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Tolman ER, Beatty CD, Bush J, Kohli MK, Frandsen PB, Gosnell JS, Ware JL. Exploring chromosome evolution in 250 million year old groups of dragonflies and damselflies (Insecta:Odonata). Mol Ecol 2023; 32:5785-5797. [PMID: 37787976 DOI: 10.1111/mec.17147] [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: 05/24/2023] [Revised: 09/04/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
Using recently published chromosome-length genome assemblies of two damselfly species, Ischnura elegans and Platycnemis pennipes, and two dragonfly species, Pantala flavescens and Tanypteryx hageni, we demonstrate that the autosomes of Odonata have undergone few fission, fusion, or inversion events, despite 250 million years of separation. In the four genomes discussed here, our results show that all autosomes have a clear ortholog in the ancestral karyotype. Despite this clear chromosomal orthology, we demonstrate that different factors, including concentration of repeat dynamics, GC content, relative position on the chromosome, and the relative proportion of coding sequence all influence the density of syntenic blocks across chromosomes. However, these factors do not interact to influence synteny the same way in any two pairs of species, nor is any one factor retained in all four species. Furthermore, it was previously unknown whether the micro-chromosomes in Odonata are descended from one ancestral chromosome. Despite structural rearrangements, our evidence suggests that the micro-chromosomes in the sampled Odonata do indeed descend from an ancestral chromosome, and that the micro-chromosome in P. flavescens was lost through fusion with autosomes.
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Affiliation(s)
- Ethan R Tolman
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA
- Graduate Center, City University of New York, New York City, New York, USA
| | - Christopher D Beatty
- Program for Conservation Genomics, Department of Biology, Stanford University, Stanford, California, USA
| | - Jonas Bush
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Manpreet K Kohli
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA
- Department of Natural Sciences, Baruch College, City University of New York, New York, New York, USA
| | - Paul B Frandsen
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| | - J Stephen Gosnell
- Graduate Center, City University of New York, New York City, New York, USA
- Department of Natural Sciences, Baruch College, City University of New York, New York, New York, USA
| | - Jessica L Ware
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, New York, USA
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Newton L, Tolman E, Kohli M, Ware JL. Evolution of Odonata: genomic insights. CURRENT OPINION IN INSECT SCIENCE 2023; 58:101073. [PMID: 37290694 DOI: 10.1016/j.cois.2023.101073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Odonata is an order of insects that comprises ∼6500 species. They are among the earliest flying insects, and one of the first diverging lineages in the Pterygota. Odonate evolution has been a topic of research for over 100 years, with studies focusing primarily on their flight behavior, color, vision, and aquatic juvenile lifestyles. Recent genomics studies have provided new interpretations about the evolution of these traits. In this paper, we look at how high-throughput sequence data (i.e. subgenomic and genomic data) have been used to answer long-standing questions in Odonata ranging from evolutionary relationships to vision evolution to flight behavior. Additionally, we evaluate these data at multiple taxonomic levels (i.e. ordinal, familial, generic, and population) and provide comparative analysis of genomes across Odonata, identifying features of these new data. Last, we discuss the next two years of Odonata genomic study, with context about what questions are currently being tackled.
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Affiliation(s)
- Lacie Newton
- American Museum of Natural History, Division of Invertebrate Zoology, New York, NY 10024, USA
| | - Ethan Tolman
- American Museum of Natural History, Division of Invertebrate Zoology, New York, NY 10024, USA; City University of New York, 365 Fifth Avenue, New York, NY 10016-4309, USA; Richard Gilder Graduate School, AMNH, New York, NY 10024, USA
| | - Manpreet Kohli
- American Museum of Natural History, Division of Invertebrate Zoology, New York, NY 10024, USA; Department of Natural Sciences, Baruch College, City University of New York, New York City, NY 10010, USA
| | - Jessica L Ware
- American Museum of Natural History, Division of Invertebrate Zoology, New York, NY 10024, USA.
