1
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Matsuda K, Adachi H, Gotoh H, Inoue Y, Kondo S. Adhesion and shrinkage transform the rounded pupal horn into an angular adult horn in Japanese rhinoceros beetle. Development 2024; 151:dev202082. [PMID: 38477641 DOI: 10.1242/dev.202082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Clarifying the mechanisms underlying shape alterations during insect metamorphosis is important for understanding exoskeletal morphogenesis. The large horn of the Japanese rhinoceros beetle Trypoxylus dichotomus is the result of drastic metamorphosis, wherein it appears as a rounded shape during pupation and then undergoes remodeling into an angular adult shape. However, the mechanical mechanisms underlying this remodeling process remain unknown. In this study, we investigated the remodeling mechanisms of the Japanese rhinoceros beetle horn by developing a physical simulation. We identified three factors contributing to remodeling by biological experiments - ventral adhesion, uneven shrinkage, and volume reduction - which were demonstrated to be crucial for transformation using a physical simulation. Furthermore, we corroborated our findings by applying the simulation to the mandibular remodeling of stag beetles. These results indicated that physical simulation applies to pupal remodeling in other beetles, and the morphogenic mechanism could explain various exoskeletal shapes.
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Affiliation(s)
- Keisuke Matsuda
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Haruhiko Adachi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Hiroki Gotoh
- Department of Biological Sciences, Faculty of Science, Shizuoka University, Shizuoka, Shizuoka 422-8529, Japan
| | - Yasuhiro Inoue
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Kyoto 616-8540, Japan
| | - Shigeru Kondo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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2
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Hoedjes KM, Grath S, Posnien N, Ritchie MG, Schlötterer C, Abbott JK, Almudi I, Coronado-Zamora M, Durmaz Mitchell E, Flatt T, Fricke C, Glaser-Schmitt A, González J, Holman L, Kankare M, Lenhart B, Orengo DJ, Snook RR, Yılmaz VM, Yusuf L. From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Mol Ecol 2024:e17382. [PMID: 38856653 DOI: 10.1111/mec.17382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/09/2024] [Accepted: 04/29/2024] [Indexed: 06/11/2024]
Abstract
RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.
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Affiliation(s)
- Katja M Hoedjes
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sonja Grath
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Nico Posnien
- Department of Developmental Biology, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany
| | - Michael G Ritchie
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
| | | | | | - Isabel Almudi
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Claudia Fricke
- Institute for Zoology/Animal Ecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain
| | - Luke Holman
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Benedict Lenhart
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Vera M Yılmaz
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Leeban Yusuf
- Centre for Biological Diversity, University of St Andrews, St Andrews, UK
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3
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Makino M, Shimizu K, Kadota K. Enhanced clustering-based differential expression analysis method for RNA-seq data. MethodsX 2024; 12:102518. [PMID: 38179066 PMCID: PMC10764243 DOI: 10.1016/j.mex.2023.102518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/10/2023] [Indexed: 01/06/2024] Open
Abstract
RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering has been widely used to classify DEGs with similar expression patterns, but rarely used to identify DEGs themselves. We recently reported that the clustering-based method (called MBCdeg1 and 2) for identifying DEGs has great potential. However, these methods left room for improvement. This study reports on the improvement (named MBCdeg3). We compared a total of six competing methods: three conventional R packages (edgeR, DESeq2, and TCC) and three versions of MBCdeg (i.e., MBCdeg1, 2, and 3) corresponding to three different normalization algorithms. As MBCdeg3 performs well in many simulation scenarios of RNA-seq count data, MBCdeg3 replaces MBCdeg1 and 2 in our previous report. •MBCdeg3 is a method for both identification and classification of DEGs from RNA-seq count data.•MBCdeg3 is available as a function of R, which is common in the field of expression analysis.•MBCdeg3 performs well in a variety of simulation scenarios for RNA-seq count data.
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Affiliation(s)
- Manon Makino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Interfaculty Initiative in Information Studies, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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4
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Le MH, Morgan B, Lu MY, Moctezuma V, Burgos O, Huang JP. The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests. Mol Ecol Resour 2024; 24:e13908. [PMID: 38063363 DOI: 10.1111/1755-0998.13908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/14/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (Dynastes grantii, D. hyllus and D. tityus) were mapped to the genome assembled using PacBio + Hi-C data (D. maya). We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the D. maya assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles. We further identified homologues of nine and three candidate-gene families that may be associated with the evolution of horn structure and body colouration respectively. Structural variations in Scr and Ebony2 were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts.
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Affiliation(s)
- My-Hanh Le
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mei-Yeh Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Victor Moctezuma
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
| | - Oscar Burgos
- Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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5
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Kiontke K, Herrera RA, Mason DA, Woronik A, Vernooy S, Patel Y, Fitch DHA. Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575210. [PMID: 38260477 PMCID: PMC10802606 DOI: 10.1101/2024.01.12.575210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the transcription factor DMD-3. To find genes regulated by DMD-3, We performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males vs. dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the UPR (unfolded protein response) pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are coregulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.
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Affiliation(s)
- Karin Kiontke
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
| | | | - D Adam Mason
- Biology Department, Siena College, 515 Loudon Road, Loudonville, NY 12211
| | - Alyssa Woronik
- Sacred Heart University, 5151 Park Avenue, Fairfield, CT 06825
| | - Stephanie Vernooy
- Biology Department, Siena College, 515 Loudon Road, Loudonville, NY 12211
| | - Yash Patel
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
| | - David H A Fitch
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
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6
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Sugiyama M, Ozawa T, Ohta K, Okada K, Niimi T, Yamaguchi K, Shigenobu S, Okada Y. Transcriptomic and functional screening of weapon formation genes implies significance of cell adhesion molecules and female-biased genes in broad-horned flour beetle. PLoS Genet 2023; 19:e1011069. [PMID: 38051754 PMCID: PMC10723671 DOI: 10.1371/journal.pgen.1011069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/15/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
For understanding the evolutionary mechanism of sexually selected exaggerated traits, it is essential to uncover its molecular basis. By using broad-horned flour beetle that has male-specific exaggerated structures (mandibular horn, head horn and gena enlargement), we investigated the transcriptomic and functional characters of sex-biased genes. Comparative transcriptome of male vs. female prepupal heads elucidated 673 sex-biased genes. Counter-intuitively, majority of them were female-biased (584 genes), and GO enrichment analysis showed cell-adhesion molecules were frequently female-biased. This pattern motivated us to hypothesize that female-biased transcripts (i.e. the transcripts diminished in males) may play a role in outgrowth formation. Potentially, female-biased genes may act as suppressors of weapon structure. In order to test the functionality of female-biased genes, we performed RNAi-mediated functional screening for top 20 female-biased genes and 3 genes in the most enriched GO term (cell-cell adhesion, fat1/2/3, fat4 and dachsous). Knockdown of one transcription factor, zinc finger protein 608 (zfp608) resulted in the formation of male-like gena in females, supporting the outgrowth suppression function of this gene. Similarly, knockdown of fat4 induced rudimental, abnormal mandibular horn in female. fat1/2/3RNAi, fat4RNAi and dachsousRNAi males exhibited thick and/or short mandibular horns and legs. These cell adhesion molecules are known to regulate tissue growth direction and known to be involved in the weapon formation in Scarabaeoidea beetles. Functional evidence in phylogenetically distant broad-horned flour beetle suggest that cell adhesion genes are repeatedly deployed in the acquisition of outgrowth. In conclusion, this study clarified the overlooked functions of female-biased genes in weapon development.
