101
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Pentinsaari M, Salmela H, Mutanen M, Roslin T. Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life. Sci Rep 2016; 6:35275. [PMID: 27734964 PMCID: PMC5062346 DOI: 10.1038/srep35275] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/15/2016] [Indexed: 11/28/2022] Open
Abstract
DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function. Overall, patterns of amino acid variation suggest convergent or parallel evolution at the protein level connected to the transition into a parasitic life style. Denser sampling of two diverse insect taxa revealed that the beetles (Coleoptera) show more amino acid variation than the butterflies and moths (Lepidoptera), indicating fundamental difference in patterns of molecular evolution in COI. Several amino acid sites were found to be under notably strong purifying selection in Lepidoptera as compared to Coleoptera. Overall, these findings demonstrate the utility of the global DNA barcode library to extend far beyond identification and taxonomy, and will hopefully be followed by a multitude of work.
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Affiliation(s)
- Mikko Pentinsaari
- Department of Genetics and Physiology, University of Oulu, P.O.Box 3000 (Pentti Kaiteran katu 1), FI-90014, Finland
| | - Heli Salmela
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Viikinkaari 1, FI-00014, Finland
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, P.O.Box 3000 (Pentti Kaiteran katu 1), FI-90014, Finland
| | - Tomas Roslin
- Spatial Foodweb Ecology Group, Department of Agricultural Sciences, University of Helsinki, Latokartanonkaari 5, FI-00014, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07 Uppsala, Sweden
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102
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The complete mitochondrial genome of Choristoneura longicellana (Lepidoptera: Tortricidae) and phylogenetic analysis of Lepidoptera. Gene 2016; 591:161-176. [DOI: 10.1016/j.gene.2016.07.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 06/30/2016] [Accepted: 07/03/2016] [Indexed: 11/20/2022]
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103
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Schachat SR, Gibbs GW. Variable wing venation in Agathiphaga (Lepidoptera: Agathiphagidae) is key to understanding the evolution of basal moths. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160453. [PMID: 27853559 PMCID: PMC5098984 DOI: 10.1098/rsos.160453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
Details of the ancestral groundplan of wing venation in moths remain uncertain, despite approximately a century of study. Here, we describe a 3-branched subcostal vein, a 5-branched medial vein and a 2-branched cubitus posterior vein on the forewing of Agathiphaga vitiensis Dumbleton 1952 from Vanuatu. Such veins had not previously been described in any Lepidoptera. Because wing veins are typically lost during lepidopteran evolutionary history, rarely-if ever-to be regained, the venation of A. vitiensis probably represents the ancestral character state for moths. Wing venation is often used to identify fossil insects as moths, because wing scales are not always preserved; the presence of a supposedly trichopteran 3-branched subcostal vein in crown Lepidoptera may decrease the certainty with which certain amphiesmenopteran fossils from the Mesozoic can be classified. And because plesiomorphic veins can influence the development of lepidopteran wing patterns even if not expressed in the adult wing, the veins described here may determine the location of wing pattern elements in many lepidopteran taxa.
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Affiliation(s)
- Sandra R. Schachat
- Mississippi Entomological Museum, Mississippi State, MS 39762, USA
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USA
| | - George W. Gibbs
- School of Biological Sciences, Victoria University, PO Box 600, Wellington 6140, New Zealand
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104
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Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles. PLoS One 2016; 11:e0163529. [PMID: 27668729 PMCID: PMC5036811 DOI: 10.1371/journal.pone.0163529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/10/2016] [Indexed: 11/19/2022] Open
Abstract
Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.
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105
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Bura VL, Kawahara AY, Yack JE. A Comparative Analysis of Sonic Defences in Bombycoidea Caterpillars. Sci Rep 2016; 6:31469. [PMID: 27510510 PMCID: PMC4980592 DOI: 10.1038/srep31469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/20/2016] [Indexed: 11/09/2022] Open
Abstract
Caterpillars have long been used as models for studying animal defence. Their impressive armour, including flamboyant warning colours, poisonous spines, irritating sprays, and mimicry of plant parts, snakes and bird droppings, has been extensively documented. But research has mainly focused on visual and chemical displays. Here we show that some caterpillars also exhibit sonic displays. During simulated attacks, 45% of 38 genera and 33% of 61 species of silk and hawkmoth caterpillars (Bombycoidea) produced sounds. Sonic caterpillars are found in many distantly-related groups of Bombycoidea, and have evolved four distinct sound types- clicks, chirps, whistles and vocalizations. We propose that different sounds convey different messages, with some designed to warn of a chemical defence and others, to startle predators. This research underscores the importance of exploring acoustic communication in juvenile insects, and provides a model system to explore how different signals have evolved to frighten, warn or even trick predators.
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Affiliation(s)
- Veronica L. Bura
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Jayne E. Yack
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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106
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Kjer KM, Simon C, Yavorskaya M, Beutel RG. Progress, pitfalls and parallel universes: a history of insect phylogenetics. J R Soc Interface 2016; 13:20160363. [PMID: 27558853 PMCID: PMC5014063 DOI: 10.1098/rsif.2016.0363] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.
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Affiliation(s)
- Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Margarita Yavorskaya
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
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107
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Zenker MM, Wahlberg N, Brehm G, Teston JA, Przybylowicz L, Pie MR, Freitas AV. Systematics and origin of moths in the subfamily Arctiinae (Lepidoptera, Erebidae) in the Neotropical region. ZOOL SCR 2016. [DOI: 10.1111/zsc.12202] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mauricio M. Zenker
- Departamento de Biologia Animal and Museu de Zoologia Instituto de Biologia Universidade Estadual de Campinas C.P. 6109 Campinas 13083‐970 Brazil
| | | | - Gunnar Brehm
- Institute of Systematic Zoology and Evolutionary Biology with Phyletic MuseumFriedrich‐Schiller‐University Jena 1 07743 Jena Germany
| | - José A. Teston
- Instituto de Ciências da Educação, Programa de Licenciatura em BiologiaUniversidade Federal do Oeste do Pará 68040070 Santarém Pará Brazil
| | - Lukasz Przybylowicz
- Institute of Systematics and Evolution of Animals Polish Academy of Sciences PolandSlawkowska 17 31–016 Krakow Poland
| | - Marcio R. Pie
- Departamento de Zoologia Universidade Federal do Paraná 81531‐990 Curitiba Paraná Brazil
| | - André V.L. Freitas
- Universidade Estadual de Campinas Departamento de Zoologia and Museu de História Natural Instituto de Biologia P.O. Box 6109 13083970 Campinas Brazil
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108
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Covarrubias-Camarillo T, Osorio-Beristain M, Legal L, Contreras-Garduño J. Baronia brevicornis caterpillars build shelters to avoid predation. J NAT HIST 2016. [DOI: 10.1080/00222933.2016.1193640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- T. Covarrubias-Camarillo
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - M. Osorio-Beristain
- Departamento de Ecología Evolutiva, Centro de Investigación en Biodiversidad y Conservación (CIByC), Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - L. Legal
- Laboratoire d’Ecologie Fonctionnelle (EcoLab), UMR 5245, Université Paul Sabatier, Toulouse, France
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109
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Cho S, Epstein SW, Mitter K, Hamilton CA, Plotkin D, Mitter C, Kawahara AY. Preserving and vouchering butterflies and moths for large-scale museum-based molecular research. PeerJ 2016; 4:e2160. [PMID: 27366654 PMCID: PMC4924120 DOI: 10.7717/peerj.2160] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
Butterflies and moths (Lepidoptera) comprise significant portions of the world’s natural history collections, but a standardized tissue preservation protocol for molecular research is largely lacking. Lepidoptera have traditionally been spread on mounting boards to display wing patterns and colors, which are often important for species identification. Many molecular phylogenetic studies have used legs from pinned specimens as the primary source for DNA in order to preserve a morphological voucher, but the amount of available tissue is often limited. Preserving an entire specimen in a cryogenic freezer is ideal for DNA preservation, but without an easily accessible voucher it can make specimen identification, verification, and morphological work difficult. Here we present a procedure that creates accessible and easily visualized “wing vouchers” of individual Lepidoptera specimens, and preserves the remainder of the insect in a cryogenic freezer for molecular research. Wings are preserved in protective holders so that both dorsal and ventral patterns and colors can be easily viewed without further damage. Our wing vouchering system has been implemented at the University of Maryland (AToL Lep Collection) and the University of Florida (Florida Museum of Natural History, McGuire Center of Lepidoptera and Biodiversity), which are among two of the largest Lepidoptera molecular collections in the world.
