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Mbanyana N, Blaimer BB, Le Roux JJ, van Noort S, Brady SG, Wossler TC. Out of the desert: Paleoclimatic changes drove the diversification of arid-adapted Ocymyrmex ants in southern Africa. Mol Phylogenet Evol 2024; 191:107977. [PMID: 38008369 DOI: 10.1016/j.ympev.2023.107977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/06/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
A highly endemic ant fauna is found in the arid regions of southern Africa, including species in the genus Ocymyrmex. This genus of ants has higher species richness in the western arid regions of southern Africa compared to tropical and subtropical parts of the continent. The processes that have produced these patterns of diversity and distribution of arid adapted ants in southern Africa have never been investigated. The diversification of many other taxa in the region has been associated with past climate fluctuations that occurred during the Miocene epoch. In this study, the nature and timing of historical processes that may have led to the diversification within Ocymyrmex were assessed. We hypothesized that past climate oscillations, characterized by long periods of aridification, have driven the current distribution of Ocymyrmex species that resulted in the highest species richness of the genus in the Deserts & xeric shrublands biome in southern Africa. Ninety-four Ocymyrmex worker specimens from Botswana, Kenya, Namibia, South Africa, Tanzania and Zimbabwe, representing 21 currently described species and six morphospecies, were included in a phylogenomic analysis. Phylogenies for the genus, based on next generation sequencing data from ultraconserved elements, were inferred using Maximum Likelihood, and a dating analysis was performed using secondary age estimates as calibration points. A distribution database of Ocymyrmex records was used to assign species ranges, which were then coded according to major biomes in southern Africa and used as input for biogeographical analysis. We explored the phylogenomic relationships of Ocymyrmex and analysed these within a biogeographical and paleoclimatic framework to disentangle the potential processes responsible for diversification in this group. Dating analyses estimated that the crown age of Ocymyrmex dates to the Oligocene, around 32 Ma. Diversification within this group occurred between the mid-Miocene (∼12.5 Ma) and Pleistocene (∼2 Ma). Our biogeographic analyses suggest that Ocymyrmex species originated in the south-western region of southern Africa, which is now part of the Deserts & xeric shrublands biome and diversified into eastern subtropical areas during the Pliocene. Paleoclimatic changes resulting in increased aridity during the Miocene likely drove the diversification of the genus Ocymyrmex. It is most likely that the diversification of grasslands, because of historical climate change, facilitated the diversification of these ants to the eastern parts of southern Africa when open grasslands replaced forests during the early Miocene.
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Affiliation(s)
- Nokuthula Mbanyana
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, P.O. Box 61, Cape Town, 8000, South Africa; Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa.
| | - Bonnie B Blaimer
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstr. 43, Berlin, 10115, Germany
| | - Johannes J Le Roux
- School of Natural Sciences, Macquarie University, Sydney, 2113, New South Wales, Australia
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, P.O. Box 61, Cape Town, 8000, South Africa; Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Theresa C Wossler
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa
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Cruaud A, Rasplus JY, Zhang J, Burks R, Delvare G, Fusu L, Gumovsky A, Huber JT, Janšta P, Mitroiu MD, Noyes JS, van Noort S, Baker A, Böhmová J, Baur H, Blaimer BB, Brady SG, Bubeníková K, Chartois M, Copeland RS, Dale-Skey Papilloud N, Dal Molin A, Dominguez C, Gebiola M, Guerrieri E, Kresslein RL, Krogmann L, Lemmon E, Murray EA, Nidelet S, Nieves-Aldrey JL, Perry RK, Peters RS, Polaszek A, Sauné L, Torréns J, Triapitsyn S, Tselikh EV, Yoder M, Lemmon AR, Woolley JB, Heraty JM. The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps. Cladistics 2024; 40:34-63. [PMID: 37919831 DOI: 10.1111/cla.12561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 11/04/2023] Open
Abstract
Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.
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Affiliation(s)
- Astrid Cruaud
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, China
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Roger Burks
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Gérard Delvare
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Lucian Fusu
- Faculty of Biology, Alexandru Ioan Cuza University, Iasi, Romania
| | - Alex Gumovsky
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - John T Huber
- Natural Resources Canada, c/o Canadian National Collection of Insects, Ottawa, Ontario, Canada
| | - Petr Janšta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
| | | | - John S Noyes
- Insects Division, Natural History Museum, London, UK
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, Cape Town, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Austin Baker
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Julie Böhmová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hannes Baur
- Department of Invertebrates, Natural History Museum Bern, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Bonnie B Blaimer
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Seán G Brady
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Kristýna Bubeníková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marguerite Chartois
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Robert S Copeland
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | | | - Ana Dal Molin
- Departamento de Microbiologia e Parasitologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Chrysalyn Dominguez
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Marco Gebiola
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Emilio Guerrieri
- Insects Division, Natural History Museum, London, UK
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Robert L Kresslein
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Lars Krogmann
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
- Institute of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Emily Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
| | - Sabine Nidelet
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | | - Ryan K Perry
- Department of Plant Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Ralph S Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | | | - Laure Sauné
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Javier Torréns
- Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja (CRILAR-CONICET), Anillaco, Argentina
| | - Serguei Triapitsyn
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | | | - Matthew Yoder
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, Florida, USA
| | - James B Woolley
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - John M Heraty
- Department of Entomology, University of California Riverside, Riverside, California, USA
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3
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Almeida EAB, Bossert S, Danforth BN, Porto DS, Freitas FV, Davis CC, Murray EA, Blaimer BB, Spasojevic T, Ströher PR, Orr MC, Packer L, Brady SG, Kuhlmann M, Branstetter MG, Pie MR. The evolutionary history of bees in time and space. Curr Biol 2023; 33:3409-3422.e6. [PMID: 37506702 DOI: 10.1016/j.cub.2023.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.
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Affiliation(s)
- Eduardo A B Almeida
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil.
| | - Silas Bossert
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA
| | - Diego S Porto
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil; Finnish Museum of Natural History - LUOMUS, University of Helsinki, Helsinki 00014, Finland
| | - Felipe V Freitas
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil; Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Tamara Spasojevic
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Life Sciences, Natural History Museum Basel, 4051 Basel, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Patrícia R Ströher
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná 81531-990, Brazil; Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Michael C Orr
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, 70191 Stuttgart, Germany; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Michael Kuhlmann
- Zoological Museum, University of Kiel, Hegewischstr. 3, 24105 Kiel, Germany
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, Utah State University, Logan, UT 84322, USA
| | - Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná 81531-990, Brazil; Department of Biology, Edge Hill University, St Helens Rd, Ormskirk, Lancashire L39 4QP, UK
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4
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Santos BF, Miller ME, Miklasevskaja M, McKeown JTA, Redmond NE, Coddington JA, Bird J, Miller SE, Smith A, Brady SG, Buffington ML, Chamorro ML, Dikow T, Gates MW, Goldstein P, Konstantinov A, Kula R, Silverson ND, Solis MA, deWaard SL, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Sones JE, Zakharov EV, deWaard JR. Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History. Biodivers Data J 2023; 11:e100904. [PMID: 38327288 PMCID: PMC10848724 DOI: 10.3897/bdj.11.e100904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 02/09/2024] Open
Abstract
The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian's National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximise sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,737 determined species in 3,886 genera and 205 families distributed in 137 countries. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximise output and minimise cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.
