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Traut W, Sahara K, ffrench-Constant RH. Lepidopteran Synteny Units reveal deep chromosomal conservation in butterflies and moths. G3 (BETHESDA, MD.) 2023; 13:jkad134. [PMID: 37310934 PMCID: PMC10411566 DOI: 10.1093/g3journal/jkad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
DNA is compacted into individual particles or chromosomes that form the basic units of inheritance. However, different animals and plants have widely different numbers of chromosomes. This means that we cannot readily tell which chromosomes are related to which. Here, we describe a simple technique that looks at the similarity of genes on each chromosome and thus gives us a true picture of their homology or similarity through evolutionary time. We use this new system to look at the chromosomes of butterflies and moths or Lepidoptera. We term the associated synteny units, Lepidopteran Synteny Units (LSUs). Using a sample of butterfly and moth genomes from across evolutionary time, we show that LSUs form a simple and reliable method of tracing chromosomal homology back through time. Surprisingly, this technique reveals that butterfly and moth chromosomes show conserved blocks dating back to their sister group the Trichoptera. As Lepidoptera have holocentric chromosomes, it will be interesting to see if similar levels of synteny are shown in groups of animals with monocentric chromosomes. The ability to define homology via LSU analysis makes it considerably easier to approach many questions in chromosomal evolution.
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Affiliation(s)
- Walther Traut
- Institut für Biologie, Zentrum für Medizinische Struktur- und Zellbiologie, Universität zu Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany
| | - Ken Sahara
- Laboratory of Molecular Entomology, Faculty of Agriculture, Iwate University, 3-18-8, Ueda, Morioka 020-8550, Japan
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2
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Laslo M, Just J, Angelini DR. Theme and variation in the evolution of insect sex determination. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:162-181. [PMID: 35239250 PMCID: PMC10078687 DOI: 10.1002/jez.b.23125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022]
Abstract
The development of dimorphic adult sexes is a critical process for most animals, one that is subject to intense selection. Work in vertebrate and insect model species has revealed that sex determination mechanisms vary widely among animal groups. However, this variation is not uniform, with a limited number of conserved factors. Therefore, sex determination offers an excellent context to consider themes and variations in gene network evolution. Here we review the literature describing sex determination in diverse insects. We have screened public genomic sequence databases for orthologs and duplicates of 25 genes involved in insect sex determination, identifying patterns of presence and absence. These genes and a 3.5 reference set of 43 others were used to infer phylogenies and compared to accepted organismal relationships to examine patterns of congruence and divergence. The function of candidate genes for roles in sex determination (virilizer, female-lethal-2-d, transformer-2) and sex chromosome dosage compensation (male specific lethal-1, msl-2, msl-3) were tested using RNA interference in the milkweed bug, Oncopeltus fasciatus. None of these candidate genes exhibited conserved roles in these processes. Amidst this variation we wish to highlight the following themes for the evolution of sex determination: (1) Unique features within taxa influence network evolution. (2) Their position in the network influences a component's evolution. Our analyses also suggest an inverse association of protein sequence conservation with functional conservation.
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Affiliation(s)
- Mara Laslo
- Department of Cell Biology, Curriculum Fellows ProgramHarvard Medical School25 Shattuck StBostonMassachusettsUSA
| | - Josefine Just
- Department of Organismic and Evolutionary BiologyHarvard University26 Oxford StCambridgeMassachusettsUSA
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
| | - David R. Angelini
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
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3
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Winkler IS, Kirk-Spriggs AH, Bayless KM, Soghigian J, Meier R, Pape T, Yeates DK, Carvalho AB, Copeland RS, Wiegmann BM. Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae. PLoS One 2022; 17:e0274292. [PMID: 36197946 PMCID: PMC9534441 DOI: 10.1371/journal.pone.0274292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/26/2022] [Indexed: 11/05/2022] Open
Abstract
The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae-the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.