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Affiliation(s)
- Soowon Cho
- Department of Plant Medicine, Chungbuk National University, Cheongju, South Korea.,Department of Entomology, University of Maryland, College Park, MD, United States
| | - Samantha W Epstein
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Kim Mitter
- Department of Entomology, University of Maryland, College Park, MD, United States
| | - Chris A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - David Plotkin
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Charles Mitter
- Department of Entomology, University of Maryland, College Park, MD, United States
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
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110
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Mutanen M, Kivelä SM, Vos RA, Doorenweerd C, Ratnasingham S, Hausmann A, Huemer P, Dincă V, van Nieukerken EJ, Lopez-Vaamonde C, Vila R, Aarvik L, Decaëns T, Efetov KA, Hebert PDN, Johnsen A, Karsholt O, Pentinsaari M, Rougerie R, Segerer A, Tarmann G, Zahiri R, Godfray HCJ. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. Syst Biol 2016; 65:1024-1040. [PMID: 27288478 PMCID: PMC5066064 DOI: 10.1093/sysbio/syw044] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 11/14/2022] Open
Abstract
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
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Affiliation(s)
- Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Finland;
| | | | - Rutger A Vos
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | - Axel Hausmann
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Peter Huemer
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Vlad Dincă
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Carlos Lopez-Vaamonde
- INRA, UR633 Zoologie Forestière, 45075 Orléans, France.,Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leif Aarvik
- Natural History Museum University of Oslo, Norway
| | - Thibaud Decaëns
- Centre d'Écologie Fonctionnelle et Évolutive, UMR 5175 CNRS / University of Montpellier / University of Montpellier 3 / EPHE / SupAgro Montpellier / INRA / IRD, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | | | - Ole Karsholt
- Zoologisk Museum, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | | | - Rodolphe Rougerie
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Andreas Segerer
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Gerhard Tarmann
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Reza Zahiri
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Ottawa Plant Laboratory, Canadian Food Inspection Agency, Canada
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111
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Wahlberg N, Peña C, Ahola M, Wheat CW, Rota J. PCR primers for 30 novel gene regions in the nuclear genomes of Lepidoptera. Zookeys 2016:129-41. [PMID: 27408580 PMCID: PMC4926658 DOI: 10.3897/zookeys.596.8399] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/27/2016] [Indexed: 12/22/2022] Open
Abstract
We report primer pairs for 30 new gene regions in the nuclear genomes of Lepidoptera that can be amplified using a standard PCR protocol. The new primers were tested across diverse Lepidoptera, including nonditrysians and a wide selection of ditrysians. These new gene regions give a total of 11,043 bp of DNA sequence data and they show similar variability to traditionally used nuclear gene regions in studies of Lepidoptera. We feel that a PCR-based approach still has its place in molecular systematic studies of Lepidoptera, particularly at the intrafamilial level, and our new set of primers now provides a route to generating phylogenomic datasets using traditional methods.
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Affiliation(s)
- Niklas Wahlberg
- Department of Biology, University of Turku, 20014 Turku, Finland; Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Carlos Peña
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Milla Ahola
- Department of Biology, University of Turku, 20014 Turku, Finland
| | | | - Jadranka Rota
- Department of Biology, University of Turku, 20014 Turku, Finland; Department of Biology, Lund University, 223 62 Lund, Sweden
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112
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Ahmed MZ, Breinholt JW, Kawahara AY. Evidence for common horizontal transmission of Wolbachia among butterflies and moths. BMC Evol Biol 2016; 16:118. [PMID: 27233666 PMCID: PMC4882834 DOI: 10.1186/s12862-016-0660-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/18/2016] [Indexed: 01/15/2023] Open
Abstract
Background Wolbachia is one of the most widespread bacteria on Earth. Previous research on Wolbachia-host interactions indicates that the bacterium is typically transferred vertically, from mother to offspring, through the egg cytoplasm. Although horizontal transmission of Wolbachia from one species to another is reported to be common in arthropods, limited direct ecological evidence is available. In this study, we examine horizontal transmission of Wolbachia using a multilocus sequence typing (MLST) strains dataset and used Wolbachia and Lepidoptera genomes to search for evidence for lateral gene transfer (LGT) in Lepidoptera, one of the most diverse cosmopolitan insect orders. We constructed a phylogeny of arthropod-associated MLST Wolbachia strains and calibrated the age of Wolbachia strains associated with lepidopteran species. Results Our results reveal inter-specific, inter-generic, inter-familial, and inter-ordinal horizontal transmission of Wolbachia strains, without discernible geographic patterns. We found at least seven probable cases of horizontal transmission among 31 species within Lepidoptera and between Lepidoptera and other arthropod hosts. The divergence time analysis revealed that Wolbachia is recently (22.6–4.7 mya, 95 % HPD) introduced in Lepidoptera. Analysis of nine Lepidoptera genomes (Bombyx mori, Danaus plexippus, Heliconius melpomene, Manduca sexta, Melitaea cinxia, Papilio glaucus, P. polytes, P. xuthus and Plutella xylostella) yielded one possible instance of Wolbachia LGT. Conclusions Our results provide evidence of high incidence of identical and multiple strains of Wolbachia among butterflies and moths, adding Lepidoptera to the growing body of evidence for common horizontal transmission of Wolbachia. This study demonstrates interesting dynamics of this remarkable and influential microorganism. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0660-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad Z Ahmed
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
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113
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Schachat SR, Brown RL. Forewing color pattern in Micropterigidae (Insecta: Lepidoptera): homologies between contrast boundaries, and a revised hypothesis for the origin of symmetry systems. BMC Evol Biol 2016; 16:116. [PMID: 27230100 PMCID: PMC4880886 DOI: 10.1186/s12862-016-0687-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/13/2016] [Indexed: 11/28/2022] Open
Abstract
Background Despite the great importance of lepidopteran wing patterns in various biological disciplines, homologies between wing pattern elements in different moth and butterfly lineages are still not understood. Among other reasons, this may be due to an incomplete understanding of the relationship between color pattern and wing venation; many individual wing pattern elements have a known relationship with venation, but a framework to unite all wing pattern elements with venation is lacking. Though plesiomorphic wing veins are known to influence color patterning even when not expressed in the adult wing, most studies of wing pattern evolution have focused on derived taxa with a reduced suite of wing veins. Results The present study aims to address this gap through an examination of Micropterigidae, a very early-diverged moth family in which all known plesiomorphic lepidopteran veins are expressed in the adult wing. The relationship between wing pattern and venation was examined in 66 species belonging to 9 genera. The relationship between venation and pattern element location, predicted based on moths in the family Tortricidae, holds for Sabatinca just as it does for Micropterix. However, the pattern elements that are lightly colored in Micropterix are dark in Sabatinca, and vice-versa. When plotted onto a hypothetical nymphalid wing in accordance with the relationship between pattern and venation discussed here, the wing pattern of Sabatinca doroxena very closely resembles the nymphalid groundplan. Conclusions The color difference in pattern elements between Micropterix and Sabatinca indicates that homologies exist among the contrast boundaries that divide wing pattern elements, and that color itself is not a reliable indicator of homology. The similarity between the wing pattern of Sabatinca doroxena and the nymphalid groundplan suggests that the nymphalid groundplan may have originated from a Sabatinca-like wing pattern subjected to changes in wing shape and reduced expression of venation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0687-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra R Schachat
- Mississippi Entomological Museum, Mississippi State, MS, 39762, USA. .,Department of Paleobiology, Smithsonian Institution, Washington, DC, 20013, USA.