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Affiliation(s)
- Miyu Sugiyama
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Takane Ozawa
- Department of Life Sciences, The University of Tokyo, Komaba, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, The University of Tokyo, Komaba, Tokyo, Japan
| | - Kensuke Okada
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Tsushima-naka, Okayama, Japan
| | - Teruyuki Niimi
- National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki, Japan
- Basic Biology Program, The Graduate University for Advanced Studies, SOKENDAI, Nishigonaka, Myodaiji, Okazaki, Japan
| | - Katsushi Yamaguchi
- National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki, Japan
- Basic Biology Program, The Graduate University for Advanced Studies, SOKENDAI, Nishigonaka, Myodaiji, Okazaki, Japan
| | - Yasukazu Okada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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7
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Erlenbach T, Haynes L, Fish O, Beveridge J, Giambrone S, Reed LK, Dyer KA, Scott Chialvo CH. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. Ecol Evol 2023; 13:e10736. [PMID: 38099137 PMCID: PMC10719611 DOI: 10.1002/ece3.10736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila, many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila. First, we inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of them could develop on diet with toxin. Finally, we asked how α-amanitin tolerance might have evolved across the immigrans-tripunctata radiation, and inferred that toxin tolerance was ancestral in mushroom-feeding Drosophila and subsequently lost multiple times. Our findings expand our understanding of toxin tolerance across the immigrans-tripunctata radiation and emphasize the uniqueness of toxin tolerance in this adaptive radiation and the complexity of biochemical adaptations.
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Affiliation(s)
| | - Lauren Haynes
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Olivia Fish
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Jordan Beveridge
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | | | - Laura K. Reed
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Kelly A. Dyer
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Clare H. Scott Chialvo
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
- Department of BiologyAppalachian State UniversityBooneNorth CarolinaUSA
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8
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Morikawa K, Morita S, Sakura K, Maeno A, Gotoh H, Niimi T, Inoue Y. Unveiling the role of differential growth in 3D morphogenesis: An inference method to analyze area expansion rate distribution in biological systems. J Theor Biol 2023; 575:111650. [PMID: 37884223 DOI: 10.1016/j.jtbi.2023.111650] [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: 03/24/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023]
Abstract
The three-dimensional (3D) morphologies of many organs in organisms, such as the curved shapes of leaves and flowers, the branching structure of lungs, and the exoskeletal shape of insects, are formed through surface growth. Although differential growth, a mode of surface growth, has been qualitatively identified as 3D morphogenesis, a quantitative understanding of the mechanical contribution of differential growth is lacking. To address this, we developed a quantitative inference method to analyze the distribution of the area expansion rate, which governs the growth of surfaces into 3D morphology. To validate the accuracy of our method, we tested it on a basic 3D morphology that allowed for the theoretical derivation of the area expansion rate distribution, and then assessed the difference between the predicted outcome and the theoretical solution. We also applied this method to complex 3D shapes and evaluated its accuracy through numerical experiments. The findings of the study revealed a linear decrease in error on a log-log scale with an increase in the number of meshes in both evaluations. This affirmed the reliability of the predictions for meshes that are sufficiently refined. Moreover, we employed our methodology to analyze the developmental process of the Japanese rhinoceros beetle Trypoxylus dichotomus, which is characterized by differential growth regulating 3D morphogenesis. The results indicated a notably high rate of area expansion on the left and right edges of the horn primordium, which is consistent with the experimental evidence of a higher rate of cell division in these regions. Hence, these findings confirm the efficacy of the proposed method in analyzing biological systems.
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Affiliation(s)
- Kentaro Morikawa
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Japan.
| | - Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Japan; Basic Biology Program, Graduate Institute for Advanced Studies, The Graduate University for Advanced Studies, SOKENDAI, Japan
| | - Kazuki Sakura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Japan
| | | | - Hiroki Gotoh
- Department of Biological Science, Faculty of Science, Shizuoka University, Japan
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Japan; Basic Biology Program, Graduate Institute for Advanced Studies, The Graduate University for Advanced Studies, SOKENDAI, Japan
| | - Yasuhiro Inoue
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Japan.
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9
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Schneider RF, Gunter HM, Salewski I, Woltering JM, Meyer A. Growth dynamics and molecular bases of evolutionary novel jaw extensions in halfbeaks and needlefishes (Beloniformes). Mol Ecol 2023; 32:5798-5811. [PMID: 37750351 DOI: 10.1111/mec.17143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/17/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
Evolutionary novelties-derived traits without clear homology found in the ancestors of a lineage-may promote ecological specialization and facilitate adaptive radiations. Examples for such novelties include the wings of bats, pharyngeal jaws of cichlids and flowers of angiosperms. Belonoid fishes (flying fishes, halfbeaks and needlefishes) feature an astonishing diversity of extremely elongated jaw phenotypes with undetermined evolutionary origins. We investigate the development of elongated jaws in a halfbeak (Dermogenys pusilla) and a needlefish (Xenentodon cancila) using morphometrics, transcriptomics and in situ hybridization. We confirm that these fishes' elongated jaws are composed of distinct base and novel 'extension' portions. These extensions are morphologically unique to belonoids, and we describe the growth dynamics of both bases and extensions throughout early development in both studied species. From transcriptomic profiling, we deduce that jaw extension outgrowth is guided by populations of multipotent cells originating from the anterior tip of the dentary. These cells are shielded from differentiation, but proliferate and migrate anteriorly during the extension's allometric growth phase. Cells left behind at the tip leave the shielded zone and undergo differentiation into osteoblast-like cells, which deposit extracellular matrix with both bone and cartilage characteristics that mineralizes and thereby provides rigidity. Such bone has characteristics akin to histological observations on the elongated 'kype' process on lower jaws of male salmon, which may hint at common conserved regulatory underpinnings. Future studies will evaluate the molecular pathways that govern the anterior migration and proliferation of these multipotent cells underlying the belonoids' evolutionary novel jaw extensions.