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Affiliation(s)
- Isaac S. Winkler
- Department of Biology, Cornell College, Mount Vernon, Iowa, United States of America
| | | | - Keith M. Bayless
- Australian National Insect Collection, CSIRO National Research Collection, Australia (NRCA), Acton, Canberra, ACT, Australia
| | - John Soghigian
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thomas Pape
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - David K. Yeates
- Australian National Insect Collection, CSIRO National Research Collection, Australia (NRCA), Acton, Canberra, ACT, Australia
| | - A. Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robert S. Copeland
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Brian M. Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
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4
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Artificial intelligence versus natural selection: Using computer vision techniques to classify bees and bee mimics. iScience 2022; 25:104924. [PMID: 36060073 PMCID: PMC9437854 DOI: 10.1016/j.isci.2022.104924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/19/2022] [Accepted: 08/09/2022] [Indexed: 12/04/2022] Open
Abstract
Many groups of stingless insects have independently evolved mimicry of bees to fool would-be predators. To investigate this mimicry, we trained artificial intelligence (AI) algorithms—specifically, computer vision—to classify citizen scientist images of bees, bumble bees, and diverse bee mimics. For detecting bees and bumble bees, our models achieved accuracies of 91.71% and 88.86%, respectively. As a proxy for a natural predator, our models were poorest in detecting bee mimics that exhibit both aggressive and defensive mimicry. Using the explainable AI method of class activation maps, we validated that our models learn from appropriate components within the image, which in turn provided anatomical insights. Our t-SNE plot yielded perfect within-group clustering, as well as between-group clustering that grossly replicated the phylogeny. Ultimately, the transdisciplinary approaches herein can enhance global citizen science efforts as well as investigations of mimicry and morphology of bees and other insects. AI models for classifying bees and bumble bees achieved 92% and 89% accuracy AI models were fooled most by bee mimics exhibiting both aggressive and defensive mimicry Class activation maps explained the anatomical reasoning of AI model classifications t-SNE plot exhibited perfect phylogenetic clustering within and between groups
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5
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Peach DA, Matthews BJ. Sensory mechanisms for the shift from phytophagy to haematophagy in mosquitoes. CURRENT OPINION IN INSECT SCIENCE 2022; 52:100930. [PMID: 35580800 DOI: 10.1016/j.cois.2022.100930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The Culicomorpha are an infraorder of several families of blood-feeding flies, including mosquitoes (Diptera: Culicidae). Here we discuss the evolutionary origins of blood-feeding within the Culicomorpha and review literature that suggests this behaviour may have evolved from ancestral plant-feeding or a combination of plant-feeding and insect-feeding. Sialomic and life-history evidence suggest that plant-feeding, concurrent or not with insect-feeding, is parsimonious as an ancestral diet for Culicomorpha. We review the chemical parsimony observed between vertebrate headspace odours, floral headspace odours, and honeydew headspace odours, which are behaviourally attractive to many of the Culicomorpha. We also review the sensory and neural mechanisms involved in changes in olfactory attraction and we propose this observed chemical parsimony as a hypothesis for an associative mechanism which may have led to the development of blood-feeding from plant-feeding that is consistent with a 'path of least resistance' for the sensory changes necessary to undergo host shifts.
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Affiliation(s)
- Daniel Ah Peach
- The University of British Columbia, Department of Zoology, 4200-6270 University Blvd, Vancouver, BC V6T1Z4, Canada.
| | - Benjamin J Matthews
- The University of British Columbia, Department of Zoology, 4200-6270 University Blvd, Vancouver, BC V6T1Z4, Canada.
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6
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Towett-Kirui S, Morrow JL, Riegler M. Substantial rearrangements, single nucleotide frameshift deletion and low diversity in mitogenome of Wolbachia-infected strepsipteran endoparasitoid in comparison to its tephritid hosts. Sci Rep 2022; 12:477. [PMID: 35013476 PMCID: PMC8748643 DOI: 10.1038/s41598-021-04398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/21/2021] [Indexed: 12/01/2022] Open
Abstract
Insect mitogenome organisation is highly conserved, yet, some insects, especially with parasitic life cycles, have rearranged mitogenomes. Furthermore, intraspecific mitochondrial diversity can be reduced by fitness-affecting bacterial endosymbionts like Wolbachia due to their maternal coinheritance with mitochondria. We have sequenced mitogenomes of the Wolbachia-infected endoparasitoid Dipterophagus daci (Strepsiptera: Halictophagidae) and four of its 22 known tephritid fruit fly host species using total genomic extracts of parasitised flies collected across > 700 km in Australia. This halictophagid mitogenome revealed extensive rearrangements relative to the four fly mitogenomes which exhibited the ancestral insect mitogenome pattern. Compared to the only four available other strepsipteran mitogenomes, the D. daci mitogenome had additional transpositions of one rRNA and two tRNA genes, and a single nucleotide frameshift deletion in nad5 requiring translational frameshifting or, alternatively, resulting in a large protein truncation. Dipterophagus daci displays an almost completely endoparasitic life cycle when compared to Strepsiptera that have maintained the ancestral state of free-living adults. Our results support the hypothesis that the transition to extreme endoparasitism evolved together with increased levels of mitogenome changes. Furthermore, intraspecific mitogenome diversity was substantially smaller in D. daci than the parasitised flies suggesting Wolbachia reduced mitochondrial diversity because of a role in D. daci fitness.
