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Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspock U, Aspock H, Bartel D, Blanke A, Berger S, Bohm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schutte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TKF, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X. Phylogenomics resolves the timing and pattern of insect evolution. Science 2014; 346:763-7. [DOI: 10.1126/science.1257570] [Citation(s) in RCA: 1672] [Impact Index Per Article: 167.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Breinholt JW, Kawahara AY. Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biol Evol 2014; 5:2082-92. [PMID: 24148944 PMCID: PMC3845638 DOI: 10.1093/gbe/evt157] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions.
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Hubert F, Grimm GW, Jousselin E, Berry V, Franc A, Kremer A. Multiple nuclear genes stabilize the phylogenetic backbone of the genusQuercus. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.941037] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Terrapon N, Li C, Robertson HM, Ji L, Meng X, Booth W, Chen Z, Childers CP, Glastad KM, Gokhale K, Gowin J, Gronenberg W, Hermansen RA, Hu H, Hunt BG, Huylmans AK, Khalil SMS, Mitchell RD, Munoz-Torres MC, Mustard JA, Pan H, Reese JT, Scharf ME, Sun F, Vogel H, Xiao J, Yang W, Yang Z, Yang Z, Zhou J, Zhu J, Brent CS, Elsik CG, Goodisman MAD, Liberles DA, Roe RM, Vargo EL, Vilcinskas A, Wang J, Bornberg-Bauer E, Korb J, Zhang G, Liebig J. Molecular traces of alternative social organization in a termite genome. Nat Commun 2014; 5:3636. [PMID: 24845553 DOI: 10.1038/ncomms4636] [Citation(s) in RCA: 273] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 03/13/2014] [Indexed: 01/28/2023] Open
Abstract
Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings of the transition towards social complexity has been confined primarily to Hymenoptera (for example, ants and bees). Here we sequence the genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) and compare them with similar data for eusocial Hymenoptera, to better identify commonalities and differences in achieving this significant transition. We show an expansion of genes related to male fertility, with upregulated gene expression in male reproductive individuals reflecting the profound differences in mating biology relative to the Hymenoptera. For several chemoreceptor families, we show divergent numbers of genes, which may correspond to the more claustral lifestyle of these termites. We also show similarities in the number and expression of genes related to caste determination mechanisms. Finally, patterns of DNA methylation and alternative splicing support a hypothesized epigenetic regulation of caste differentiation.
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Affiliation(s)
- Nicolas Terrapon
- 1] Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany [2] [3]
| | - Cai Li
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350, Denmark [3]
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lu Ji
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xuehong Meng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Warren Booth
- 1] Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA [2]
| | - Zhensheng Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Karl M Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kaustubh Gokhale
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Johannes Gowin
- 1] Behavioural Biology, University of Osnabrück, Osnabrück D49076, Germany [2]
| | - Wulfila Gronenberg
- Department of Neuroscience, University of Arizona, Tucson, Arizona 85721, USA
| | - Russell A Hermansen
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - Haofu Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Brendan G Hunt
- 1] School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA [2]
| | - Ann Kathrin Huylmans
- 1] Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany [2]
| | - Sayed M S Khalil
- 1] Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA [2] Department of Microbial Molecular Biology, Agricultural Genetic Engineering Research Institute, Giza 12619, Egypt
| | - Robert D Mitchell
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Monica C Munoz-Torres
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Julie A Mustard
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Hailin Pan
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Justin T Reese
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Fengming Sun
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhikai Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zuoquan Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiajian Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiwei Zhu
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Colin S Brent
- Arid Land Agricultural Research Center, United States Department of Agriculture, Maricopa, Arizona 85138, USA
| | - Christine G Elsik
- 1] Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA [2] Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | | | - David A Liberles
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - R Michael Roe
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Edward L Vargo
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Andreas Vilcinskas
- Institut für Phytopathologie und Angewandte Zoologie, Justus-Liebig-Universität Giessen, Giessen D35390, Germany
| | - Jun Wang
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Copenhagen DK-1165, Denmark [3] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, 21589 Jeddah, Saudi Arabia [4] Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China [5] Department of Medicine, University of Hong Kong, Hong Kong
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany
| | - Judith Korb
- 1] Behavioural Biology, University of Osnabrück, Osnabrück D49076, Germany [2]
| | - Guojie Zhang
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Jürgen Liebig
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
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55
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Poteat MD, Buchwalter DB. Phylogeny and size differentially influence dissolved Cd and Zn bioaccumulation parameters among closely related aquatic insects. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:5274-5281. [PMID: 24730589 DOI: 10.1021/es501096a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Evolutionarily distinct lineages can vary markedly in their accumulation of, and sensitivity to, contaminants. However, less is known about variability among closely related species. Here, we compared dissolved Cd and Zn bioaccumulation in 19 species spanning two species-rich aquatic insect families: Ephemerellidae (order Ephemeroptera (mayflies)), generalized to be metal sensitive, and Hydropsychidae (order Trichoptera (caddisflies)), generalized to be metal tolerant. Across all species, Zn and Cd uptake rate constants (k(u)s), efflux rate constants (k(e)s) and bioconcentration factors (BCFs) strongly covaried, suggesting that these metals share transport pathways in these distinct lineages. K(u)s and BCFs were substantially larger in Ephemerellidae than in Hydropsychidae, whereas k(e)s did not dramatically differ between the two families. Body size played an important role in driving ku differences among species, but had no influence on k(e)s. While familial differences in metal bioconcentration were striking, each family exhibited tremendous variability in all bioaccumulation parameters. At finer levels of taxonomic resolution (within families), phylogeny did not account for differences in metal bioaccumulation. These findings suggest that intrafamily variability can be profound and have important practical implications in that we need to better understand how well "surrogate species" represent their fellow congeners and family members.