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Affiliation(s)
- Bernardo F. Santos
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UAParisFrance
| | - Meredith E. Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Margarita Miklasevskaja
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jaclyn T. A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Niamh E. Redmond
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jonathan A. Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jessica Bird
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Ashton Smith
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Seán G. Brady
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Matthew L. Buffington
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - M. Lourdes Chamorro
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Michael W. Gates
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Paul Goldstein
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Alexander Konstantinov
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Robert Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Nicholas D. Silverson
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - M. Alma Solis
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Stephanie L. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jayme E. Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Jeremy R. deWaard
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- School of Environmental Sciences, University of Guelph, Guelph, CanadaSchool of Environmental Sciences, University of GuelphGuelphCanada
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Blaimer BB, Santos BF, Cruaud A, Gates MW, Kula RR, Mikó I, Rasplus JY, Smith DR, Talamas EJ, Brady SG, Buffington ML. Key innovations and the diversification of Hymenoptera. Nat Commun 2023; 14:1212. [PMID: 36869077 PMCID: PMC9984522 DOI: 10.1038/s41467-023-36868-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.
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Affiliation(s)
- Bonnie B Blaimer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany.
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA.
| | - Bernardo F Santos
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Astrid Cruaud
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Michael W Gates
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Robert R Kula
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - István Mikó
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Jean-Yves Rasplus
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - David R Smith
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Elijah J Talamas
- Florida State Collection of Arthropods, Division of Plant Industry, Florida Department of Agriculture and Consumer Services, 1911 SW 34th St, Gainesville, FL, 32608, USA
| | - Seán G Brady
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
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6
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Jasso-Martínez JM, Santos BF, Zaldívar-Riverón A, Fernandez-Triana J, Sharanowski BJ, Richter R, Dettman JR, Blaimer BB, Brady SG, Kula RR. Phylogenomics of braconid wasps (Hymenoptera, Braconidae) sheds light on classification and the evolution of parasitoid life history traits. Mol Phylogenet Evol 2022; 173:107452. [DOI: 10.1016/j.ympev.2022.107452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/17/2022] [Accepted: 03/01/2022] [Indexed: 01/05/2023]
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7
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Cruaud A, Delvare G, Nidelet S, Sauné L, Ratnasingham S, Chartois M, Blaimer BB, Gates M, Brady SG, Faure S, van Noort S, Rossi JP, Rasplus JY. Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics 2021; 37:1-35. [PMID: 34478176 DOI: 10.1111/cla.12416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2020] [Indexed: 11/30/2022] Open
Abstract
Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.
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Affiliation(s)
- Astrid Cruaud
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Gérard Delvare
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France.,UMR CBGP, CIRAD, F-34398, Montpellier, France
| | - Sabine Nidelet
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Laure Sauné
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Marguerite Chartois
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Michael Gates
- USDA, ARS, SEL, c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Seán G Brady
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sariana Faure
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, PO Box 61, Cape Town, 8000, South Africa.,Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, Cape Town, South Africa
| | - Jean-Pierre Rossi
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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8
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Bossert S, Murray EA, Pauly A, Chernyshov K, Brady SG, Danforth BN. Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees. Syst Biol 2020; 70:803-821. [PMID: 33367855 DOI: 10.1093/sysbio/syaa097] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 11/12/2022] Open
Abstract
Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree, and RAxML. We study their performance in the phylogenomic framework of $>$800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus Pseudapis, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (ModelFinder program). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for Pseudapis s. l. and map the distribution of distinct morphological features of the group. [ASTRAL; Bees; concordance; gene tree estimation error; IQ-Tree; MrBayes, Nomiinae; PhyloBayes; RAxML; phylogenomics; stemminess].
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, Washington State University, Pullman, Washington 99164, USA
| | - Elizabeth A Murray
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, Washington State University, Pullman, Washington 99164, USA
| | - Alain Pauly
- O.D. Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000 Brussels, Belgium
| | - Kyrylo Chernyshov
- College of Arts and Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA
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9
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Blaimer BB, Gotzek D, Brady SG, Buffington ML. Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps. BMC Evol Biol 2020; 20:155. [PMID: 33228574 PMCID: PMC7686688 DOI: 10.1186/s12862-020-01716-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/31/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior known as galling. Less commonly, cynipoid wasps exhibit inquilinism, a strategy where some species have adapted to usurp other species' galls instead of inducing their own. Using a phylogenomic data set of ultraconserved elements from nearly all lineages of Cynipoidea, we here generate a robust phylogenetic framework and timescale to understand cynipoid systematics and the evolution of these life histories. RESULTS Our reconstructed evolutionary history for Cynipoidea differs considerably from previous hypotheses. Rooting our analyses with non-cynipoid outgroups, the Paraulacini, a group of inquilines, emerged as sister-group to the rest of Cynipoidea, rendering the gall wasp family Cynipidae paraphyletic. The families Ibaliidae and Liopteridae, long considered archaic and early-branching parasitoid lineages, were found nested well within the Cynipoidea as sister-group to the parasitoid Figitidae. Cynipoidea originated in the early Jurassic around 190 Ma. Either inquilinism or parasitoidism is suggested as the ancestral and dominant strategy throughout the early evolution of cynipoids, depending on whether a simple (three states: parasitoidism, inquilinism and galling) or more complex (seven states: parasitoidism, inquilinism and galling split by host use) model is employed. CONCLUSIONS Our study has significant impact on understanding cynipoid evolution and highlights the importance of adequate outgroup sampling. We discuss the evolutionary timescale of the superfamily in relation to their insect hosts and host plants, and outline how phytophagous galling behavior may have evolved from entomophagous, parasitoid cynipoids. Our study has established the framework for further physiological and comparative genomic work between gall-making, inquiline and parasitoid lineages, which could also have significant implications for the evolution of diverse life histories in other Hymenoptera.
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Affiliation(s)
- Bonnie B Blaimer
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Berlin, Germany.
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
- North Carolina State University, Raleigh, NC, USA.
| | - Dietrich Gotzek
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Seán G Brady
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS-USDA, C/O NMNH, Smithsonian Institution, Washington, DC, USA.
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10
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Legeai F, Santos BF, Robin S, Bretaudeau A, Dikow RB, Lemaitre C, Jouan V, Ravallec M, Drezen JM, Tagu D, Baudat F, Gyapay G, Zhou X, Liu S, Webb BA, Brady SG, Volkoff AN. Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. BMC Biol 2020; 18:89. [PMID: 32703219 PMCID: PMC7379367 DOI: 10.1186/s12915-020-00822-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/29/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Polydnaviruses (PDVs) are mutualistic endogenous viruses inoculated by some lineages of parasitoid wasps into their hosts, where they facilitate successful wasp development. PDVs include the ichnoviruses and bracoviruses that originate from independent viral acquisitions in ichneumonid and braconid wasps respectively. PDV genomes are fully incorporated into the wasp genomes and consist of (1) genes involved in viral particle production, which derive from the viral ancestor and are not encapsidated, and (2) proviral segments harboring virulence genes, which are packaged into the viral particle. To help elucidating the mechanisms that have facilitated viral domestication in ichneumonid wasps, we analyzed the structure of the viral insertions by sequencing the whole genome of two ichnovirus-carrying wasp species, Hyposoter didymator and Campoletis sonorensis. RESULTS Assemblies with long scaffold sizes allowed us to unravel the organization of the endogenous ichnovirus and revealed considerable dispersion of the viral loci within the wasp genomes. Proviral segments contained species-specific sets of genes and occupied distinct genomic locations in the two ichneumonid wasps. In contrast, viral machinery genes were organized in clusters showing highly conserved gene content and order, with some loci located in collinear wasp genomic regions. This genomic architecture clearly differs from the organization of PDVs in braconid wasps, in which proviral segments are clustered and viral machinery elements are more dispersed. CONCLUSIONS The contrasting structures of the two types of ichnovirus genomic elements are consistent with their different functions: proviral segments are vehicles for virulence proteins expected to adapt according to different host defense systems, whereas the genes involved in virus particle production in the wasp are likely more stable and may reflect ancestral viral architecture. The distinct genomic architectures seen in ichnoviruses versus bracoviruses reveal different evolutionary trajectories that have led to virus domestication in the two wasp lineages.