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Affiliation(s)
- Sharon Towett-Kirui
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Jennifer L Morrow
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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7
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Albayrak T, Yorulmaz S, İnak E, Toprak U, Van Leeuwen T. Pirimicarb resistance and associated mechanisms in field-collected and selected populations of Neoseiulus californicus. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 180:104984. [PMID: 34955177 DOI: 10.1016/j.pestbp.2021.104984] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 06/14/2023]
Abstract
The predatory mite Neoseiulus californicus McGregor (Acari: Phytoseiidae) is an important natural enemy of phytophagous mites, and naturally established populations are often found in apple orchards. However, insecticide applications to control pests cause side effects to non-target organisms such as N. californicus. Pirimicarb, a widely used carbamate insecticide in apple orchards, is generally considered a selective aphidicide, however, toxicity to beneficial insects and predatory mites has been reported. Furthermore, the molecular basis for this selectivity, if present in N. californicus, is still largely unknown. In this study, 8 field-collected N. californicus populations were investigated and showed up to 27-fold resistance compared to a susceptible laboratory population. Selection in the laboratory for 5 consecutive generations resulted in a 69-fold pirimicarb resistance. Although there were no significant difference in terms of the acetlycholinesterase (AChE) activity between susceptible and field-collected populations, the selected population exhibited a significantly higher AChE activity. In addition, gene copy number variation of acetylcholinesterase (ace) gene among populations was detected and ranged from 1.6 to 2.1-fold relative to the susceptible population. All field-collected populations, but not the selected population, had a significantly higher ace copy number compared to the susceptible population (t-test, p < 0.05). Molecular analysis of the target-site (AChE) revealed, for the first time, a phenylalanine to tryptophan substition at position 331 in AChE (Torpedo californica numbering), both in field-collected and the selected population, but not in the susceptible population. Last, the selected F5 population consumed significantly more Tetranychusurticae adults than the parental population. Together, the results of this study shed light on the molecular determinants of acaricide selectivity in predatory mites, and will contribute to a better design of an integrated mite management program, including the use of pesticide resistant N. californicus in apple orchards.
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Affiliation(s)
- Tuba Albayrak
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Isparta University of Applied Sciences, Isparta, Turkey
| | - Sibel Yorulmaz
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Isparta University of Applied Sciences, Isparta, Turkey
| | - Emre İnak
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Diskapi, 06110 Ankara, Turkey
| | - Umut Toprak
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Diskapi, 06110 Ankara, Turkey
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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8
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Pohl H, Wipfler B, Boudinot B, Georg Beutel R. On the value of Burmese amber for understanding insect evolution: Insights from †Heterobathmilla - an exceptional stem group genus of Strepsiptera (Insecta). Cladistics 2021; 37:211-229. [PMID: 34478185 DOI: 10.1111/cla.12433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Burmese amber and amber from other periods and regions became a rich source of new extinct insect species and yielded important insights in insect evolution in the dimension of time. Amber fossils have contributed to the understanding of the phylogeny, biology, and biogeography of insects and other groups, and have also gained great importance for dating molecular trees. Another major potential is the documentation of faunal, floral and climatic shifts. Evolutionary transitions can be well-documented in amber fossils and can reveal anatomical transformations and the age of appearance of structural features. Here, using a new stem group species of Strepsiptera from Burmite, we evaluate this potential of amber insect fossils to assess the current phylogeny of Strepsiptera, with the main emphasis on the early splitting events in the stem group. Amber fossils have greatly contributed to the understanding of the evolution of Strepsiptera in the late Mesozoic and the Cenozoic. †Heterobathmilla kakopoios Pohl and Beutel gen. et sp. n. described here is placed in the stem group of the order, in a clade with †Kinzelbachilla (†Kinzelbachillidae) and †Phthanoxenos (†Phthanoxenidae). †Phthanoxenidae has priority over †Kinzelbachillidae, and the latter is synonymised. The superb details available from this new fossil allowed us to explore unique features of the antennae, mouthparts, and male copulatory apparatus, and to provide a phylogenetic hypothesis for the order. The younger †Protoxenos from Eocene Baltic amber was confirmed as sister to all remaining extinct and extant groups of Strepsiptera, whereas the position of the Cretaceous †Cretostylops in the stem group remains ambivalent. While the value of Burmite and amber from other periods has a recognized impact on our knowledge of the evolution in various lineages, this new fossil does not fundamentally change our picture of the phylogeny and evolution of early Strepsiptera. However, it offers new insights into the morphological diversity in the early evolution of the group.