| | - Richard L Brown
- Mississippi Entomological Museum, Mississippi State, MS, 39762, USA
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114
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Lieb B, Ebner B, Kayser H. cDNA sequences of two arylphorin subunits of an insect biliprotein: phylogenetic differences and gene duplications during evolution of hexamerins-implications for hexamer formation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:136-48. [DOI: 10.1002/jez.b.22672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Bernhard Lieb
- Institut für Zoologie; Johannes Gutenberg-Universität; Mainz Germany
| | - Bettina Ebner
- Institut für Zoologie; Johannes Gutenberg-Universität; Mainz Germany
| | - Hartmut Kayser
- Institute of General Zoology and Endocrinology; Ulm University; Ulm Germany
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Buenaventura E, Whitmore D, Pape T. Molecular phylogeny of the hyperdiverse genusSarcophaga(Diptera: Sarcophagidae), and comparison between algorithms for identification of rogue taxa. Cladistics 2016; 33:109-133. [DOI: 10.1111/cla.12161] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Eliana Buenaventura
- Natural History Museum of Denmark; Universitetsparken 15 Copenhagen DK-2100 Denmark
| | - Daniel Whitmore
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Thomas Pape
- Natural History Museum of Denmark; Universitetsparken 15 Copenhagen DK-2100 Denmark
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116
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Yeates DK, Meusemann K, Trautwein M, Wiegmann B, Zwick A. Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution. CURRENT OPINION IN INSECT SCIENCE 2016; 13:16-23. [PMID: 27436549 DOI: 10.1016/j.cois.2015.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/08/2015] [Accepted: 10/18/2015] [Indexed: 06/06/2023]
Abstract
Our understanding on the phylogenetic relationships of insects has been revolutionised in the last decade by the proliferation of next generation sequencing technologies (NGS). NGS has allowed insect systematists to assemble very large molecular datasets that include both model and non-model organisms. Such datasets often include a large proportion of the total number of protein coding sequences available for phylogenetic comparison. We review some early entomological phylogenomic studies that employ a range of different data sampling protocols and analyses strategies, illustrating a fundamental renaissance in our understanding of insect evolution all driven by the genomic revolution. The analysis of phylogenomic datasets is challenging because of their size and complexity, and it is obvious that the increasing size alone does not ensure that phylogenetic signal overcomes systematic biases in the data. Biases can be due to various factors such as the method of data generation and assembly, or intrinsic biological feature of the data per se, such as similarities due to saturation or compositional heterogeneity. Such biases often cause violations in the underlying assumptions of phylogenetic models. We review some of the bioinformatics tools available and being developed to detect and minimise systematic biases in phylogenomic datasets. Phylogenomic-scale data coupled with sophisticated analyses will revolutionise our understanding of insect functional genomics. This will illuminate the relationship between the vast range of insect phenotypic diversity and underlying genetic diversity. In combination with rapidly developing methods to estimate divergence times, these analyses will also provide a compelling view of the rates and patterns of lineagenesis (birth of lineages) over the half billion years of insect evolution.
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Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia.
| | - Karen Meusemann
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Michelle Trautwein
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Brian Wiegmann
- Department of Entomology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
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Ma L, Dong WW, Jiang GF, Wang X. The Complete Mitochondrial Genome of Brachmia macroscopa (Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:9. [PMID: 26810560 PMCID: PMC4725263 DOI: 10.1093/jisesa/iev157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 12/11/2015] [Indexed: 06/05/2023]
Abstract
The sweet potato leaf folder, Brachmia macroscopa, is an important pest in China. The complete mitogenome, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region, was sequenced and found to be 15,394 bp in length (GeneBank no. KT354968). The gene order and orientation of the B. macroscopa mitogenome were similar to those of other sequenced lepidopteran species. All of the PCGs started with ATN as the canonical start codon except for cox1, which started with CGA. In regard to stop codons, most PCGs stopped at TAA except for cox2, which stopped at TA, and nad4, which stopped at a single T. Thirteen PCGs of the available species (33 taxa) were used to demonstrate phylogenetic relationships. The ditrysian cluster was supported as a monophyletic clade at high levels by using maximum likelihood and Bayesian methods. The apoditrysian group, covering the Gelechioidea, formed a monophyletic clade with a bootstrap value of 88% and a posterior probability of 1.00. The superfamily Gelechioidea was supported as a monophyletic lineage by a posterior probability of 1.00.
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Affiliation(s)
- Li Ma
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Wan-Wei Dong
- Jiangsu Key Laboratory for Bioresource Technology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China, and
| | - Guo-Fang Jiang
- Jiangsu Key Laboratory for Bioresource Technology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China, and
| | - Xing Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China ,
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Rainford JL, Hofreiter M, Mayhew PJ. Phylogenetic analyses suggest that diversification and body size evolution are independent in insects. BMC Evol Biol 2016; 16:8. [PMID: 26746988 PMCID: PMC4706648 DOI: 10.1186/s12862-015-0570-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. RESULTS The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. CONCLUSIONS Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.
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Affiliation(s)
- James L Rainford
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Peter J Mayhew
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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119
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Zaspel J, Weller S, Epstein M. Origin of the hungry caterpillar: Evolution of fasting in slug moths (Insecta: Lepidoptera: Limacodidae). Mol Phylogenet Evol 2016; 94:827-832. [DOI: 10.1016/j.ympev.2015.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/05/2015] [Accepted: 09/18/2015] [Indexed: 10/23/2022]
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Heikkilä M, Mutanen M, Wahlberg N, Sihvonen P, Kaila L. Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera). BMC Evol Biol 2015; 15:260. [PMID: 26589618 PMCID: PMC4654798 DOI: 10.1186/s12862-015-0520-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only. RESULTS Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov. CONCLUSIONS The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The "backbone" of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.
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Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, PO Box 3000, Oulu, 90014, Finland.
| | - Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, Turku, 20014, Finland.
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Pasi Sihvonen
- University of Helsinki, Research Affairs, PO Box 33, Helsinki, 00014, Finland.
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
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122
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Lehnert MS, Beard CE, Gerard PD, Kornev KG, Adler PH. Structure of the lepidopteran proboscis in relation to feeding guild. J Morphol 2015; 277:167-82. [DOI: 10.1002/jmor.20487] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/10/2015] [Accepted: 10/18/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Matthew S. Lehnert
- Department of Biological Sciences; Kent State University at Stark; North Canton Ohio 44720
- Department of Agricultural and Environmental Sciences; Clemson University; Clemson South Carolina 29634
| | - Charles E. Beard
- Department of Agricultural and Environmental Sciences; Clemson University; Clemson South Carolina 29634
| | - Patrick D. Gerard
- Department of Mathematical Sciences; Clemson University; Clemson South Carolina 29634
| | - Konstantin G. Kornev
- Department of Materials Science and Engineering; Clemson University; Clemson South Carolina 29634
| | - Peter H. Adler
- Department of Agricultural and Environmental Sciences; Clemson University; Clemson South Carolina 29634
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123
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Sugimoto TN, Kayukawa T, Shinoda T, Ishikawa Y, Tsuchida T. Misdirection of dosage compensation underlies bidirectional sex-specific death in Wolbachia-infected Ostrinia scapulalis. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 66:72-76. [PMID: 26453817 DOI: 10.1016/j.ibmb.2015.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 06/05/2023]
Abstract
Endosymbiotic bacteria of the genus Wolbachia often manipulate the reproductive system of their hosts to propagate themselves in host populations. Ostrinia scapulalis moths infected with Wolbachia (wSca) produce female-only progeny (sex chromosomes: ZW), whereas females cured of the infection by antibiotic treatment produce male-only progeny (ZZ). The occurrence of female- and male-only progeny has been attributed to the specific death of the opposite sex during embryonic and larval development. In this bidirectional sex-specific lethality, embryos destined to die express a phenotypic sex opposite to their genotypic sex. On the basis of these findings, we suggested that wSca carries a genetic factor that feminizes the male host, the W chromosome of the host has lost its feminizing function, and discordance between the genotypic and phenotypic sexes underlies this sex-specific death. In the present study, we examined whether the failure of dosage compensation was responsible for this sex-specific mortality. Quantitative PCRs showed that Z-linked gene expression levels in embryos destined to die were not properly dosage compensated; they were approximately two-fold higher in the male progeny of wSca-infected females and approximately two-fold lower in the female progeny of infected-and-cured females. These results support our hypothesis that misdirection of dosage compensation underlies the sex-specific death.