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Affiliation(s)
- Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Bernardo F Santos
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Rebecca B Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
| | - Claire Lemaitre
- Université Rennes 1, INRIA, CNRS, IRISA, F-35000, Rennes, France
| | - Véronique Jouan
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Marc Ravallec
- DGIMI, INRAE, University of Montpellier, 34095, Montpellier, France
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - Université de Tours, UFR des Sciences et Techniques, Parc de Grandmont, Tours, France
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650, Le Rheu, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, CNRS, University of Montpellier, 34396, Montpellier, France
| | - Gabor Gyapay
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, People's Republic of China
| | - Bruce A Webb
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC, 20560-0165, USA
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11
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Supeleto FA, Santos BF, Brady SG, Aguiar AP. Phylogenomic analyses reveal a rare new genus of wasp (Hymenoptera, Ichneumonidae, Cryptinae) from the Brazilian Atlantic Forest. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1787551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Fernanda A. Supeleto
- Depto de Ciências Biológicas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari 514, Goiabeiras, Vitória, 29075–010, ES, Brazil
| | - Bernardo F. Santos
- Department of Entomology, National Museum of Natural History, 10th & Constitution NW, Washington, 20560, DC, USA
| | - Seán G. Brady
- Department of Entomology, National Museum of Natural History, 10th & Constitution NW, Washington, 20560, DC, USA
| | - Alexandre P. Aguiar
- Depto de Ciências Biológicas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari 514, Goiabeiras, Vitória, 29075–010, ES, Brazil
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12
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Menezes RST, Lloyd MW, Brady SG. Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity. Proc Biol Sci 2020; 287:20200480. [PMID: 32486978 DOI: 10.1098/rspb.2020.0480] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Neotropical realm harbours unparalleled species richness and hence has challenged biologists to explain the cause of its high biotic diversity. Empirical studies to shed light on the processes underlying biological diversification in the Neotropics are focused mainly on vertebrates and plants, with little attention to the hyperdiverse insect fauna. Here, we use phylogenomic data from ultraconserved element (UCE) loci to reconstruct for the first time the evolutionary history of Neotropical swarm-founding social wasps (Hymenoptera, Vespidae, Epiponini). Using maximum likelihood, Bayesian, and species tree approaches we recovered a highly resolved phylogeny for epiponine wasps. Additionally, we estimated divergence dates, diversification rates, and the biogeographic history for these insects in order to test whether the group followed a 'museum' (speciation events occurred gradually over many millions of years) or 'cradle' (lineages evolved rapidly over a short time period) model of diversification. The origin of many genera and all sampled extant Epiponini species occurred during the Miocene and Plio-Pleistocene. Moreover, we detected no major shifts in the estimated diversification rate during the evolutionary history of Epiponini, suggesting a relatively gradual accumulation of lineages with low extinction rates. Several lines of evidence suggest that the Amazonian region played a major role in the evolution of Epiponini wasps. This spatio-temporal diversification pattern, most likely concurrent with climatic and landscape changes in the Neotropics during the Miocene and Pliocene, establishes the Amazonian region as the major source of Neotropical swarm-founding social wasp diversity.
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Affiliation(s)
- Rodolpho S T Menezes
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0188, USA.,Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras - Universidade de São Paulo (FFCLRP/USP), Av. Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil
| | - Michael W Lloyd
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0188, USA.,Computational Sciences, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0188, USA
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13
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Rasplus JY, Blaimer BB, Brady SG, Burks RA, Delvare G, Fisher N, Gates M, Gauthier N, Gumovsky AV, Hansson C, Heraty JM, Fusu L, Nidelet S, Pereira RA, Sauné L, Ubaidillah R, Cruaud A. A first phylogenomic hypothesis for Eulophidae (Hymenoptera, Chalcidoidea). J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1762941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jean-Yves Rasplus
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Bonnie B. Blaimer
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Seán G. Brady
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Roger A. Burks
- Department of Entomology, University of California, Riverside, CA, USA
| | | | - Nicole Fisher
- Digital Collections and Informatics, National Research Collections Australia (NRCA), CSIRO, Canberra, Australia
| | - Michael Gates
- USDA, ARS, SEL, C/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Nathalie Gauthier
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Alex V. Gumovsky
- Schmalhausen Institute of Zoology, NAS of Ukraine, Kiev, Ukraine
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christer Hansson
- Museum of Biology (Entomology), Lund University, Lund, Sweden
- Faculty of Biology and CERNESIM, Al. I. Cuza University, Iasi, Romania
| | - John M. Heraty
- Department of Entomology, University of California, Riverside, CA, USA
| | - Lucian Fusu
- Departamento de Biologia, FFCLRP – USP, Ribeirão Preto, Brazil
| | - Sabine Nidelet
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Laure Sauné
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Astrid Cruaud
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
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14
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Abstract
Female army ants cannot fly, making them very poor dispersers across water barriers. This dependence on terrestrial corridors motivated the investigation by Winston et al. (), published in this issue of Molecular Ecology, into the role of Panamanian isthmus formation in the diversification of Eciton army ants. Complete closure of this isthmus occurred around three million years ago (3 Ma), but it has also been hypothesized that earlier, temporary land connections facilitated additional colonization events between South and Central America over the past 13 million years or more. The phylogenomic and population genomic analyses by Winston et al. () uncovered multiple incursions of Eciton lineages into Central America between 4 and 7 Ma. Their study contributes to a growing body of evidence arguing that transitory land bridges predating 3 Ma supported substantial intercontinental biotic exchange.
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Affiliation(s)
- Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
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15
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Borowiec ML, Rabeling C, Brady SG, Fisher BL, Schultz TR, Ward PS. Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants. Mol Phylogenet Evol 2019; 134:111-121. [DOI: 10.1016/j.ympev.2019.01.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 10/27/2022]
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16
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Santos BF, Perrard A, Brady SG. Running in circles in phylomorphospace: host environment constrains morphological diversification in parasitic wasps. Proc Biol Sci 2019; 286:20182352. [PMID: 30963952 PMCID: PMC6364584 DOI: 10.1098/rspb.2018.2352] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/04/2019] [Indexed: 11/12/2022] Open
Abstract
Understanding phenotypic diversification and the conditions that spur morphological novelty or constraint is a major theme in evolutionary biology. Unequal morphological diversity between sister clades can result from either differences in the rate of morphological change or in the ability of clades to explore novel phenotype ranges. We combine an existing phylogenetic framework with new phylogenomic data and geometric morphometrics to explore the relative roles of rate versus mode of morphological evolution for a hyperdiverse group: cryptine ichneumonid wasps. Data from genomic ultraconserved elements confirm that cryptines are divided into two large clades: one specialized in the use of hosts that are deeply concealed under hard substrates, and another with a much more diversified host range. Using a phylomorphospace approach, we show that both clades have experienced similar rates of morphological evolution. Nonetheless, the more specialized group is much more restricted in morphospace occupation, indicating that it repeatedly evolved morphological change through the same morphospace regions. This is in agreement with our prediction that host use imposes constraints in the morphospace available to lineages, and reinforces an important distinction between evolutionary stasis as opposed to a scenario of continual morphological change restricted to a certain range of morphotypes.