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Affiliation(s)
- Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Marine Ecology, GEOMAR, Kiel, Germany
| | - Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Inken Salewski
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Joost M Woltering
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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10
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Weber JN, Kojima W, Boisseau RP, Niimi T, Morita S, Shigenobu S, Gotoh H, Araya K, Lin CP, Thomas-Bulle C, Allen CE, Tong W, Lavine LC, Swanson BO, Emlen DJ. Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus. Curr Biol 2023; 33:4285-4297.e5. [PMID: 37734374 DOI: 10.1016/j.cub.2023.08.066] [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: 03/13/2023] [Revised: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
What limits the size of nature's most extreme structures? For weapons like beetle horns, one possibility is a tradeoff associated with mechanical levers: as the output arm of the lever system-the beetle horn-gets longer, it also gets weaker. This "paradox of the weakening combatant" could offset reproductive advantages of additional increases in weapon size. However, in contemporary populations of most heavily weaponed species, males with the longest weapons also tend to be the strongest, presumably because selection drove the evolution of compensatory changes to these lever systems that ameliorated the force reductions of increased weapon size. Therefore, we test for biomechanical limits by reconstructing the stages of weapon evolution, exploring whether initial increases in weapon length first led to reductions in weapon force generation that were later ameliorated through the evolution of mechanisms of mechanical compensation. We describe phylogeographic relationships among populations of a rhinoceros beetle and show that the "pitchfork" shaped head horn likely increased in length independently in the northern and southern radiations of beetles. Both increases in horn length were associated with dramatic reductions to horn lifting strength-compelling evidence for the paradox of the weakening combatant-and these initial reductions to horn strength were later ameliorated in some populations through reductions to horn length or through increases in head height (the input arm for the horn lever system). Our results reveal an exciting geographic mosaic of weapon size, weapon force, and mechanical compensation, shedding light on larger questions pertaining to the evolution of extreme structures.
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Affiliation(s)
- Jesse N Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Wataru Kojima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Romain P Boisseau
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Hiroki Gotoh
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oya, Suruga Ward, Shizuoka, Japan
| | - Kunio Araya
- Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-city Fukuoka 819-0395, Japan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, No.88 Sec. 4, Tingzhou Rd, Taipei 11677, Taiwan
| | - Camille Thomas-Bulle
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA; Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Cerisse E Allen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Wenfei Tong
- Cornell Laboratory of Ornithology, Ithaca, NY 14850, USA
| | - Laura Corley Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Brook O Swanson
- Department of Biology, Gonzaga University, 502 East Boone Avenue, Spokane, WA 99258-0102, USA
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.
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11
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Erlenbach T, Haynes L, Fish O, Beveridge J, Bingolo E, Giambrone SA, Kropelin G, Rudisill S, Chialvo P, Reed LK, Dyer KA, Chialvo CS. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551872. [PMID: 37577671 PMCID: PMC10418198 DOI: 10.1101/2023.08.03.551872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila , many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila . We first inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of these species could develop on diet with toxin. Third, we examined fly development on a diet containing a natural mix of toxins extracted from the Death Cap Amanita phalloides mushroom. Both tolerant and susceptible species developed on diet with this mix, though tolerant species survived at significantly higher concentrations. Finally, we asked how cyclopeptide tolerance might have evolved across the immigrans-tripunctata radiation and inferred that toxin tolerance was ancestral and subsequently lost multiple times. Our results suggest the evolutionary history of cyclopeptide tolerance is complex, and simply describing this trait as present or absent does not fully capture the occurrence or impact on this adaptive radiation. More broadly, the evolution of novelty can be more complex than previously thought, and that accurate descriptions of such novelties are critical in studies examining their evolution.
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12
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Morita S, Shibata TF, Nishiyama T, Kobayashi Y, Yamaguchi K, Toga K, Ohde T, Gotoh H, Kojima T, Weber JN, Salvemini M, Bino T, Mase M, Nakata M, Mori T, Mori S, Cornette R, Sakura K, Lavine LC, Emlen DJ, Niimi T, Shigenobu S. The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation. Sci Rep 2023; 13:8735. [PMID: 37253792 DOI: 10.1038/s41598-023-35246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
The Japanese rhinoceros beetle Trypoxylus dichotomus is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as a research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10 × Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. We focused on the genes related to horn formation and obtained new insights into the evolution of the gene repertoire and sexual dimorphism as exemplified by the sex-specific splicing pattern of the doublesex gene. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.
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Grants
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- 23128505, 25128706, 16H01452, 18H04766, 20H04933, 20H05944, 17H06384, 22128008, 19K16181, 21K15135 Japan Society for the Promotion of Science
- IOS-1456133 National Science Foundation
- IOS-1456133 National Science Foundation
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Affiliation(s)
- Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
| | - Tomoko F Shibata
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Tomoaki Nishiyama
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Yuuki Kobayashi
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Kouhei Toga
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- URA Division, Office of Research and Academia-Government-Community Collaboration, Hiroshima University, Hiroshima, Japan
| | - Takahiro Ohde
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroki Gotoh
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, Nagoya, Japan
| | - Jesse N Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Takahiro Bino
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Mutsuki Mase
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Moe Nakata
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tomoko Mori
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Shogo Mori
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kazuki Sakura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Laura C Lavine
- Department of Entomology, Washington State University, Pullman, WA, USA
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, MT, USA
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan.
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.
- Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
| | - Shuji Shigenobu
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan.
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Japan.
- Trans-Omics Facility, National Institute for Basic Biology, Okazaki, Japan.
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13
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Wilcox AS, Vea IM, Frankino WA, Shingleton AW. Genetic variation of morphological scaling in Drosophila melanogaster. Heredity (Edinb) 2023; 130:302-311. [PMID: 36878946 PMCID: PMC10162999 DOI: 10.1038/s41437-023-00603-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/08/2023] Open
Abstract
Morphological scaling relationships between the sizes of individual traits and the body captures the characteristic shape of a species, and their evolution is the primary mechanism of morphological diversification. However, we have almost no knowledge of the genetic variation of scaling, which is critical if we are to understand how scaling evolves. Here we explore the genetics of population scaling relationships (scaling relationships fit to multiple genetically-distinct individuals in a population) by describing the distribution of individual scaling relationships (genotype-specific scaling relationships that are unseen or cryptic). These individual scaling relationships harbor the genetic variation in the developmental mechanisms that regulate trait growth relative to body growth, and theoretical studies suggest that their distribution dictates how the population scaling relationship will respond to selection. Using variation in nutrition to generate size variation within 197 isogenic lineages of Drosophila melanogaster, we reveal extensive variation in the slopes of the wing-body and leg-body individual scaling relationships among genotypes. This variation reflects variation in the nutritionally-induced size plasticity of the wing, leg, and body. Surprisingly, we find that variation in the slope of individual scaling relationships primarily results from variation in nutritionally-induced plasticity of body size, not leg or wing size. These data allow us to predict how different selection regimes affect scaling in Drosophila, and is the first step in identifying the genetic targets of such selection. More generally, our approach provides a framework for understanding the genetic variation of scaling, an important prerequisite to explaining how selection changes scaling and morphology.
