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Li X, Mao C, He J, Bin X, Liu G, Dong Z, Zhao R, Wan X, Li X. The first chromosome-level genome of the stag beetle Dorcus hopei Saunders, 1854 (Coleoptera: Lucanidae). Sci Data 2024; 11:396. [PMID: 38637640 PMCID: PMC11026507 DOI: 10.1038/s41597-024-03251-x] [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: 10/05/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Stag beetles (Coleoptera: Lucanidae) represent a significant saproxylic assemblage in forest ecosystems and are noted for their enlarged mandibles and male polymorphism. Despite their relevance as ideal models for the study of exaggerated mandibles that aid in attracting mates, the regulatory mechanisms associated with these traits remain understudied, and restricted by the lack of high-quality reference genomes for stag beetles. To address this limitation, we successfully assembled the first chromosome-level genome of a representative species Dorcus hopei. The genome was 496.58 Mb in length, with a scaffold N50 size of 54.61 Mb, BUSCO values of 99.8%, and 96.8% of scaffolds anchored to nine pairs of chromosomes. We identified 285.27 Mb (57.45%) of repeat sequences and annotated 11,231 protein-coding genes. This genome will be a valuable resource for further understanding the evolution and ecology of stag beetles, and provides a basis for studying the mechanisms of exaggerated mandibles through comparative analysis.
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Affiliation(s)
- Xiaolu Li
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Chuyang Mao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Jinwu He
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Xiaoyan Bin
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Guichun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Zhiwei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Ruoping Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Xia Wan
- Department of Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
| | - Xueyan Li
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China.
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Žikić V, Lazarević M, Stanković SS, Milošević MI, Kavallieratos NG, Skourti A, Boukouvala MC. Effect of α-cypermethrin and pirimiphos-methyl on wing morphology of Tribolium castaneum (Herbst) and T. confusum Jacquelin du Val: a comparative study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:895-908. [PMID: 38036905 PMCID: PMC10789656 DOI: 10.1007/s11356-023-30783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023]
Abstract
Tribolium castaneum (Herbst) and Tribolium confusum Jacquelin du Val (Coleoptera: Tenebrionidae) are widespread and serious pests of stored products. Various insecticides are applied aiming to effectively manage both species. Here, two insecticides are tested, the pyrethroid α-cypermethrin and the organophosphate pirimiphos-methyl, hypothesizing that they can lead to morphological changes in the certain body parts of the adult offspring of treated T. castaneum and T. confusum parental female adults. For this purpose, the geometric morphometric method to the elytra and hindwings was applied. Both males and females were included in the analysis. The results showed that adult individuals of T. confusum showed higher tolerance to both insecticides compared to T. castaneum adults. This finding is reflected in analyses of both pairs of wings in T. confusum where changes in shape were negligible. The hindwings of T. castaneum experienced deformations to both insecticides. More significant changes in wing shape were observed in the α-cypermethrin treatment compared to pirimiphos-methyl. In the case of T. castaneum, even the shortest exposure to insecticides (5 min) is enough to provoke shape changes in the hindwings. Deformities in offspring, caused after treatment of their parents with insecticides, could moderate the frequency of insecticidal applications in storages.
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Affiliation(s)
- Vladimir Žikić
- Faculty of Sciences and Mathematics, Department of Biology and Ecology, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Maja Lazarević
- Faculty of Sciences and Mathematics, Department of Biology and Ecology, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Saša S Stanković
- Faculty of Sciences and Mathematics, Department of Biology and Ecology, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Marijana Ilić Milošević
- Faculty of Sciences and Mathematics, Department of Biology and Ecology, University of Niš, Višegradska 33, 18000, Niš, Serbia
| | - Nickolas G Kavallieratos
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Str, 11855, Athens, Attica, Greece.
| | - Anna Skourti
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Str, 11855, Athens, Attica, Greece
| | - Maria C Boukouvala
- Laboratory of Agricultural Zoology and Entomology, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Str, 11855, Athens, Attica, Greece
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Feng S, Bai M, Rivas-González I, Li C, Liu S, Tong Y, Yang H, Chen G, Xie D, Sears KE, Franco LM, Gaitan-Espitia JD, Nespolo RF, Johnson WE, Yang H, Brandies PA, Hogg CJ, Belov K, Renfree MB, Helgen KM, Boomsma JJ, Schierup MH, Zhang G. Incomplete lineage sorting and phenotypic evolution in marsupials. Cell 2022; 185:1646-1660.e18. [PMID: 35447073 PMCID: PMC9200472 DOI: 10.1016/j.cell.2022.03.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/22/2021] [Accepted: 03/21/2022] [Indexed: 12/19/2022]
Abstract
Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.