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Affiliation(s)
- Monica D Poteat
- Environmental and Molecular Toxicology Program, Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina 27695, United States
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56
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Wipfler B, Klug R, Ge SQ, Bai M, Göbbels J, Yang XK, Hörnschemeyer T. The thorax of Mantophasmatodea, the morphology of flightlessness, and the evolution of the neopteran insects. Cladistics 2014; 31:50-70. [DOI: 10.1111/cla.12068] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Benjamin Wipfler
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Rebecca Klug
- Johann-Friedrich-Blumenbach Institut für Zoologie und Anthropologie; Universität Göttingen; Berliner Straße 28 Göttingen 37073 Germany
| | - Si-Qin Ge
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Jürgen Göbbels
- Bundesanstalt für Materialforschung Berlin; Unter den Eichen 87 Berlin 12205 Germany
| | - Xing-Ke Yang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Thomas Hörnschemeyer
- Johann-Friedrich-Blumenbach Institut für Zoologie und Anthropologie; Universität Göttingen; Berliner Straße 28 Göttingen 37073 Germany
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57
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Rosas-Guerrero V, Aguilar R, Martén-Rodríguez S, Ashworth L, Lopezaraiza-Mikel M, Bastida JM, Quesada M. A quantitative review of pollination syndromes: do floral traits predict effective pollinators? Ecol Lett 2014; 17:388-400. [DOI: 10.1111/ele.12224] [Citation(s) in RCA: 284] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/17/2013] [Accepted: 10/27/2013] [Indexed: 11/25/2022]
Affiliation(s)
- Víctor Rosas-Guerrero
- Centro de Investigaciones en Ecosistemas; Universidad Nacional Autónoma de México; Apartado Postal 27-3 (Xangari) 58089 Morelia Michoacán México
- Unidad Académica en Desarrollo Sustentable; Campus Costa Grande; Universidad Autónoma de Guerrero; Carretera Nacional Acapulco Zihuatanejo Km 106 + 900; Colonia Las Tunas Tecpan de Galeana Guerrero 40900 México
| | - Ramiro Aguilar
- Instituto Multidisciplinario de Biología Vegetal; Universidad Nacional de Córdoba - CONICET; C.C. 495 (5000) Córdoba Argentina
| | - Silvana Martén-Rodríguez
- Departamento de Biología Evolutiva, Instituto de Ecología A. C., Carretera Antigua a Coatepec No. 351, El Haya; Xalapa Veracruz 91070 México
- Centro Regional del Bajío, Instituto de Ecología, A. C.; Pátzcuaro, Michoacán 61600 México
| | - Lorena Ashworth
- Instituto Multidisciplinario de Biología Vegetal; Universidad Nacional de Córdoba - CONICET; C.C. 495 (5000) Córdoba Argentina
| | - Martha Lopezaraiza-Mikel
- Centro de Investigaciones en Ecosistemas; Universidad Nacional Autónoma de México; Apartado Postal 27-3 (Xangari) 58089 Morelia Michoacán México
- Unidad Académica en Desarrollo Sustentable; Campus Costa Grande; Universidad Autónoma de Guerrero; Carretera Nacional Acapulco Zihuatanejo Km 106 + 900; Colonia Las Tunas Tecpan de Galeana Guerrero 40900 México
| | - Jesús M. Bastida
- Centro de Investigaciones en Ecosistemas; Universidad Nacional Autónoma de México; Apartado Postal 27-3 (Xangari) 58089 Morelia Michoacán México
| | - Mauricio Quesada
- Centro de Investigaciones en Ecosistemas; Universidad Nacional Autónoma de México; Apartado Postal 27-3 (Xangari) 58089 Morelia Michoacán México
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58
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Broad polyphyly and historical biogeography of the neotropical wasp genus Notiospathius (Braconidae: Doryctinae). Mol Phylogenet Evol 2013; 69:142-52. [DOI: 10.1016/j.ympev.2013.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/28/2013] [Accepted: 05/03/2013] [Indexed: 11/24/2022]
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59
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Ren Z, Zhong Y, Kurosu U, Aoki S, Ma E, von Dohlen CD, Wen J. Historical biogeography of Eastern Asian-Eastern North American disjunct Melaphidina aphids (Hemiptera: Aphididae: Eriosomatinae) on Rhus hosts (Anacardiaceae). Mol Phylogenet Evol 2013; 69:1146-58. [PMID: 23973894 DOI: 10.1016/j.ympev.2013.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/24/2013] [Accepted: 08/06/2013] [Indexed: 12/17/2022]
Abstract
Intercontinental biotic disjunctions have been documented and analyzed in numerous Holarctic taxa. Patterns previously synthesized for animals compared to plants suggest that the timing of animal disjunctions are mostly Early Tertiary and were generated by migration and vicariance events occurring in the North Atlantic, while plant disjunctions are mostly Mid-Late Tertiary and imply migration and vicariance over Beringia. Melaphidina aphids (Hemiptera: Aphididae: Fordini) exhibit host-alternating life cycles comprising an obligate seasonal shift between Rhus subgenus Rhus species (Anacardiaceae) and mosses (Bryophyta). Similar to their Rhus hosts, melaphidines are distributed disjunctly between Eastern Asia and Eastern North America. We examined evolutionary relationships within Melaphidina to determine the position of the North American lineage, date its divergence from Asian relatives, and compare these results to a previous historical biogeographic study of Rhus. We sampled nine species and three subspecies representing all six genera of Melaphidina. Data included sequences of mitochondrial cytochrome c oxidase subunits I and II+leucine tRNA, cytochrome b, and nuclear elongation factor 1α genes. Phylogenetic analyses (Bayesian, maximum-likelihood, parsimony) of the combined data (3282 bp) supported the monophyly of all genera except Nurudea and Schlechtendalia, due to the position of N. ibofushi. While the exact position of the North American Melaphis was not well resolved, there was high support for a derived position within Asian taxa. The divergence of Melaphis from Asian relatives centered on the Eocene-Oligocene boundary (~33-35Ma), which coincides with closure of Beringian Land Bridge I. This also corresponded to the Asian-North American disjunction previously estimated for subgenus Rhus spp. We suggest the late-Eocene Bering Land Bridge as the most likely migration route for Melaphis ancestors, as was also hypothesized for North American Rhus ancestors. Results for the Melaphidina disjunction depart from the modal pattern in animal lineages, and present a case where insect and host-plant taxa apparently responded similarly to Tertiary climate change.
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Affiliation(s)
- Zhumei Ren
- School of Life Science, Shanxi University, 92 Wucheng Rd., Taiyuan Shanxi 030006, China.
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60
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Fior S, Li M, Oxelman B, Viola R, Hodges SA, Ometto L, Varotto C. Spatiotemporal reconstruction of the Aquilegia rapid radiation through next-generation sequencing of rapidly evolving cpDNA regions. THE NEW PHYTOLOGIST 2013; 198:579-592. [PMID: 23379348 DOI: 10.1111/nph.12163] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/20/2012] [Indexed: 05/02/2023]
Abstract
Aquilegia is a well-known model system in the field of evolutionary biology, but obtaining a resolved and well-supported phylogenetic reconstruction for the genus has been hindered by its recent and rapid diversification. Here, we applied 454 next-generation sequencing to PCR amplicons of 21 of the most rapidly evolving regions of the plastome to generate c. 24 kb of sequences from each of 84 individuals from throughout the genus. The resulting phylogeny has well-supported resolution of the main lineages of the genus, although recent diversification such as in the European taxa remains unresolved. By producing a chronogram of the whole Ranunculaceae family based on published data, we inferred calibration points for dating the Aquilegia radiation. The genus originated in the upper Miocene c. 6.9 million yr ago (Ma) in Eastern Asia, and diversification occurred c. 4.8 Ma with the split of two main clades, one colonizing North America, and the other Western Eurasia through the mountains of Central Asia. This was followed by a back-to-Asia migration, originating from the European stock using a North Asian route. These results provide the first backbone phylogeny and spatiotemporal reconstruction of the Aquilegia radiation, and constitute a robust framework to address the adaptative nature of speciation within the group.
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Affiliation(s)
- Simone Fior
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Mingai Li
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Bengt Oxelman
- Department of Biology and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30, Gothenburg, Sweden
| | - Roberto Viola
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Scott A Hodges
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Lino Ometto
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Claudio Varotto
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
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61
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Characterization of an ancient lepidopteran lateral gene transfer. PLoS One 2013; 8:e59262. [PMID: 23533610 PMCID: PMC3606386 DOI: 10.1371/journal.pone.0059262] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/13/2013] [Indexed: 02/03/2023] Open
Abstract
Bacteria to eukaryote lateral gene transfers (LGT) are an important potential source of material for the evolution of novel genetic traits. The explosion in the number of newly sequenced genomes provides opportunities to identify and characterize examples of these lateral gene transfer events, and to assess their role in the evolution of new genes. In this paper, we describe an ancient lepidopteran LGT of a glycosyl hydrolase family 31 gene (GH31) from an Enterococcus bacteria. PCR amplification between the LGT and a flanking insect gene confirmed that the GH31 was integrated into the Bombyx mori genome and was not a result of an assembly error. Database searches in combination with degenerate PCR on a panel of 7 lepidopteran families confirmed that the GH31 LGT event occurred deep within the Order approximately 65–145 million years ago. The most basal species in which the LGT was found is Plutella xylostella (superfamily: Yponomeutoidea). Array data from Bombyx mori shows that GH31 is expressed, and low dN/dS ratios indicates the LGT coding sequence is under strong stabilizing selection. These findings provide further support for the proposition that bacterial LGTs are relatively common in insects and likely to be an underappreciated source of adaptive genetic material.