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Affiliation(s)
- Bernardo F. Santos
- Department of Entomology, National Museum of Natural History, 10th and Constitution Avenue NW, Washington, DC 20560-0165, USA
| | - Adrien Perrard
- Université Paris Diderot, Sorbonne Université, CNRS, IRD, INRA, Institute of Ecology and Environmental Sciences (UMR7618), 4 Place Jussieu, 75005 Paris, France
| | - Seán G. Brady
- Department of Entomology, National Museum of Natural History, 10th and Constitution Avenue NW, Washington, DC 20560-0165, USA
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17
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Santos BF, Alvarado M, Sääksjärvi IE, van Noort S, Villemant C, Brady SG. Molecular phylogeny of Ateleutinae (Hymenoptera: Ichneumonidae): systematics and biogeography of a widespread parasitoid wasp lineage. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Bernardo F Santos
- Department of Entomology, National Museum of Natural History, Washington DC, USA
- Department of Systematics & Evolution, Muséum National d’Histoire Naturelle, France
| | - Mabel Alvarado
- Department of Ecology and Evolutionary Biology, University of Kansas, USA
| | | | - Simon van Noort
- Research and Exhibitions Department, Iziko South African Museum, South Africa
- Department of Biological Sciences, University of Cape Town, South Africa
| | - Claire Villemant
- Department of Systematics & Evolution, Muséum National d’Histoire Naturelle, France
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Washington DC, USA
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Bossert S, Murray EA, Almeida EAB, Brady SG, Blaimer BB, Danforth BN. Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae. Mol Phylogenet Evol 2018; 130:121-131. [PMID: 30326287 DOI: 10.1016/j.ympev.2018.10.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023]
Abstract
Two increasingly popular approaches to reconstruct the Tree of Life involve whole transcriptome sequencing and the target capture of ultraconserved elements (UCEs). Both methods can be used to generate large, multigene datasets for analysis of phylogenetic relationships in non-model organisms. While targeted exon sequencing across divergent lineages is now a standard method, it is still not clear if UCE data can be readily combined with published transcriptomes. In this study, we evaluate the combination of UCEs and transcriptomes in a single analysis using genome-, transcriptome-, and UCE data for 79 bees in the largest and most biologically diverse bee family, Apidae. Using existing tools, we first developed a workflow to assemble phylogenomic data from different sources and produced two large nucleotide matrices of combined data. We then reconstructed the phylogeny of the Apidae using concatenation- and coalescent-based methods, and critically evaluated the resulting phylogenies in the context of previously published genetic, genomic, and morphological data sets. Our estimated phylogenetic trees are robustly supported and largely congruent with previous molecular hypotheses, from deep nodes to shallow species-level phylogenies. Moreover, the combined approach allows us to resolve controversial nodes of the apid Tree of Life, by clarifying the relationships among the genera of orchid bees (Euglossini) and the monophyly of the Centridini. Additionally, we present novel phylogenetic evidence supporting the monophyly of the diverse clade of cleptoparasitic Apidae and the placement of two enigmatic, oil-collecting genera (Ctenoplectra and Tetrapedia). Lastly, we propose a revised classification of the family Apidae that reflects our improved understanding of apid higher-level relationships.
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Cornell University, Ithaca, NY, USA.
| | | | - Eduardo A B Almeida
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
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Blaimer BB, Mawdsley JR, Brady SG. Multiple origins of sexual dichromatism and aposematism within large carpenter bees. Evolution 2018; 72:1874-1889. [PMID: 30039868 DOI: 10.1111/evo.13558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 07/05/2018] [Accepted: 07/15/2018] [Indexed: 12/24/2022]
Abstract
The evolution of reversed sexual dichromatism and aposematic coloration has long been of interest to both theoreticians and empiricists. Yet despite the potential connections between these phenomena, they have seldom been jointly studied. Large carpenter bees (genus Xylocopa) are a promising group for such comparative investigations as they are a diverse clade in which both aposematism and reversed sexual dichromatism can occur either together or separately. We investigated the evolutionary history of dichromatism and aposematism and a potential correlation of these traits with diversification rates within Xylocopa, using a newly generated phylogeny for 179 Xylocopa species based on ultraconserved elements (UCEs). A monochromatic, inconspicuous ancestor is indicated for the genus, with subsequent convergent evolution of sexual dichromatism and aposematism in multiple lineages. Aposematism is found to covary with reversed sexual dichromatism in many species; however, reversed dichromatism also evolved in non-aposematic species. Bayesian Analysis of Macroevolutionary Models (BAMM) did not show increased diversification in any specific clade in Xylocopa, whereas support from Hidden State Speciation and Extinction (HiSSE) models remained inconclusive regarding an association of increased diversification rates with dichromatism or aposematism. We discuss the evolution of color patterns and diversification in Xylocopa by considering potential drivers of dichromatism and aposematism.
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Affiliation(s)
- Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20560.,Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27695
| | - Jonathan R Mawdsley
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20560
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20560
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Branstetter MG, Ješovnik A, Sosa-Calvo J, Lloyd MW, Faircloth BC, Brady SG, Schultz TR. Dry habitats were crucibles of domestication in the evolution of agriculture in ants. Proc Biol Sci 2017; 284:rspb.2017.0095. [PMID: 28404776 PMCID: PMC5394666 DOI: 10.1098/rspb.2017.0095] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/14/2017] [Indexed: 11/12/2022] Open
Abstract
The evolution of ant agriculture, as practised by the fungus-farming 'attine' ants, is thought to have arisen in the wet rainforests of South America about 55-65 Ma. Most subsequent attine agricultural evolution, including the domestication event that produced the ancestor of higher attine cultivars, is likewise hypothesized to have occurred in South American rainforests. The 'out-of-the-rainforest' hypothesis, while generally accepted, has never been tested in a phylogenetic context. It also presents a problem for explaining how fungal domestication might have occurred, given that isolation from free-living populations is required. Here, we use phylogenomic data from ultra-conserved element (UCE) loci to reconstruct the evolutionary history of fungus-farming ants, reduce topological uncertainty, and identify the closest non-fungus-growing ant relative. Using the phylogeny we infer the history of attine agricultural systems, habitat preference and biogeography. Our results show that the out-of-the-rainforest hypothesis is correct with regard to the origin of attine ant agriculture; however, contrary to expectation, we find that the transition from lower to higher agriculture is very likely to have occurred in a seasonally dry habitat, inhospitable to the growth of free-living populations of attine fungal cultivars. We suggest that dry habitats favoured the isolation of attine cultivars over the evolutionary time spans necessary for domestication to occur.
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Affiliation(s)
- Michael G Branstetter
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA .,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Ana Ješovnik
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Jeffrey Sosa-Calvo
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Center for Social Insect Research, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael W Lloyd
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Ted R Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
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Branstetter MG, Danforth BN, Pitts JP, Faircloth BC, Ward PS, Buffington ML, Gates MW, Kula RR, Brady SG. Phylogenomic Insights into the Evolution of Stinging Wasps and the Origins of Ants and Bees. Curr Biol 2017; 27:1019-1025. [DOI: 10.1016/j.cub.2017.03.027] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/10/2017] [Accepted: 03/13/2017] [Indexed: 11/30/2022]
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Mulcahy DG, Macdonald KS, Brady SG, Meyer C, Barker KB, Coddington J. Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA. PeerJ 2016; 4:e2528. [PMID: 27761327 DOI: 10.7287/peerj.preprints.2202v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/04/2016] [Indexed: 05/26/2023] Open
Abstract
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples-and their quantifiable metadata-preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall "genome-quality" DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA "greater than X kb" as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards ("DNA Threshold" and "Percent above Threshold") introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.