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Affiliation(s)
- Takafumi N Sugimoto
- Graduate School of Science and Engineering, University of Toyama, Toyama, Toyama 930-8555, Japan.
| | - Takumi Kayukawa
- National Institute of Agrobiological Sciences, Ohwashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
| | - Tetsuro Shinoda
- National Institute of Agrobiological Sciences, Ohwashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
| | - Yukio Ishikawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tsutomu Tsuchida
- Graduate School of Science and Engineering, University of Toyama, Toyama, Toyama 930-8555, Japan
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124
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Schachat SR, Brown RL. Color Pattern on the Forewing of Micropterix (Lepidoptera: Micropterigidae): Insights into the Evolution of Wing Pattern and Wing Venation in Moths. PLoS One 2015; 10:e0139972. [PMID: 26437004 PMCID: PMC4593546 DOI: 10.1371/journal.pone.0139972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/18/2015] [Indexed: 12/26/2022] Open
Abstract
Wing patterns are key taxonomic characters that have long been used in descriptions of Lepidoptera; however, wing pattern homologies are not understood among different moth lineages. Here, we examine the relationship between wing venation and wing pattern in the genus Micropterix, among the most basal extant Lepidoptera, in order to evaluate the two existing predictive models that have the potential to establish wing pattern element homologies for the order. The location of wing pattern elements along the costal margin of the wing in Micropterix is consistent with the predictions of the model proposed for Tortricidae by Brown and Powell in 1991, later modified by Baixeras in 2002. The predictive power of this model for such distantly related taxa suggests that the model may hold across various superfamilies within Lepidoptera, and supports the long-held notion that fasciae, not spots, are the most likely primitive wing pattern elements for the order. In addition, the location of wing pattern elements suggests that the wing vein commonly termed Sc1 may in fact be a different vein, which Comstock identified in Trichoptera and referred to as "a."
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Affiliation(s)
- Sandra R. Schachat
- Mississippi Entomological Museum, Mississippi State, Mississippi, United States of America
- Department of Paleobiology, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Richard L. Brown
- Mississippi Entomological Museum, Mississippi State, Mississippi, United States of America
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125
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Walters JR, Hardcastle TJ, Jiggins CD. Sex Chromosome Dosage Compensation in Heliconius Butterflies: Global yet Still Incomplete? Genome Biol Evol 2015; 7:2545-59. [PMID: 26338190 PMCID: PMC4607515 DOI: 10.1093/gbe/evv156] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of heterogametic sex chromosomes is often—but not always—accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) species but not in female-heterogametic (ZW) species, which will consequently exhibit “incomplete” sex chromosome dosage compensation. However, recent results suggest that at least some Lepidoptera (moths and butterflies) may prove to be an exception to this prediction. Studies in bombycoid moths indicate the presence of a chromosome-wide epigenetic mechanism that effectively balances Z chromosome gene expression between the sexes by reducing Z-linked expression in males. In contrast, strong sex chromosome dosage effects without any reduction in male Z-linked expression were previously reported in a pyralid moth, suggesting a lack of any such dosage compensating mechanism. Here we report an analysis of sex chromosome dosage compensation in Heliconius butterflies, sampling multiple individuals for several different adult tissues (head, abdomen, leg, mouth, and antennae). Methodologically, we introduce a novel application of linear mixed-effects models to assess dosage compensation, offering a unified statistical framework that can estimate effects specific to chromosome, to sex, and their interactions (i.e., a dosage effect). Our results show substantially reduced Z-linked expression relative to autosomes in both sexes, as previously observed in bombycoid moths. This observation is consistent with an increasing body of evidence that some lepidopteran species possess an epigenetic dosage compensating mechanism that reduces Z chromosome expression in males to levels comparable with females. However, this mechanism appears to be imperfect in Heliconius, resulting in a modest dosage effect that produces an average 5–20% increase in male expression relative to females on the Z chromosome, depending on the tissue. Thus our results in Heliconius reflect a mixture of previous patterns reported for Lepidoptera. In Heliconius, a moderate pattern of incomplete dosage compensation persists apparently despite the presence of an epigenetic dosage compensating mechanism. The chromosomal distributions of sex-biased genes show an excess of male-biased and a dearth of female-biased genes on the Z chromosome relative to autosomes, consistent with predictions of sexually antagonistic evolution.
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Affiliation(s)
- James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, United Kingdom
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126
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Goodheart JA, Bazinet AL, Collins AG, Cummings MP. Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150196. [PMID: 26473045 PMCID: PMC4593679 DOI: 10.1098/rsos.150196] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/26/2015] [Indexed: 05/28/2023]
Abstract
Cladobranchia (Gastropoda: Nudibranchia) is a diverse (approx. 1000 species) but understudied group of sea slug molluscs. In order to fully comprehend the diversity of nudibranchs and the evolution of character traits within Cladobranchia, a solid understanding of evolutionary relationships is necessary. To date, only two direct attempts have been made to understand the evolutionary relationships within Cladobranchia, neither of which resulted in well-supported phylogenetic hypotheses. In addition to these studies, several others have addressed some of the relationships within this clade while investigating the evolutionary history of more inclusive groups (Nudibranchia and Euthyneura). However, all of the resulting phylogenetic hypotheses contain conflicting topologies within Cladobranchia. In this study, we address some of these long-standing issues regarding the evolutionary history of Cladobranchia using RNA-Seq data (transcriptomes). We sequenced 16 transcriptomes and combined these with four transcriptomes from the NCBI Sequence Read Archive. Transcript assembly using Trinity and orthology determination using HaMStR yielded 839 orthologous groups for analysis. These data provide a well-supported and almost fully resolved phylogenetic hypothesis for Cladobranchia. Our results support the monophyly of Cladobranchia and the sub-clade Aeolidida, but reject the monophyly of Dendronotida.
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Affiliation(s)
- Jessica A. Goodheart
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
- NMFS, National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, MRC-153, PO Box 37012, Washington, DC 20013, USA
| | - Adam L. Bazinet
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Allen G. Collins
- NMFS, National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, MRC-153, PO Box 37012, Washington, DC 20013, USA
| | - Michael P. Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
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127
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Abbasi R, Marcus JM. Colour pattern homology and evolution inVanessabutterflies (Nymphalidae: Nymphalini): eyespot characters. J Evol Biol 2015; 28:2009-26. [DOI: 10.1111/jeb.12716] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 06/11/2015] [Accepted: 07/31/2015] [Indexed: 11/30/2022]
Affiliation(s)
- R. Abbasi
- Department of Biological Sciences; University of Manitoba; Winnipeg MB Canada
| | - J. M. Marcus
- Department of Biological Sciences; University of Manitoba; Winnipeg MB Canada
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128
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A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm. Heredity (Edinb) 2015; 116:75-83. [PMID: 26264548 DOI: 10.1038/hdy.2015.72] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/29/2015] [Accepted: 06/29/2015] [Indexed: 11/08/2022] Open
Abstract
A significant feature of the genomes of Lepidoptera, butterflies and moths, is the high conservation of chromosome organization. Recent remarkable progress in genome sequencing of Lepidoptera has revealed that syntenic gene order is extensively conserved across phylogenetically distant species. The ancestral karyotype of Lepidoptera is thought to be n=31; however, that of the most well-studied moth, Bombyx mori, is n=28, and diverse studies suggest that three chromosomal fusion events occurred in this lineage. To identify the boundaries between predicted ancient fusions involving B. mori chromosomes 11, 23 and 24, we constructed fluorescence in situ hybridization (FISH)-based chromosome maps of the European corn borer, Ostrinia nubilalis (n=31). We first determined a 511 Mb genomic sequence of the Asian corn borer, O. furnacalis, a congener of O. nubilalis, and isolated bacterial artificial chromosomes and fosmid clones that were expected to localize in candidate regions for the boundaries using these sequences. Combined with FISH and genetic analysis, we narrowed down the candidate regions to 40 kb-1.5 Mb, in strong agreement with a previous estimate based on the genome of a butterfly, Melitaea cinxia. The significant difference in the lengths of the candidate regions where no functional genes were observed may reflect the evolutionary time after fusion events.
