among three species of grasshoppers (Orthoptera: Acridoidea: Gomphocerinae) and their phylogenetic implications. PeerJ 2023; 11:e16550. [PMID: 38111661 PMCID: PMC10726767 DOI: 10.7717/peerj.16550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Whole mitochondrial genomes have been widely used in phylogenetic analysis, population genetics and biogeography studies. This study sequenced and characterized three complete mitochondrial genomes (Dasyhippus peipingensis, Myrmeleotettix palpalis, Aeropedellus prominemarginis) and determined their phylogenetic position in Acrididae. The length of the mitochondrial genomes ranged from 15,621-15,629 bp and composed of 13 PCGs, 2 rRNA, 22 tRNA genes and an AT control region. The arrangement and structure of the mitochondrial genomes were similar to those of other invertebrates. Comparative genomics revealed that the three mitochondrial genomes were highly conserved in terms of gene size, structure, and codon usage, all PCGs were purified selections with an ATN start codon and a TAN stop codon. All tRNAs could be folded into the typical clover-leaf structure, except tRNA Ser (AGN) that lacked a dihydrouridine (DHU) arm. Phylogenetic analysis based on 13 PCGs of 34 Acrididae species and seven outgroup species revealed that differences in the shape of antennae within the family Acrididae should be given less weight as a taxonomic character for higher-level classification. Moreover, the divergence time estimates indicates that in Gomphocerinae, the species with clubbed antennae were formed within the nearest 18 Mya, and Pacris xizangensis is more ancient.
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Affiliation(s)
- Li Wang
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Jianyu Chen
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xiaobao Xue
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Guoqing Qin
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Yuanyi Gao
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Kai Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Yulong Zhang
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Xin-Jiang Li
- The Key Laboratory of Zoological Systematics and Application, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
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Gaugel SM, Hawlitschek O, Dey LS, Husemann M. Evolution of mitogenomic gene order in Orthoptera. INSECT MOLECULAR BIOLOGY 2023. [PMID: 36883292 DOI: 10.1111/imb.12838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Mitochondrial gene order has contributed to the elucidation of evolutionary relationships in several animal groups. It generally has found its application as a phylogenetic marker for deep nodes. Yet, in Orthoptera limited research has been performed on the gene order, although the group represents one of the oldest insect orders. We performed a comprehensive study on mitochondrial genome rearrangements (MTRs) within Orthoptera in the context of mitogenomic sequence-based phylogeny. We used 280 published mitogenome sequences from 256 species, including three outgroup species, to reconstruct a molecular phylogeny. Using a heuristic approach, we assigned MTR scenarios to the edges of the phylogenetic tree and reconstructed ancestral gene orders to identify possible synapomorphies in Orthoptera. We found all types of MTRs in our dataset: inversions, transpositions, inverse transpositions, and tandem-duplication/random loss events (TDRL). Most of the suggested MTRs were in single and unrelated species. Out of five MTRs which were unique in subgroups of Orthoptera, we suggest four of them to be synapomorphies; those were in the infraorder Acrididea, in the tribe Holochlorini, in the subfamily Pseudophyllinae, and in the two families Phalangopsidae and Gryllidae or their common ancestor (leading to the relationship ((Phalangopsidae + Gryllidae) + Trigonidiidae)). However, similar MTRs have been found in distant insect lineages. Our findings suggest convergent evolution of specific mitochondrial gene orders in several species, deviant from the evolution of the mitogenome DNA sequence. As most MTRs were detected at terminal nodes, a phylogenetic inference of deeper nodes based on MTRs is not supported. Hence, the marker does not seem to aid resolving the phylogeny of Orthoptera, but adds further evidence for the complex evolution of the whole group, especially at the genetic and genomic levels. The results indicate a high demand for more research on patterns and underlying mechanisms of MTR events in Orthoptera.