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62
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van Velzen R, Wahlberg N, Sosef MSM, Bakker FT. Effects of changing climate on species diversification in tropical forest butterflies of the genusCymothoe(Lepidoptera: Nymphalidae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Robin van Velzen
- Biosystematics Group; Wageningen University; PO box 647 6708PB Wageningen the Netherlands
- Naturalis Biodiversity Centre (Section NHN); Wageningen University; Generaal Foulkesweg 37, 6703 BL Wageningen the Netherlands
| | - Niklas Wahlberg
- Laboratory of Genetics; Department of Biology; University of Turku; Turku 20014 Finland
| | - Marc S. M. Sosef
- Biosystematics Group; Wageningen University; PO box 647 6708PB Wageningen the Netherlands
- Naturalis Biodiversity Centre (Section NHN); Wageningen University; Generaal Foulkesweg 37, 6703 BL Wageningen the Netherlands
| | - Freek T. Bakker
- Biosystematics Group; Wageningen University; PO box 647 6708PB Wageningen the Netherlands
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63
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Thomas JA, Trueman JWH, Rambaut A, Welch JJ. Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny. Syst Biol 2013; 62:285-97. [DOI: 10.1093/sysbio/sys093] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jessica A. Thomas
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - John W. H. Trueman
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Andrew Rambaut
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - John J. Welch
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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Wang Y, Engel MS, Rafael JA, Dang K, Wu H, Wang Y, Xie Q, Bu W. A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera. PLoS One 2013; 8:e53679. [PMID: 23301099 PMCID: PMC3536744 DOI: 10.1371/journal.pone.0053679] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/03/2012] [Indexed: 01/30/2023] Open
Abstract
The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.
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Affiliation(s)
- Yanhui Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Michael S. Engel
- Division of Entomology (Paleoentomology), Natural History Museum, London, England
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Jose A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Haoyang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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65
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Zahiri R, Lafontaine JD, Holloway JD, Kitching IJ, Schmidt BC, Kaila L, Wahlberg N. Major lineages of Nolidae (Lepidoptera, Noctuoidea) elucidated by molecular phylogenetics. Cladistics 2012; 29:337-359. [DOI: 10.1111/cla.12001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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66
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Garwood R, Ross A, Sotty D, Chabard D, Charbonnier S, Sutton M, Withers PJ. Tomographic reconstruction of neopterous carboniferous insect nymphs. PLoS One 2012; 7:e45779. [PMID: 23049858 PMCID: PMC3458060 DOI: 10.1371/journal.pone.0045779] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/22/2012] [Indexed: 11/18/2022] Open
Abstract
Two new polyneopteran insect nymphs from the Montceau-les-Mines Lagerstätte of France are presented. Both are preserved in three dimensions, and are imaged with the aid of X-ray micro-tomography, allowing their morphology to be recovered in unprecedented detail. One-Anebos phrixos gen. et sp. nov.-is of uncertain affinities, and preserves portions of the antennae and eyes, coupled with a heavily spined habitus. The other is a roachoid with long antennae and chewing mouthparts very similar in form to the most generalized mandibulate mouthparts of extant orthopteroid insects. Computer reconstructions reveal limbs in both specimens, allowing identification of the segments and annulation in the tarsus, while poorly developed thoracic wing pads suggest both are young instars. This work describes the morphologically best-known Palaeozoic insect nymphs, allowing a better understanding of the juveniles' palaeobiology and palaeoecology. We also consider the validity of evidence from Palaeozoic juvenile insects in wing origin theories. The study of juvenile Palaeozoic insects is currently a neglected field, yet these fossils provide direct evidence on the evolution of insect development. It is hoped this study will stimulate a renewed interest in such work.
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Affiliation(s)
- Russell Garwood
- School of Materials, The University of Manchester, Manchester, United Kingdom.
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67
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Yang Q, Makarkin VN, Winterton SL, Khramov AV, Ren D. A remarkable new family of Jurassic insects (Neuroptera) with primitive wing venation and its phylogenetic position in Neuropterida. PLoS One 2012; 7:e44762. [PMID: 23028608 PMCID: PMC3445537 DOI: 10.1371/journal.pone.0044762] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 08/07/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lacewings (insect order Neuroptera), known in the fossil record since the Early Permian, were most diverse in the Mesozoic. A dramatic variety of forms ranged in that time from large butterfly-like Kalligrammatidae to minute two-winged Dipteromantispidae. PRINCIPAL FINDINGS We describe the intriguing new neuropteran family Parakseneuridae fam. nov. with three new genera and 15 new species from the Middle Jurassic of Daohugou (Inner Mongolia, China) and the Early/Middle Jurassic of Sai-Sagul (Kyrgyzstan): Parakseneura undula gen. et sp. nov., P. albomacula gen. et sp. nov., P. curvivenis gen. et sp. nov., P. nigromacula gen. et sp. nov., P. nigrolinea gen. et sp. nov., P. albadelta gen. et sp. nov., P. cavomaculata gen. et sp. nov., P. inflata gen. et sp. nov., P. metallica gen. et sp. nov., P. emarginata gen. et sp. nov., P. directa gen. et sp. nov., Pseudorapisma jurassicum gen. et sp. nov., P. angustipenne gen. et sp. nov., P. maculatum gen. et sp. nov. (Daohugou); Shuraboneura ovata gen. et sp. nov. (Sai-Sagul). The family comprises large neuropterans with most primitive wing venation in the order indicated by the presence of ScA and AA1+2, and the dichotomous branching of MP, CuA, CuP, AA3+4, AP1+2. The phylogenetic position of Parakseneuridae was investigated using a phylogenetic analysis of morphological scoring for 33 families of extinct and extant Neuropterida combined with DNA sequence data for representatives of all extant families. Parakseneuridae were recovered in a clade with Osmylopsychopidae, Prohemerobiidae, and Ithonidae. CONCLUSIONS/SIGNIFICANCE The presence of the presumed AA1+2 in wings of Parakseneuridae is a unique plesiomorphic condition hitherto unknown in Neuropterida, the clade comprising Neuroptera, Megaloptera, Raphidioptera. The relative uncertainty of phylogenetic position of Parakseneuridae and the majority of other families of Neuroptera reflects deficient paleontological data, especially from critical important periods for the order, earliest Triassic and latest Triassic/earliest Jurassic.
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Affiliation(s)
- Qiang Yang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Vladimir N. Makarkin
- College of Life Sciences, Capital Normal University, Beijing, China
- Institute of Biology and Soil Sciences, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
- * E-mail: (VM); (DR)
| | - Shaun L. Winterton
- California State Collection of Arthropods, California Department of Food and Agriculture, Sacramento, California, United States of America
| | - Alexander V. Khramov
- Borissiak Paleontological Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Dong Ren
- College of Life Sciences, Capital Normal University, Beijing, China
- * E-mail: (VM); (DR)
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68
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Letsch HO, Meusemann K, Wipfler B, Schütte K, Beutel R, Misof B. Insect phylogenomics: results, problems and the impact of matrix composition. Proc Biol Sci 2012; 279:3282-90. [PMID: 22628473 PMCID: PMC3385742 DOI: 10.1098/rspb.2012.0744] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 05/02/2012] [Indexed: 11/12/2022] Open
Abstract
In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data ('EST': short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.