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Affiliation(s)
- Hans Pohl
- Entomology Group, Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Erbertstrasse 1, Jena, D-07743, Germany
| | | | - Brendon Boudinot
- Department of Entomology/Nematology, University of California, One Shields Ave., Davis,Davis, CA, 95616, USA
| | - Rolf Georg Beutel
- Entomology Group, Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Erbertstrasse 1, Jena, D-07743, Germany
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9
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Beutel RG, Friedrich F, Economo EP. Patterns of morphological simplification and innovation in the megadiverse Holometabola (Insecta). Cladistics 2021; 38:227-245. [DOI: 10.1111/cla.12483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rolf Georg Beutel
- Entomology Group Institut für Zoologie und Evolutionsforschung Friedrich‐Schiller‐Universität Jena Erbertstrasse 1 Jena D‐07743 Germany
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University 1919‐1 Tancha, Onna‐son Kunigami‐gun Okinawa 904‐0495 Japan
| | - Frank Friedrich
- Institut für Zoologie Universität Hamburg Martin‐Luther‐King‐Platz 3 Hamburg D‐20146 Germany
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University 1919‐1 Tancha, Onna‐son Kunigami‐gun Okinawa 904‐0495 Japan
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10
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Moreira F, Arenas M, Videira A, Pereira F. Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. J Mol Evol 2021; 89:384-395. [PMID: 33999213 DOI: 10.1007/s00239-021-10011-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/30/2021] [Indexed: 12/14/2022]
Abstract
DNA topoisomerase III beta (TOP3B) is unique by operating on both DNA and RNA substrates to regulate gene expression and genomic stability. Mutations in human TOP3B are linked to neurodevelopmental and cognitive disorders, highlighting its relevance for human health. Despite the emerging importance of TOP3B, its precise cellular functions and evolutionary history remain poorly understood. Here, we show that TOP3B is conserved across main metazoan groups and evolved under strong purifying selection. Subdomain IV was identified as the most conserved TOP3B region, in agreement with its role in providing the structural foundation of the protein. On the contrary, subdomain II is the less conserved, possibly because it is the most structurally flexible region of all TOP3B regions. Interestingly, TOP3B residue at position 472, previously associated with schizophrenia, is highly variable across animals, suggesting a more specific role in humans and related species. Finally, we show that all TOP3B CXXC zinc finger motifs previously identified at the protein C-terminal region are retained across metazoans. We also found that the two major methylation sites known to regulate TOP3B activity are located in the most conserved region of the C-terminal arginine-glycine-glycine (RGG) box, suggesting that a similar regulatory mechanism may operate throughout animals. Overall, our results provide a better understanding of the evolution and functional roles of TOP3B.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 36310, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal. .,Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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11
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Fischer S, Laue M, Müller CHG, Meinertzhagen IA, Pohl H. Ultrastructural 3D reconstruction of the smallest known insect photoreceptors: The stemmata of a first instar larva of Strepsiptera (Hexapoda). ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 62:101055. [PMID: 33975098 DOI: 10.1016/j.asd.2021.101055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Stemmata of strepsipteran insects represent the smallest arthropod eyes known, having photoreceptors which form fused rhabdoms measuring an average size of 1.69 × 1.21 × 1.04 μm and each occupying a volume of only 0.97-1.16 μm3. The morphology of the stemmata of the extremely miniaturized first instar larva of Stylops ovinae (Strepsiptera, Stylopidae) was investigated using serial-sectioning transmission electron microscopy (ssTEM). Our 3D reconstruction revealed that, despite different proportions, all three stemmata maintain the same organization: a biconvex corneal lens, four corneagenous cells and five photoreceptor (retinula) cells. No pigment-containing cell-types were found to adjoin the corneagenous cells. Whereas the retinula cells are adapted to the limited space by having laterally bulged median regions, containing mitochondria and the smallest nuclei yet reported for arthropods (1.37 μm3), special adaptations are found in the corneagenous cells which have cell volumes down to 1 μm3. The corneagenous cells lack nuclei and pigment granules and bear only a few mitochondria (up to three) or none at all. Morphological adaptations due to miniaturization are discussed in the context of photoreceptor function and the visual needs of the larva.
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Affiliation(s)
- Stefan Fischer
- Tübingen Structural Microscopy Core Facility, Center for Applied Geoscience, Eberhard-Karls-University Tübingen, Schnarrenbergstrasse 94-96, 72076 Tübingen, Germany; Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, NS, Canada B3H 4R2.