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Affiliation(s)
- Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution , Washingtion, DC , USA
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Katharine B Barker
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Jonathan Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washingtion, DC, USA
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Mulcahy DG, Macdonald KS, Brady SG, Meyer C, Barker KB, Coddington J. Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA. PeerJ 2016; 4:e2528. [PMID: 27761327 PMCID: PMC5068448 DOI: 10.7717/peerj.2528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/04/2016] [Indexed: 12/02/2022] Open
Abstract
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall “genome-quality” DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA “greater than X kb” as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (“DNA Threshold” and “Percent above Threshold”) introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.
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Affiliation(s)
- Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution , Washingtion, DC , USA
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Katharine B Barker
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Jonathan Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washingtion, DC, USA
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Blaimer BB, LaPolla JS, Branstetter MG, Lloyd MW, Brady SG. Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga. Mol Phylogenet Evol 2016; 102:20-9. [DOI: 10.1016/j.ympev.2016.05.030] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 12/29/2022]
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Blaimer BB, Lloyd MW, Guillory WX, Brady SG. Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens. PLoS One 2016; 11:e0161531. [PMID: 27556533 PMCID: PMC4996520 DOI: 10.1371/journal.pone.0161531] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/08/2016] [Indexed: 01/15/2023] Open
Abstract
Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/μL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE approach for large-scale projects in insect phylogenomics using museum specimens.
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Affiliation(s)
- Bonnie B. Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Michael W. Lloyd
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Wilson X. Guillory
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Seán G. Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America
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Nygaard S, Hu H, Li C, Schiøtt M, Chen Z, Yang Z, Xie Q, Ma C, Deng Y, Dikow RB, Rabeling C, Nash DR, Wcislo WT, Brady SG, Schultz TR, Zhang G, Boomsma JJ. Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. Nat Commun 2016; 7:12233. [PMID: 27436133 PMCID: PMC4961791 DOI: 10.1038/ncomms12233] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/14/2016] [Indexed: 02/02/2023] Open
Abstract
The attine ant-fungus agricultural symbiosis evolved over tens of millions of years, producing complex societies with industrial-scale farming analogous to that of humans. Here we document reciprocal shifts in the genomes and transcriptomes of seven fungus-farming ant species and their fungal cultivars. We show that ant subsistence farming probably originated in the early Tertiary (55-60 MYA), followed by further transitions to the farming of fully domesticated cultivars and leaf-cutting, both arising earlier than previously estimated. Evolutionary modifications in the ants include unprecedented rates of genome-wide structural rearrangement, early loss of arginine biosynthesis and positive selection on chitinase pathways. Modifications of fungal cultivars include loss of a key ligninase domain, changes in chitin synthesis and a reduction in carbohydrate-degrading enzymes as the ants gradually transitioned to functional herbivory. In contrast to human farming, increasing dependence on a single cultivar lineage appears to have been essential to the origin of industrial-scale ant agriculture.
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Affiliation(s)
- Sanne Nygaard
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Haofu Hu
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
| | - Cai Li
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Zhensheng Chen
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhikai Yang
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiaolin Xie
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
| | - Chunyu Ma
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yuan Deng
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
| | - Rebecca B. Dikow
- Smithsonian Institute for Biodiversity Genomics, Smithsonian Institution, Washington DC 20013-7012, USA
| | - Christian Rabeling
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - David R. Nash
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - William T. Wcislo
- Smithsonian Tropical Research Institute, Balboa, Ancón 03092, Panama
| | - Seán G. Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Ted R. Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
- China National Genbank, BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jacobus J. Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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Blaimer BB, Brady SG, Schultz TR, Lloyd MW, Fisher BL, Ward PS. Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants. BMC Evol Biol 2015; 15:271. [PMID: 26637372 PMCID: PMC4670518 DOI: 10.1186/s12862-015-0552-5] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/26/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with that of traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, including insects, are sparse. We compared the phylogenetic informativeness of 959 UCE loci with a multi-locus data set of ten nuclear markers obtained via Sanger sequencing, testing the ability of these two types of data to resolve and date the evolutionary history of the second most species-rich subfamily of ants in the world, the Formicinae. RESULTS Phylogenetic analyses show that UCEs are superior in resolving ancient and shallow relationships in formicine ants, demonstrated by increased node support and a more resolved phylogeny. Phylogenetic informativeness metrics indicate a twofold improvement relative to the 10-gene data matrix generated from the identical set of taxa. We were able to significantly improve formicine classification based on our comprehensive UCE phylogeny. Our divergence age estimations, using both UCE and Sanger data, indicate that crown-group Formicinae are older (104-117 Ma) than previously suggested. Biogeographic analyses infer that the diversification of the subfamily has occurred on all continents with no particular hub of cladogenesis. CONCLUSIONS We found UCEs to be far superior to the multi-locus data set in estimating formicine relationships. The early history of the clade remains uncertain due to ancient rapid divergence events that are unresolvable even with our genomic-scale data, although this might be largely an effect of several problematic taxa subtended by long branches. Our comparison of divergence ages from both Sanger and UCE data demonstrates the effectiveness of UCEs for dating analyses. This comparative study highlights both the promise and limitations of UCEs for insect phylogenomics, and will prove useful to the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.
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Affiliation(s)
- Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Ted R Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Michael W Lloyd
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Brian L Fisher
- Department of Entomology, California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - Philip S Ward
- Department of Entomology and Nematology, University of California-Davis, Davis, CA, 95616, USA.
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Smith CR, Helms Cahan S, Kemena C, Brady SG, Yang W, Bornberg-Bauer E, Eriksson T, Gadau J, Helmkampf M, Gotzek D, Okamoto Miyakawa M, Suarez AV, Mikheyev A. How Do Genomes Create Novel Phenotypes? Insights from the Loss of the Worker Caste in Ant Social Parasites. Mol Biol Evol 2015; 32:2919-31. [PMID: 26226984 PMCID: PMC4651238 DOI: 10.1093/molbev/msv165] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A central goal of biology is to uncover the genetic basis for the origin of new
phenotypes. A particularly effective approach is to examine the genomic
architecture of species that have secondarily lost a phenotype with respect to
their close relatives. In the eusocial Hymenoptera, queens and workers have
divergent phenotypes that may be produced via either expression of alternative
sets of caste-specific genes and pathways or differences in expression patterns
of a shared set of multifunctional genes. To distinguish between these two
hypotheses, we investigated how secondary loss of the worker phenotype in
workerless ant social parasites impacted genome evolution across two independent
origins of social parasitism in the ant genera Pogonomyrmex and
Vollenhovia. We sequenced the genomes of three social
parasites and their most-closely related eusocial host species and compared gene
losses in social parasites with gene expression differences between host queens
and workers. Virtually all annotated genes were expressed to some degree in both
castes of the host, with most shifting in queen-worker bias across developmental
stages. As a result, despite >1 My of divergence from the last common
ancestor that had workers, the social parasites showed strikingly little
evidence of gene loss, damaging mutations, or shifts in selection regime
resulting from loss of the worker caste. This suggests that regulatory changes
within a multifunctional genome, rather than sequence differences, have played a
predominant role in the evolution of social parasitism, and perhaps also in the
many gains and losses of phenotypes in the social insects.
