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Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M. Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evol Biol 2023; 50:395-412. [PMID: 37854269 PMCID: PMC10579158 DOI: 10.1007/s11692-023-09612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-023-09612-5.
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Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
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2
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Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T. High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance. NAR Genom Bioinform 2022; 4:lqac029. [PMID: 35387384 PMCID: PMC8982440 DOI: 10.1093/nargab/lqac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Non-biting midges (Chironomidae) are known to inhabit a wide range of environments, and certain species can tolerate extreme conditions, where the rest of insects cannot survive. In particular, the sleeping chironomid Polypedilum vanderplanki is known for the remarkable ability of its larvae to withstand almost complete desiccation by entering a state called anhydrobiosis. Chromosome numbers in chironomids are higher than in other dipterans and this extra genomic resource might facilitate rapid adaptation to novel environments. We used improved sequencing strategies to assemble a chromosome-level genome sequence for P. vanderplanki for deep comparative analysis of genomic location of genes associated with desiccation tolerance. Using whole genome-based cross-species and intra-species analysis, we provide evidence for the unique functional specialization of Chromosome 4 through extensive acquisition of novel genes. In contrast to other insect genomes, in the sleeping chironomid a uniquely high degree of subfunctionalization in paralogous anhydrobiosis genes occurs in this chromosome, as well as pseudogenization in a highly duplicated gene family. Our findings suggest that the Chromosome 4 in Polypedilum is a site of high genetic turnover, allowing it to act as a 'sandbox' for evolutionary experiments, thus facilitating the rapid adaptation of midges to harsh environments.
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Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Nurislam Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 21205, Russian Federation
| | - Olga Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Masayoshi Itoh
- Preventive Medicine & Diagnosis Innovation Program (PMI), RIKEN, Wako, Saitama 351-0198, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | | | - Miki Kojima-Ishiyama
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shohei Noma
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Alexander Cherkasov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Guzel Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Aigul Nasibullina
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Alina Ryabova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yugo Miyata
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
- Faculty of Environment and Information studies, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- Department of Regulatory Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
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Melicher D, Bowsher JH, Rinehart JP. Fluctuating temperatures extend longevity in pupae and adult stages of the sepsid Themira biloba. J Therm Biol 2021; 99:102959. [PMID: 34420614 DOI: 10.1016/j.jtherbio.2021.102959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022]
Abstract
Fluctuating Thermal Regimes (FTR), where organisms are held at low temperatures with a brief, daily warm pulse, have been shown to increase longevity in adult insects and improve pupa survival while reducing sublethal effects. We used FTR to extend the longevity and thus generation time of the fly species Themira biloba (Diptera: Sepsidae). T. biloba can be maintained in continuous culture and requires an insecticide-free dung substrate for larval growth and development. Our objective was to decrease labor and consumable materials required to maintain insect species in critical scientific collections using FTR. We extended pupation time from 4 days up to 8 weeks with no increase in mortality, and mean adult longevity was increased from 12 days to 50 days. FTR is a valuable tool for reducing the investment required to maintain rare and exotic insects.
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Affiliation(s)
- Dacotah Melicher
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Station, 1605 Albrecht Boulevard, Fargo, ND, 58105, USA.
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND, 58102, USA
| | - Joseph P Rinehart
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Station, 1605 Albrecht Boulevard, Fargo, ND, 58105, USA
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Riccardi PR, Amorim DDS. Phylogenetic relationships and classification of the Chloropinae of the world (Diptera: Chloropidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The Chloropidae is a species-rich family of flies with about 3000 species in four subfamilies. The Chloropinae is the second most species-rich subfamily with almost 1000 described species in 75 accepted genera. There is agreement about the monophyly of the subfamily; however, the relationships among the genera are still poorly understood and some genera are clearly paraphyletic. Thus, the interpretation of the evolution of morphological traits, such as male terminalia sclerites, remains challenging. This is the first phylogenetic study of the Chloropinae using a formal analytical approach, including representatives of 73 genera of the subfamily and 124 morphological characters. The monophyly of the Chloropinae is corroborated. Chloropella is sister to the remainder of the subfamily. Slightly different analytical procedures show stable clades and rogue taxa. We propose a system for the subfamily with ten tribes, three of which are newly proposed here—Chloropellini trib. nov., Chloropini, Chloropsinini trib. nov., Diplotoxini, Eurinini stat. nov., Lasiosinini, Mepachymerini, Meromyzini, Mindini and Pseudothaumatomyini. Eight genera are kept incertae sedis and two new genera are erected. There is compelling evidence that Chlorops and Ectecephalina are paraphyletic.