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3
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Alfieri JM, Jonika MM, Dulin JN, Blackmon H. Tempo and Mode of Genome Structure Evolution in Insects. Genes (Basel) 2023; 14:336. [PMID: 36833264 PMCID: PMC9957073 DOI: 10.3390/genes14020336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The division of the genome into discrete chromosomes is a fundamental characteristic of eukaryotic life. Insect taxonomists' early adoption of cytogenetics has led to an incredible amount of data describing genome structure across insects. In this article, we synthesize data from thousands of species and use biologically realistic models to infer the tempo and mode of chromosome evolution among insect orders. Our results show that orders vary dramatically in the overall rate of chromosome number evolution (a proxy of genome structural stability) and the pattern of evolution (e.g., the balance between fusions and fissions). These findings have important implications for our understanding of likely modes of speciation and offer insight into the most informative clades for future genome sequencing.
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Affiliation(s)
- James M. Alfieri
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
| | - Michelle M. Jonika
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
| | - Jennifer N. Dulin
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, USA
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Mola LM, Vrbová I, Tosto DS, Zrzavá M, Marec F. On the Origin of Neo-Sex Chromosomes in the Neotropical Dragonflies Rhionaeschna bonariensis and R. planaltica (Aeshnidae, Odonata). INSECTS 2022; 13:1159. [PMID: 36555069 PMCID: PMC9784284 DOI: 10.3390/insects13121159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Odonata have holokinetic chromosomes. About 95% of species have an XX/X0 sex chromosome system, with heterogametic males. There are species with neo-XX/neo-XY sex chromosomes resulting from an X chromosome/autosome fusion. The genus Rhionaeschna includes 42 species found in the Americas. We analyzed the distribution of the nucleolar organizer region (NOR) using FISH with rDNA probes in Rhionaeschna bonariensis (n = 12 + neo-XY), R. planaltica (n = 7 + neo-XY), and Aeshna cyanea (n = 13 + X0). In R. bonariensis and A. cyanea, the NOR is located on a large pair of autosomes, which have a secondary constriction in the latter species. In R. planaltica, the NOR is located on the ancestral part of the neo-X chromosome. Meiotic analysis and FISH results in R. planaltica led to the conclusion that the neo-XY system arose by insertion of the ancestral X chromosome into an autosome. Genomic in situ hybridization, performed for the first time in Odonata, highlighted the entire neo-Y chromosome in meiosis of R. bonariensis, suggesting that it consists mainly of repetitive DNA. This feature and the terminal chiasma localization suggest an ancient origin of the neo-XY system. Our study provides new information on the origin and evolution of neo-sex chromosomes in Odonata, including new types of chromosomal rearrangements, NOR transposition, and heterochromatin accumulation.
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Affiliation(s)
- Liliana M. Mola
- Laboratory of Cytogenetics and Evolution, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EGA, Argentina
- Institute of Ecology, Genetics and Evolution of Buenos Aires, National Council of Scientific and Technical Research, Buenos Aires C1428EGA, Argentina
| | - Iva Vrbová
- Biology Centre CAS, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Biology Centre CAS, Institute of Plant Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Daniela S. Tosto
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires 1686, Argentina
| | - Magda Zrzavá
- Biology Centre CAS, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - František Marec
- Biology Centre CAS, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
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Barros LAC, Chaul JCM, Teixeira GA, Lod RB, Orivel J, de Aguiar HJAC. First Report of the Tramp ant Technomyrmex vitiensis Mann, 1921 (Formicidae: Dolichoderinae) in Brazil with Cytogenetic and Sperm Structure Data and an Updated Key to Brazilian Dolichoderinae Genera. Zool Stud 2022; 60:e29. [PMID: 36245915 PMCID: PMC9522628 DOI: 10.6620/zs.2022.61-29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/13/2022] [Indexed: 06/16/2023]
Abstract
Invasive ants are usually harmful taxa and are considered a potential problem to biodiversity due to their negative ecological impacts, as they can outcompete native ant species. Ten such species are reported in Brazil. In this study, we report for the first time the Asian tramp ant Technomyrmex vitiensis Mann, 1921 at the municipality of Oiapoque, in the Brazilian Amazon. The colony studied contained workers, intercastes, males and larvae, which provided sperm structure and cytogenetic data. Considering the unprecedented report of the genus Technomyrmex as well as the recent finding of the primarily Australian genus Leptomyrmex in Brazil, we present a revised key for the workers of Brazilian Dolichoderinae genera. Technomyrmex vitiensis presented 2n = 16 chromosomes; all metacentrics and comparative cytogenetics on the genus is provided. A single rDNA 18S site located in intrachromosomal region was observed in this species, which is a common trait in ants. The spermatozoa of T. vitiensis had a filiform shape, with 78.13 (± 1.96) μm of total length and 11.43 (± 0.51) μm of nucleus length. Total and nucleus sperm size length fit with the known variation observed in other ant species. The occurrence of T. vitiensis in Brazil is probably a result of traffic between French Guiana and the Amapá state. Cytogenetics and sperm structures of T. vitiensis enhance the biological knowledge of this tramp species. We highlight the scarce knowledge of ant diversity in the state of Amapá and the consequences that the presence of this species may have in this region.