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Affiliation(s)
- Harald O Letsch
- Department für Tropenökologie und Biodiversität der Tiere, Universität Wien, Rennweg 14, 1030 Wien, Austria.
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69
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Blanke A, Wipfler B, Letsch H, Koch M, Beckmann F, Beutel R, Misof B. Revival of Palaeoptera-head characters support a monophyletic origin of Odonata and Ephemeroptera (Insecta). Cladistics 2012; 28:560-581. [DOI: 10.1111/j.1096-0031.2012.00405.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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70
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Tettweiler G, Kowanda M, Lasko P, Sonenberg N, Hernández G. The Distribution of eIF4E-Family Members across Insecta. Comp Funct Genomics 2012; 2012:960420. [PMID: 22745595 PMCID: PMC3382400 DOI: 10.1155/2012/960420] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 03/14/2012] [Indexed: 11/20/2022] Open
Abstract
Insects are part of the earliest faunas that invaded terrestrial environments and are the first organisms that evolved controlled flight. Nowadays, insects are the most diverse animal group on the planet and comprise the majority of extant animal species described. Moreover, they have a huge impact in the biosphere as well as in all aspects of human life and economy; therefore understanding all aspects of insect biology is of great importance. In insects, as in all cells, translation is a fundamental process for gene expression. However, translation in insects has been mostly studied only in the model organism Drosophila melanogaster. We used all publicly available genomic sequences to investigate in insects the distribution of the genes encoding the cap-binding protein eIF4E, a protein that plays a crucial role in eukaryotic translation. We found that there is a diversity of multiple ortholog genes encoding eIF4E isoforms within the genus Drosophila. In striking contrast, insects outside this genus contain only a single eIF4E gene, related to D. melanogaster eIF4E-1. We also found that all insect species here analyzed contain only one Class II gene, termed 4E-HP. We discuss the possible evolutionary causes originating the multiplicity of eIF4E genes within the genus Drosophila.
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Affiliation(s)
- Gritta Tettweiler
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada H3A 1A3
| | - Michelle Kowanda
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
| | - Paul Lasko
- Department of Biology, McGill University, 1205 Dr. Penfield, Montreal, QC, Canada H3A 1B1
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada H3A 1A3
| | - Greco Hernández
- Division of Basic Research, National Institute for Cancer (INCan), Avenida San Fernando No. 22, Tlalpan, 14080 Mexico City, DF, Mexico
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71
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Predel R, Neupert S, Huetteroth W, Kahnt J, Waidelich D, Roth S. Peptidomics-Based Phylogeny and Biogeography of Mantophasmatodea (Hexapoda). Syst Biol 2012; 61:609-29. [DOI: 10.1093/sysbio/sys003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Reinhard Predel
- Biocenter, Institute for Zoology, University of Cologne, Zülpicher Strasse 47b, 50674 Cologne, Germany
| | - Susanne Neupert
- Biocenter, Institute for Zoology, University of Cologne, Zülpicher Strasse 47b, 50674 Cologne, Germany
| | - Wolf Huetteroth
- Department of Biology, Animal Physiology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | | | - Steffen Roth
- The Natural History Collections, University Museum of Bergen, PO Box 7800, N-5020 Bergen, Norway
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72
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Pilgrim EM, von Dohlen CD. Phylogeny of the dragonfly genus Sympetrum (Odonata: Libellulidae). ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0081-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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73
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Heikkilä M, Kaila L, Mutanen M, Peña C, Wahlberg N. Cretaceous origin and repeated tertiary diversification of the redefined butterflies. Proc Biol Sci 2012; 279:1093-9. [PMID: 21920981 PMCID: PMC3267136 DOI: 10.1098/rspb.2011.1430] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 08/23/2011] [Indexed: 11/12/2022] Open
Abstract
Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous-Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis, a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.
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Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, University of Helsinki, PO Box 17, Helsinki 00014, Finland
| | - Lauri Kaila
- Finnish Museum of Natural History, University of Helsinki, PO Box 17, Helsinki 00014, Finland
| | - Marko Mutanen
- Zoological Museum, Department of Biology, University of Oulu, PO Box 3000, Oulu 90014, Finland
| | - Carlos Peña
- Laboratory of Genetics, Department of Biology, University of Turku, Turku 20014, Finland
| | - Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, Turku 20014, Finland
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74
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Yeates DK, Cameron SL, Trautwein M. A view from the edge of the forest: recent progress in understanding the relationships of the insect orders. ACTA ACUST UNITED AC 2012. [DOI: 10.1111/j.1440-6055.2012.00857.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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75
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Evolution of a large, conserved, and syntenic gene family in insects. G3-GENES GENOMES GENETICS 2012; 2:313-9. [PMID: 22384409 PMCID: PMC3284338 DOI: 10.1534/g3.111.001412] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/16/2011] [Indexed: 11/18/2022]
Abstract
The Osiris gene family, first described in Drosophila melanogaster, is clustered in the genomes of all Drosophila species sequenced to date. In D. melanogaster, it explains the enigmatic phenomenon of the triplo-lethal and haploinsufficient locus Tpl. The synteny of Osiris genes in flies is well conserved, and it is one of the largest syntenic blocks in the Drosophila group. By examining the genome sequences of other insects in a wide range of taxonomic orders, we show here that the gene family is well-conserved and syntenic not only in the diptera but across the holometabolous and hemimetabolous insects. Osiris gene homologs have also been found in the expressed sequence tag sequences of various other insects but are absent from all groups that are not insects, including crustacea and arachnids. It is clear that the gene family evolved by gene duplication and neofunctionalization very soon after the divergence of the insects from other arthropods but before the divergence of the insects from one another and that the sequences and synteny have been maintained by selection ever since.
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76
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Trautwein MD, Wiegmann BM, Beutel R, Kjer KM, Yeates DK. Advances in insect phylogeny at the dawn of the postgenomic era. ANNUAL REVIEW OF ENTOMOLOGY 2012; 57:449-468. [PMID: 22149269 DOI: 10.1146/annurev-ento-120710-100538] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).
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Affiliation(s)
- Michelle D Trautwein
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA.
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77
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Mavrodiev EV, Gitzendanner M, Calaminus AK, Baldini RM, Soltis PS, Soltis DE. Molecular phylogeny ofTragopogonL. (Asteraceae) based on seven nuclear loci (Adh, GapC, LFY, AP3, PI, ITS, and ETS). ACTA ACUST UNITED AC 2012. [DOI: 10.1080/00837792.2012.10670912] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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78
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Liu Y, Budke JM, Goffinet B. Phylogenetic inference rejects sporophyte based classification of the Funariaceae (Bryophyta): Rapid radiation suggests rampant homoplasy in sporophyte evolution. Mol Phylogenet Evol 2012; 62:130-45. [DOI: 10.1016/j.ympev.2011.09.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/09/2011] [Accepted: 09/17/2011] [Indexed: 10/17/2022]
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79
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Kaila L, Mutanen M, Nyman T. Phylogeny of the mega-diverse Gelechioidea (Lepidoptera): adaptations and determinants of success. Mol Phylogenet Evol 2011; 61:801-9. [PMID: 21903172 DOI: 10.1016/j.ympev.2011.08.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 11/26/2022]
Abstract
The Gelechioidea, with 18,000 described and many more unnamed species ranks among the most diverse lepidopteran superfamilies. Nevertheless, their taxonomy has remained largely unresolved, and phylogenetic affinities among gelechioid families and lower taxa have been insufficiently understood. We constructed, for the first time, a comprehensive molecular phylogeny for the Gelechioidea. We sampled seven genes, in total 5466 base pairs, of 109 gelechioid taxa representing 32 of 37 recognized subfamilies, and two outgroup taxa. We used maximum likelihood methods and Bayesian inference to construct phylogenetic trees. We found that the families Autostichidae, Lecithoceridae, Xyloryctidae, and Oecophoridae s. str., in this order, are the most basally arising clades. Elachistidae s. l. was found to be paraphyletic, with families such as Gelechiidae and Cosmopterigidae nested within it, and Parametriotinae associated with several families previously considered unrelated to them. Using the phylogenetic trees, we examined patterns of life history evolution and determinants of the success of different lineages. Gelechioids express unusually wide variability in life-history strategies, including herbivorous, saprophagous, fungivorous, and carnivorous lineages. Most species are highly specialized in diet and other life history traits. The results suggest that either saprophagy was the ancestral feeding strategy from which herbivory evolved independently on multiple occasions, or that the ancestor was herbivorous with repeated origins of saprophagy. External feeding is an ancestral trait from which internal feeding evolved independently several times. In terms of species number, saprophages are dominant in Australia, while elsewhere several phytophagous lineages have extensively specialized and diversified. Internal feeding has remained a somewhat less generally adopted feeding mode, although in a few lineages significant radiations of leaf mining species have occurred. We conclude that diverse feeding modes, specialization among saprophages, repeated shifts to phytophagy, and a generally high specialization rate on single plant species (monophagy) are the major factors behind the success of the Gelechioidea.