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Affiliation(s)
- Austin S Wilcox
- Department of Biological Sciences, University of Illinois Chicago, 840 W Taylor St, Chicago, IL, 60607, USA
| | - Isabelle M Vea
- Department of Biological Sciences, University of Illinois Chicago, 840 W Taylor St, Chicago, IL, 60607, USA
| | - W Anthony Frankino
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Alexander W Shingleton
- Department of Biological Sciences, University of Illinois Chicago, 840 W Taylor St, Chicago, IL, 60607, USA.
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14
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The function and evolution of a genetic switch controlling sexually dimorphic eye differentiation in honeybees. Nat Commun 2023; 14:463. [PMID: 36709321 PMCID: PMC9884244 DOI: 10.1038/s41467-023-36153-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Animals develop sex-specific morphological structures that are diverse between organisms. However, understanding the developmental and evolutionary mechanisms governing these traits is still limited and largely restricted to DM domain genes, which are conserved, sex-specific developmental regulators identified in genetic models. Here, we report a sex-specific developmental regulator gene, glubschauge (glu) that selectively regulates sexually dimorphic eye differentiation in honeybees. We found that the sex determination gene feminizer (fem) controls sex-specific splicing of glu transcripts, establishing a genetic switch in which Glu proteins with a zinc finger (ZnF) domain are only expressed in females. We showed that female coding sequence was essential and sufficient for partial feminization. Comparative sequence and functional studies revealed that the evolutionary origination of the genetic switch was followed by the mutational origin of the essential ZnF domain. Our results demonstrate that glu is a newly evolved sex-specific genetic switch for region-specific regulation of a dimorphic character.
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15
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Ohtsu I, Chikami Y, Umino T, Gotoh H. Evaluation of Body Size Indicators for Morphological Analyses in Two Sister Species of Genus Dorcus (Coleoptera, Lucanidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:7. [PMID: 36130316 PMCID: PMC9492273 DOI: 10.1093/jisesa/ieac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Indexed: 06/15/2023]
Abstract
The relationship between trait and body size, i.e., the scaling relationship or static allometry, is an essential concept for investigating trait size. However, usage of an inappropriate body size indicator can lead to misinterpretation of morphology. In this study, we examined several possible body size indicators in two closely related stag beetle species, Dorcus rectus and Dorcus amamianus. We raised animals in captivity and used pupal weight as a measure of true, or overall body size, and then evaluated six adult morphological traits to test whether these traits could be reliably used as body size indicators in static scaling relationship comparisons. We analyzed two comparisons, between sexes in same species and between species in same sex. We showed that the most appropriate body size indicators differ depending on the comparisons. Our results indicated that the scaling relationship of focal traits could be over- or under-estimated depending on which body size indicators are used.
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Affiliation(s)
- Itsuki Ohtsu
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yasuhiko Chikami
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Taichi Umino
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Ueda, Nagano, 386-2204, Japan
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16
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Morita S, Sakura K, Gotoh H, Emlen DJ, Niimi T. Recent advances in understanding horn formation in the Japanese rhinoceros beetle Trypoxylus dichotomus using next-generation sequencing technology. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100901. [PMID: 35301164 DOI: 10.1016/j.cois.2022.100901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/20/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
The exaggerated horns of beetles are attractive models for studying the origin of novel traits and morphological evolution. Closely related species often differ profoundly in the size, number, and shape of their horns, and in the body region from which they extend. In addition, beetle horns exhibit exquisite nutrition-dependent phenotypic plasticity, leading to disproportionate growth of the horns in the largest, best-condition individuals and much smaller - even stunted - horn sizes in poor-condition individuals. These exciting phenomena in beetle horns have recently been revealed at the molecular level with the advent of next-generation sequencing. This section reviews the latest research on a horned beetle, the Japanese rhinoceros beetle Trypoxylus dichotomus, whose genome was recently sequenced.
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Affiliation(s)
- Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Kazuki Sakura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Hiroki Gotoh
- Department of Biological Science, Faculty of Sciences, Shizuoka University, Shizuoka 422-8529, Japan
| | - Douglas J Emlen
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan.
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17
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Sex-specific regulation of development, growth and metabolism. Semin Cell Dev Biol 2022; 138:117-127. [PMID: 35469676 DOI: 10.1016/j.semcdb.2022.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/07/2022] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
Adult females and males of most species differ in many aspects of their morphology, physiology and behavior, in response to sex-specific selective pressures that maximize fitness. While we have an increasingly good understanding of the genetic mechanisms that initiate these differences, the sex-specific developmental trajectories that generate them are much less well understood. Here we review recent advances in the sex-specific regulation of development focusing on two models where this development is increasingly well understood: Sexual dimorphism of body size in the fruit fly Drosophila melanogaster and sexual dimorphism of horns in the horned beetle Onthophagus taurus. Because growth and development are also supported by metabolism, the regulation of sex-specific metabolism during and after development is an important aspect of the generation of female and male phenotypes. Hitherto, the study of sex-specific development has largely been independent of the study of sex-specific metabolism. Nevertheless, as we discuss in this review, recent research has begun to reveal considerable overlap in the cellular and physiological mechanisms that regulate sex-specific development and metabolism.
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18
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Sakura K, Morita S, Niimi T. RNA Interference Method for Gene Function Analysis in the Japanese Rhinoceros Beetle Trypoxylus dichotomus. Bio Protoc 2022; 12:e4396. [PMID: 35800098 PMCID: PMC9081472 DOI: 10.21769/bioprotoc.4396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/20/2021] [Accepted: 03/14/2022] [Indexed: 12/29/2022] Open
Abstract
In the Japanese rhinoceros beetle Trypoxylus dichotomus, various candidate genes required for a specific phenotype of interest are listed by next-generation sequencing analysis. Their functions were investigated using RNA interference (RNAi) method, the only gene function analysis tool for T. dichotomusdeveloped so far. The summarized procedure for the RNAi method used for T. dichotomusis to synthesize double-stranded RNA (dsRNA), and inject it in larvae or pupae of T. dichotomus. Although some dedicated materials or equipment are generally required to inject dsRNA in insects, the advantage of the protocol described here is that it is possible to inject dsRNA in T. dichotomuswith one syringe.