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Robert Koch-Institut, Seestr. 10, 13353 Berlin, Germany
| | - Carsten H G Müller
- Zoological Institute and Museum, Department of General and Systematic Zoology, University of Greifswald, Loitzer Str. 26, 17489 Greifswald, Germany
| | - Ian A Meinertzhagen
- Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, NS, Canada B3H 4R2
| | - Hans Pohl
- Entomology Group, Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
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12
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Smýkal V, Pivarči M, Provazník J, Bazalová O, Jedlička P, Lukšan O, Horák A, Vaněčková H, Beneš V, Fiala I, Hanus R, Doležel D. Complex Evolution of Insect Insulin Receptors and Homologous Decoy Receptors, and Functional Significance of Their Multiplicity. Mol Biol Evol 2021; 37:1775-1789. [PMID: 32101294 PMCID: PMC7253209 DOI: 10.1093/molbev/msaa048] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Evidence accumulates that the functional plasticity of insulin and insulin-like growth factor signaling in insects could spring, among others, from the multiplicity of insulin receptors (InRs). Their multiple variants may be implemented in the control of insect polyphenism, such as wing or caste polyphenism. Here, we present a comprehensive phylogenetic analysis of insect InR sequences in 118 species from 23 orders and investigate the role of three InRs identified in the linden bug, Pyrrhocoris apterus, in wing polymorphism control. We identified two gene clusters (Clusters I and II) resulting from an ancestral duplication in a late ancestor of winged insects, which remained conserved in most lineages, only in some of them being subject to further duplications or losses. One remarkable yet neglected feature of InR evolution is the loss of the tyrosine kinase catalytic domain, giving rise to decoys of InR in both clusters. Within the Cluster I, we confirmed the presence of the secreted decoy of insulin receptor in all studied Muscomorpha. More importantly, we described a new tyrosine kinase-less gene (DR2) in the Cluster II, conserved in apical Holometabola for ∼300 My. We differentially silenced the three P. apterus InRs and confirmed their participation in wing polymorphism control. We observed a pattern of Cluster I and Cluster II InRs impact on wing development, which differed from that postulated in planthoppers, suggesting an independent establishment of insulin/insulin-like growth factor signaling control over wing development, leading to idiosyncrasies in the co-option of multiple InRs in polyphenism control in different taxa.
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Affiliation(s)
- Vlastimil Smýkal
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Martin Pivarči
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Jan Provazník
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Olga Bazalová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Pavel Jedlička
- Chemistry of Social Insects, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondřej Lukšan
- Chemistry of Social Insects, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Hana Vaněčková
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Vladimír Beneš
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ivan Fiala
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Robert Hanus
- Chemistry of Social Insects, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Doležel
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic.,Department of Molecular Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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13
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Medina Munoz M, Spencer N, Enomoto S, Dale C, Rio RVM. Quorum sensing sets the stage for the establishment and vertical transmission of Sodalis praecaptivus in tsetse flies. PLoS Genet 2020; 16:e1008992. [PMID: 32797092 PMCID: PMC7449468 DOI: 10.1371/journal.pgen.1008992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial virulence factors facilitate host colonization and set the stage for the evolution of parasitic and mutualistic interactions. The Sodalis-allied clade of bacteria exhibit striking diversity in the range of both plant and animal feeding insects they inhabit, suggesting the appropriation of universal molecular mechanisms that facilitate establishment. Here, we report on the infection of the tsetse fly by free-living Sodalis praecaptivus, a close relative of many Sodalis-allied symbionts. Key genes involved in quorum sensing, including the homoserine lactone synthase (ypeI) and response regulators (yenR and ypeR) are integral for the benign colonization of S. praecaptivus. Mutants lacking ypeI, yenR and ypeR compromised tsetse survival as a consequence of their inability to repress virulence. Genes under quorum sensing, including homologs of the binary insecticidal toxin PirAB and a putative symbiosis-promoting factor CpmAJ, demonstrated negative and positive impacts, respectively, on tsetse survival. Taken together with results obtained from experiments involving weevils, this work shows that quorum sensing virulence suppression plays an integral role in facilitating the establishment of Sodalis-allied symbionts in diverse insect hosts. This knowledge contributes to the understanding of the early evolutionary steps involved in the formation of insect-bacterial symbiosis. Further, despite having no established history of interaction with tsetse, S. praecaptivus can infect reproductive tissues, enabling vertical transmission through adenotrophic viviparity within a single host generation. This creates an option for the use of S. praecaptivus in the biocontrol of insect disease vectors via paratransgenesis.
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Affiliation(s)
- Miguel Medina Munoz
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Noah Spencer
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Shinichiro Enomoto
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Colin Dale
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Rita V. M. Rio
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
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14
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van der Burg KRL, Lewis JJ, Martin A, Nijhout HF, Danko CG, Reed RD. Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis. Cell Rep 2020; 27:1027-1038.e3. [PMID: 31018121 DOI: 10.1016/j.celrep.2019.03.092] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/22/2019] [Accepted: 03/25/2019] [Indexed: 01/24/2023] Open
Abstract
Development requires highly coordinated changes in chromatin accessibility in order for proper gene regulation to occur. Here, we identify factors associated with major, discrete changes in chromatin accessibility during butterfly wing metamorphosis. By combining mRNA sequencing (mRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and machine learning analysis of motifs, we show that distinct sets of transcription factors are predictive of chromatin opening at different developmental stages. Our data suggest an important role for nuclear hormone receptors early in metamorphosis, whereas PAS-domain transcription factors are strongly associated with later chromatin opening. Chromatin immunoprecipitation sequencing (ChIP-seq) validation of select candidate factors showed spineless binding to be a major predictor of opening chromatin. Surprisingly, binding of ecdysone receptor (EcR), a candidate accessibility factor in Drosophila, was not predictive of opening but instead marked persistent sites. This work characterizes the chromatin dynamics of insect wing metamorphosis, identifies candidate chromatin remodeling factors in insects, and presents a genome assembly of the model butterfly Junonia coenia.