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Affiliation(s)
- Lauri Kaila
- Finnish Museum of Natural History, University of Helsinki, PO Box 17, Helsinki 00014, Finland.
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80
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Kawahara AY, Ohshima I, Kawakita A, Regier JC, Mitter C, Cummings MP, Davis DR, Wagner DL, De Prins J, Lopez-Vaamonde C. Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae). BMC Evol Biol 2011; 11:182. [PMID: 21702958 PMCID: PMC3145599 DOI: 10.1186/1471-2148-11-182] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 06/24/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Researchers conducting molecular phylogenetic studies are frequently faced with the decision of what to do when weak branch support is obtained for key nodes of importance. As one solution, the researcher may choose to sequence additional orthologous genes of appropriate evolutionary rate for the taxa in the study. However, generating large, complete data matrices can become increasingly difficult as the number of characters increases. A few empirical studies have shown that augmenting genes even for a subset of taxa can improve branch support. However, because each study differs in the number of characters and taxa, there is still a need for additional studies that examine whether incomplete sampling designs are likely to aid at increasing deep node resolution. We target Gracillariidae, a Cretaceous-age (~100 Ma) group of leaf-mining moths to test whether the strategy of adding genes for a subset of taxa can improve branch support for deep nodes. We initially sequenced ten genes (8,418 bp) for 57 taxa that represent the major lineages of Gracillariidae plus outgroups. After finding that many deep divergences remained weakly supported, we sequenced eleven additional genes (6,375 bp) for a 27-taxon subset. We then compared results from different data sets to assess whether one sampling design can be favored over another. The concatenated data set comprising all genes and all taxa and three other data sets of different taxon and gene sub-sampling design were analyzed with maximum likelihood. Each data set was subject to five different models and partitioning schemes of non-synonymous and synonymous changes. Statistical significance of non-monophyly was examined with the Approximately Unbiased (AU) test. RESULTS Partial augmentation of genes led to high support for deep divergences, especially when non-synonymous changes were analyzed alone. Increasing the number of taxa without an increase in number of characters led to lower bootstrap support; increasing the number of characters without increasing the number of taxa generally increased bootstrap support. More than three-quarters of nodes were supported with bootstrap values greater than 80% when all taxa and genes were combined. Gracillariidae, Lithocolletinae + Leucanthiza, and Acrocercops and Parectopa groups were strongly supported in nearly every analysis. Gracillaria group was well supported in some analyses, but less so in others. We find strong evidence for the exclusion of Douglasiidae from Gracillarioidea sensu Davis and Robinson (1998). Our results strongly support the monophyly of a G.B.R.Y. clade, a group comprised of Gracillariidae + Bucculatricidae + Roeslerstammiidae + Yponomeutidae, when analyzed with non-synonymous changes only, but this group was frequently split when synonymous and non-synonymous substitutions were analyzed together. CONCLUSIONS 1) Partially or fully augmenting a data set with more characters increased bootstrap support for particular deep nodes, and this increase was dramatic when non-synonymous changes were analyzed alone. Thus, the addition of sites that have low levels of saturation and compositional heterogeneity can greatly improve results. 2) Gracillarioidea, as defined by Davis and Robinson (1998), clearly do not include Douglasiidae, and changes to current classification will be required. 3) Gracillariidae were monophyletic in all analyses conducted, and nearly all species can be placed into one of six strongly supported clades though relationships among these remain unclear. 4) The difficulty in determining the phylogenetic placement of Bucculatricidae is probably attributable to compositional heterogeneity at the third codon position. From our tests for compositional heterogeneity and strong bootstrap values obtained when synonymous changes are excluded, we tentatively conclude that Bucculatricidae is closely related to Gracillariidae + Roeslerstammiidae + Yponomeutidae.
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Affiliation(s)
- Akito Y Kawahara
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Issei Ohshima
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Japan
| | | | - Jerome C Regier
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Charles Mitter
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Michael P Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Donald R Davis
- Department of Entomology, Smithsonian Institution, Washington, D.C., USA
| | - David L Wagner
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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81
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Trautwein MD, Wiegmann BM, Yeates DK. Overcoming the effects of rogue taxa: Evolutionary relationships of the bee flies. PLOS CURRENTS 2011; 3:RRN1233. [PMID: 21686308 PMCID: PMC3088465 DOI: 10.1371/currents.rrn1233] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/05/2011] [Indexed: 11/18/2022]
Abstract
Bombyliidae (5000 sp.), or bee flies, are a lower brachyceran family of flower-visiting flies that, as larvae, act as parasitoids of other insects. The evolutionary relationships are known from a morphological analysis that yielded minimal support for higher-level groupings. We use the protein-coding gene CAD and 28S rDNA to determine phylogeny and to test the monophyly of existing subfamilies, the divisions Tomophtalmae, and 'the sand chamber subfamilies'. Additionally, we demonstrate that consensus networks can be used to identify rogue taxa in a Bayesian framework. Pruning rogue taxa post-analysis from the final tree distribution results in increased posterior probabilities. We find 8 subfamilies to be monophyletic and the subfamilies Heterotropinae and Mythicomyiinae to be the earliest diverging lineages. The large subfamily Bombyliinae is found to be polyphyletic and our data does not provide evidence for the monophyly of Tomophthalmae or the 'sand chamber subfamilies'.
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Affiliation(s)
- Michelle D Trautwein
- Department of Entomology, North Carolina State University, Raleigh NC 27695 and CSIRO Ecosystem Sciences, Australian National Insect Collection, PO Box 1700 Canberra ACT 2601
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82
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Stolle E, Wilfert L, Schmid-Hempel R, Schmid-Hempel P, Kube M, Reinhardt R, Moritz RFA. A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae. BMC Genomics 2011; 12:48. [PMID: 21247459 PMCID: PMC3034698 DOI: 10.1186/1471-2164-12-48] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 01/19/2011] [Indexed: 12/30/2022] Open
Abstract
Background The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL) mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level. Results The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs) and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG. Conclusions This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae.