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Affiliation(s)
- Kazuki Sakura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan
| | - Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki, Japan,*For correspondence:
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19
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Zittra C, Vitecek S, Schwaha T, Handschuh S, Martini J, Vieira A, Kuhlmann HC, Waringer J. Comparing head muscles among Drusinae clades (Insecta: Trichoptera) reveals high congruence despite strong contrasts in head shape. Sci Rep 2022; 12:1047. [PMID: 35058493 PMCID: PMC8776961 DOI: 10.1038/s41598-022-04790-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 12/29/2021] [Indexed: 11/09/2022] Open
Abstract
AbstractThe subfamily Drusinae (Limnephilidae, Trichoptera) comprises a range of species exhibiting differently shaped head capsules in their larval stages. These correspond to evolutionary lineages pursuing different larval feeding ecologies, each of which uses a different hydraulic niche: scraping grazers and omnivorous shredders sharing rounded head capsules and filtering carnivores with indented and corrugated head capsules. In this study, we assess whether changes in head capsule morphology are reflected by changes in internal anatomy of Drusinae heads. To this end, internal and external head morphology was visualized using µCT methods and histological sections in three Drusinae species—Drusus franzi, D. discolor and D. bosnicus—representing the three evolutionary lineages. Our results indicate that Drusinae head musculature is highly conserved across the evolutionary lineages with only minute changes between taxa. Conversely, the tentorium is reduced in D. discolor, the species with the most aberrant head capsule investigated here. Integrating previous research on Drusinae head anatomy, we propose a fundamental Drusinae blueprint comprising 29 cephalic muscles and discuss significance of larval head capsule corrugation in Trichoptera.
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20
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Osabe T, Shimizu K, Kadota K. Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data. BMC Bioinformatics 2021; 22:511. [PMID: 34670485 PMCID: PMC8527798 DOI: 10.1186/s12859-021-04438-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering is used to classify DEGs with similar expression patterns for the subsequent analyses of data from experiments such as time-courses or multi-group comparisons. However, gene clustering has rarely been used for analyzing simple two-group data or differential expression (DE). In this study, we report that a model-based clustering algorithm implemented in an R package, MBCluster.Seq, can also be used for DE analysis. Results The input data originally used by MBCluster.Seq is DEGs, and the proposed method (called MBCdeg) uses all genes for the analysis. The method uses posterior probabilities of genes assigned to a cluster displaying non-DEG pattern for overall gene ranking. We compared the performance of MBCdeg with conventional R packages such as edgeR, DESeq2, and TCC that are specialized for DE analysis using simulated and real data. Our results showed that MBCdeg outperformed other methods when the proportion of DEG (PDEG) was less than 50%. However, the DEG identification using MBCdeg was less consistent than with conventional methods. We compared the effects of different normalization algorithms using MBCdeg, and performed an analysis using MBCdeg in combination with a robust normalization algorithm (called DEGES) that was not implemented in MBCluster.Seq. The new analysis method showed greater stability than using the original MBCdeg with the default normalization algorithm. Conclusions MBCdeg with DEGES normalization can be used in the identification of DEGs when the PDEG is relatively low. As the method is based on gene clustering, the DE result includes information on which expression pattern the gene belongs to. The new method may be useful for the analysis of time-course and multi-group data, where the classification of expression patterns is often required. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04438-4.
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Affiliation(s)
- Takayuki Osabe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,Interfaculty Initiative in Information Studies, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Interfaculty Initiative in Information Studies, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
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21
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Ogata N. Whole-Genome Sequence of the Trypoxylus dichotomus Japanese rhinoceros beetle. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000487. [PMID: 34723147 PMCID: PMC8553429 DOI: 10.17912/micropub.biology.000487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/06/2022]
Abstract
The draft whole-genome sequence of the Japanese rhinoceros beetle, Trypoxylus dichotomus was obtained using long-read PacBio sequence technology. The final assembled genome consisted of 739 Mbp in 2,347 contigs, with 24.5× mean coverage and a G+C content of 35.99%.
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Affiliation(s)
- Norichika Ogata
- Nihon BioData Corporation,
Correspondence to: Norichika Ogata ()
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22
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Toubiana W, Armisén D, Dechaud C, Arbore R, Khila A. Impact of male trait exaggeration on sex-biased gene expression and genome architecture in a water strider. BMC Biol 2021; 19:89. [PMID: 33931057 PMCID: PMC8088084 DOI: 10.1186/s12915-021-01021-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 04/01/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Exaggerated secondary sexual traits are widespread in nature and often evolve under strong directional sexual selection. Although heavily studied from both theoretical and empirical viewpoints, we have little understanding of how sexual selection influences sex-biased gene regulation during the development of exaggerated secondary sexual phenotypes, and how these changes are reflected in genomic architecture. This is primarily due to the limited availability of representative genomes and associated tissue and sex transcriptomes to study the development of these traits. Here we present the genome and developmental transcriptomes, focused on the legs, of the water strider Microvelia longipes, a species where males exhibit strikingly long third legs compared to females, which they use as weapons. RESULTS We generated a high-quality genome assembly with 90% of the sequence captured in 13 scaffolds. The most exaggerated legs in males were particularly enriched in both sex-biased and leg-biased genes, indicating a specific signature of gene expression in association with trait exaggeration. We also found that male-biased genes showed patterns of fast evolution compared to non-biased and female-biased genes, indicative of directional or relaxed purifying selection. By contrast to male-biased genes, female-biased genes that are expressed in the third legs, but not the other legs, are over-represented in the X chromosome compared to the autosomes. An enrichment analysis for sex-biased genes along the chromosomes revealed also that they arrange in large genomic regions or in small clusters of two to four consecutive genes. The number and expression of these enriched regions were often associated with the exaggerated legs of males, suggesting a pattern of common regulation through genomic proximity in association with trait exaggeration. CONCLUSION Our findings indicate how directional sexual selection may drive sex-biased gene expression and genome architecture along the path to trait exaggeration and sexual dimorphism.
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Affiliation(s)
- William Toubiana
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon Cedex 07, France
- Present address: Department of Ecology and Evolution, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon Cedex 07, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon Cedex 07, France
| | - Roberto Arbore
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon Cedex 07, France
- Present address: Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon Cedex 07, France.
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23
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Gotoh H, Adachi H, Matsuda K, Lavine LC. Epithelial folding determines the final shape of beetle horns. Curr Opin Genet Dev 2021; 69:122-128. [PMID: 33848957 DOI: 10.1016/j.gde.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 11/18/2022]
Abstract
The elaborate ornaments and weapons of sexual selection, such as the vast array of horns observed in scarab beetles, are some of the most striking outcomes of evolution. How these novel traits have arisen, develop, and respond to condition is governed by a complex suite of interactions that require coordination between the environment, whole-animal signals, cell-cell signals, and within-cell signals. Endocrine factors, developmental patterning genes, and sex-specific gene expression have been shown to regulate beetle horn size, shape, and location, yet no overarching mechanism of horn shape has been described. Recent advances in microscopy and computational analyses combined with a functional genetic approach have revealed that patterning genes combined with intricate epithelial folding and movement are responsible for the final shape of a beetle head horn.
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Affiliation(s)
- Hiroki Gotoh
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 401-8540, Japan
| | - Haruhiko Adachi
- Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Keisuke Matsuda
- Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka, 565-0871, Japan; Osaka University Hospital, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Laura C Lavine
- Department of Entomology, Washington State University, Pullman, WA, 99163 USA.