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Affiliation(s)
- Karin R L van der Burg
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA; Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | | | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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15
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Vasilikopoulos A, Misof B, Meusemann K, Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U. An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). BMC Evol Biol 2020; 20:64. [PMID: 32493355 PMCID: PMC7268685 DOI: 10.1186/s12862-020-01631-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations. RESULTS Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera. CONCLUSION Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.
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Affiliation(s)
- Alexandros Vasilikopoulos
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
- Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Doria Lieberz
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743, Jena, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum Darmstadt, 64283, Darmstadt, Germany
| | - Jes Rust
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Ralph S Peters
- Centre for Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325, Frankfurt, Germany
| | - James E Jepson
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, T23 N73K, Cork, Ireland
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), 1090, Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
- Zoological Department II, Natural History Museum of Vienna, 1010, Vienna, Austria
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16
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Miyata MN, Kageyama D, Nomura M. Multiplex PCR for identification of two butterfly sister species: Eurema mandarina and Eurema hecabe. BMC Res Notes 2020; 13:260. [PMID: 32460868 PMCID: PMC7251659 DOI: 10.1186/s13104-020-05093-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/16/2020] [Indexed: 11/18/2022] Open
Abstract
Objective In insects, closely related species are often difficult or impossible to distinguish solely by morphological traits. Mitochondrial DNA (mtDNA) markers are often useful and reliable for distinguishing closely related species. However, useful mtDNA markers can be unavailable, particularly when such species pairs experienced hybrid introgression in the past. Although polymorphic nuclear DNA markers would be necessary to distinguish such species pairs, recombination, multiple copies, and slower mutation rates of the nuclear DNA compared with those of mtDNA often make it challenging. The objective of this study was to develop a multiplex polymerase chain reaction that can reliably amplify and distinguish the Tpi sequences of Eurema mandarina and Eurema hecabe. Results We successfully analyzed the nucleotide sequences of the Z chromosome-linked triose phosphate isomerase (Tpi) gene to develop a multiplex polymerase chain reaction (PCR) that amplified ca. 120-bp products for E. mandarina and ca. 375-bp products for E. hecabe. We suggest that multiplex PCR using Tpi with appropriately designed primers can be used to accurately and reliably distinguish between other closely related Lepidoptera species.
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Affiliation(s)
- Mai N Miyata
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8510, Japan
| | - Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-0851, Japan.
| | - Masashi Nomura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8510, Japan.
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17
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Gäde G, Šimek P, Marco HG. The Adipokinetic Peptides in Diptera: Structure, Function, and Evolutionary Trends. Front Endocrinol (Lausanne) 2020; 11:153. [PMID: 32296388 PMCID: PMC7136388 DOI: 10.3389/fendo.2020.00153] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Nineteen species of various families of the order Diptera and one species from the order Mecoptera are investigated with mass spectrometry for the presence and primary structure of putative adipokinetic hormones (AKHs). Additionally, the peptide structure of putative AKHs in other Diptera are deduced from data mining of publicly available genomic or transcriptomic data. The study aims to demonstrate the structural biodiversity of AKHs in this insect order and also possible evolutionary trends. Sequence analysis of AKHs is achieved by liquid chromatography coupled to mass spectrometry. The corpora cardiaca of almost all dipteran species contain AKH octapeptides, a decapeptide is an exception found only in one species. In general, the dipteran AKHs are order-specific- they are not found in any other insect order with two exceptions only. Four novel AKHs are revealed by mass spectrometry: two in the basal infraorder of Tipulomorpha and two in the brachyceran family Syrphidae. Data mining revealed another four novel AKHs: one in various species of the infraorder Culicumorpha, one in the brachyceran superfamily Asiloidea, one in the family Diopsidae and in a Drosophilidae species, and the last of the novel AKHs is found in yet another Drosophila. In general, there is quite a biodiversity in the lower Diptera, whereas the majority of the cyclorraphan Brachycera produce the octapeptide Phote-HrTH. A hypothetical molecular peptide evolution of dipteran AKHs is suggested to start with an ancestral AKH, such as Glomo-AKH, from which all other AKHs in Diptera to date can evolve via point mutation of one of the base triplets, with one exception.