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Affiliation(s)
- Shaohong Feng
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Agriculture, Ningxia University, Yinchuan 750021, China; College of Plant Protection, Hebei Agricultural University, Baoding 071001, China
| | | | - Cai Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yijie Tong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071001, China; Hainan Yazhou Bay Seed Lab, Building 1, No. 7 Yiju Road, Yazhou District, Sanya, Hainan 572024, China
| | - Haidong Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Guangji Chen
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duo Xie
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Lida M Franco
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué, Colombia
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remont Road, Front Royal, VA 22630, USA; The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746-2863, USA; Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Parice A Brandies
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacobus J Boomsma
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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Study on the Relationship between Richness and Morphological Diversity of Higher Taxa in the Darkling Beetles (Coleoptera: Tenebrionidae). DIVERSITY 2022. [DOI: 10.3390/d14010060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Many studies have found that the correlation between species richness (SR) and morphological diversity (MD) is positive, but the correlation degree of these parameters is not always consistent due to differences in categories and various ecological factors in the living environment. Based on this, related studies have revealed the good performance of using higher taxa in biodiversity research, not only by shifting the testing group scale from local communities to worldwide datasets but also by adding different taxonomic levels, such as the genus level. However, it remains unclear whether this positive correlation can also be applied to other categories or groups. Here, we evaluated the applicability of higher taxa in the biodiversity study of darkling beetles by using 3407 species (9 subfamilies, 89 tribes, and 678 genera), based on the correlation between taxa richness and morphological diversity in the tribe/genus/species. In addition, the continuous features prevalent in the tenebrionids, pronotum and elytron, were selected, and the morphological diversity of various groups was obtained by the geometric morphometric approach to quantify the morphologic information of features. This study found that genus/species richness in subfamilies Pimelinae and Stenochiinae was positively correlated with the change trend of MD, and the correlation between the MD of elytron and taxa richness gradually decreased from the tribe-level to the genus-level to the species-level test. The results confirm the stable morphology and simple function of the elytron and the applicability of tribe level in biodiversity research.
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The Relationship between Genus/Species Richness and Morphological Diversity among Subfamilies of Jewel Beetles. INSECTS 2021; 12:insects12010024. [PMID: 33401400 PMCID: PMC7830872 DOI: 10.3390/insects12010024] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022]
Abstract
Simple Summary Morphological diversity and species richness provide insights into biodiversity and have been studied extensively in recent years. Most researchers have found a positive correlation between these factors in many groups at the local community scale; however, this documented relationship has not always been consistent because of diverse niches and the status of an organism in a given ecosystem. Here we propose a new paradigm for the analysis of higher taxa biodiversity based on a cosmopolitan dataset to further investigate this contradiction. The morphological diversity of 1106 buprestid species from around the world was quantified based on the contours of the pronotum and elytron in dorsal view using a geometric morphometric approach. We found a positive correlation between morphological diversity and genus richness while no significance was found in the species-level test. Furthermore, the correlation between morphological diversity and genus richness is higher than it is in the species-level test. Our results demonstrate the superiority of higher taxa in biodiversity, and that the geometric morphometric approach could quite accurately reveal diversity patterns of the family Buprestidae. These conclusions complement the crucial aspect in several disciplines, including biodiversity, phylogeny and evolutionary strategy. Abstract A positive correlation between the species richness and morphological diversity of some organisms has been found in almost all studies at the local community scale. However, this documented relationship has not always been consistent because of diverse niches and the status of an organism in an ecosystem. Global taxon sampling, new morphological approaches, and consideration of more taxonomic categories other than species level are possible methods to further investigate this contradiction. In this study, we proposed a new paradigm for higher taxa biodiversity analysis based on a cosmopolitan dataset. A total of 1106 species from around the world representing all subfamilies and 33% genera of Buprestidae (jewel beetles) were selected to test the correlation between morphological diversity (MD) and genus/species richness (GR/SR) among subfamilies. The MD was quantified by the contours of the pronotum and elytron in dorsal view based on a geometric morphometric approach. The positive correlation between MD and GR was found in all test combinations, but was irrelevant in the species-level test. Interestingly, the correlation between MD and GR was higher than MD and SR in both pronotum and elytron measurements. Additionally, the MD of the pronotum is obviously higher than the MD of the elytron. Our results demonstrate that the geometric morphometric approach could quite accurately reveal diversity patterns of the family Buprestidae. Future studies on different groups, using more characters, more analyses and detailed biological interpretations, are required to fully understand the relationship between MD and SR.
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