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24
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Emberts Z, Wiens JJ. Do sexually selected weapons drive diversification? Evolution 2021; 75:2411-2424. [PMID: 33738793 DOI: 10.1111/evo.14212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
Sexual selection is often thought to promote speciation. This expectation is largely driven by the fact that sexually selected traits can influence mating patterns and contribute to reproductive isolation. Indeed, some comparative studies have shown that clades with sexually selected traits have increased rates of speciation and diversification. However, these studies have almost exclusively focused on one mechanism of sexual selection: female choice. Another widespread mechanism is male-male competition. Few empirical studies (if any) have investigated the role of this alternative mechanism in driving diversification. Nevertheless, recent reviews have suggested that male-male competition can increase speciation rates. Here, we investigated whether traits associated with precopulatory male-male competition (i.e., sexually selected weapons) have promoted speciation and diversification in insects. We focused on three clades with both weapons and suitable phylogenies: leaf-footed and broad-headed bugs (Coreidae+Alydidae; ∼2850 species), stick insects and relatives (Phasmatodea; ∼3284 species), and scarab beetles (Scarabaeoidea; ∼39,717 species). We found no evidence that weapon-bearing lineages in these clades have higher rates of speciation or diversification than their weaponless relatives. Thus, our results suggest that precopulatory male-male competition may not have strong, general effects on speciation and diversification in insects, a group encompassing ∼60% of all described species.
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Affiliation(s)
- Zachary Emberts
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721
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25
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Mowles SL, Skicko IM, Sturrock CJ, Durrant KL. Differential effects of aerobic capacities on fight outcome in giant hissing cockroaches. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2021.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Computational analyses decipher the primordial folding coding the 3D structure of the beetle horn. Sci Rep 2021; 11:1017. [PMID: 33441712 PMCID: PMC7806817 DOI: 10.1038/s41598-020-79757-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/07/2020] [Indexed: 01/18/2023] Open
Abstract
The beetle horn primordium is a complex and compactly folded epithelial sheet located beneath the larval cuticle. Only by unfolding the primordium can the complete 3D shape of the horn appear, suggesting that the morphology of beetle horns is encoded in the primordial folding pattern. To decipher the folding pattern, we developed a method to manipulate the primordial local folding on a computer and clarified the contribution of the folding of each primordium region to transformation. We found that the three major morphological changes (branching of distal tips, proximodistal elongation, and angular change) were caused by the folding of different regions, and that the folding mechanism also differs according to the region. The computational methods we used are applicable to the morphological study of other exoskeletal animals.
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27
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Yang H, You CJ, Tsui CKM, Tembrock LR, Wu ZQ, Yang DP. Phylogeny and biogeography of the Japanese rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae) based on SNP markers. Ecol Evol 2021; 11:153-173. [PMID: 33437420 PMCID: PMC7790660 DOI: 10.1002/ece3.6982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/23/2020] [Accepted: 10/16/2020] [Indexed: 12/05/2022] Open
Abstract
The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific-locus amplified fragment sequencing (SLAF-seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., T. d. septentrionalis) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise F ST values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF-seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species' range.
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Affiliation(s)
- Huan Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Chong Juan You
- Beijing Key Laboratory for Forest Pest ControlBeijing Forestry UniversityBeijingChina
| | - Clement K. M. Tsui
- Department of PathologySidra MedicineDohaQatar
- Department of Pathology and Laboratory MedicineWeill Cornell Medicine‐QatarAr‐RayyanQatar
- Division of Infectious DiseasesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Luke R. Tembrock
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Zhi Qiang Wu
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - De Po Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
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28
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Adachi H, Matsuda K, Niimi T, Kondo S, Gotoh H. Genetical control of 2D pattern and depth of the primordial furrow that prefigures 3D shape of the rhinoceros beetle horn. Sci Rep 2020; 10:18687. [PMID: 33122767 PMCID: PMC7596553 DOI: 10.1038/s41598-020-75709-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
The head horn of the Asian rhinoceros beetle develops as an extensively folded primordium before unfurling into its final 3D shape at the pupal molt. The information of the final 3D structure of the beetle horn is prefigured in the folding pattern of the developing primordium. However, the developmental mechanism underlying epithelial folding of the primordium is unknown. In this study, we addressed this gap in our understanding of the developmental patterning of the 3D horn shape of beetles by focusing on the formation of furrows at the surface of the primordium that become the bifurcated 3D shape of the horn. By gene knockdown analysis via RNAi, we found that knockdown of the gene Notch disturbed overall horn primordial furrow depth without affecting the 2D furrow pattern. In contrast, knockdown of CyclinE altered 2D horn primordial furrow pattern without affecting furrow depth. Our results show how the depth and 2D pattern of primordial surface furrows are regulated at least partially independently during beetle horn development, and how both can alter the final 3D shape of the horn.
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Affiliation(s)
- Haruhiko Adachi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Keisuke Matsuda
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.,Osaka University Hospital, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Shigeru Kondo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hiroki Gotoh
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
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29
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Monteiro A. Distinguishing serial homologs from novel traits: Experimental limitations and ideas for improvements. Bioessays 2020; 43:e2000162. [PMID: 33118632 DOI: 10.1002/bies.202000162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022]
Abstract
One of the central but yet unresolved problems in evolutionary biology concerns the origin of novel complex traits. One hypothesis is that complex traits derive from pre-existing gene regulatory networks (GRNs) reused and modified to specify a novel trait somewhere else in the body. This simple explanation encounters problems when the novel trait that emerges in a body is in a region that is known to harbor a latent or repressed trait that has been silent for millions of years. Is the novel trait merely a re-emerged de-repressed trait or a truly novel trait that emerged via a novel deployment of an old GRN? A couple of new studies sided on opposite sides of this question when investigating the origin of horns in dung beetles and helmets in treehoppers that develop in the first thoracic segment (T1) of their bodies, a segment known to harbor a pair of repressed/modified wings in close relatives. Here, I point to some key limitations of the experimental approaches used and highlight additional experiments that could be done in future to resolve the developmental origin of these and other traits.
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Affiliation(s)
- Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Science Division, Yale-NUS College, Singapore, Singapore
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30
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Del Sol JF, Hongo Y, Boisseau RP, Berman GH, Allen CE, Emlen DJ. Population differences in the strength of sexual selection match relative weapon size in the Japanese rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae)†. Evolution 2020; 75:394-413. [PMID: 33009663 DOI: 10.1111/evo.14101] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/07/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Exaggerated weapons of sexual selection often diverge more rapidly and dramatically than other body parts, suggesting that relevant agents of selection may be discernible in contemporary populations. We examined the ecology, reproductive behavior, and strength of sexual selection on horn length in five recently diverged rhinoceros beetle (Trypoxylus dichotomus) populations that differ in relative horn size. Males with longer horns were better at winning fights in all locations, but the link between winning fights and mating success differed such that selection favored large males with long horns at the two long-horned populations, but was relaxed or nonexistent at the populations with relatively shorter horns. Observations of local habitat conditions and breeding ecology point to shifts in the relative abundance of feeding territories as the most likely cause of population differences in selection on male weapon size in this species. Comparisons of ecological conditions and selection strength across populations offer critical first steps toward meaningfully linking mating system dynamics, selection patterns, and diversity in sexually selected traits.