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Affiliation(s)
- Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Petr Šimek
- Biology Centre, Czech Academy of Sciences, Ceské Budejovice, Czechia
| | - Heather G. Marco
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
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18
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Hua Y, Zhang BB, Miao Y, Hua BZ, Tao SH. Vasa deferentia and associated structures of the male Panorpodes kuandianensis (Mecoptera: Panorpodidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2020; 55:100926. [PMID: 32172209 DOI: 10.1016/j.asd.2020.100926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
The male reproductive system may provide significant evidence for the taxonomic and phylogenetic analyses of insects. However, current knowledge of the male reproductive system in Mecoptera is mainly concentrated on the external genitalia, and is rarely involved in the internal reproductive system. Here, we investigated the morphology and the fine structure of the vasa deferentia and associated structures of the male reproductive system of Panorpodes kuandianensis Zhong et al., 2011 (Panorpodidae) using light, scanning, and transmission electron microscopy. The male reproductive system of P. kuandianensis consists of a pair of symmetrical testes with three tubular testicular follicles, two epididymides, two distinctly partitioned vasa deferentia, a pair of mesadenia, one ejaculatory sac, and the external genitalia. A pair of expanded seminal vesicles are modified from the median part of the vasa deferentia, and evolve into secretory organs. The seminal vesicles have elongated cylindrical epithelial cells, which contain abundant secretory materials in the cytoplasm and form a small central lumen, likely serving a secretory function rather than provisionally storing sperm as in most other insects. Alternatively, the sperm are stored temporarily in the epididymis, the greatly coiled portion of the vasa deferentia. The morphology of the male reproductive system supports the close relationships of Panorpidae and Panorpodidae.
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Affiliation(s)
- Yuan Hua
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bei-Bei Zhang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Institute of Tropical Agriculture and Forestry, Hainan University, Danzhou, Hainan 571737, China
| | - Ying Miao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bao-Zhen Hua
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shi-Heng Tao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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19
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Meng J, Lei J, Davitt A, Holt JR, Huang J, Gold R, Vargo EL, Tarone AM, Zhu-Salzman K. Suppressing tawny crazy ant (Nylanderia fulva) by RNAi technology. INSECT SCIENCE 2020; 27:113-121. [PMID: 29790281 DOI: 10.1111/1744-7917.12604] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
The tawny crazy ant (Nylanderia fulva) is a new invasive pest in the United States. At present, its management mainly relies on the use of synthetic insecticides, which are generally ineffective at producing lasting control of the pest, necessitating alternative environmentally friendly measures. In this study, we evaluated the feasibility of gene silencing to control this ant species. Six housekeeping genes encoding actin (NfActin), coatomer subunit β (NfCOPβ), arginine kinase (NfArgK), and V-type proton ATPase subunits A (NfvATPaseA), B (NfvATPaseB) and E (NfvATPaseE) were cloned. Phylogenetic analysis revealed high sequence similarity to homologs from other ant species, particularly the Florida carpenter ant (Camponotus floridanus). To silence these genes, vector L4440 was used to generate six specific RNAi constructs for bacterial expression. Heat-inactivated, dsRNA-expressing Escherichia coli were incorporated into artificial diet. Worker ants exhibited reduced endogenous gene expression after feeding on such diet for 9 d. However, only ingestion of dsRNAs of NfCOPβ (a gene involved in protein trafficking) and NfArgK (a cellular energy reserve regulatory gene in invertebrates) caused modest but significantly higher ant mortality than the control. These results suggest that bacterially expressed dsRNA can be orally delivered to ant cells as a mean to target its vulnerabilities. Improved efficacy is necessary for the RNAi-based approach to be useful in tawny crazy ant management.
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Affiliation(s)
- Jia Meng
- College of Plant Protection, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
- Department of Entomology, Texas A&M University, College Station, Texas, USA
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, Texas, USA
| | - Jiaxin Lei
- Department of Entomology, Texas A&M University, College Station, Texas, USA
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, Texas, USA
| | - Andrew Davitt
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Jocelyn R Holt
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Jian Huang
- College of Plant Protection, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Roger Gold
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Edward L Vargo
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Aaron M Tarone
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M University, College Station, Texas, USA
- Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, Texas, USA
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20
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Meisel RP, Delclos PJ, Wexler JR. The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence. BMC Biol 2019; 17:100. [PMID: 31806031 PMCID: PMC6894488 DOI: 10.1186/s12915-019-0721-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022] Open
Abstract
Background Sex chromosome evolution is a dynamic process that can proceed at varying rates across lineages. For example, different chromosomes can be sex-linked between closely related species, whereas other sex chromosomes have been conserved for > 100 million years. Cases of long-term sex chromosome conservation could be informative of factors that constrain sex chromosome evolution. Cytological similarities between the X chromosomes of the German cockroach (Blattella germanica) and most flies suggest that they may be homologous—possibly representing an extreme case of long-term conservation. Results To test the hypothesis that the cockroach and fly X chromosomes are homologous, we analyzed whole-genome sequence data from cockroaches. We found evidence in both sequencing coverage and heterozygosity that a significant excess of the same genes are on both the cockroach and fly X chromosomes. We also present evidence that the candidate X-linked cockroach genes may be dosage compensated in hemizygous males. Consistent with this hypothesis, three regulators of transcription and chromatin on the fly X chromosome are conserved in the cockroach genome. Conclusions Our results support our hypothesis that the German cockroach shares the same X chromosome as most flies. This may represent the convergent evolution of the X chromosome in the lineages leading to cockroaches and flies. Alternatively, the common ancestor of most insects may have had an X chromosome that resembled the extant cockroach and fly X. Cockroaches and flies diverged ∼ 400 million years ago, which would be the longest documented conservation of a sex chromosome. Cockroaches and flies have different mechanisms of sex determination, raising the possibility that the X chromosome was conserved despite the evolution of the sex determination pathway.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd., Houston, 77204, TX, USA.