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Affiliation(s)
| | - Júlio Cezar Mário Chaul
- Programa de Pós-graduação em Ecologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. E-mail: (Chaul)
| | - Gisele Amaro Teixeira
- Programa de Pós-graduação em Biologia Celular e Estrutural, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. E-mail: (Teixeira)
| | - Rodrigo Batista Lod
- Universidade Federal do Amapá, Campus Binacional, Oiapoque, Amapá, Brazil. E-mail: (Barros); (Lod)
| | - Jérôme Orivel
- CNRS, UMR EcoFoG, AgroParisTech, CIRAD, INRAE, Université de Guyane, Université des Antilles, Campus Agronomique, BP 316, 97379, Kourou Cedex, France. E-mail: (Orivel)
| | - Hilton Jeferson Alves Cardoso de Aguiar
- Universidade Federal do Amapá, Campus Binacional, Oiapoque, Amapá, Brazil. E-mail: (Barros); (Lod)
- Programa de Pós-graduação em Biodiversidade Tropical, Universidade Federal do Amapá, Macapá, Brazil. E-mail: (Aguiar)
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Mola LM, Fourastié MF, Agopian SS. High karyotypic variation in Orthemis Hagen, 1861 species, with insights about the neo-XY in Orthemisambinigra Calvert, 1909 (Libellulidae, Odonata). COMPARATIVE CYTOGENETICS 2021; 15:355-374. [PMID: 34804379 PMCID: PMC8580954 DOI: 10.3897/compcytogen.v15.i4.68761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023]
Abstract
The American dragonfly genus Orthemis Hagen, 1861 is mainly found in the Neotropical region. Seven of 28 taxonomically described species have been reported from Argentina. Chromosome studies performed on this genus showed a wide variation in chromosome number and a high frequency of the neoXY chromosomal sex-determination system, although the sexual pair was not observed in all cases. This work analyzes the spermatogenesis of Orthemisdiscolor (Burmeister, 1839), O.nodiplaga Karsch, 1891 and O.ambinigra Calvert, 1909 in individuals from the provinces of Misiones and Buenos Aires, Argentina. Orthemisdiscolor has 2n=23, n=11+X and one larger bivalent. Orthemisnodiplaga exhibits the largest chromosome number of the order, 2n=41, n=20+X and small chromosomes. Orthemisambinigra shows a reduced complement, 2n=12, n=5+neo-XY, large-sized chromosomes, and a homomorphic sex bivalent. Fusions and fragmentations are the main evolutionary mechanisms in Odonata, as well as in other organisms with holokinetic chromosomes. Orthemisnodiplaga would have originated by nine autosomal fragmentations from the ancestral karyotype of the genus (2n=22A+X in males). We argue that the diploid number 23 in Orthemis has a secondary origin from the ancestral karyotype of family Libellulidae (2n=25). The complement of O.ambinigra would have arisen from five autosomal fusions and the insertion of the X chromosome into a fused autosome. C-banding and DAPI/CMA3 staining allowed the identification of the sexual bivalent, which revealed the presence of constitutive heterochromatin. We propose that the chromosome with intermediate C-staining intensity and three medial heterochromatic regions corresponds to the neo-Y and that the neo-system of this species has an ancient evolutionary origin. Moreover, we discuss on the mechanisms involved in the karyotypic evolution of this genus, the characteristics of the neo sex-determining systems and the patterns of heterochromatin distribution, quantity and base pair richness.
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Affiliation(s)
- Liliana M Mola
- Laboratorio de Citogenética y Evolución - Departamento de Ecología, Genética y Evolución, Instituto de Ecología, Genética y Evolución (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Florencia Fourastié
- Instituto de Ecología, Genética y Evolución (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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