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Henríquez-Piskulich P, Hugall AF, Stuart-Fox D. A supermatrix phylogeny of the world's bees (Hymenoptera: Anthophila). Mol Phylogenet Evol 2024; 190:107963. [PMID: 37967640 DOI: 10.1016/j.ympev.2023.107963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
The increasing availability of large molecular phylogenies has provided new opportunities to study the evolution of species traits, their origins and diversification, and biogeography; yet there are limited attempts to synthesise existing phylogenetic information for major insect groups. Bees (Hymenoptera: Anthophila) are a large group of insect pollinators that have a worldwide distribution, and a wide variation in ecology, morphology, and life-history traits, including sociality. For these reasons, as well as their major economic importance as pollinators, numerous molecular phylogenetic studies of family and genus-level relationships have been published, providing an opportunity to assemble a bee 'tree-of-life'. We used publicly available genetic sequence data, including phylogenomic data, reconciled to a taxonomic database, to produce a concatenated supermatrix phylogeny for the Anthophila comprising 4,586 bee species, representing 23% of species and 82% of genera. At family, subfamily, and tribe levels, support for expected relationships was robust, but between and within some genera relationships remain uncertain. Within families, sampling of genera ranged from 67 to 100% but species coverage was lower (17-41%). Our phylogeny mostly reproduces the relationships found in recent phylogenomic studies with a few exceptions. We provide a summary of these differences and the current state of molecular data available and its gaps. We discuss the advantages and limitations of this bee supermatrix phylogeny (available online at beetreeoflife.org), which may enable new insights into long standing questions about evolutionary drivers in bees, and potentially insects more generally.
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Affiliation(s)
| | - Andrew F Hugall
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia; Department of Sciences, Museums Victoria, Melbourne, Victoria, Australia.
| | - Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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2
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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: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [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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3
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Alajmi R, Haddadi R, Abdel-Gaber R, Alkuriji M. Molecular phylogeny of Monomorium pharaonis (Hymenoptera: Formicidae) based on rRNA sequences of mitochondrial gene. J Genet 2020. [DOI: 10.1007/s12041-020-1186-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Comparative mitogenomics of Hymenoptera reveals evolutionary differences in structure and composition. Int J Biol Macromol 2020; 144:460-472. [DOI: 10.1016/j.ijbiomac.2019.12.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/06/2019] [Accepted: 12/15/2019] [Indexed: 01/26/2023]
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Tang P, Zhu JC, Zheng BY, Wei SJ, Sharkey M, Chen XX, Vogler AP. Mitochondrial phylogenomics of the Hymenoptera. Mol Phylogenet Evol 2019; 131:8-18. [DOI: 10.1016/j.ympev.2018.10.040] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/02/2018] [Accepted: 10/30/2018] [Indexed: 11/16/2022]
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6
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Niu G, Korkmaz EM, Doğan Ö, Zhang Y, Aydemir MN, Budak M, Du S, Başıbüyük HH, Wei M. The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference. Int J Biol Macromol 2018; 124:185-199. [PMID: 30448489 DOI: 10.1016/j.ijbiomac.2018.11.129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/30/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
The Pamphilioidea represents a small superfamily of the phytophagous suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genomes (mitogenomes) of three pamphilioid species: Chinolyda flagellicornis (Pamphiliidae), Megalodontes spiraeae and M. cephalotes (Megalodontesidae) were newly sequenced using next generation sequencing and comparatively analysed with the previously reported symphytan mitogenomes. A positive AT skew (0.013) and a negative GC skew (-0.194) were found in pamphilioid mitogenome, and a deviation from strand asymmetry was also observed in the PCGs encoded on both strands. Several gene rearrangement events were observed in four tRNA gene clusters (WCY, IQM, ARNS1EF and TP clusters), which have not been reported from symphytan mitogenomes to date. As the most parsimonious explanation, compared with the inferred insect ancestral mitogenome architecture, the occurrence of gene rearrangements in pamphilioid mitogenomes requires totally five evolutionary steps, including four transpositions and one inversion. The predicted secondary structures of tRNAs, rrnS and rrnL genes are mostly consistent with reported hymenopteran species. Phylogenetic analyses recovered the monophyly of superfamily Pamphilioidea and indicated the relationship Tenthredinoidea + (Pamphilioidea + (Cephoidea + (Orussoidea + Apocrita))) with strong nodal supports.
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Affiliation(s)
- Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang 330022, PR China
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey.
| | - Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Yaoyao Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, PR China
| | - Merve Nur Aydemir
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Shiyu Du
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, PR China
| | | | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang 330022, PR China
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Molecular Phylogeny, Diversity and Zoogeography of Net-Winged Beetles (Coleoptera: Lycidae). INSECTS 2018; 9:insects9040154. [PMID: 30388727 PMCID: PMC6315567 DOI: 10.3390/insects9040154] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/18/2018] [Accepted: 10/28/2018] [Indexed: 01/23/2023]
Abstract
We synthesize the evidence from molecular phylogenetics, extant distribution, and plate tectonics to present an insight in ancestral areas, dispersal routes and the effectiveness of geographic barriers for net-winged beetle tribes (Coleoptera: Lycidae). Samples from all zoogeographical realms were assembled and phylogenetic relationships for ~550 species and 25 tribes were inferred using nuclear rRNA and mtDNA markers. The analyses revealed well-supported clades at the rank of tribes as they have been defined using morphology, but a low support for relationships among them. Most tribes started their diversification in Southeast and East Asia or are endemic to this region. Slipinskiini and Dexorini are Afrotropical endemics and Calopterini, Eurrhacini, Thonalmini, and Leptolycini remained isolated in South America and the Caribbean after their separation from northern continents. Lycini, Calochromini, and Erotini support relationships between the Nearctic and eastern Palearctic faunas; Calochromini colonized the Afrotropical realm from East Asia and Metriorrhynchini Afrotropical and Oriental realms from the drifting Indian subcontinent. Most tribes occur in the Oriental and Sino-Japanese realms, the highest alpha-taxonomic diversity was identified in Malesian tropical rainforests. The turn-over at zoogeographical boundaries is discussed when only short distance over-sea colonization events were inferred. The lycid phylogeny shows that poor dispersers can be used for reconstruction of dispersal and vicariance history over a long time-span, but the current data are insufficient for reconstruction of the early phase of their diversification.