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129
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Li Y, Dou K, Gao S, Sun J, Wang M, Fu K, Yu C, Wu Q, Li Y, Chen J. Impacts on silkworm larvae midgut proteomics by transgenic Trichoderma strain and analysis of glutathione S-transferase sigma 2 gene essential for anti-stress response of silkworm larvae. J Proteomics 2015; 126:218-27. [DOI: 10.1016/j.jprot.2015.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 02/07/2023]
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130
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Wang HL, Geertsema H, van Nieukerken EJ, Löfstedt C. Identification of the Female-Produced Sex Pheromone of the Leafminer Holocacista capensis Infesting Grapevine in South Africa. J Chem Ecol 2015; 41:724-31. [PMID: 26271672 PMCID: PMC4568023 DOI: 10.1007/s10886-015-0611-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/25/2015] [Accepted: 07/10/2015] [Indexed: 11/18/2022]
Abstract
We report the first identification of a sex pheromone in a heliozelid moth, Holocacista capensis van Nieukerken & Geertsema. This leafminer recently infested grapevine in South Africa. Compared to solvent extraction of pheromone glands, solid phase microextraction (SPME) proved to be highly effective for collection of the pheromone from calling females. The volatiles collected by SPME were analyzed by gas chromatography with electroantennographic detection (GC/EAD). Three compounds eliciting electrophysiological activity from the male antenna were identified as (Z)-5-tetradecenal, (Z)-7-tetradecenal, and (Z)-9-hexadecenal by coupled gas chromatography-mass spectrometry (GC/MS). GC/MS analysis of dimethyldisulphide (DMDS) derivatives of fatty acyl moieties in pheromone gland extracts confirmed the presence of the corresponding putative pheromone precursors with double bonds in the same position and with Z geometry. Field trapping experiments in a South African vineyard confirmed that both (Z)-5-tetradecenal and (Z)-7-tetradecenal are essential for the attraction of male H. capensis, whereas addition of (Z)-9-hexadecenal to the blend did not affect the attractiveness. The composition of the pheromone is discussed in relation to the phylogeny of this family of moths.
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Affiliation(s)
- Hong-Lei Wang
- Department of Biology, Lund University, SE-223 62, Lund, Sweden.
| | - Henk Geertsema
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa
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Ahmed MZ, Araujo-Jnr EV, Welch JJ, Kawahara AY. Wolbachia in butterflies and moths: geographic structure in infection frequency. Front Zool 2015; 12:16. [PMID: 26180539 PMCID: PMC4502936 DOI: 10.1186/s12983-015-0107-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/18/2015] [Indexed: 02/03/2023] Open
Abstract
INTRODUCTION Butterflies and moths (Lepidoptera) constitute one of the most diverse insect orders, and play an important role in ecosystem function. However, little is known in terms of their bacterial communities. Wolbachia, perhaps the most common and widespread intracellular bacterium on Earth, can manipulate the physiology and reproduction of its hosts, and is transmitted vertically from mother to offspring, or sometimes horizontally between species. While its role in some hosts has been studied extensively, its incidence across Lepidoptera is poorly understood. A recent analysis using a beta-binomial model to infer the between-species distribution of prevalence estimated that approximately 40 % of arthropod species are infected with Wolbachia, but particular taxonomic groups and ecological niches seem to display substantially higher or lower incidences. In this study, we took an initial step and applied a similar, maximum likelihood approach to 300 species of Lepidoptera (7604 individuals from 660 populations) belonging to 17 families and 10 superfamilies, and sampled from 36 countries, representing all continents excluding Antarctica. RESULTS Approximately a quarter to a third of individuals appear to be infected with Wolbachia, and around 80 % of Lepidoptera species are infected at a non-negligible frequency. This incidence estimate is very high compared to arthropods in general. Wolbachia infection in Lepidoptera is shown to vary between families, but there is no evidence for closely related groups to show similar infection levels. True butterflies (Papilionoidea) are overrepresented in our data, however, our estimates show this group can be taken as a representative for the other major lepidopteran superfamilies. We also show substantial variation in infection level according to geography - closer locations tend to show similar infection levels. We further show that variation in geography is due to a latitudinal gradient in Wolbachia infection, with lower frequencies towards higher latitudes. CONCLUSIONS Our comprehensive survey of Wolbachia infection in Lepidoptera suggests that infection incidence is very high, and provides evidence that climate and geography are strong predictors of infection frequency.
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Affiliation(s)
- Muhammad Z. Ahmed
- />Florida Museum of Natural History, University of Florida, 32611 Gainesville, FL USA
- />Institute of Food and Agricultural Sciences, Tropical Research and Education Center, University of Florida, 18905 SW 280th Street, 33031 Homestead, FL USA
| | - Eli V. Araujo-Jnr
- />Institute of Food and Agricultural Sciences, Tropical Research and Education Center, University of Florida, 18905 SW 280th Street, 33031 Homestead, FL USA
| | - John J. Welch
- />Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK
| | - Akito Y. Kawahara
- />Institute of Food and Agricultural Sciences, Tropical Research and Education Center, University of Florida, 18905 SW 280th Street, 33031 Homestead, FL USA
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132
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The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications. Meta Gene 2015; 5:68-83. [PMID: 26106582 PMCID: PMC4475787 DOI: 10.1016/j.mgene.2015.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/19/2015] [Accepted: 05/11/2015] [Indexed: 11/21/2022] Open
Abstract
Due to the intriguing morphology, lifecycle, and diversity of butterflies and moths, Lepidoptera are emerging as model organisms for the study of genetics, evolution and speciation. The progress of these studies relies on decoding Lepidoptera genomes, both nuclear and mitochondrial. Here we describe a protocol to obtain mitogenomes from Next Generation Sequencing reads performed for whole-genome sequencing and report the complete mitogenome of Papilio (Pterourus) glaucus. The circular mitogenome is 15,306 bp in length and rich in A and T. It contains 13 protein-coding genes (PCGs), 22 transfer-RNA-coding genes (tRNA), and 2 ribosomal-RNA-coding genes (rRNA), with a gene order typical for mitogenomes of Lepidoptera. We performed phylogenetic analyses based on PCG and RNA-coding genes or protein sequences using Bayesian Inference and Maximum Likelihood methods. The phylogenetic trees consistently show that among species with available mitogenomes Papilio glaucus is the closest to Papilio (Agehana) maraho from Asia.
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133
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Yuan X, Gao K, Yuan F, Wang P, Zhang Y. Phylogenetic relationships of subfamilies in the family Hesperiidae (Lepidoptera: Hesperioidea) from China. Sci Rep 2015; 5:11140. [PMID: 26059470 PMCID: PMC4461911 DOI: 10.1038/srep11140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/11/2015] [Indexed: 11/09/2022] Open
Abstract
Hesperiidae is one of the largest families of butterflies. Our knowledge of the higher systematics on hesperiids from China is still very limited. We infer the phylogenetic relationships of the subfamilies of Chinese skippers based on three mitochondrial genes (cytochrome b (Cytb), the NADH dehydrogenase subunit 1 (ND1) and cytochrome oxidase I (COI)). In this study, 30 species in 23 genera were included in the Bayesian and maximum likelihood analyses. The subfamily Coeliadinae, Eudaminae, Pyrginae and Heteropterinae were recovered as a monophyletic clade with strong support. The subfamily Hesperiinae formed a clade, but support for monophyly was weak. Our results imply that the five subfamilies of Chinese Hesperiidae should be divided into: Coeliadinae, Eudaminae, Pyrginae, Heteropterinae and Hesperiinae. The relationships of the five subfamilies should be as follows: Coeliadinae + (Eudaminae + (Pyrginae + (Heteropterinae + Hesperiinae))).
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Affiliation(s)
- Xiangqun Yuan
- 1] Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum of Northwest A&F University, 712100, Yangling, Shaanxi, China [2] Department of Entomology, Cornell University, 14456, Geneva, NY, USA
| | - Ke Gao
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum of Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Feng Yuan
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum of Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Ping Wang
- Department of Entomology, Cornell University, 14456, Geneva, NY, USA
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum of Northwest A&F University, 712100, Yangling, Shaanxi, China
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134
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Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation. Proc Natl Acad Sci U S A 2015; 112:6407-12. [PMID: 25941377 DOI: 10.1073/pnas.1416679112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bat-moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼ 26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18-14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.
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135
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Montgomery SH, Ott SR. Brain composition in Godyris zavaleta, a diurnal butterfly, Reflects an increased reliance on olfactory information. J Comp Neurol 2015; 523:869-91. [PMID: 25400217 PMCID: PMC4354442 DOI: 10.1002/cne.23711] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/17/2014] [Accepted: 11/04/2014] [Indexed: 11/15/2022]
Abstract
Interspecific comparisons of brain structure can inform our functional understanding of brain regions, identify adaptations to species-specific ecologies, and explore what constrains adaptive changes in brain structure, and coevolution between functionally related structures. The value of such comparisons is enhanced when the species considered have known ecological differences. The Lepidoptera have long been a favored model in evolutionary biology, but to date descriptions of brain anatomy have largely focused on a few commonly used neurobiological model species. We describe the brain of Godyris zavaleta (Ithomiinae), a member of a subfamily of Neotropical butterflies with enhanced reliance on olfactory information. We demonstrate for the first time the presence of sexually dimorphic glomeruli within a distinct macroglomerular complex (MGC) in the antennal lobe of a diurnal butterfly. This presents a striking convergence with the well-known moth MGC, prompting a discussion of the potential mechanisms behind the independent evolution of specialized glomeruli. Interspecific analyses across four Lepidoptera further show that the relative size of sensory neuropils closely mirror interspecific variation in sensory ecology, with G. zavaleta displaying levels of sensory investment intermediate between the diurnal monarch butterfly (Danaus plexippus), which invests heavily in visual neuropil, and night-flying moths, which invest more in olfactory neuropil. We identify several traits that distinguish butterflies from moths, and several that distinguish D. plexippus and G. zavaleta. Our results illustrate that ecological selection pressures mold the structure of invertebrate brains, and exemplify how comparative analyses across ecologically divergent species can illuminate the functional significance of variation in brain structure.