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Affiliation(s)
- Eckart Stolle
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
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83
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The mitochondrial genome of Bacillus stick insects (Phasmatodea) and the phylogeny of orthopteroid insects. Mol Phylogenet Evol 2010; 58:304-16. [PMID: 21167949 DOI: 10.1016/j.ympev.2010.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 12/06/2010] [Accepted: 12/11/2010] [Indexed: 11/23/2022]
Abstract
The Order Phasmatodea (stick and leaf insects) includes many well-known species of cryptic phytophagous insects. In this work, we sequenced the almost complete mitochondrial genomes of two stick insect species of the genus Bacillus. Phasmatodea pertain to the Polyneoptera, and represent one of the major clades of heterometabolous insects. Orthopteroid insect lineages arose through rapid evolutionary radiation events, which likely blurred the phylogenetic reconstructions obtained so far; we therefore performed a phylogenetic analysis to resolve and date all major splits of orthopteroid phylogeny, including the relationships between Phasmatodea and other polyneopterans. We explored several molecular models, with special reference to data partitioning, to correctly detect any phylogenetic signal lying in rough data. Phylogenetic Informativeness analysis showed that the maximum resolving power on the orthopteroid mtDNA dataset is expected for the Upper Cretaceous, about 80millionyears ago (Mya), but at least 70% of the maximum informativeness is also expected for the 150-200 Mya timespan, which makes mtDNA a suitable marker to study orthopteroid splits. A complete chronological calibration has also been computed following a Penalized Likelihood method. In summary, our analysis confirmed the monophyly of Phasmatodea, Dictyoptera and Orthoptera, and retrieved Mantophasmatodea as sister group of Phasmatodea. The origin of orthopteroid insects was also estimated to be in the Middle Triassic, while the order Phasmatodea seems to appear in the Upper Jurassic. The obtained results evidenced that mtDNA is a suitable marker to unravel the ancient splits leading to the orthopteroid orders, given a proper methodological approach.
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84
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Ishiwata K, Sasaki G, Ogawa J, Miyata T, Su ZH. Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences. Mol Phylogenet Evol 2010; 58:169-80. [PMID: 21075208 DOI: 10.1016/j.ympev.2010.11.001] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 10/20/2010] [Accepted: 11/06/2010] [Indexed: 10/18/2022]
Abstract
Many attempts to resolve the phylogenetic relationships of higher groups of insects have been made based on both morphological and molecular evidence; nonetheless, most of the interordinal relationships of insects remain unclear or are controversial. As a new approach, in this study we sequenced three nuclear genes encoding the catalytic subunit of DNA polymerase delta and the two largest subunits of RNA polymerase II from all insect orders. The predicted amino acid sequences (In total, approx. 3500 amino acid sites) of these proteins were subjected to phylogenetic analyses based on the maximum likelihood and Bayesian analysis methods with various models. The resulting trees strongly support the monophyly of Palaeoptera, Neoptera, Polyneoptera, and Holometabola, while within Polyneoptera, the groupings of Isoptera/"Blattaria"/Mantodea (Superorder Dictyoptera), Dictyoptera/Zoraptera, Dermaptera/Plecoptera, Mantophasmatodea/Grylloblattodea, and Embioptera/Phasmatodea are supported. Although Paraneoptera is not supported as a monophyletic group, the grouping of Phthiraptera/Psocoptera is robustly supported. The interordinal relationships within Holometabola are well resolved and strongly supported that the order Hymenoptera is the sister lineage to all other holometabolous insects. The other orders of Holometabola are separated into two large groups, and the interordinal relationships of each group are (((Siphonaptera, Mecoptera), Diptera), (Trichoptera, Lepidoptera)) and ((Coleoptera, Strepsiptera), (Neuroptera, Raphidioptera, Megaloptera)). The sister relationship between Strepsiptera and Diptera are significantly rejected by all the statistical tests (AU, KH and wSH), while the affinity between Hymenoptera and Mecopterida are significantly rejected only by AU and KH tests. Our results show that the use of amino acid sequences of these three nuclear genes is an effective approach for resolving the relationships of higher groups of insects.
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Affiliation(s)
- Keisuke Ishiwata
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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85
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Gotzek D, Clarke J, Shoemaker D. Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae). BMC Evol Biol 2010; 10:300. [PMID: 20929580 PMCID: PMC2958920 DOI: 10.1186/1471-2148-10-300] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 10/07/2010] [Indexed: 01/02/2023] Open
Abstract
Background Complete mitochondrial genome sequences have become important tools for the study of genome architecture, phylogeny, and molecular evolution. Despite the rapid increase in available mitogenomes, the taxonomic sampling often poorly reflects phylogenetic diversity and is often also biased to represent deeper (family-level) evolutionary relationships. Results We present the first fully sequenced ant (Hymenoptera: Formicidae) mitochondrial genomes. We sampled four mitogenomes from three species of fire ants, genus Solenopsis, which represent various evolutionary depths. Overall, ant mitogenomes appear to be typical of hymenopteran mitogenomes, displaying a general A+T-bias. The Solenopsis mitogenomes are slightly more compact than other hymentoperan mitogenomes (~15.5 kb), retaining all protein coding genes, ribosomal, and transfer RNAs. We also present evidence of recombination between the mitogenomes of the two conspecific Solenopsis mitogenomes. Finally, we discuss potential ways to improve the estimation of phylogenies using complete mitochondrial genome sequences. Conclusions The ant mitogenome presents an important addition to the continued efforts in studying hymenopteran mitogenome architecture, evolution, and phylogenetics. We provide further evidence that the sampling across many taxonomic levels (including conspecifics and congeners) is useful and important to gain detailed insights into mitogenome evolution. We also discuss ways that may help improve the use of mitogenomes in phylogenetic analyses by accounting for non-stationary and non-homogeneous evolution among branches.
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Affiliation(s)
- Dietrich Gotzek
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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86
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Mutanen M, Wahlberg N, Kaila L. Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies. Proc Biol Sci 2010; 277:2839-48. [PMID: 20444718 PMCID: PMC2981981 DOI: 10.1098/rspb.2010.0392] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 04/12/2010] [Indexed: 11/12/2022] Open
Abstract
Lepidoptera (butterflies and moths) represent one of the most diverse animals groups. Yet, the phylogeny of advanced ditrysian Lepidoptera, accounting for about 99 per cent of lepidopteran species, has remained largely unresolved. We report a rigorous and comprehensive analysis of lepidopteran affinities. We performed phylogenetic analyses of 350 taxa representing nearly 90 per cent of lepidopteran families. We found Ditrysia to be a monophyletic taxon with the clade Tischerioidea + Palaephatoidea being the sister group of it. No support for the monophyly of the proposed major internested ditrysian clades, Apoditrysia, Obtectomera and Macrolepidoptera, was found as currently defined, but each of these is supported with some modification. The monophyly or near-monophyly of most previously identified lepidopteran superfamilies is reinforced, but several species-rich superfamilies were found to be para- or polyphyletic. Butterflies were found to be more closely related to 'microlepidopteran' groups of moths rather than the clade Macrolepidoptera, where they have traditionally been placed. There is support for the monophyly of Macrolepidoptera when butterflies and Calliduloidea are excluded. The data suggest that the generally short diverging nodes between major groupings in basal non-tineoid Ditrysia are owing to their rapid radiation, presumably in correlation with the radiation of flowering plants.
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Affiliation(s)
- Marko Mutanen
- Zoological Museum, Department of Biology, University of Oulu, , PO Box 3000, Oulu 90014, Finland.
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87
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Ober KA, Heider TN. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae). BMC Evol Biol 2010; 10:262. [PMID: 20799952 PMCID: PMC2939577 DOI: 10.1186/1471-2148-10-262] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 08/27/2010] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. RESULTS According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. CONCLUSIONS Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.