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Affiliation(s)
| | | | - Carsten Kemena
- Institute for Evolution and Biodiversity, Westfälische Wilhems-Universität Münster, Münster, Germany
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington DC
| | - Wei Yang
- Department of Computer Science, University of Illinois Urbana-Champaign
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfälische Wilhems-Universität Münster, Münster, Germany
| | - Ti Eriksson
- School of Life Sciences, Arizona State University
| | | | | | - Dietrich Gotzek
- Department of Entomology, University of Georgia Department of Animal Biology, University of Illinois Urbana-Champaign
| | - Misato Okamoto Miyakawa
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Andrew V Suarez
- Department of Animal Biology, University of Illinois Urbana-Champaign Department of Entomology, University of Illinois Urbana-Champaign
| | - Alexander Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
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Schultz TR, Sosa-Calvo J, Brady SG, Lopes CT, Mueller UG, Bacci M, Vasconcelos HL. The Most Relictual Fungus-Farming Ant Species Cultivates the Most Recently Evolved and Highly Domesticated Fungal Symbiont Species. Am Nat 2015; 185:693-703. [DOI: 10.1086/680501] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Faircloth BC, Branstetter MG, White ND, Brady SG. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol Ecol Resour 2015; 15:489-501. [PMID: 25207863 PMCID: PMC4407909 DOI: 10.1111/1755-0998.12328] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 08/31/2014] [Accepted: 09/05/2014] [Indexed: 12/30/2022]
Abstract
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.
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Affiliation(s)
- Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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Rinkevich FD, Hedtke SM, Leichter CA, Harris SA, Su C, Brady SG, Taskin V, Qiu X, Scott JG. Multiple origins of kdr-type resistance in the house fly, Musca domestica. PLoS One 2012; 7:e52761. [PMID: 23285178 PMCID: PMC3532202 DOI: 10.1371/journal.pone.0052761] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 11/22/2012] [Indexed: 11/19/2022] Open
Abstract
Insecticide resistance is a model phenotype that can be used to investigate evolutionary processes underlying the spread of alleles across a global landscape, while offering valuable insights into solving the problems that resistant pests present to human health and agriculture. Pyrethroids are one of the most widely used classes of insecticides world-wide and they exert their toxic effects through interactions with the voltage-sensitive sodium channel (Vssc). Specific mutations in Vssc (kdr, kdr-his and super-kdr) are known to cause resistance to pyrethroid insecticides in house flies. In order to determine the number of evolutionary origins of kdr, kdr-his and super-kdr, we sequenced a region of Vssc from house flies collected in the USA, Turkey and China. Our phylogenetic analysis of Vssc unequivocally supports the hypothesis of multiple independent origins of kdr, super-kdr and kdr-his on an unprecedented geographic scale. The implications of these evolutionary processes on pest management are discussed.
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Affiliation(s)
- Frank D. Rinkevich
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York, United States of America
| | - Shannon M. Hedtke
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York, United States of America
| | - Cheryl A. Leichter
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York, United States of America
| | - Sarah A. Harris
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York, United States of America
| | - Cathy Su
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York, United States of America
| | - Seán G. Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D. C., United States of America
| | - Vatan Taskin
- Department of Biology, Faculty of Science, Muğla Sitki Kocman University, Muğla, Turkey
| | - Xinghui Qiu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jeffrey G. Scott
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Gibbs J, Brady SG, Kanda K, Danforth BN. Phylogeny of halictine bees supports a shared origin of eusociality for Halictus and Lasioglossum (Apoidea: Anthophila: Halictidae). Mol Phylogenet Evol 2012; 65:926-39. [DOI: 10.1016/j.ympev.2012.08.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/30/2012] [Accepted: 08/17/2012] [Indexed: 11/24/2022]
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Ward PS, Brady SG, Fisher BL, Schultz TR. Phylogeny and biogeography of dolichoderine ants: effects of data partitioning and relict taxa on historical inference. Syst Biol 2010; 59:342-62. [PMID: 20525640 DOI: 10.1093/sysbio/syq012] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ants (Hymenoptera: Formicidae) are conspicuous organisms in most terrestrial ecosystems, often attaining high levels of abundance and diversity. In this study, we investigate the evolutionary history of a major clade of ants, the subfamily Dolichoderinae, whose species frequently achieve ecological dominance in ant communities. This group has also produced some of the world's most successful invasive ants. We use an extensive molecular data set ( approximately 9 kb of sequence data from 10 nuclear genes, covering 48 dolichoderine species and 6 outgroup taxa) to infer the phylogenetic relationships, divergence dates, and biogeographic history of these ants. We evaluate the effects of data partitioning and outgroup composition on phylogenetic inference by estimating relationships under a series of increasingly partitioned data sets and by running analyses both with and without Aneuretus simoni, a rare and localized species that is the nearest living relative of Dolichoderinae. We also examine the effects of excluding 2 data partitions with significant base composition heterogeneity. Our results reveal 4 well-supported and mutually exclusive clades of dolichoderines, corresponding to 4 newly defined tribes: Bothriomyrmecini (B), Dolichoderini (D), Leptomyrmecini (L), and Tapinomini (T). All Bayesian and likelihood analyses yield the same unrooted (ingroup-only) topology, ((D,L),(B,T)), with the outgroups attaching either on the Dolichoderini branch or on the Tapinomini branch. Placement of the root is highly sensitive to choice of model partition and to inclusion/exclusion of Aneuretus. Bayes' factors strongly favor the more partitioned models, and in these Tapinomini is recovered as sister to the remaining dolichoderines, but only if Aneuretus is included. Exclusion of Aneuretus precludes recovery of this topology in all but the most highly partitioned Bayesian analyses and then only with nonsignificant support, underscoring the importance of relict, taxonomically isolated taxa for phylogenetic inference. Removal of 2 partitions with heterogeneous base composition also markedly increases support for placement of the root on the Tapinomini branch. Our divergence date estimates and biogeographic analyses indicate that crown-group dolichoderines arose about 65 million years ago (Ma), although this was preceded by a substantial period (30 million years) of stem group evolution. The 4 extant tribes are estimated to have crown-group origins in the late Paleocene or Eocene (40-60 Ma). Tapinomini and Bothriomyrmecini originated in the Paleotropics and subsequently dispersed to other biogeographic regions. Crown-group Leptomyrmecini arose and diversified in the Neotropics, but they also gave rise to one clade that colonized Australia about 30 Ma and subsequently experienced a massive radiation on that continent. This event occurred later than the diversification of dolichoderines in the northern hemisphere, so that by the time dolichoderines came to dominate the Australian fauna they had already declined in abundance in the Holarctic region.
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Affiliation(s)
- Philip S Ward
- Department of Entomology, University of California, Davis, CA 95616, USA.
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Wernegreen JJ, Kauppinen SN, Brady SG, Ward PS. One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects. BMC Evol Biol 2009; 9:292. [PMID: 20015388 PMCID: PMC2810300 DOI: 10.1186/1471-2148-9-292] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 12/16/2009] [Indexed: 11/28/2022] Open
Abstract
Background Bacterial endosymbiosis has a recurring significance in the evolution of insects. An estimated 10-20% of insect species depend on bacterial associates for their nutrition and reproductive viability. Members of the ant tribe Camponotini, the focus of this study, possess a stable, intracellular bacterial mutualist. The bacterium, Blochmannia, was first discovered in Camponotus and has since been documented in a distinct subgenus of Camponotus, Colobopsis, and in the related genus Polyrhachis. However, the distribution of Blochmannia throughout the Camponotini remains in question. Documenting the true host range of this bacterial mutualist is an important first step toward understanding the various ecological contexts in which it has evolved, and toward identifying its closest bacterial relatives. In this study, we performed a molecular screen, based on PCR amplification of 16S rDNA, to identify bacterial associates of diverse Camponotini species. Results Phylogenetic analyses of 16S rDNA gave four important insights: (i) Blochmannia occurs in a broad range of Camponotini genera including Calomyrmex, Echinopla, and Opisthopsis, and did not occur in outgroups related to this tribe (e.g., Notostigma). This suggests that the mutualism originated in the ancestor of the tribe Camponotini. (ii) The known bacteriocyte-associated symbionts of ants, in Formica, Plagiolepis, and the Camponotini, arose independently. (iii) Blochmannia is nestled within a diverse clade of endosymbionts of sap-feeding hemipteran insects, such as mealybugs, aphids, and psyllids. In our analyses, a group of secondary symbionts of mealybugs are the closest relatives of Blochmannia. (iv) Blochmannia has cospeciated with its known hosts, although deep divergences at the genus level remain uncertain. Conclusions The Blochmannia mutualism occurs in Calomyrmex, Echinopla, and Opisthopsis, in addition to Camponotus, and probably originated in the ancestral lineage leading to the Camponotini. This significant expansion of its known host range implies that the mutualism is more ancient and ecologically diverse than previously documented. Blochmannia is most closely related to endosymbionts of sap-feeding hemipterans, which ants tend for their carbohydrate-rich honeydew. Based on phylogenetic results, we propose Camponotini might have originally acquired this bacterial mutualist through a nutritional symbiosis with other insects.