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Linard B, Crampton-Platt A, Moriniere J, Timmermans MJ, Andújar C, Arribas P, Miller KE, Lipecki J, Favreau E, Hunter A, Gómez-Rodríguez C, Barton C, Nie R, Gillett CP, Breeschoten T, Bocak L, Vogler AP. The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera. Mol Phylogenet Evol 2018; 128:1-11. [DOI: 10.1016/j.ympev.2018.07.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 03/09/2018] [Indexed: 12/16/2022]
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Mikó I, van de Kamp T, Trietsch C, Ulmer JM, Zuber M, Baumbach T, Deans AR. A new megaspilid wasp from Eocene Baltic amber (Hymenoptera: Ceraphronoidea), with notes on two non-ceraphronoid families: Radiophronidae and Stigmaphronidae. PeerJ 2018; 6:e5174. [PMID: 30140594 PMCID: PMC6103384 DOI: 10.7717/peerj.5174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/14/2018] [Indexed: 11/24/2022] Open
Abstract
Ceraphronoids are some of the most commonly collected hymenopterans, yet they remain rare in the fossil record. Conostigmus talamasi Mikó and Trietsch, sp. nov. from Baltic amber represents an intermediate form between the type genus, Megaspilus, and one of the most species-rich megaspilid genera, Conostigmus. We describe the new species using 3D data collected with synchrotron-based micro-CT equipment. This non-invasive technique allows for quick data collection in unusually high resolution, revealing morphological traits that are otherwise obscured by the amber. In describing this new species, we revise the diagnostic characters for Ceraphronoidea and discuss possible reasons why minute wasps with a pterostigma are often misidentified as ceraphronoids. Based on the lack of ceraphronoid characteristics, we remove Dendrocerus dubitatus Brues, 1937, Stigmaphronidae, and Radiophronidae from Ceraphronoidea and consider them as incertae sedis. We also provide some guidance for their future classification.
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Affiliation(s)
- István Mikó
- Frost Entomological Museum, Department of Entomology, Pennsylvania State University, University Park, PA, United States of America
| | - Thomas van de Kamp
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Carolyn Trietsch
- Frost Entomological Museum, Department of Entomology, Pennsylvania State University, University Park, PA, United States of America
| | - Jonah M. Ulmer
- Frost Entomological Museum, Department of Entomology, Pennsylvania State University, University Park, PA, United States of America
| | - Marcus Zuber
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tilo Baumbach
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Andrew R. Deans
- Frost Entomological Museum, Department of Entomology, Pennsylvania State University, University Park, PA, United States of America
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10
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Tvedte ES, Forbes AA, Logsdon JM. Retention of Core Meiotic Genes Across Diverse Hymenoptera. J Hered 2018; 108:791-806. [PMID: 28992199 DOI: 10.1093/jhered/esx062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
The cellular mechanisms of meiosis are critical for proper gamete formation in sexual organisms. Functional studies in model organisms have identified genes essential for meiosis, yet the extent to which this core meiotic machinery is conserved across non-model systems is not fully understood. Moreover, it is unclear whether deviation from canonical modes of sexual reproduction is accompanied by modifications in the genetic components involved in meiosis. We used a robust approach to identify and catalogue meiosis genes in Hymenoptera, an insect order typically characterized by haplodiploid reproduction. Using newly available genome data, we searched for 43 genes involved in meiosis in 18 diverse hymenopterans. Seven of eight genes with roles specific to meiosis were found across a majority of surveyed species, suggesting the preservation of core meiotic machinery in haplodiploid hymenopterans. Phylogenomic analyses of the inventory of meiosis genes and the identification of shared gene duplications and losses provided support for the grouping of species within Proctotrupomorpha, Ichneumonomorpha, and Aculeata clades, along with a paraphyletic Symphyta. The conservation of meiosis genes across Hymenoptera provides a framework for studying transitions between reproductive modes in this insect group.
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Affiliation(s)
- Eric S Tvedte
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA 52242
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11
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Chesters D. Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling. Syst Biol 2018; 66:426-439. [PMID: 27798407 DOI: 10.1093/sysbio/syw099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.].