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Affiliation(s)
- Karen A Ober
- Department of Biology, College of the Holy Cross, 1 College St., Worcester, MA 01610 USA
| | - Thomas N Heider
- Department of Biology, College of the Holy Cross, 1 College St., Worcester, MA 01610 USA
- Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 USA
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88
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ESPELAND M, JOHANSON KA. The diversity and radiation of the largest monophyletic animal group on New Caledonia (Trichoptera: Ecnomidae: Agmina). J Evol Biol 2010; 23:2112-2122. [DOI: 10.1111/j.1420-9101.2010.02072.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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89
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Lin CP, Chen MY, Huang JP. The complete mitochondrial genome and phylogenomics of a damselfly, Euphaea formosa support a basal Odonata within the Pterygota. Gene 2010; 468:20-9. [PMID: 20699111 DOI: 10.1016/j.gene.2010.08.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2010] [Revised: 08/03/2010] [Accepted: 08/03/2010] [Indexed: 11/29/2022]
Abstract
This study determined the first complete mitochondrial genome of a damselfly, Euphaea formosa (Insecta: Odonata: Zygoptera), and reconstructed a phylogeny based on thirteen protein-coding genes of mitochondrial genomes in twenty-five representative hexapods to examine the relationships among the basal Pterygota. The damselfly's mitochondrial genome is a circular molecule of 15,700bp long, and contains the entire set of thirty-seven genes typically found in insects. The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar across the three odonate species, suggesting a conserved genome evolution within the Odonata. The presence of the intergenic spacer s5 likely represents a synapomorphy for the dragonflies (Anisoptera). Maximum parsimony, maximum likelihood, and Bayesian analyses of both nucleotide and amino acid sequences cannot support the three existing phylogenetic hypotheses of the basal Pterygota (Palaeoptera, Metapterygota, and Chiastomyaria). In contrast, the phylogenetic results indicate an alternative hypothesis of a strongly supported basal Odonata and a sister relationship of the Ephemeroptera and Plecoptera. The unexpected sister Ephemeroptera+Plecoptera clade, which contradicts with the widely accepted hypothesis of a monophyletic Neoptera, requires further analyses with additional mitochondrial genome sampling at the base of the Neoptera.
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Affiliation(s)
- Chung-Ping Lin
- Department of Life Science, Tunghai University, Taichung, Taiwan.
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90
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Kodandaramaiah U, Lees DC, Müller CJ, Torres E, Karanth KP, Wahlberg N. Phylogenetics and biogeography of a spectacular Old World radiation of butterflies: the subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrini). BMC Evol Biol 2010; 10:172. [PMID: 20537168 PMCID: PMC2898688 DOI: 10.1186/1471-2148-10-172] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 06/10/2010] [Indexed: 02/07/2023] Open
Abstract
Background Butterflies of the subtribe Mycalesina (Nymphalidae: Satyrinae) are important model organisms in ecology and evolution. This group has radiated spectacularly in the Old World tropics and presents an exciting opportunity to better understand processes of invertebrate rapid radiations. However, the generic-level taxonomy of the subtribe has been in a constant state of flux, and relationships among genera are unknown. There are six currently recognized genera in the group. Mycalesis, Lohora and Nirvanopsis are found in the Oriental region, the first of which is the most speciose genus among mycalesines, and extends into the Australasian region. Hallelesis and Bicyclus are found in mainland Africa, while Heteropsis is primarily Madagascan, with a few species in Africa. We infer the phylogeny of the group with data from three genes (total of 3139 bp) and use these data to reconstruct events in the biogeographic history of the group. Results The results indicate that the group Mycalesina radiated rapidly around the Oligocene-Miocene boundary. Basal relationships are unresolved, but we recover six well-supported clades. Some species of Mycalesis are nested within a primarily Madagascan clade of Heteropsis, while Nirvanopsis is nested within Lohora. The phylogeny suggests that the group had its origin either in Asia or Africa, and diversified through dispersals between the two regions, during the late Oligocene and early Miocene. The current dataset tentatively suggests that the Madagascan fauna comprises two independent radiations. The Australasian radiation shares a common ancestor derived from Asia. We discuss factors that are likely to have played a key role in the diversification of the group. Conclusions We propose a significantly revised classification scheme for Mycalesina. We conclude that the group originated and radiated from an ancestor that was found either in Asia or Africa, with dispersals between the two regions and to Australasia. Our phylogeny paves the way for further comparative studies on this group that will help us understand the processes underlying diversification in rapid radiations of invertebrates.
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91
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Meusemann K, von Reumont BM, Simon S, Roeding F, Strauss S, Kück P, Ebersberger I, Walzl M, Pass G, Breuers S, Achter V, von Haeseler A, Burmester T, Hadrys H, Wägele JW, Misof B. A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol 2010; 27:2451-64. [PMID: 20534705 DOI: 10.1093/molbev/msq130] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Arthropods were the first animals to conquer land and air. They encompass more than three quarters of all described living species. This extraordinary evolutionary success is based on an astoundingly wide array of highly adaptive body organizations. A lack of robustly resolved phylogenetic relationships, however, currently impedes the reliable reconstruction of the underlying evolutionary processes. Here, we show that phylogenomic data can substantially advance our understanding of arthropod evolution and resolve several conflicts among existing hypotheses. We assembled a data set of 233 taxa and 775 genes from which an optimally informative data set of 117 taxa and 129 genes was finally selected using new heuristics and compared with the unreduced data set. We included novel expressed sequence tag (EST) data for 11 species and all published phylogenomic data augmented by recently published EST data on taxonomically important arthropod taxa. This thorough sampling reduces the chance of obtaining spurious results due to stochastic effects of undersampling taxa and genes. Orthology prediction of genes, alignment masking tools, and selection of most informative genes due to a balanced taxa-gene ratio using new heuristics were established. Our optimized data set robustly resolves major arthropod relationships. We received strong support for a sister group relationship of onychophorans and euarthropods and strong support for a close association of tardigrades and cycloneuralia. Within pancrustaceans, our analyses yielded paraphyletic crustaceans and monophyletic hexapods and robustly resolved monophyletic endopterygote insects. However, our analyses also showed for few deep splits that were recently thought to be resolved, for example, the position of myriapods, a remarkable sensitivity to methods of analyses.
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Affiliation(s)
- Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Molecular Biology Unit, Bonn, Germany
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92
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On the phylogenetic position of the palaeopteran Syntonopteroidea (Insecta: Ephemeroptera), with a new species from the Upper Carboniferous of England. ORG DIVERS EVOL 2010. [DOI: 10.1007/s13127-010-0022-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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93
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Letsch HO, Kück P, Stocsits RR, Misof B. The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. Mol Biol Evol 2010; 27:2507-21. [PMID: 20530152 DOI: 10.1093/molbev/msq140] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The use of secondary structures has been advocated to improve both the alignment and the tree reconstruction processes of ribosomal RNA (rRNA) data sets. We used simulated and empirical rRNA data to test the impact of secondary structure consideration in both steps of molecular phylogenetic analyses. A simulation approach was used to generate realistic rRNA data sets based on real 16S, 18S, and 28S sequences and structures in combination with different branch length and topologies. Alignment and tree reconstruction performance of four recent structural alignment methods was compared with exclusively sequence-based approaches. As empirical data, we used a hexapod rRNA data set to study the influence of nucleotide interdependencies in sequence alignment and tree reconstruction. Structural alignment methods delivered significantly better sequence alignments compared with pure sequence-based methods. Also, structural alignment methods delivered better trees judged by topological congruence to simulation base trees. However, the advantage of structural alignments was less pronounced and even vanished in several instances. For simulated data, application of mixed RNA/DNA models to stems and loops, respectively, led to significantly shorter branches. The application of mixed RNA/DNA models in the hexapod analyses delivered partly implausible relationships. This can be interpreted as a stronger sensitivity of mixed model setups to nonphylogenetic signal. Secondary structure consideration clearly influenced sequence alignment and tree reconstruction of ribosomal genes. Although sequence alignment quality can considerably be improved by the use of secondary structure information, the application of mixed models in tree reconstructions needs further studies to understand the observed effects.