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Affiliation(s)
- Stephen H Montgomery
- Department of Genetics, Evolution & Environment, University College LondonLondon, UK, WC1E 6BT
| | - Swidbert R Ott
- Department of Biology, University of LeicesterLeicester, UK, LE1 7RH
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136
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Winkler IS, Blaschke JD, Davis DJ, Stireman JO, O'Hara JE, Cerretti P, Moulton JK. Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae). Mol Phylogenet Evol 2015; 88:38-54. [PMID: 25841383 DOI: 10.1016/j.ympev.2015.03.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 12/01/2022]
Abstract
Molecular phylogenetic studies at all taxonomic levels often infer rapid radiation events based on short, poorly resolved internodes. While such rapid episodes of diversification are an important and widespread evolutionary phenomenon, much of this poor phylogenetic resolution may be attributed to the continuing widespread use of "traditional" markers (mitochondrial, ribosomal, and some nuclear protein-coding genes) that are often poorly suited to resolve difficult, higher-level phylogenetic problems. Here we reconstruct phylogenetic relationships among a representative set of taxa of the parasitoid fly family Tachinidae and related outgroups of the superfamily Oestroidea. The Tachinidae are one of the most species rich, yet evolutionarily recent families of Diptera, providing an ideal case study for examining the differential performance of loci in resolving phylogenetic relationships and the benefits of adding more loci to phylogenetic analyses. We assess the phylogenetic utility of nine genes including both traditional genes (e.g., CO1 mtDNA, 28S rDNA) and nuclear protein-coding genes newly developed for phylogenetic analysis. Our phylogenetic findings, based on a limited set of taxa, include: a close relationship between Tachinidae and the calliphorid subfamily Polleninae, monophyly of Tachinidae and the subfamilies Exoristinae and Dexiinae, subfamily groupings of Dexiinae+Phasiinae and Tachininae+Exoristinae, and robust phylogenetic placement of the somewhat enigmatic genera Strongygaster, Euthera, and Ceracia. In contrast to poor resolution and phylogenetic incongruence of "traditional genes," we find that a more selective set of highly informative genes is able to more precisely identify regions of the phylogeny that experienced rapid radiation of lineages, while more accurately depicting their phylogenetic context. Although much expanded taxon sampling is necessary to effectively assess the monophyly of and relationships among major tachinid lineages and their relatives, we show that a small number of well-chosen nuclear protein-coding genes can successfully resolve even difficult phylogenetic problems.
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Affiliation(s)
- Isaac S Winkler
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA; Department of Biology, Linfield College, McMinnville, OR 97128, USA
| | - Jeremy D Blaschke
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel J Davis
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA
| | - John O Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
| | - James E O'Hara
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Pierfilippo Cerretti
- DAFNAE-Entomology, Università degli Studi di Padova, Viale dell'Università 16, 35020 Legnaro (Padova), Italy; Dipartimento di Biologia e Biotecnologie 'Charles Darwin', 'Sapienza' Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy
| | - John K Moulton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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137
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A mitochondrial genome phylogeny of owlet moths (Lepidoptera: Noctuoidea), and examination of the utility of mitochondrial genomes for lepidopteran phylogenetics. Mol Phylogenet Evol 2015; 85:230-7. [DOI: 10.1016/j.ympev.2015.02.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 01/27/2015] [Accepted: 02/06/2015] [Indexed: 11/17/2022]
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138
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Rajaei H, Greve C, Letsch H, Stüning D, Wahlberg N, Minet J, Misof B. Advances in Geometroidea phylogeny, with characterization of a new family based onPseudobiston pinratanai(Lepidoptera, Glossata). ZOOL SCR 2015. [DOI: 10.1111/zsc.12108] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hossein Rajaei
- Stuttgart State Museum of Natural History; Rosenstein 1 70191 Stuttgart Germany
| | - Carola Greve
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160 53113 Bonn Germany
| | - Harald Letsch
- Department of Botany and Biodiversity Research; University of Vienna; Rennweg 14 1030 Vienna Austria
| | - Dieter Stüning
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160 53113 Bonn Germany
| | - Niklas Wahlberg
- Laboratory of Genetics; Department of Biology; University of Turku; 20014 Turku Finland
| | - Joël Minet
- Institut de Systématique, Evolution; Biodiversité (ISYEB); UMR 7205 (CNRS, MNHN, UPMC, EPHE); Muséum National d'Histoire Naturelle (Sorbonne Universités); 57, rue Cuvier Case Postale 50 (Entomologie) 75005 Paris France
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160 53113 Bonn Germany
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139
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Gupta A, Fernández-Triana JL. Four new species of the genus Diolcogaster Ashmead, 1900 (Hymenoptera: Braconidae: Microgastrinae) from South East Asia with a key to the Indian species. Syst Parasitol 2015; 90:285-300. [PMID: 25693462 DOI: 10.1007/s11230-014-9546-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/24/2014] [Indexed: 11/30/2022]
Abstract
Four new species of the genus Diolcogaster Ashmead, 1900 (Hymenoptera: Braconidae: Microgastrinae) are described and illustrated: Diolcogaster andamanensis n. sp. from the Andaman Islands, and D. duocolor n. sp., D. longistria n. sp. and D. solitarium n. sp. from mainland India. The solitary larval parasitoid D. solitarium was reared from Gatesclarkeana sp. (Lepidoptera: Tortricidae). A new combination, Diolcogaster tomentosae (Wilkinson, 1930) n. comb., is proposed for the Indian species Protomicroplitis tomentosae (Wilkinson, 1930) along with its redescription and documentation of the gregarious cocoons associated with the pyralid (Epipaschiinae) host feeding on Terminalia cattappa L.
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Affiliation(s)
- Ankita Gupta
- National Bureau of Agriculturally Important Insects, Post Bag No. 2491, H. A. Farm Post, Bellary Road, Hebbal, Bangalore, 560 024, Karnataka, India,
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140
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Sohn JC, Labandeira CC, Davis DR. The fossil record and taphonomy of butterflies and moths (Insecta, Lepidoptera): implications for evolutionary diversity and divergence-time estimates. BMC Evol Biol 2015; 15:12. [PMID: 25649001 PMCID: PMC4326409 DOI: 10.1186/s12862-015-0290-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/15/2015] [Indexed: 11/22/2022] Open
Abstract
Background It is conventionally accepted that the lepidopteran fossil record is significantly incomplete when compared to the fossil records of other, very diverse, extant insect orders. Such an assumption, however, has been based on cumulative diversity data rather than using alternative statistical approaches from actual specimen counts. Results We reviewed documented specimens of the lepidopteran fossil record, currently consisting of 4,593 known specimens that are comprised of 4,262 body fossils and 331 trace fossils. The temporal distribution of the lepidopteran fossil record shows significant bias towards the late Paleocene to middle Eocene time interval. Lepidopteran fossils also record major shifts in preservational style and number of represented localities at the Mesozoic stage and Cenozoic epoch level of temporal resolution. Only 985 of the total known fossil specimens (21.4%) were assigned to 23 of the 40 extant lepidopteran superfamilies. Absolute numbers and proportions of preservation types for identified fossils varied significantly across superfamilies. The secular increase of lepidopteran family-level diversity through geologic time significantly deviates from the general pattern of other hyperdiverse, ordinal-level lineages. Conclusion Our statistical analyses of the lepidopteran fossil record show extreme biases in preservation type, age, and taxonomic composition. We highlight the scarcity of identified lepidopteran fossils and provide a correspondence between the latest lepidopteran divergence-time estimates and relevant fossil occurrences at the superfamily level. These findings provide caution in interpreting the lepidopteran fossil record through the modeling of evolutionary diversification and in determination of divergence time estimates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0290-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jae-Cheon Sohn
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA. .,Department of Paleobiology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA. .,Department of Entomology, University of Maryland, College Park, MD, USA.
| | - Conrad C Labandeira
- Department of Paleobiology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA. .,Department of Entomology, University of Maryland, College Park, MD, USA. .,College of Life Sciences, Capital Normal University, Beijing, China.
| | - Donald R Davis
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.