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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12
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Peters RS, Krogmann L, Mayer C, Donath A, Gunkel S, Meusemann K, Kozlov A, Podsiadlowski L, Petersen M, Lanfear R, Diez PA, Heraty J, Kjer KM, Klopfstein S, Meier R, Polidori C, Schmitt T, Liu S, Zhou X, Wappler T, Rust J, Misof B, Niehuis O. Evolutionary History of the Hymenoptera. Curr Biol 2017; 27:1013-1018. [DOI: 10.1016/j.cub.2017.01.027] [Citation(s) in RCA: 340] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/13/2016] [Accepted: 01/16/2017] [Indexed: 10/24/2022]
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13
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Zhou X, Frandsen PB, Holzenthal RW, Beet CR, Bennett KR, Blahnik RJ, Bonada N, Cartwright D, Chuluunbat S, Cocks GV, Collins GE, deWaard J, Dean J, Flint OS, Hausmann A, Hendrich L, Hess M, Hogg ID, Kondratieff BC, Malicky H, Milton MA, Morinière J, Morse JC, Mwangi FN, Pauls SU, Gonzalez MR, Rinne A, Robinson JL, Salokannel J, Shackleton M, Smith B, Stamatakis A, StClair R, Thomas JA, Zamora-Muñoz C, Ziesmann T, Kjer KM. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160025. [PMID: 27481793 PMCID: PMC4971193 DOI: 10.1098/rstb.2016.0025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2016] [Indexed: 12/15/2022] Open
Abstract
DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Paul B Frandsen
- Office of Research Information Services, Office of the Chief Information Officer, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Ralph W Holzenthal
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Clare R Beet
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Kristi R Bennett
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Roger J Blahnik
- Department of Entomology, University of Minnesota, 1980 Folwell Avenue, St Paul, MN 55108, USA
| | - Núria Bonada
- Grup de Recerca Freshwater Ecology and Management (FEM), Departament d'Ecologia, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal, 643, 08028 Barcelona, Catalonia, Spain
| | | | - Suvdtsetseg Chuluunbat
- Department of Biology, Mongolian National University of Education, 3rd Palace, Beijing Street, Ulaanbaatar 14191, Mongolia
| | - Graeme V Cocks
- 44 Marks Street, Hermit Park, Queensland 4812, Australia
| | - Gemma E Collins
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Jeremy deWaard
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - John Dean
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Oliver S Flint
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Axel Hausmann
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Lars Hendrich
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - Monika Hess
- Büro H2-Ökologische Gutachten, Hess+Heckes GbR, Rumfordstraße 42, 80469 München, Germany
| | - Ian D Hogg
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Boris C Kondratieff
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523, USA
| | - Hans Malicky
- Biologische Station Lunz, Austrian Academy of Sciences, A-3293 Lunz am see, Austria
| | - Megan A Milton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Jérôme Morinière
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
| | - John C Morse
- Department of Plant and Environmental Sciences, Clemson University, PO Box 340310, Clemson, SC 29634-0310, USA
| | | | - Steffen U Pauls
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - María Razo Gonzalez
- Unidad Multidisciplinaria de Docencia e Investigación, Universidad Nacional Autónoma de Mexcio, Facultad de Ciencias, Campus Juriquilla, Querétaro, 76230, México
| | - Aki Rinne
- Finnish Environment Institute, Merikasarminkatu 8 D, 00160 Helsinki, Finland
| | - Jason L Robinson
- Illinois Natural History Survey, Prairie Research Institute at the University of Illinois at Urbana-Champaign, 1816 S. Oak Street, MC 652, Champaign, IL 61820, USA
| | - Juha Salokannel
- Aquatic Insects Expert Group of Finland, Siikinkatu 13, 33710, Tampere, Finland
| | - Michael Shackleton
- Murray-Darling Freshwater Research Centre, La Trobe University, 133 McKoy Street, Wodonga, Victoria 3691, Australia
| | - Brian Smith
- National Institute of Water and Atmospheric Research, PO Box, 11115, Hamilton 3240, New Zealand
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, 35 D-69118 Heidelberg, Germany
| | - Ros StClair
- Environment Protection Authority Victoria, Ernest Jones Drive, Macleod 3085, Australia
| | - Jessica A Thomas
- BioArch, Environment Building, Department of Biology, University of York, York, YO10 5DD, UK
| | - Carmen Zamora-Muñoz
- Department of Zoology, Faculty of Sciences, University of Granada, C/Severo Ochoa s/n, 18071 Granada, Spain
| | - Tanja Ziesmann
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum fu¨r Molekulare Biodiversitätsforschung (ZMB), Bonn 5 76131 Karlsruhe, Germany
| | - Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
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Kjer KM, Simon C, Yavorskaya M, Beutel RG. Progress, pitfalls and parallel universes: a history of insect phylogenetics. J R Soc Interface 2016; 13:20160363. [PMID: 27558853 PMCID: PMC5014063 DOI: 10.1098/rsif.2016.0363] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.
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Affiliation(s)
- Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Margarita Yavorskaya
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
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15
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Ogutcen E, Vamosi JC. A phylogenetic study of the tribe Antirrhineae: Genome duplications and long-distance dispersals from the Old World to the New World. AMERICAN JOURNAL OF BOTANY 2016; 103:1071-81. [PMID: 27283021 DOI: 10.3732/ajb.1500464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/14/2016] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Antirrhineae is a large tribe within Plantaginaceae. Mostly concentrated in the Mediterranean Basin, the tribe members are present both in the Old World and the New World. Current Antirrhineae phylogenies have different views on taxonomic relationships, and they lack homogeneity in terms of geographic distribution and ploidy levels. This study aims to investigate the changes in the chromosome numbers along with dispersal routes as definitive characters identifying clades. METHODS With the use of multiple DNA regions and taxon sampling enriched with de novo sequences, we provide an extensive phylogeny for Antirrhineae. The reconstructed phylogeny was then used to investigate changes in ploidy levels and dispersal patterns in the tribe using ChromEvol and RASP, respectively. KEY RESULTS Antirrhineae is a monophyletic group with six highly supported clades. ChromEvol analysis suggests the ancestral haploid chromosome number for the tribe is six, and that the tribe has experienced several duplications and gain events. The Mediterranean Basin was estimated to be the origin for the tribe with four long-distance dispersals from the Old World to the New World, three of which were associated with genome duplications. CONCLUSIONS On an updated Antirrhineae phylogeny, we showed that the three out of four dispersals from the Old World to the New World were coupled with changes in ploidy levels. The observed patterns suggest that increases in ploidy levels may facilitate dispersing into new environments.