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Affiliation(s)
- Harald O Letsch
- Molecular Biodiversity Research Unit, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.
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94
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Trautwein MD, Wiegmann BM, Yeates DK. A multigene phylogeny of the fly superfamily Asiloidea (Insecta): Taxon sampling and additional genes reveal the sister-group to all higher flies (Cyclorrhapha). Mol Phylogenet Evol 2010; 56:918-30. [PMID: 20399874 DOI: 10.1016/j.ympev.2010.04.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 03/31/2010] [Accepted: 04/12/2010] [Indexed: 11/26/2022]
Abstract
Asiloidea are a group of 9 lower brachyceran fly families, considered to be the closest relative to the large Metazoan radiation Eremoneura (Cyclorrhapha+Empidoidea). The evidence for asiloid monophyly is limited, and few characters define the relationships between the families of Asiloidea and Eremoneura. Additionally, enigmatic genera, Hilarimorpha and Apystomyia, retain morphological characters of both asiloids and higher flies. We use the nuclear protein-coding gene CAD and 28S rDNA to test the monophyly of Asiloidea and to resolve its relationship to Eremoneura. We explore the effects of taxon sampling on support values and topological stability, the resolving power of additional genes, and hypothesis testing using four-cluster likelihood mapping. We find that: (1) the 'asiloid' genus Apystomyia is sister to Cyclorrhapha, (2) the remaining asiloids are monophyletic at the exclusion of the family Bombyliidae, and (3) our best estimate of relationships places the asiloid flies excluding Bombyliidae as the sister-group to Eremoneura, though high support is lacking.
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Affiliation(s)
- Michelle D Trautwein
- Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA.
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95
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Ribosomal protein genes of holometabolan insects reject the Halteria, instead revealing a close affinity of Strepsiptera with Coleoptera. Mol Phylogenet Evol 2010; 55:846-59. [PMID: 20348001 DOI: 10.1016/j.ympev.2010.03.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 02/18/2010] [Accepted: 03/19/2010] [Indexed: 11/23/2022]
Abstract
The phylogenetic relationships among holometabolan insect orders remain poorly known, despite a wealth of previous studies. In particular, past attempts to clarify the sister-group of the enigmatic order Strepsiptera with rRNA genes have led to intense debate about long-branch attraction (the 'Strepsiptera problem'), without resolving the taxonomic question at hand. Here, we appealed to alternative nuclear sequences of 27 ribosomal proteins (RPs) to generate a data matrix of 10,731 nucleotides for 22 holometabolan taxa, including two strepsipteran species. Phylogenetic relationships among holometabolan insects were analyzed under several nucleotide-coding schemes to explore differences in signal and systematic biases. Saturation and compositional bias particularly affected third positions, which greatly differed in AT content (18-72%). Such confounding factors were best reduced by R-Y coding and removal of third codon positions, resulting in more strongly supported topologies, whereas amino acid coding gave poor resolution. The placement of Strepsiptera with Coleoptera (the Coleopterida) was recovered under most coding schemes and analytical methods, if often with modest support and ambiguity. In contrast, an alternative sister-group with Diptera (the Halteria) was only found in one analysis using parsimony, and weakly supported. The topologies here generally support a Coleoptera+Strepsiptera as sister-group to Mecopterida (Siphonaptera+Mecoptera+Diptera+Lepidoptera+Trichoptera), while Hymenoptera were always recovered as sister-group to the remaining Holometabola.
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96
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Can the tight co-speciation between reed beetles (Col., Chrysomelidae, Donaciinae) and their bacterial endosymbionts, which provide cocoon material, clarify the deeper phylogeny of the hosts? Mol Phylogenet Evol 2010; 54:810-21. [DOI: 10.1016/j.ympev.2009.10.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 10/29/2009] [Accepted: 10/31/2009] [Indexed: 11/23/2022]
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97
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Huerta-Cepas J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldón T. The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes. INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 2:13-21. [PMID: 20482636 DOI: 10.1111/j.1365-2583.2009.00947.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phylogenetic analyses serve many purposes, including the establishment of orthology relationships, the prediction of protein function and the detection of important evolutionary events. Within the context of the sequencing of the genome of the pea aphid, Acyrthosiphon pisum, we undertook a phylogenetic analysis for every protein of this species. The resulting phylome includes the evolutionary relationships of all predicted aphid proteins and their homologues among 13 other fully-sequenced arthropods and three out-group species. Subsequent analyses have revealed multiple gene expansions that are specific to aphids and have served to transfer functional annotations to 4058 pea aphid genes that display one-to-one orthology relationships with Drosophila melanogaster annotated genes. All phylogenies and alignments are accessible through the PhylomeDB database. Here we provide a description of this dataset and provide some examples on how can it be exploited.
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98
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Simon S, Schierwater B, Hadrys H. On the value of Elongation factor-1α for reconstructing pterygote insect phylogeny. Mol Phylogenet Evol 2010; 54:651-6. [DOI: 10.1016/j.ympev.2009.09.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 09/12/2009] [Accepted: 09/22/2009] [Indexed: 11/25/2022]
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99
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Phylogenetics of Coenonymphina (Nymphalidae: Satyrinae) and the problem of rooting rapid radiations. Mol Phylogenet Evol 2010; 54:386-94. [DOI: 10.1016/j.ympev.2009.08.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 08/10/2009] [Accepted: 08/12/2009] [Indexed: 11/23/2022]
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100
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Rehan SM, Chapman TW, Craigie AI, Richards MH, Cooper SJB, Schwarz MP. Molecular phylogeny of the small carpenter bees (Hymenoptera: Apidae: Ceratinini) indicates early and rapid global dispersal. Mol Phylogenet Evol 2010; 55:1042-54. [PMID: 20079861 DOI: 10.1016/j.ympev.2010.01.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 12/16/2009] [Accepted: 01/08/2010] [Indexed: 10/19/2022]
Abstract
The small carpenter bees (tribe Ceratinini, family Apidae) are recorded from all continents except Antarctica. The Ceratinini have a near-global distribution which contrasts strongly with their sister tribe, the Allodapini which has a largely southern Old World distribution. The Ceratinini therefore provides an excellent group to understand the factors that help determine the biogeography and radiation of the bees. This is the first molecular study of ceratinine bees covering representatives from both northern and southern hemisphere Old and New World regions. We use two mitochondrial and one nuclear marker (totalling 2807 nucleotides) to examine the age, cladogenesis and historical biogeography of this tribe. Tree topology and molecular dating support an African origin at about 47 Mya with subsequent dispersal into Eurasia 44 Mya, and followed by an American invasion 32 Mya. Concentrated African and Malagasy sampling revealed there were two or three dispersals events into Madagascar ranging from 25 to 9 Mya. Lineage through time analyses suggest higher rates of cladogenesis close to the origin of the tribe, and this corresponds to both major dispersal events and divergences of lineages leading to extant subgenera. Ceratinini have potentially great importance for future studies to understand the relative roles of dispersal ability and time of origin in determining bee biogeography.
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Affiliation(s)
- Sandra M Rehan
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5000, Australia.
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