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Affiliation(s)
- Paula Raile Riccardi
- Departamento de Entomologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro, Brazil
| | - Dalton De Souza Amorim
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, Brazil
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Mao Y, Zhang N, Nie Y, Zhang X, Li X, Huang Y. Genome Size of 17 Species From Caelifera (Orthoptera) and Determination of Internal Standards With Very Large Genome Size in Insecta. Front Physiol 2020; 11:567125. [PMID: 33192564 PMCID: PMC7642767 DOI: 10.3389/fphys.2020.567125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Comparative studies of insect genome size show that Orthoptera is a unique group of Insecta with a significantly enlarged genome. To determine a suitable internal standard for a large genome and to compare the effects of different internal standards on estimates of genome size, we used four internal standards to estimate nuclear DNA content in nine insect species with large genomes. The results showed that the combination of two internal standards, Locusta migratoria (♂1C = 6.20 pg, ♀1C = 6.60 pg) and Periplaneta americana♂ (1C = 3.41 pg), was suitable for estimating large genome of Caelifera by flow cytometry. Using these two internal standards, we estimated the genome sizes of 17 species of Caelifera (12 genera in Acrididae, 2 genera in Pamphagidae, 1 genus in Pyrgomorphidae) using flow cytometry. Genomes ranged from 6.57 pg (Shirakiacris shirakii) to 18.64 pg (Bryodemella holdereri), the largest described in insects to date. These species showed significant genomic dimorphism based on sex: females had a 0.56 pg larger genome than males on average, which might be due to the sex chromosome determinism mechanism of X0(♂)/XX(♀). To test the results obtained by flow cytometry, we used k-mers of Illumina sequencing data to gauge the C-value of Calliptamus abbreviatus and Haplotropis brunneriana. The results of the two methods are slightly different. Genomes were estimated to be about 0.28 and 0.26 pg smaller, respectively, than the flow cytometry values. Furthermore, we also reconstructed the evolutionary relationships of these taxa and discuss the genome size evolution in a phylogenetic framework.
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Affiliation(s)
| | | | | | | | | | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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6
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Melicher D, Su KFY, Meier R, Bowsher JH. Comparative analysis reveals the complex role of histoblast nest size in the evolution of novel insect abdominal appendages in Sepsidae (Diptera). BMC Evol Biol 2018; 18:151. [PMID: 30314458 PMCID: PMC6186081 DOI: 10.1186/s12862-018-1265-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The males of some sepsid species (Sepsidae: Diptera) have abdominal appendages that are remarkable in several ways. They are sexually dimorphic, have a complex evolutionary history of gain and loss, and can be jointed and thus highly mobile. The sternite brushes are used extensively in complex courtship behaviors that differ considerably between species and during mating. The abdominal appendages have a novel developmental pathway developing from histoblast nests rather than imaginal discs. RESULTS We focus on the evolution of cell number, nest area, and segment length in both sexes to understand how this tissue relates to the formation of novel abdominal appendages. We map histoblast nest size of wandering-phase larvae of 17 species across 10 genera to a phylogenetic tree of Sepsidae and demonstrate that abdominal appendages require significant increases of histoblast nest size and cell number in most species while one species produces small appendages even without such modifications. In species with particularly large appendages, not only the nests on the fourth, but nests in neighboring segments are enlarged (Themira biloba, Themira putris). The loss of abdominal appendages corresponds to the loss of an enlarged fourth histoblast nest, although one species showed an exception to this pattern. One species that constitutes an independent origin of abdominal appendages (Perochaeta dikowi) uses an unusual developmental mechanism in that the histoblast nest sizes are not sexually dimorphic. CONCLUSIONS The surprisingly high diversity in histoblast size and degree of sexual dimorphism suggests that the developmental mechanism used for abdominal appendage formation in sepsids is highly adaptable. The presence of appendages usually correlate with increased histoblast cell number and in most cases appendage loss results in a return to ancestral histoblast morphology. However, we also identify several exceptions that indicate the abdominal appendages have a malleable developmental origin that is responsive to selection.
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Affiliation(s)
- Dacotah Melicher
- U.S. Department of Agriculture/Agricultural Research Station, Bioscience Research Laboratory, 1605 Albrecht Boulevard, Fargo, ND 58102 USA
| | - Kathy F Y Su
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore, 117543 Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore, 117543 Singapore
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND 58102 USA
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