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Affiliation(s)
- Ezgi Ogutcen
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
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16
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Chernomor O, Minh BQ, von Haeseler A. Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference. J Comput Biol 2015; 22:1129-42. [PMID: 26448206 PMCID: PMC4663649 DOI: 10.1089/cmb.2015.0146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.
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Affiliation(s)
- Olga Chernomor
- 1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria .,2 Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna , Vienna, Austria
| | - Bui Quang Minh
- 1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria
| | - Arndt von Haeseler
- 1 Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna , Vienna, Austria .,2 Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna , Vienna, Austria
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17
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Evolution of Cuticular Hydrocarbons in the Hymenoptera: a Meta-Analysis. J Chem Ecol 2015; 41:871-83. [PMID: 26410609 PMCID: PMC4619461 DOI: 10.1007/s10886-015-0631-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/30/2015] [Accepted: 09/01/2015] [Indexed: 12/21/2022]
Abstract
Chemical communication is the oldest form of communication, spreading across all forms of life. In insects, cuticular hydrocarbons (CHC) function as chemical cues for the recognition of mates, species, and nest-mates in social insects. Although much is known about the function of individual hydrocarbons and their biosynthesis, a phylogenetic overview is lacking. Here, we review the CHC profiles of 241 species of Hymenoptera, one of the largest and most important insect orders, which includes the Symphyta (sawflies), the polyphyletic Parasitica (parasitoid wasps), and the Aculeata (wasps, bees, and ants). We investigated whether these taxonomic groups differed in the presence and absence of CHC classes and whether the sociality of a species (solitarily vs. social) had an effect on CHC profile complexity. We found that the main CHC classes (i.e., n-alkanes, alkenes, and methylalkanes) were all present early in the evolutionary history of the Hymenoptera, as evidenced by their presence in ancient Symphyta and primitive Parasitica wasps. Throughout all groups within the Hymenoptera, the more complex a CHC the fewer species that produce it, which may reflect the Occam’s razor principle that insects’ only biosynthesize the most simple compound that fulfil its needs. Surprisingly, there was no difference in the complexity of CHC profiles between social and solitary species, with some of the most complex CHC profiles belonging to the Parasitica. This profile complexity has been maintained in the ants, but some specialization in biosynthetic pathways has led to a simplification of profiles in the aculeate wasps and bees. The absence of CHC classes in some taxa or species may be due to gene silencing or down-regulation rather than gene loss, as demonstrated by sister species having highly divergent CHC profiles, and cannot be predicted by their phylogenetic history. The presence of highly complex CHC profiles prior to the vast radiation of the social Hymenoptera indicates a ‘spring-loaded’ system where the diversity of CHC needed for the complex communication systems of social insects were already present for natural selection to act upon, rather than having evolved independently. This diversity may have aided the multiple independent evolution of sociality within the Aculeata.
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18
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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] [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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19
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Chesters D, Zheng W, Zhu C. A
DNA
Barcoding system integrating multigene sequence data. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution (CAS) Institute of Zoology Chinese Academy of Sciences Beijing 100101 China
| | - Wei‐Min Zheng
- Institute of Information Engineering Chinese Academy of Sciences Beijing 100093 China
| | - Chao‐Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution (CAS) Institute of Zoology Chinese Academy of Sciences Beijing 100101 China
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20
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McMahon MM, Deepak A, Fernández-Baca D, Boss D, Sanderson MJ. STBase: one million species trees for comparative biology. PLoS One 2015; 10:e0117987. [PMID: 25679219 PMCID: PMC4332655 DOI: 10.1371/journal.pone.0117987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/05/2015] [Indexed: 11/29/2022] Open
Abstract
Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user's query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees.
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Affiliation(s)
- Michelle M. McMahon
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Akshay Deepak
- Department of Computer Science, Iowa State University, Ames, IA, 50011, United States of America
| | - David Fernández-Baca
- Department of Computer Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Darren Boss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Michael J. Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, United States of America
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21
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Mao M, Gibson T, Dowton M. Higher-level phylogeny of the Hymenoptera inferred from mitochondrial genomes. Mol Phylogenet Evol 2014; 84:34-43. [PMID: 25542648 DOI: 10.1016/j.ympev.2014.12.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/27/2014] [Accepted: 12/16/2014] [Indexed: 11/25/2022]
Abstract
Higher-level hymenopteran relationships remain unresolved in both morphological and molecular analyses. In this study, we present the most comprehensive analyses of hymenopteran relationships based on 48 mitochondrial (mt) genomes. One complete and two nearly complete mt genomes representing three hymenopteran superfamilies were newly sequenced. We assessed the influence of inclusion/exclusion of 3rd codon positions, alignment approaches, partition schemes and phylogenetic approaches on topology and nodal support within the Hymenoptera. The results showed that the topologies were sensitive to the variation of dataset and analytical approach. However, some robust and highly supported relationships were recovered: the Ichneumonomorpha was monophyletic; the Trigonalyoidea+Megalyroidea and the Diaprioidea+Chalcidoidea were consistently recovered; the Cynipoidea was generally recovered as the sister group to the Diaprioidea+Chalcidoidea. In addition, the monophyletic Aculeata and Proctotrupomorpha were recovered in some analyses. Several gene rearrangements were detected in each of the three newly sequenced mt genomes. Specifically, the Ibalia leucospoides mt genome harbors a large inversion of a gene block from trnE to trnS2. Inverted, duplicated A+T rich regions were detected in the Ibalia leucospoides mt genome, which probably played an important role during the formation of the large gene block inversion via recombination.