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Affiliation(s)
- Jennifer J Wernegreen
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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Bradley TJ, Briscoe AD, Brady SG, Contreras HL, Danforth BN, Dudley R, Grimaldi D, Harrison JF, Kaiser JA, Merlin C, Reppert SM, Vandenbrooks JM, Yanoviak SP. Episodes in insect evolution. Integr Comp Biol 2009; 49:590-606. [PMID: 21665843 DOI: 10.1093/icb/icp043] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This article derives from a society-wide symposium organized by Timothy Bradley and Adriana Briscoe and presented at the 2009 annual meeting of the Society for Integrative and Comparative Biology in Boston, Massachusetts. David Grimaldi provided the opening presentation in which he outlined the major evolutionary events in the formation and subsequent diversification of the insect clade. This presentation was followed by speakers who detailed the evolutionary history of specific physiological and/or behavioral traits that have caused insects to be both ecologically successful and fascinating as subjects for biological study. These include a review of the evolutionary history of the insects, the origins of flight, osmoregulation, the evolution of tracheal systems, the evolution of color vision, circadian clocks, and the evolution of eusociality. These topics, as covered by the speakers, provide an overview of the pattern and timing of evolutionary diversification and specialization in the group of animals we know as insects.
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Affiliation(s)
- Timothy J Bradley
- *Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697-2525, USA;Department of Entomology and Laboratories of Analytical Biology, National Museum of the Smithsonian Institution, Washington, D.C. 20013-7012, USA;Department of Entomology, Cornell University, Ithaca, NY 14853, USA;Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA;Division of Invertebrate Zoology, Museum of Natural History, New York, NY 10024, USA;Section of Organismal, Integrative and Systems Biology, School of Life Sciences, Arizona State University, Tempe AZ 85287-4501, USA;Department of Basic Sciences, Midwestern University, Glendale, AZ 85308, USA;Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA;Department of Biology, University of Arkansas Little Rock, Little Rock, AR 72204, USA
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Brady SG, Schultz TR, Fisher BL, Ward PS. Evaluating alternative hypotheses for the early evolution and diversification of ants. Proc Natl Acad Sci U S A 2006; 103:18172-7. [PMID: 17079492 PMCID: PMC1838725 DOI: 10.1073/pnas.0605858103] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Indexed: 11/18/2022] Open
Abstract
Ants are the world's most diverse and ecologically dominant eusocial organisms. Resolving the phylogeny and timescale for major ant lineages is vital to understanding how they achieved this success. Morphological, molecular, and paleontological studies, however, have presented conflicting views on early ant evolution. To address these issues, we generated the largest ant molecular phylogenetic data set published to date, containing approximately 6 kb of DNA sequence from 162 species representing all 20 ant subfamilies and 10 aculeate outgroup families. When these data were analyzed with and without outgroups, which are all distantly related to ants and hence long-branched, we obtained conflicting ingroup topologies for some early ant lineages. This result casts strong doubt on the existence of a poneroid clade as currently defined. We compare alternate attachments of the outgroups to the ingroup tree by using likelihood tests, and find that several alternative rootings cannot be rejected by the data. These alternatives imply fundamentally different scenarios for the early evolution of ant morphology and behavior. Our data strongly support several notable relationships within the more derived formicoid ants, including placement of the enigmatic subfamily Aenictogitoninae as sister to Dorylus army ants. We use the molecular data to estimate divergence times, employing a strategy distinct from previous work by incorporating the extensive fossil record of other aculeate Hymenoptera as well as that of ants. Our age estimates for the most recent common ancestor of extant ants range from approximately 115 to 135 million years ago, indicating that a Jurassic origin is highly unlikely.
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Affiliation(s)
- Seán G. Brady
- *Department of Entomology and
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | | | - Brian L. Fisher
- Department of Entomology, California Academy of Sciences, San Francisco, CA 94103; and
| | - Philip S. Ward
- Department of Entomology and Center for Population Biology, University of California, Davis, CA 95616
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Abstract
Bees, the largest (>16,000 species) and most important radiation of pollinating insects, originated in early to mid-Cretaceous, roughly in synchrony with the angiosperms (flowering plants). Understanding the diversification of the bees and the coevolutionary history of bees and angiosperms requires a well supported phylogeny of bees (as well as angiosperms). We reconstructed a robust phylogeny of bees at the family and subfamily levels using a data set of five genes (4,299 nucleotide sites) plus morphology (109 characters). The molecular data set included protein coding (elongation factor-1alpha, RNA polymerase II, and LW rhodopsin), as well as ribosomal (28S and 18S) nuclear gene data. Analyses of both the DNA data set and the DNA+morphology data set by parsimony and Bayesian methods yielded a single well supported family-level tree topology that places Melittidae as a paraphyletic group at the base of the phylogeny of bees. This topology ("Melittidae-LT basal") is significantly better than a previously proposed alternative topology ("Colletidae basal") based both on likelihood and Bayesian methods. Our results have important implications for understanding the early diversification, historical biogeography, host-plant evolution, and fossil record of bees. The earliest branches of bee phylogeny include lineages that are predominantly host-plant specialists, suggesting that host-plant specificity is an ancestral trait in bees. Our results suggest an African origin for bees, because the earliest branches of the tree include predominantly African lineages. These results also help explain the predominance of Melittidae, Apidae, and Megachilidae among the earliest fossil bees.
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Affiliation(s)
- Bryan N Danforth
- Department of Entomology, 3119 Comstock Hall, Cornell University, Ithaca, NY 14853, USA.
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Abstract
Eusocial organisms are characterized by cooperative brood care, generation overlap and reproductive division of labour. Traits associated with eusociality are most developed in ants, termites, paper wasps and corbiculate bees; the fossil record indicates that each of these advanced eusocial taxa evolved in the Late Cretaceous or earlier (greater than 65 Myr ago). Halictid bees also include a large and diverse number of eusocial members, but, in contrast to advanced eusocial taxa, they are characterized by substantial intra- and inter-specific variation in social behaviour, which may be indicative of more recent eusocial evolution. To test this hypothesis, we used over 2400 bp of DNA sequence data gathered from three protein-coding nuclear genes (opsin, wingless and EF-1a) to infer the phylogeny of eusocial halictid lineages and their relatives. Results from relaxed molecular clock dating techniques that utilize a combination of molecular and fossil data indicate that the three independent origins of eusociality in halictid bees occurred within a narrow time frame between approximately 20 and 22 Myr ago. This relatively recent evolution helps to explain the pronounced levels of social variation observed within these bees. The three origins of eusociality appear to be temporally correlated with a period of global warming, suggesting that climate may have had an important role in the evolution and maintenance of eusociality in these bees.