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Affiliation(s)
- Jillian F Del Sol
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Yoshihito Hongo
- Department of Life Sciences, Ritsumeikan University, Kyoto, 603-8577, Japan
| | - Romain P Boisseau
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Gabriella H Berman
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Cerisse E Allen
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Douglas J Emlen
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
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31
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Walton A, Sheehan MJ, Toth AL. Going wild for functional genomics: RNA interference as a tool to study gene-behavior associations in diverse species and ecological contexts. Horm Behav 2020; 124:104774. [PMID: 32422196 DOI: 10.1016/j.yhbeh.2020.104774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/25/2022]
Abstract
Identifying the genetic basis of behavior has remained a challenge for biologists. A major obstacle to this goal is the difficulty of examining gene function in an ecologically relevant context. New tools such as CRISPR/Cas9, which alter the germline of an organism, have taken center stage in functional genomics in non-model organisms. However, germline modifications of this nature cannot be ethically implemented in the wild as a part of field experiments. This impediment is more than technical. Gene function is intimately tied to the environment in which the gene is expressed, especially for behavior. Most lab-based studies fail to recapitulate an organism's ecological niche, thus most published functional genomics studies of gene-behavior relationships may provide an incomplete or even inaccurate assessment of gene function. In this review, we highlight RNA interference as an especially effective experimental method to deepen our understanding of the interplay between genes, behavior, and the environment. We highlight the utility of RNAi for researchers investigating behavioral genetics, noting unique attributes of RNAi including transience of effect and the feasibility of releasing treated animals into the wild, that make it especially useful for studying the function of behavior-related genes. Furthermore, we provide guidelines for planning and executing an RNAi experiment to study behavior, including challenges to consider. We urge behavioral ecologists and functional genomicists to adopt a more fully integrated approach which we call "ethological genomics". We advocate this approach, utilizing tools such as RNAi, to study gene-behavior relationships in their natural context, arguing that such studies can provide a deeper understanding of how genes can influence behavior, as well as ecological aspects beyond the organism that houses them.
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Affiliation(s)
- Alexander Walton
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Amy L Toth
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA; Department of Entomology, Iowa State University, Ames, IA, USA
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32
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Linz DM, Moczek AP. Integrating evolutionarily novel horns within the deeply conserved insect head. BMC Biol 2020; 18:41. [PMID: 32312271 PMCID: PMC7171871 DOI: 10.1186/s12915-020-00773-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND How novel traits integrate within ancient trait complexes without compromising ancestral functions is a foundational challenge in evo-devo. The insect head represents an ancient body region patterned by a deeply conserved developmental genetic network, yet at the same time constitutes a hot spot for morphological innovation. However, the mechanisms that facilitate the repeated emergence, integration, and diversification of morphological novelties within this body region are virtually unknown. Using horned Onthophagus beetles, we investigated the mechanisms that instruct the development of the dorsal adult head and the formation and integration of head horns, one of the most elaborate classes of secondary sexual weapons in the animal kingdom. RESULTS Using region-specific RNAseq and gene knockdowns, we (i) show that the head is compartmentalized along multiple axes, (ii) identify striking parallels between morphological and transcriptional complexity across regions, yet (iii) fail to identify a horn-forming gene module. Instead, (iv) our results support that sex-biased regulation of a shared transcriptional repertoire underpins the formation of horned and hornless heads. Furthermore, (v) we show that embryonic head patterning genes frequently maintain expression within the dorsal head well into late post-embryonic development, thereby possibly facilitating the repurposing of such genes within novel developmental contexts. Lastly, (vi) we identify novel functions for several genes including three embryonic head patterning genes in the integration of both posterior and anterior head horns. CONCLUSIONS Our results illuminate how the adult insect head is patterned and suggest mechanisms capable of integrating novel traits within ancient trait complexes in a sex- and species-specific manner. More generally, our work underscores how significant morphological innovation in developmental evolution need not require the recruitment of new genes, pathways, or gene networks but instead may be scaffolded by pre-existing developmental machinery.
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Affiliation(s)
- David M Linz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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33
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Hu Y, Linz DM, Moczek AP. Beetle horns evolved from wing serial homologs. Science 2019; 366:1004-1007. [DOI: 10.1126/science.aaw2980] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 09/16/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022]
Abstract
Understanding how novel complex traits originate is a foundational challenge in evolutionary biology. We investigated the origin of prothoracic horns in scarabaeine beetles, one of the most pronounced examples of secondary sexual traits in the animal kingdom. We show that prothoracic horns derive from bilateral source tissues; that diverse wing genes are functionally required for instructing this process; and that, in the absence of Hox input, prothoracic horn primordia transform to contribute to ectopic wings. Once induced, however, the transcriptional profile of prothoracic horns diverges markedly from that of wings and other wing serial homologs. Our results substantiate the serial homology between prothoracic horns and insects wings and suggest that other insect innovations may derive similarly from wing serial homologs and the concomitant establishment of structure-specific transcriptional landscapes.
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34
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Variation in an Extreme Weapon: Horn Performance Differences across Rhinoceros Beetle ( Trypoxylus dichotomus) Populations. INSECTS 2019; 10:insects10100346. [PMID: 31618906 PMCID: PMC6835817 DOI: 10.3390/insects10100346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 01/02/2023]
Abstract
Japanese rhinoceros beetle (Trypoxylus dichotomus) males have exaggerated head horns that they use as weapons in combat over reproductive opportunities. In these contests, there is an advantage to having a longer horn, and there seems to be little cost to horn exaggeration. However, populations vary in the amount of horn exaggeration across this widespread species. Here, we examine four populations and quantify scaling and functional morphology of the horn. We then measure force production by the horn system in a combat-relevant movement. We find that not only does horn length vary among populations, but allometry of lever mechanics and force production varies in a complex way. For instance, some beetle populations make relatively long horns, but exert relatively low forces. Other populations make shorter horns and produce higher forces during fights. We suggest that this performance variation could be associated with differences in the intensity or type of sexual selection across the species.
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35
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Osabe T, Shimizu K, Kadota K. Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data. Bioinform Biol Insights 2019; 13:1177932219860817. [PMID: 31312083 PMCID: PMC6614939 DOI: 10.1177/1177932219860817] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/10/2019] [Indexed: 12/13/2022] Open
Abstract
Empirical Bayes is a choice framework for differential expression (DE) analysis
for multi-group RNA-seq count data. Its characteristic ability to compute
posterior probabilities for predefined expression patterns allows users to
assign the pattern with the highest value to the gene under consideration.