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Affiliation(s)
- Meng Mao
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia.
| | - Tracey Gibson
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Mark Dowton
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
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22
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Babbucci M, Basso A, Scupola A, Patarnello T, Negrisolo E. Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and Lepidoptera. Genome Biol Evol 2014; 6:3326-43. [PMID: 25480682 PMCID: PMC4466343 DOI: 10.1093/gbe/evu265] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2014] [Indexed: 11/18/2022] Open
Abstract
Insect mitochondrial genomes (mtDNA) are usually double helical and circular molecules containing 37 genes that are encoded on both strands. The arrangement of the genes is not constant for all species, and produces distinct gene orders (GOs) that have proven to be diagnostic in defining clades at different taxonomic levels. In general, it is believed that distinct taxa have a very low chance of sharing identically arranged GOs. However, examples of identical, homoplastic local rearrangements occurring in distinct taxa do exist. In this study, we sequenced the complete mtDNAs of the ants Formica fusca and Myrmica scabrinodis (Formicidae, Hymenoptera) and compared their GOs with those of other Insecta. The GO of F. fusca was found to be identical to the GO of Dytrisia (the largest clade of Lepidoptera). This finding is the first documented case of an identical GO shared by distinct groups of Insecta, and it is the oldest known event of GO convergent evolution in animals. Both Hymenoptera and Lepidoptera acquired this GO early in their evolution. Using a phylogenetic approach combined with new bioinformatic tools, the chronological order of the evolutionary events that produced the diversity of the hymenopteran GOs was determined. Additionally, new local homoplastic rearrangements shared by distinct groups of insects were identified. Our study showed that local and global homoplasies affecting the insect GOs are more widespread than previously thought. Homoplastic GOs can still be useful for characterizing the various clades, provided that they are appropriately considered in a phylogenetic and taxonomic context.
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Affiliation(s)
- Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy Department of Agronomy, Food, Natural Resources, Animal and Environment (DAFNE), University of Padova, Agripolis, Legnaro (PD), Italy Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Antonio Scupola
- Natural History Museum (Museo di Storia Naturale), Verona, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
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23
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Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches. Mol Phylogenet Evol 2014; 78:334-48. [DOI: 10.1016/j.ympev.2014.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/30/2014] [Accepted: 06/01/2014] [Indexed: 11/17/2022]
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24
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Mao M, Gibson T, Dowton M. Evolutionary dynamics of the mitochondrial genome in the evaniomorpha (hymenoptera)—a group with an intermediate rate of gene rearrangement. Genome Biol Evol 2014; 6:1862-74. [PMID: 25115010 PMCID: PMC4122943 DOI: 10.1093/gbe/evu145] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2014] [Indexed: 11/30/2022] Open
Abstract
We determined the complete mitochondrial (mt) genomes of three evaniomorph species, Ceraphron sp. (Ceraphronoidea), Gasteruption sp. (Evanioidea), and Orthogonalys pulchella (Trigonalyoidea) as well as the nearly complete mt genome from another evaniomorph species, Megalyra sp. (Megalyroidea). Each of them possesses dramatic gene rearrangements, including protein-coding or rRNA genes. Gene inversions were identified in all of these mt genomes; for example, the two rRNA genes have inverted and moved into the nad2-cox1 junction in the Megalyra sp. mt genome. In addition, we found two copies of a 10-bp complementary repeat at the beginning of rrnS and at the end of trnL(2) in the Gasteruption sp. mt genome, consistent with recombination as the possible mechanism for gene inversion and long-range movement. Although each of the genomes contains a number of repeats of varying size, there was no consistent association of the size or number of repeats with the extent or type of gene rearrangement. The breakpoint distance analysis showed the Evaniomorpha has an intermediate rate of gene rearrangement. Sequence-based phylogenetic analyses of 13 protein-coding and 2 rRNA genes in 22 hymenopteran taxa recovered a paraphyletic Evaniomorpha with the Aculeata nested within it. Within the Evaniomorpha, our analyses confirmed the Trigonalyoidea + Megalyroidea as the sister group to the Aculeata and recovered a novel clade, Ceraphronoidea + Evanioidea. In contrast to previous hymenopteran phylogenetic studies, the internal relationships of the Evaniomorpha were highly supported and robust to the variation of alignment approach and phylogenetic inference approach.