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141
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Quah S, Hui JHL, Holland PWH. A Burst of miRNA Innovation in the Early Evolution of Butterflies and Moths. Mol Biol Evol 2015; 32:1161-74. [PMID: 25576364 PMCID: PMC4408404 DOI: 10.1093/molbev/msv004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in posttranscriptional regulation of gene expression. Because several miRNAs are known to affect the stability or translation of developmental regulatory genes, the origin of novel miRNAs may have contributed to the evolution of developmental processes and morphology. Lepidoptera (butterflies and moths) is a species-rich clade with a well-established phylogeny and abundant genomic resources, thereby representing an ideal system in which to study miRNA evolution. We sequenced small RNA libraries from developmental stages of two divergent lepidopterans, Cameraria ohridella (Horse chestnut Leafminer) and Pararge aegeria (Speckled Wood butterfly), discovering 90 and 81 conserved miRNAs, respectively, and many species-specific miRNA sequences. Mapping miRNAs onto the lepidopteran phylogeny reveals rapid miRNA turnover and an episode of miRNA fixation early in lepidopteran evolution, implying that miRNA acquisition accompanied the early radiation of the Lepidoptera. One lepidopteran-specific miRNA gene, miR-2768, is located within an intron of the homeobox gene invected, involved in insect segmental and wing patterning. We identified cubitus interruptus (ci) as a likely direct target of miR-2768, and validated this suppression using a luciferase assay system. We propose a model by which miR-2768 modulates expression of ci in the segmentation pathway and in patterning of lepidopteran wing primordia.
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Affiliation(s)
- Shan Quah
- Department of Zoology, University of Oxford
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142
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Breinholt JW, Kawahara AY. Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biol Evol 2014; 5:2082-92. [PMID: 24148944 PMCID: PMC3845638 DOI: 10.1093/gbe/evt157] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions.
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143
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Environmental determinism of community structure across trophic levels: moth assemblages and substrate type in the rain forests of south-western China. JOURNAL OF TROPICAL ECOLOGY 2014. [DOI: 10.1017/s026646741400056x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract:Soil type may drive vegetation structure. In turn, the richness, identity and diversity of arthropod herbivores may be related to plant diversity through specific host plant relationships in a location. We test the hypothesis that the soil type (calcicolous vs alluvial soils) will drive the assemblage structure of a dominant group of arthropod herbivores: the moths. We used sampling sites in rain-forest fragments in south-western China around the Xishuangbanna Tropical Botanical Gardens (21°41′N, 101°25′E) to test this hypothesis. We used Pennsylvania style light traps to take point samples of macromoths and pyraloids from four sampling sites in forest remnants on a limestone geological base and four from alluvial-based forest. A total of 3165 moths (1739 from limestone-based and 1255 from alluvium-based forests) was collected representing 1255 species. The limestone-based sites showed statistically similar levels of species richness and other alpha diversity indices to the four alluvium-based site. Nevertheless the sites were clearly significantly different in terms of species composition. Analysis of contrasting similarity (‘beta’ diversity) indices suggested that there was ‘leakage’ between the two classes of sites when ‘rare’ species were emphasized in the calculations. We used an indicator value procedure to select species that most characterized this separation. We expect that these differences reflect associated changes in plant assemblage structure acting through the herbivorous habits of larval moths. Accordingly, in any assessment of landscape level diversity the nature of the substrate and its associated vegetation is clearly of great importance. This observation also has consequences for the design of conservation programmes.
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144
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Rainford JL, Hofreiter M, Nicholson DB, Mayhew PJ. Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects. PLoS One 2014; 9:e109085. [PMID: 25275450 PMCID: PMC4183542 DOI: 10.1371/journal.pone.0109085] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/08/2014] [Indexed: 11/18/2022] Open
Abstract
Insects and their six-legged relatives (Hexapoda) comprise more than half of all described species and dominate terrestrial and freshwater ecosystems. Understanding the macroevolutionary processes generating this richness requires a historical perspective, but the fossil record of hexapods is patchy and incomplete. Dated molecular phylogenies provide an alternative perspective on divergence times and have been combined with birth-death models to infer patterns of diversification across a range of taxonomic groups. Here we generate a dated phylogeny of hexapod families, based on previously published sequence data and literature derived constraints, in order to identify the broad pattern of macroevolutionary changes responsible for the composition of the extant hexapod fauna. The most prominent increase in diversification identified is associated with the origin of complete metamorphosis, confirming this as a key innovation in promoting insect diversity. Subsequent reductions are recovered for several groups previously identified as having a higher fossil diversity during the Mesozoic. In addition, a number of recently derived taxa are found to have radiated following the development of flowering plant (angiosperm) floras during the mid-Cretaceous. These results reveal that the composition of the modern hexapod fauna is a product of a key developmental innovation, combined with multiple and varied evolutionary responses to environmental changes from the mid Cretaceous floral transition onward.
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Affiliation(s)
- James L. Rainford
- Department of Biology, University of York, York, United Kingdom
- * E-mail:
| | - Michael Hofreiter
- Department of Biology, University of York, York, United Kingdom
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - David B. Nicholson
- Department of Biology, University of York, York, United Kingdom
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
- Department of Earth Sciences, The Natural History Museum, London, United Kingdom
| | - Peter J. Mayhew
- Department of Biology, University of York, York, United Kingdom
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145
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Ferguson L, Marlétaz F, Carter JM, Taylor WR, Gibbs M, Breuker CJ, Holland PWH. Ancient expansion of the hox cluster in lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation. PLoS Genet 2014; 10:e1004698. [PMID: 25340822 PMCID: PMC4207634 DOI: 10.1371/journal.pgen.1004698] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/22/2014] [Indexed: 01/15/2023] Open
Abstract
Gene duplications within the conserved Hox cluster are rare in animal evolution, but in Lepidoptera an array of divergent Hox-related genes (Shx genes) has been reported between pb and zen. Here, we use genome sequencing of five lepidopteran species (Polygonia c-album, Pararge aegeria, Callimorpha dominula, Cameraria ohridella, Hepialus sylvina) plus a caddisfly outgroup (Glyphotaelius pellucidus) to trace the evolution of the lepidopteran Shx genes. We demonstrate that Shx genes originated by tandem duplication of zen early in the evolution of large clade Ditrysia; Shx are not found in a caddisfly and a member of the basally diverging Hepialidae (swift moths). Four distinct Shx genes were generated early in ditrysian evolution, and were stably retained in all descendent Lepidoptera except the silkmoth which has additional duplications. Despite extensive sequence divergence, molecular modelling indicates that all four Shx genes have the potential to encode stable homeodomains. The four Shx genes have distinct spatiotemporal expression patterns in early development of the Speckled Wood butterfly (Pararge aegeria), with ShxC demarcating the future sites of extraembryonic tissue formation via strikingly localised maternal RNA in the oocyte. All four genes are also expressed in presumptive serosal cells, prior to the onset of zen expression. Lepidopteran Shx genes represent an unusual example of Hox cluster expansion and integration of novel genes into ancient developmental regulatory networks.