However, current Bayesian methods such as baySeq and EBSeq can be improved,
especially with respect to normalization. Two R packages
(baySeq and EBSeq) with their default normalization settings and with other
normalization methods (MRN and TCC) were compared using three-group simulation
data and real count data. Our findings were as follows: (1) the Bayesian methods
coupled with TCC normalization performed comparably or better than those with
the default normalization settings under various simulation scenarios, (2)
default DE pipelines provided in TCC that implements a generalized linear model
framework was still superior to the Bayesian methods with TCC normalization when
overall degree of DE was evaluated, and (3) baySeq with TCC was robust against
different choices of possible expression patterns. In practice, we recommend
using the default DE pipeline provided in TCC for obtaining overall gene ranking
and then using the baySeq with TCC normalization for assigning the most
plausible expression patterns to individual genes.
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Affiliation(s)
- Takayuki Osabe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
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36
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Ando T, Niimi T. Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis. Dev Growth Differ 2019; 61:73-84. [PMID: 30644547 DOI: 10.1111/dgd.12592] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 12/18/2022]
Abstract
Many organisms show various geometric color patterns on their bodies, and the developmental, evolutionary, genetic, and ecological bases of these patterns have been intensely studied in various organisms. Ladybird beetles display highly diverse patterns of wing (elytral) color and are one of the most attractive model organisms for studying these characteristics. In this study, we reviewed the genetic history of elytral color patterns in the Asian multicolored ladybird beetle Harmonia axyridis from the classical genetic studies led by the pupils of Thomas Hunt Morgan and Theodosius Dobzhansky to recent genomic studies that revealed that a single GATA transcription factor gene, pannier, regulates the highly diverse elytral color patterns in this species. We also reviewed and discussed the developmental and evolutionary mechanisms driven by the pannier locus in H. axyridis. In the development sections, we focused on the following two topics: (a) how the red (carotenoid) and black (melanin) pigmentation of elytra is regulated by the pannier and pigmentation genes and (b) how the diverse color patterns are formed by integrating regulatory inputs from other genes involved in wing development. In the evolution section, we subsequently focused on the highly diversified DNA sequences within the first intron of pannier that are 56-76 kb long and that were generated through recurrent multiple inversions. Furthermore, we discussed how these recurrent inversions have driven the diversification of color patterns throughout evolution.
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Affiliation(s)
- Toshiya Ando
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
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37
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Morita S, Ando T, Maeno A, Mizutani T, Mase M, Shigenobu S, Niimi T. Precise staging of beetle horn formation in Trypoxylus dichotomus reveals the pleiotropic roles of doublesex depending on the spatiotemporal developmental contexts. PLoS Genet 2019; 15:e1008063. [PMID: 30969957 PMCID: PMC6457530 DOI: 10.1371/journal.pgen.1008063] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/03/2019] [Indexed: 11/19/2022] Open
Abstract
Many scarab beetles have sexually dimorphic exaggerated horns that are an evolutionary novelty. Since the shape, number, size, and location of horns are highly diverged within Scarabaeidae, beetle horns are an attractive model for studying the evolution of sexually dimorphic and novel traits. In beetles including the Japanese rhinoceros beetle Trypoxylus dichotomus, the sex differentiation gene doublesex (dsx) plays a crucial role in sexually dimorphic horn formation during larval-pupal development. However, knowledge of when and how dsx drives the gene regulatory network (GRN) for horn formation to form sexually dimorphic horns during development remains elusive. To address this issue, we identified a Trypoxylus-ortholog of the sex determination gene, transformer (tra), that regulates sex-specific splicing of the dsx pre-mRNA, and whose loss of function results in sex transformation. By knocking down tra function at multiple developmental timepoints during larval-pupal development, we estimated the onset when the sex-specific GRN for horn formation is driven. In addition, we also revealed that dsx regulates different aspects of morphogenetic activities during the prepupal and pupal developmental stages to form appropriate morphologies of pupal head and thoracic horn primordia as well as those of adult horns. Based on these findings, we discuss the evolutionary developmental background of sexually dimorphic trait growth in horned beetles. Beetles in the family Scarabaeidae have various types of horns on their heads and thoraces, and the shape, size, number, and location of these horns are highly diversified within the group. In addition, many scarab beetle horns are sexually dimorphic. The acquisition of these evolutionarily novel horns, and the mechanisms for the diversification of these structures is an interesting question. To address this question, we focused on the rhinoceros beetle Tripoxylus dichotomus. Here we identified the exact developmental timepoints during which the morphological sexual dimorphism of horn primordia appears, estimated the onset of the developmental program for sexually dimorphic horn formation driven by doublesex, and revealed that doublesex regulates different aspects of cell activities during horn formation depending on particular spatiotemporal developmental contexts. Our study provides insights into regulatory shifts in these mechanisms during the evolution of sexually dimorphic traits in horned beetles.
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Affiliation(s)
- Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan
| | - Toshiya Ando
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, Japan
| | - Akiteru Maeno
- Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takeshi Mizutani
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan
| | - Mutsuki Mase
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Shuji Shigenobu
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, Japan
- NIBB Core Research Facilities, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki, Japan
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
- * E-mail:
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Su W, Sun J, Shimizu K, Kadota K. TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data. BMC Res Notes 2019; 12:133. [PMID: 30867032 PMCID: PMC6417217 DOI: 10.1186/s13104-019-4179-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/11/2019] [Indexed: 11/19/2022] Open
Abstract
Objective Differential expression (DE) is a fundamental step in the analysis of RNA-Seq count data. We had previously developed an R/Bioconductor package (called TCC) for this purpose. While this package has the unique feature of an in-built robust normalization method, its use has so far been limited to R users only. There is thus, a need for an alternative to DE analysis by TCC for non-R users. Results Here, we present a graphical user interface for TCC (called TCC-GUI). Non-R users only need a web browser as the minimum requirement for its use (https://infinityloop.shinyapps.io/TCC-GUI/). TCC-GUI is implemented in R and encapsulated in Shiny application. It contains all the major functionalities of TCC, including DE pipelines with robust normalization and simulation data generation under various conditions. It also contains (i) tools for exploratory analysis, including a useful score termed average silhouette that measures the degree of separation of compared groups, (ii) visualization tools such as volcano plot and heatmap with hierarchical clustering, and (iii) a reporting tool using R Markdown. By virtue of the Shiny-based GUI framework, users can obtain results simply by mouse navigation. The source code for TCC-GUI is available at https://github.com/swsoyee/TCC-GUI under MIT license. Electronic supplementary material The online version of this article (10.1186/s13104-019-4179-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Su
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Jianqiang Sun
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Koji Kadota
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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