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Affiliation(s)
- Meng Mao
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, New South Wales, Australia
| | - Tracey Gibson
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, New South Wales, Australia
| | - Mark Dowton
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, New South Wales, Australia
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25
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Chesters D, Zhu CD. A protocol for species delineation of public DNA databases, applied to the Insecta. Syst Biol 2014; 63:712-25. [PMID: 24929897 DOI: 10.1093/sysbio/syu038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Public DNA databases are composed of data from many different taxa, although the taxonomic annotation on sequences is not always complete, which impedes the utilization of mined data for species-level applications. There is much ongoing work on species identification and delineation based on the molecular data itself, although applying species clustering to whole databases requires consolidation of results from numerous undefined gene regions, and introduces significant obstacles in data organization and computational load. In the current paper, we demonstrate an approach for species delineation of a sequence database. All DNA sequences for the insects were obtained and processed. After filtration of duplicated data, delineation of the database into species or molecular operational taxonomic units (MOTUs) followed a three-step process in which (i) the genetic loci L are partitioned, (ii) the species S are delineated within each locus, then (iii) species units are matched across loci to form the matrix L × S, a set of global (multilocus) species units. Partitioning the database into a set of homologous gene fragments was achieved by Markov clustering using edge weights calculated from the amount of overlap between pairs of sequences, then delineation of species units and assignment of species names were performed for the set of genes necessary to capture most of the species diversity. The complexity of computing pairwise similarities for species clustering was substantial at the cytochrome oxidase subunit I locus in particular, but made feasible through the development of software that performs pairwise alignments within the taxonomic framework, while accounting for the different ranks at which sequences are labeled with taxonomic information. Over 24 different homologs, the unidentified sequences numbered approximately 194,000, containing 41,525 species IDs (98.7% of all found in the insect database), and were grouped into 59,173 single-locus MOTUs by hierarchical clustering under parameters optimized independently for each locus. Species units from different loci were matched using a multipartite matching algorithm to form multilocus species units with minimal incongruence between loci. After matching, the insect database as represented by these 24 loci was found to be composed of 78,091 species units in total. 38,574 of these units contained only species labeled data, 34,891 contained only unlabeled data, leaving 4,626 units composed both of labeled and unlabeled sequences. In addition to giving estimates of species diversity of sequence repositories, the protocol developed here will facilitate species-level applications of modern-day sequence data sets. In particular, the L × S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity.
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution (CAS), Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
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26
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Simmons MP. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Mol Phylogenet Evol 2014; 74:1-14. [DOI: 10.1016/j.ympev.2014.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 11/16/2022]
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27
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Grant JR, Katz LA. Building a phylogenomic pipeline for the eukaryotic tree of life - addressing deep phylogenies with genome-scale data. PLOS CURRENTS 2014; 6. [PMID: 24707447 PMCID: PMC3973741 DOI: 10.1371/currents.tol.c24b6054aebf3602748ac042ccc8f2e9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Background
Understanding the evolutionary relationships of all eukaryotes on Earth remains a paramount goal of modern biology, yet analyzing homologous sequences across 1.8 billion years of eukaryotic evolution is challenging. Many existing tools for identifying gene orthologs are inadequate when working with heterogeneous rates of evolution and endosymbiotic/lateral gene transfer. Moreover, genomic-scale sequencing, which was once the domain of large sequencing centers, has advanced to the point where small laboratories can now generate the data needed for phylogenomic studies. This has opened the door for increased taxonomic sampling as individual research groups have the ability to conduct genome-scale projects on their favorite non-model organism.
Results
Here we present some of the tools developed, and insights gained, as we created a pipeline that combines data-mining from public databases and our own transcriptome data to study the eukaryotic tree of life. The first steps of a phylogenomic pipeline involve choosing taxa and loci, and making decisions about how to handle alleles, paralogs and non-overlapping sequences. Next, orthologs are aligned for analyses including gene tree reconstruction and concatenation for supermatrix approaches. To build our pipeline, we created scripts written in Python that integrate third-party tools with custom methods. As a test case, we present the placement of five amoebae on the eukaryotic tree of life based on analyses of transcriptome data. Our scripts available on GitHUb and may be used as-is for automated analyses of large scale phylogenomics, or adapted for use in other types of studies.
Conclusion
Analyses on the scale of all eukaryotes present challenges not necessarily found in studies of more closely related organisms. Our approach will be of relevance to others for whom existing third-party tools fail to fully answer desired phylogenetic questions.
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Affiliation(s)
- Jessica R Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
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28
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Van Oystaeyen A, Oliveira RC, Holman L, van Zweden JS, Romero C, Oi CA, d'Ettorre P, Khalesi M, Billen J, Wäckers F, Millar JG, Wenseleers T. Conserved class of queen pheromones stops social insect workers from reproducing. Science 2014; 343:287-90. [PMID: 24436417 DOI: 10.1126/science.1244899] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A major evolutionary transition to eusociality with reproductive division of labor between queens and workers has arisen independently at least 10 times in the ants, bees, and wasps. Pheromones produced by queens are thought to play a key role in regulating this complex social system, but their evolutionary history remains unknown. Here, we identify the first sterility-inducing queen pheromones in a wasp, bumblebee, and desert ant and synthesize existing data on compounds that characterize female fecundity in 64 species of social insects. Our results show that queen pheromones are strikingly conserved across at least three independent origins of eusociality, with wasps, ants, and some bees all appearing to use nonvolatile, saturated hydrocarbons to advertise fecundity and/or suppress worker reproduction. These results suggest that queen pheromones evolved from conserved signals of solitary ancestors.