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Affiliation(s)
- Laura Ferguson
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Jean-Michel Carter
- Evolutionary Developmental Biology Research Group, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Headington, Oxford, United Kingdom
| | - William R. Taylor
- MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Melanie Gibbs
- NERC Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom
| | - Casper J. Breuker
- Evolutionary Developmental Biology Research Group, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Headington, Oxford, United Kingdom
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146
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Combover/CG10732, a novel PCP effector for Drosophila wing hair formation. PLoS One 2014; 9:e107311. [PMID: 25207969 PMCID: PMC4160248 DOI: 10.1371/journal.pone.0107311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/10/2014] [Indexed: 01/22/2023] Open
Abstract
The polarization of cells is essential for the proper functioning of most organs. Planar Cell Polarity (PCP), the polarization within the plane of an epithelium, is perpendicular to apical-basal polarity and established by the non-canonical Wnt/Fz-PCP signaling pathway. Within each tissue, downstream PCP effectors link the signal to tissue specific readouts such as stereocilia orientation in the inner ear and hair follicle orientation in vertebrates or the polarization of ommatidia and wing hairs in Drosophila melanogaster. Specific PCP effectors in the wing such as Multiple wing hairs (Mwh) and Rho Kinase (Rok) are required to position the hair at the correct position and to prevent ectopic actin hairs. In a genome-wide screen in vitro, we identified Combover (Cmb)/CG10732 as a novel Rho kinase substrate. Overexpression of Cmb causes the formation of a multiple hair cell phenotype (MHC), similar to loss of rok and mwh. This MHC phenotype is dominantly enhanced by removal of rok or of other members of the PCP effector gene family. Furthermore, we show that Cmb physically interacts with Mwh, and cmb null mutants suppress the MHC phenotype of mwh alleles. Our data indicate that Cmb is a novel PCP effector that promotes to wing hair formation, a function that is antagonized by Mwh.
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147
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Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nat Commun 2014; 5:4737. [PMID: 25189940 PMCID: PMC4164777 DOI: 10.1038/ncomms5737] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/17/2014] [Indexed: 12/30/2022] Open
Abstract
Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths. Butterflies and moths (Lepidoptera) vary in chromosome number. Here, the authors sequence the genome of the Glanville fritillary butterfly, Melitaea cinxia, show it has the ancestral lepidopteran karyotype and provide insight into how chromosomal fusions have shaped karyotype evolution in butterflies and moths.
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Affiliation(s)
- Virpi Ahola
- 1] Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland [2]
| | - Rainer Lehtonen
- 1] Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland [2] Genome-Scale Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland [3] Institute of Biomedicine, University of Helsinki, FI-00014 Helsinki, Finland [4] Center of Excellence in Cancer Genetics, University of Helsinki, FI-00014 Helsinki, Finland [5] [6]
| | - Panu Somervuo
- 1] Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland [2] Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland [3]
| | - Leena Salmela
- Department of Computer Science &Helsinki Institute for Information Technology HIIT, University of Helsinki, FI-00014 Helsinki, Finland
| | - Patrik Koskinen
- 1] Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland [2] Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pasi Rastas
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Niko Välimäki
- 1] Genome-Scale Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland [2] Institute of Biomedicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jouni Kvist
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Niklas Wahlberg
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Jaakko Tanskanen
- 1] Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland [2] Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland
| | - Emily A Hornett
- 1] Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK [2] Department of Biology, Pennsylvania State University, Pennsylvania 16802, USA
| | | | - Shiqi Luo
- College of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Zijuan Cao
- College of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Maaike A de Jong
- 1] Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland [2] School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
| | - Anne Duplouy
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Rajiv C McCoy
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Kui Qian
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Wong Swee Chong
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Qin Zhang
- BioMediTech, University of Tampere, FI-33520 Tampere, Finland
| | - Freed Ahmad
- Department of Information Technology, University of Turku, FI-20014 Turku, Finland
| | - Jani K Haukka
- BioMediTech, University of Tampere, FI-33520 Tampere, Finland
| | - Aruj Joshi
- BioMediTech, University of Tampere, FI-33520 Tampere, Finland
| | - Jarkko Salojärvi
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Ewald Grosse-Wilde
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Daniel Hughes
- 1] European Bioinformatics Institute, Hinxton CB10 1SD, UK [2] Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas 77030-3411, USA
| | - Riku Katainen
- 1] Genome-Scale Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland [2] Institute of Biomedicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Esa Pitkänen
- 1] Genome-Scale Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland [2] Institute of Biomedicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Johannes Ylinen
- Department of Computer Science &Helsinki Institute for Information Technology HIIT, University of Helsinki, FI-00014 Helsinki, Finland
| | - Robert M Waterhouse
- 1] Department of Genetic Medicine and Development, University of Geneva Medical School &Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland [2] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Mikko Turunen
- Genome-Scale Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland
| | - Anna Vähärautio
- 1] Genome-Scale Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland [2] Department of Pathology, University of Helsinki, FI-00014 Helsinki, Finland [3] Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, SE-14183 Stockholm, Sweden
| | - Sami P Ojanen
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
| | - Alan H Schulman
- 1] Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland [2] Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland
| | - Minna Taipale
- 1] Genome-Scale Biology Research Program, University of Helsinki, FI-00014 Helsinki, Finland [2] Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, SE-14183 Stockholm, Sweden
| | - Daniel Lawson
- European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Esko Ukkonen
- Department of Computer Science &Helsinki Institute for Information Technology HIIT, University of Helsinki, FI-00014 Helsinki, Finland
| | - Veli Mäkinen
- Department of Computer Science &Helsinki Institute for Information Technology HIIT, University of Helsinki, FI-00014 Helsinki, Finland
| | - Marian R Goldsmith
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881-0816, USA
| | - Liisa Holm
- 1] Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland [2] Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland [3]
| | - Petri Auvinen
- 1] Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland [2]
| | - Mikko J Frilander
- 1] Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland [2]
| | - Ilkka Hanski
- Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland
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148
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Kawahara AY, Breinholt JW. Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc Biol Sci 2014; 281:20140970. [PMID: 24966318 PMCID: PMC4083801 DOI: 10.1098/rspb.2014.0970] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/04/2014] [Indexed: 11/12/2022] Open
Abstract
Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly-moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order.
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Affiliation(s)
- Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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149
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Doorenweerd C, van Haren MM, Schermer M, Pieterse S, van Nieukerken EJ. A Linnaeus NG (TM) interactive key to the Lithocolletinae of North-West Europe aimed at accelerating the accumulation of reliable biodiversity data (Lepidoptera, Gracillariidae). Zookeys 2014:87-101. [PMID: 25061390 PMCID: PMC4109447 DOI: 10.3897/zookeys.422.7446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/22/2014] [Indexed: 11/12/2022] Open
Abstract
We present an interactive key that is available online through any web browser without the need to install any additional software, making it an easily accessible tool for the larger public. The key can be found at http://identify.naturalis.nl/lithocolletinae. The key includes all 86 North-West European Lithocolletinae, a subfamily of smaller moths (“micro-moths”) that is commonly not treated in field guides. The user can input data on several external morphological character systems in addition to distribution, host plant and even characteristics of the larval feeding traces to reach an identification. We expect that this will enable more people to contribute with reliable observation data on this group of moths and alleviate the workload of taxonomic specialists, allowing them to focus on other new keys or taxonomic work.
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Affiliation(s)
- Camiel Doorenweerd
- Naturalis Biodiversity Center, Department of Terrestrial Zoology, P.O. Box 9517, 2300 RA, Leiden, the Netherlands
| | - Merel M van Haren
- Naturalis Biodiversity Center, Department of Terrestrial Zoology, P.O. Box 9517, 2300 RA, Leiden, the Netherlands ; Radboud University, RU-Institute for Water and Wetland research, Department of Animal ecology and ecophysiology, P.O. Box 9010, 6500 GL, Nijmegen, the Netherlands
| | - Maarten Schermer
- Naturalis Biodiversity Center, ETI BioInformatics, P.O. Box 9517, 2300 RA, Leiden, the Netherlands
| | - Sander Pieterse
- Naturalis Biodiversity Center, Educational Development, P.O. Box 9517, 2300 RA, Leiden, the Netherlands
| | - Erik J van Nieukerken
- Naturalis Biodiversity Center, Department of Terrestrial Zoology, P.O. Box 9517, 2300 RA, Leiden, the Netherlands
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150
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Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera. Gene 2014; 549:97-112. [PMID: 25058696 DOI: 10.1016/j.gene.2014.07.052] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/02/2014] [Accepted: 07/18/2014] [Indexed: 11/24/2022]
Abstract
We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A+T composition (79.3%-80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNA(Gln) and ND2 (64-87 bp), conserved ATACTAA motif between tRNA(Ser (UCN)) and ND1, and characteristic features of the A+T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNA(Asn)/tRNA(Ser (AGN)), instead of the rearrangement tRNA(Ser (AGN))/tRNA(Asn), found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea+Noctuoidea+Geometroidea)+Pyraloidea)+Papilionoidea)+Tortricoidea)+Yponomeutoidea)+Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae+(Hesperiidae+(Pieridae+((Lycaenidae+Riodinidae)+Nymphalidae)))) were strongly supported in all analyses (0.98-1 by BI and 96-100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.
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