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Affiliation(s)
- Sarah Maria Gaugel
- University of Hamburg, Hamburg, Germany
- Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Oliver Hawlitschek
- University of Hamburg, Hamburg, Germany
- Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Lara-Sophie Dey
- University of Hamburg, Hamburg, Germany
- Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Martin Husemann
- University of Hamburg, Hamburg, Germany
- Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
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Sevastianov N, Neretina T, Vedenina V. Evolution of calling songs in the grasshopper subfamily Gomphocerinae (Orthoptera, Acrididae). ZOOL SCR 2023. [DOI: 10.1111/zsc.12579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nikita Sevastianov
- Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russia
| | - Tatiana Neretina
- White Sea Biological Station, Biological Faculty M.V. Lomonosov Moscow State University Moscow Russia
| | - Varvara Vedenina
- Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russia
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Hawlitschek O, Sadílek D, Dey LS, Buchholz K, Noori S, Baez IL, Wehrt T, Brozio J, Trávníček P, Seidel M, Husemann M. New estimates of genome size in Orthoptera and their evolutionary implications. PLoS One 2023; 18:e0275551. [PMID: 36920952 PMCID: PMC10016648 DOI: 10.1371/journal.pone.0275551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Animal genomes vary widely in size, and much of their architecture and content remains poorly understood. Even among related groups, such as orders of insects, genomes may vary in size by orders of magnitude-for reasons unknown. The largest known insect genomes were repeatedly found in Orthoptera, e.g., Podisma pedestris (1C = 16.93 pg), Stethophyma grossum (1C = 18.48 pg) and Bryodemella holdereri (1C = 18.64 pg). While all these species belong to the suborder of Caelifera, the ensiferan Deracantha onos (1C = 19.60 pg) was recently found to have the largest genome. Here, we present new genome size estimates of 50 further species of Ensifera (superfamilies Gryllidea, Tettigoniidea) and Caelifera (Acrididae, Tetrigidae) based on flow cytometric measurements. We found that Bryodemella tuberculata (Caelifera: Acrididae) has the so far largest measured genome of all insects with 1C = 21.96 pg (21.48 gBp). Species of Orthoptera with 2n = 16 and 2n = 22 chromosomes have significantly larger genomes than species with other chromosome counts. Gryllidea genomes vary between 1C = 0.95 and 2.88 pg, and Tetrigidae between 1C = 2.18 and 2.41, while the genomes of all other studied Orthoptera range in size from 1C = 1.37 to 21.96 pg. Reconstructing ancestral genome sizes based on a phylogenetic tree of mitochondrial genomic data, we found genome size values of >15.84 pg only for the nodes of Bryodemella holdereri / B. tuberculata and Chrysochraon dispar / Euthystira brachyptera. The predicted values of ancestral genome sizes are 6.19 pg for Orthoptera, 5.37 pg for Ensifera, and 7.28 pg for Caelifera. The reasons for the large genomes in Orthoptera remain largely unknown, but a duplication or polyploidization seems unlikely as chromosome numbers do not differ much. Sequence-based genomic studies may shed light on the underlying evolutionary mechanisms.
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Affiliation(s)
- Oliver Hawlitschek
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- * E-mail:
| | - David Sadílek
- Institute of Medical Biochemistry and Laboratory Diagnostics, Centre of Oncocytogenomics, General University Hospital in Prague, Prague, Czech Republic
| | - Lara-Sophie Dey
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Katharina Buchholz
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Sajad Noori
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Inci Livia Baez
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig, Bonn, Germany
| | - Timo Wehrt
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Jason Brozio
- Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | | | - Martin Husemann
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
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Ma Y, Miao Y. Mitogenomic Comparison of the Mole Crickets Gryllotalpidae with the Phylogenetic Implications (Orthoptera: Ensifera). INSECTS 2022; 13:919. [PMID: 36292867 PMCID: PMC9604337 DOI: 10.3390/insects13100919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Owing to limited molecular data, the phylogenetic position of the family Gryllotalpidae is still controversial in the infraorder Gryllidea. Mitochondrial genome (mitogenome) plays a crucial role in reconstructing phylogenetic relationships and revealing the molecular evolution of insects. However, only four mitogenomes have been reported in Gryllotalpidae to date. Herein, we obtained the first mitogenomes of Gryllotalpa henana Cai & Niu, 1998 and the Chinese G. orientalis Burmeister, 1838, made a detailed comparison of all mitogenomes available in Gryllotalpidae and reconstructed the phylogeny of Gryllidea based on mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. The results show that the complete mitogenome sequences of G. henana (15,504 bp) and G. orientalis (15,497 bp) are conserved, both exhibiting the double-stranded circular structure, typical gene content and the ancestral insect gene arrangement. The complete mitogenome of G.henana exhibits the lowest average AT content ever detected in Gryllotalpidae, and even Gryllidea. The gene nad2 of both species has atypical initiation codon GTG. All tRNAs exhibit typical clover-leaf structure, except for trnS1 lacking the dihydrouridine (DHU) arm. A potential stem-loop structure, containing a (T)n(TC)2(T)n sequence, is detected in the control region of all gryllotalpids investigated and is likely related to the replication initiation of the minority strand. The phylogenetic analyses recover the six families of Gryllidea as Gryllotalpidae + (Myrmecophilidae + (Mogoplistidae + (Trigonidiidae + (Phalangopsidae + Gryllidae)))), similar to the trees based on transcriptomic and mitogenomic data. However, the trees are slightly different from the multilocus phylogenies, which show the sister-group relationship of Gryllotalpidae and Myrmecophilidae. The contradictions between mitogenomic and multilocus trees are briefly discussed.
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