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Affiliation(s)
- Annette Van Oystaeyen
- Laboratory of Socioecology and Social Evolution, Zoological Institute, University of Leuven, Naamsestraat 59-Box 2466, 3000 Leuven, Belgium
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Malm T, Nyman T. Phylogeny of the symphytan grade of Hymenoptera: new pieces into the old jigsaw(fly) puzzle. Cladistics 2014; 31:1-17. [DOI: 10.1111/cla.12069] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
- Tobias Malm
- Department of Biology; University of Eastern Finland; PO Box 111 Joensuu FI-80101 Finland
- Department of Biology; Laboratory of Genetics; University of Turku; Turku FI-20014 Finland
| | - Tommi Nyman
- Department of Biology; University of Eastern Finland; PO Box 111 Joensuu FI-80101 Finland
- Institute for Systematic Botany; University of Zurich; Zollikerstrasse 107 Zurich CH-8008 Switzerland
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Payne A, Barden PM, Wheeler WC, Carpenter JM. Direct Optimization, Sensitivity Analysis, and the Evolution of the Hymenopteran Superfamilies. AMERICAN MUSEUM NOVITATES 2013. [DOI: 10.1206/3789.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters. Mol Phylogenet Evol 2013; 69:265-75. [DOI: 10.1016/j.ympev.2013.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 05/28/2013] [Accepted: 06/01/2013] [Indexed: 11/22/2022]
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Klopfstein S, Vilhelmsen L, Heraty JM, Sharkey M, Ronquist F. The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data. PLoS One 2013; 8:e69344. [PMID: 23936325 PMCID: PMC3732274 DOI: 10.1371/journal.pone.0069344] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
Previous molecular analyses of higher hymenopteran relationships have largely been based on subjectively aligned ribosomal sequences (18S and 28S). Here, we reanalyze the 18S and 28S data (unaligned about 4.4 kb) using an objective and a semi-objective alignment approach, based on MAFFT and BAli-Phy, respectively. Furthermore, we present the first analyses of a substantial protein-coding data set (4.6 kb from one mitochondrial and four nuclear genes). Our results indicate that previous studies may have suffered from inflated support values due to subjective alignment of the ribosomal sequences, but apparently not from significant biases. The protein data provide independent confirmation of several earlier results, including the monophyly of non-xyelid hymenopterans, Pamphilioidea + Unicalcarida, Unicalcarida, Vespina, Apocrita, Proctotrupomorpha and core Proctotrupomorpha. The protein data confirm that Aculeata are nested within a paraphyletic Evaniomorpha, but cast doubt on the monophyly of Evanioidea. Combining the available morphological, ribosomal and protein-coding data, we examine the total-evidence signal as well as congruence and conflict among the three data sources. Despite an emerging consensus on many higher-level hymenopteran relationships, several problems remain unresolved or contentious, including rooting of the hymenopteran tree, relationships of the woodwasps, placement of Stephanoidea and Ceraphronoidea, and the sister group of Aculeata.
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Affiliation(s)
- Seraina Klopfstein
- Department of Biodiversity Informatics, Swedish Museum of Natural History, Stockholm, Sweden.
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33
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Pearse WD, Purvis A. phyloGenerator: an automated phylogeny generation tool for ecologists. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12055] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Andy Purvis
- Department of Life Sciences; Imperial College London; Silwood Park Campus; Ascot; SL5 7PY; UK
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34
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Affiliation(s)
- Martin Kaltenpoth
- Max Planck Institute for Chemical Ecology; Insect Symbiosis Research Group; Hans-Knoell-Str. 8 Jena 07745 Germany
| | - Tobias Engl
- Max Planck Institute for Chemical Ecology; Insect Symbiosis Research Group; Hans-Knoell-Str. 8 Jena 07745 Germany
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35
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Simmons MP, Norton AP. Quantification and relative severity of inflated branch-support values generated by alternative methods: An empirical example. Mol Phylogenet Evol 2013; 67:277-96. [DOI: 10.1016/j.ympev.2013.01.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/18/2013] [Accepted: 01/31/2013] [Indexed: 10/27/2022]
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36
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Chesters D, Vogler AP. Resolving Ambiguity of Species Limits and Concatenation in Multilocus Sequence Data for the Construction of Phylogenetic Supermatrices. Syst Biol 2013; 62:456-66. [DOI: 10.1093/sysbio/syt011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Douglas Chesters
- Department of Entomology, Natural History Museum, London SW7 5BD, UK; 2Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and 3Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Entomology, Natural History Museum, London SW7 5BD, UK; 2Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and 3Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Entomology, Natural History Museum, London SW7 5BD, UK; 2Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and 3Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Alfried P. Vogler
- Department of Entomology, Natural History Museum, London SW7 5BD, UK; 2Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and 3Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Entomology, Natural History Museum, London SW7 5BD, UK; 2Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; and 3Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Ferreira PG, Patalano S, Chauhan R, Ffrench-Constant R, Gabaldón T, Guigó R, Sumner S. Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol 2013; 14:R20. [PMID: 23442883 PMCID: PMC4053794 DOI: 10.1186/gb-2013-14-2-r20] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/26/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Understanding how alternative phenotypes arise from the same genome is a major challenge in modern biology. Eusociality in insects requires the evolution of two alternative phenotypes - workers, who sacrifice personal reproduction, and queens, who realize that reproduction. Extensive work on honeybees and ants has revealed the molecular basis of derived queen and worker phenotypes in highly eusocial lineages, but we lack equivalent deep-level analyses of wasps and of primitively eusocial species, the latter of which can reveal how phenotypic decoupling first occurs in the early stages of eusocial evolution. RESULTS We sequenced 20 Gbp of transcriptomes derived from brains of different behavioral castes of the primitively eusocial tropical paper wasp Polistes canadensis. Surprisingly, 75% of the 2,442 genes differentially expressed between phenotypes were novel, having no significant homology with described sequences. Moreover, 90% of these novel genes were significantly upregulated in workers relative to queens. Differential expression of novel genes in the early stages of sociality may be important in facilitating the evolution of worker behavioral complexity in eusocial evolution. We also found surprisingly low correlation in the identity and direction of expression of differentially expressed genes across similar phenotypes in different social lineages, supporting the idea that social evolution in different lineages requires substantial de novo rewiring of molecular pathways. CONCLUSIONS These genomic resources for aculeate wasps and first transcriptome-wide insights into the origin of castes bring us closer to a more general understanding of eusocial evolution and how phenotypic diversity arises from the same genome.