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Affiliation(s)
- Seán G Brady
- Department of Entomology and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
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Rinkevich FD, Zhang L, Hamm RL, Brady SG, Lazzaro BP, Scott JG. Frequencies of the pyrethroid resistance alleles of Vssc1 and CYP6D1 in house flies from the eastern United States. Insect Mol Biol 2006; 15:157-67. [PMID: 16640726 DOI: 10.1111/j.1365-2583.2006.00620.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
House flies were collected from four dairies in Maine, New York, North Carolina, and Florida, where high levels of resistance to permethrin have been documented. Regions of two genes, CYP6D1 and Vssc1, having alleles that confer resistance to permethrin (and other pyrethroids) were analysed from individuals at each collection site. The combinations of resistance alleles for Vssc1 and CYP6D1 were highly variable between each state. The resistance allele CYP6D1v1 was found at a high frequency (0.63-0.91) at all sites. Individuals homozygous susceptible for CYP6D1 were very rare and detected only at the dairy in Maine. In addition to the typical Vssc1 mutation responsible for resistance, kdr (L1014F), we also identified individuals with a L1014H mutation. Although house flies homozygous for the L1014H mutation had a lower level of resistance to permethrin, compared to L1014F, the H1014 resistance allele was frequently detected. No individuals with the super-kdr allele (M918T + L1014F) were detected from the field collections. The intron 3 bp downstream of the kdr mutation was found to be extremely variable, providing an opportunity to reconstruct a phylogeny of Vssc1 alleles. Based on this analysis it appears the kdr-his mutation had multiple evolutionary origins, but that the kdr mutation may have had a single origin. The impacts of these findings on resistance management are discussed.
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Affiliation(s)
- F D Rinkevich
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York 14853-0901, USA
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Abstract
We analyzed the higher level phylogeny of the bee family Halictidae based on the coding regions of three single-copy nuclear genes (long-wavelength [LW] opsin, wingless, and elongation factor 1-alpha [EF-1 alpha]). Our combined data set consisted of 2,234 aligned nucleotide sites (702 base pairs [bp] for LW opsin, 405 bp for wingless, and 1,127 bp for EF-1 alpha) and 779 parsimony-informative sites. We included 58 species of halictid bees from 33 genera, representing all subfamilies and tribes, and rooted the trees using seven outgroups from other bee families: Colletidae, Andrenidae, Melittidae, and Apidae. We analyzed the separate and combined data sets by a variety of methods, including equal weights parsimony, maximum likelihood, and Bayesian methods. Analysis of the combined data set produced a strong phylogenetic signal with high bootstrap and Bremer support and high posterior probability well into the base of the tree. The phylogeny recovered the monophyly of the Halictidae and of all four subfamilies and both tribes, recovered relationships among the subfamilies and tribes congruent with morphology, and provided robust support for the relationships among the numerous genera in the tribe Halictini, sensu Michener (2000). Using our combined nucleotide data set, several recently described halictid fossils from the Oligocene and Eocene, and recently developed Bayesian methods, we estimated the antiquity of major clades within the family. Our results indicate that each of the four subfamilies arose well before the Cretaceous-Tertiary boundary and suggest that the early radiation of halictid bees involved substantial African-South American interchange roughly coincident with the separation of these two continents in the late Cretaceous. This combination of single-copy nuclear genes is capable of recovering Cretaceous-age divergences in bees with high levels of support. We propose that LW opsin, wingless, and EF-1 alpha(F2 copy) may be useful in resolving relationships among bee families and other Cretaceous-age insect lineages.
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Affiliation(s)
- Bryan N Danforth
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York 14853, USA.
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Abstract
We discovered the presence of a unique spliceosomal intron in the F1 copy of elongation factor-1alpha (EF-1alpha) restricted to the bee family Colletidae (Hymenoptera: Apoidae). The intron ranges in size from 101 to 1044 bp and shows no positional sliding. Our data also demonstrate the complete absence of this intron from exemplars representing all other bee families, as well as from close hymenopteran relatives. A review of the literature finds that this intron is likewise absent from all other arthropods for which data are available. This provides unambiguous evidence for a relatively recent intron insertion event in the colletid common ancestor and, at least in this specific instance, lends support to the introns-late hypothesis. The comparative distribution of this novel intron also supports the monophyly of Colletidae and the exclusion of the Stenotritidae from this family, providing an example of the potential of some introns to act as robust markers of shared descent.
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Affiliation(s)
- Seán G Brady
- Department of Entomology, Cornell University, Ithaca, New York, USA.
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Brady SG. Evolution of the army ant syndrome: the origin and long-term evolutionary stasis of a complex of behavioral and reproductive adaptations. Proc Natl Acad Sci U S A 2003; 100:6575-9. [PMID: 12750466 PMCID: PMC164488 DOI: 10.1073/pnas.1137809100] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2002] [Indexed: 11/18/2022] Open
Abstract
The army ant syndrome of behavioral and reproductive traits (obligate collective foraging, nomadism, and highly specialized queens) has allowed these organisms to become the premiere social hunters of the tropics, yet we know little about how or why these strategies evolved. The currently accepted view holds that army ants evolved multiple times on separate continents. I generated data from three nuclear genes, a mitochondrial gene, and morphology to test this hypothesis. Results strongly indicate that the suite of behavioral and reproductive adaptations found in army ants throughout the world is inherited from a unique common ancestor, and did not evolve convergently in the New World and Old World as previously thought. New Bayesian methodology for dating the antiquity of lineages by using a combination of fossil and molecular information places the origin of army ants in the mid-Cretaceous, consistent with a Gondwanan origin. Because no known army ant species lacks any component of the army ant syndrome, this group represents an extraordinary case of long-term evolutionary stasis in these adaptations.
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Affiliation(s)
- Seán G Brady
- Center for Population Biology and Department of Entomology, University of California, Davis 95616, USA.
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Abstract
We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.
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Abstract
We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.
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Abstract
The accuracy of phylogenetic inference was examined in simulated data sets up to nearly 10,000 taxa, the size of the largest set of homologous genes in existing molecular sequence databases. Even with a simple search algorithm (maximum parsimony without branch swapping), the number of characters needed to estimate 80% of a tree correctly can scale remarkably well at optimal substitution rates (on the order of log N, where N is the number of taxa). In other words, the number of taxa in an analysis can be doubled and only an arithmetic increase in the number of characters is required to maintain the same level of accuracy. Even substitution rates that are much higher than normally used in phylogenetic studies did not affect the scaling too adversely. However, scaling is usually worse than log N for more stringent levels of accuracy. Moreover, errors are not distributed randomly throughout the tree. Shallow nodes are remarkably easy to reconstruct and display favourable log-linear scaling. The deepest nodes are extremely difficult to reconstruct accurately, even with branch swapping, and the scaling is poor. Therefore, the strategy of sequencing large numbers of homologous genes may not always provide global solutions to extreme phylogenetic problems and alternative strategies may be required.
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Affiliation(s)
- O R Bininda-Emonds
- Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
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Sanderson MJ, Wojciechowski MF, Hu JM, Khan TS, Brady SG. Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants. Mol Biol Evol 2000; 17:782-97. [PMID: 10779539 DOI: 10.1093/oxfordjournals.molbev.a026357] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern "anthophyte hypothesis," which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups.
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Affiliation(s)
- M J Sanderson
- Section of Evolution and Ecology, University of California at Davis, 95616, USA.
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