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Hartig G, Peters RS, Borner J, Etzbauer C, Misof B, Niehuis O. Oligonucleotide primers for targeted amplification of single-copy nuclear genes in apocritan Hymenoptera. PLoS One 2012; 7:e39826. [PMID: 22768134 PMCID: PMC3387199 DOI: 10.1371/journal.pone.0039826] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/27/2012] [Indexed: 11/19/2022] Open
Abstract
Background Published nucleotide sequence data from the mega-diverse insect order Hymenoptera (sawflies, bees, wasps, and ants) are taxonomically scattered and still inadequate for reconstructing a well-supported phylogenetic tree for the order. The analysis of comprehensive multiple gene data sets obtained via targeted PCR could provide a cost-effective solution to this problem. However, oligonucleotide primers for PCR amplification of nuclear genes across a wide range of hymenopteran species are still scarce. Findings Here we present a suite of degenerate oligonucleotide primer pairs for PCR amplification of 154 single-copy nuclear protein-coding genes from Hymenoptera. These primers were inferred from genome sequence data from nine Hymenoptera (seven species of ants, the honeybee, and the parasitoid wasp Nasonia vitripennis). We empirically tested a randomly chosen subset of these primer pairs for amplifying target genes from six Hymenoptera, representing the families Chrysididae, Crabronidae, Gasteruptiidae, Leucospidae, Pompilidae, and Stephanidae. Based on our results, we estimate that these primers are suitable for studying a large number of nuclear genes across a wide range of apocritan Hymenoptera (i.e., all hymenopterans with a wasp-waist) and of aculeate Hymenoptera in particular (i.e., apocritan wasps with stingers). Conclusions The amplified nucleotide sequences are (a) with high probability from single-copy genes, (b) easily generated at low financial costs, especially when compared to phylogenomic approaches, (c) easily sequenced by means of an additionally provided set of sequencing primers, and (d) suitable to address a wide range of phylogenetic questions and to aid rapid species identification via barcoding, as many amplicons contain both exonic and fast-evolving intronic nucleotides.
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Affiliation(s)
- Gerrit Hartig
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
- Universität Münster, Institut für Bioinformatik, Münster, Germany
| | - Ralph S. Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Bonn, Germany
| | - Janus Borner
- Universität Hamburg, Biozentrum Grindel und Zoologisches Museum, Hamburg, Germany
| | - Claudia Etzbauer
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
| | - Oliver Niehuis
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany
- * E-mail:
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39
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Voloch CM, Schrago CG. Impact of the partitioning scheme on divergence times inferred from Mammalian genomic data sets. Evol Bioinform Online 2012; 8:207-18. [PMID: 22654486 PMCID: PMC3362329 DOI: 10.4137/ebo.s9627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Data partitioning has long been regarded as an important parameter for phylogenetic inference. The division of heterogeneous multigene data sets into partitions with similar substitution patterns is known to increase the performance of probabilistic phylogenetic methods. However, the effect of the partitioning scheme on divergence time estimates has generally been ignored. To investigate the impact of data partitioning on the estimation of divergence times, we have constructed two genomic data sets. The first one with 15 nuclear genes comprising 50,928 bp were selected from the OrthoMam database; the second set was composed of complete mitochondrial genomes. We studied two partitioning schemes: concatenated supermatrices and partitioned gene analysis. We have also measured the impact of taxonomic sampling on the estimates. After drawing divergence time inferences using the uncorrelated relaxed clock in BEAST, we have compared the age estimates between the partitioning schemes. Our results show that, in general, both schemes resulted in similar chronological estimates, however the concatenated data sets were more efficient than the partitioned ones in attaining suitable effective sample sizes.
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Affiliation(s)
- Carolina M Voloch
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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40
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Kaltenpoth M, Showers Corneli P, Dunn DM, Weiss RB, Strohm E, Seger J. Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps. PLoS One 2012; 7:e32826. [PMID: 22412929 PMCID: PMC3295772 DOI: 10.1371/journal.pone.0032826] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/06/2012] [Indexed: 12/03/2022] Open
Abstract
Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes.
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Affiliation(s)
- Martin Kaltenpoth
- Research Group Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany.
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Inferring the Tree of Life: chopping a phylogenomic problem down to size? BMC Biol 2011; 9:59. [PMID: 21933452 PMCID: PMC3176480 DOI: 10.1186/1741-7007-9-59] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 09/13/2011] [Indexed: 11/30/2022] Open
Abstract
The combination of molecular sequence data and bioinformatics has revolutionized phylogenetic inference over the past decade, vastly increasing the scope of the evolutionary trees that we are able to infer. A recent paper in BMC Biology describing a new phylogenomic pipeline to help automate the inference of evolutionary trees from public sequence databases provides another important tool in our efforts to derive the Tree of Life. See research article: http://www.biomedcentral.com/1741-7007/9/55
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