| | - Pablo J Delclos
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd., Houston, 77204, TX, USA
| | - Judith R Wexler
- Department of Ecology and Evolution, University of California, Davis, One Shields Ave, Davis, 95616, CA, USA.,Department of Entomology, University of Maryland, 4112 Plant Sciences Building, College Park, 20742, MD, USA
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21
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Rödelsperger C, Prabh N, Sommer RJ. New Gene Origin and Deep Taxon Phylogenomics: Opportunities and Challenges. Trends Genet 2019; 35:914-922. [DOI: 10.1016/j.tig.2019.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/29/2019] [Indexed: 01/22/2023]
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22
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Cuquetto‐Leite L, Barbosa A, Salles FF, Mancini KC. Sperm Ultrastructure of corydalid
Corydalus diasi
Navás (Megaloptera, Neuropterida, Insecta) with phylogenetic considerations. ACTA ZOOL-STOCKHOLM 2019. [DOI: 10.1111/azo.12312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lívia Cuquetto‐Leite
- Department of Structural and Functional Biology Campinas State University (UNICAMP) Campinas São Paulo Brazil
| | - Aline Barbosa
- Department of Agrarian and Biological Sciences Federal University of Espírito Santo (UFES) São Mateus Espírito Santo Brazil
| | | | - Karina Carvalho Mancini
- Department of Agrarian and Biological Sciences Federal University of Espírito Santo (UFES) São Mateus Espírito Santo Brazil
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23
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Montagna M, Tong KJ, Magoga G, Strada L, Tintori A, Ho SYW, Lo N. Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction. Proc Biol Sci 2019; 286:20191854. [PMID: 31594499 PMCID: PMC6790769 DOI: 10.1098/rspb.2019.1854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland-Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised time scale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera: Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.
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Affiliation(s)
- Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - K. Jun Tong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Laura Strada
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Andrea Tintori
- Dipartimento di Scienze della Terra ‘Ardito Desio’, Università degli Studi di Milano, Via Mangiagalli 34, 20133 Milano, Italy
| | - Simon Y. W. Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Sydney, Australia
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Wang Y, White MM, Moncalvo JM. Diversification of the gut fungi Smittium and allies (Harpellales) co-occurred with the origin of complete metamorphosis of their symbiotic insect hosts (lower Diptera). Mol Phylogenet Evol 2019; 139:106550. [DOI: 10.1016/j.ympev.2019.106550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 05/30/2019] [Accepted: 06/28/2019] [Indexed: 01/26/2023]
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25
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Li N, Hu GL, Hua BZ. Complete mitochondrial genomes of Bittacus strigosus and Panorpa debilis and genomic comparisons of Mecoptera. Int J Biol Macromol 2019; 140:672-681. [PMID: 31437496 DOI: 10.1016/j.ijbiomac.2019.08.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/17/2019] [Accepted: 08/17/2019] [Indexed: 11/19/2022]
Abstract
Mitochondrial genomes play a significant role in reconstructing phylogenetic relationships and revealing molecular evolution of insects. However, only four mitochondrial genomes were reported in Mecoptera to date. Here, we obtained two new complete mitochondrial genomes of the hangingfly Bittacus strigosus Hagen, 1861 and the scorpionfly Panorpa debilis Westwood, 1846. The results show that the complete mitogenome sequences of B. strigosus and P. debilis are 15,825 and 17,018 bp, respectively, both containing 37 genes and one control region. The mecopteran mitogenomes are highly similar in A + T bias, AT-skew, and GC-skew. Tandem repeats of the control region were discovered in Mecoptera for the first time. The sliding window, genetic distance, and Ka/Ks ratio analyses indicate the purifying selection of 13 protein-coding genes, the lowest evolutionary rate of cox1, and the highest sequence variability of atp8. Considering the sufficiently large size, fast evolution, and high ratio of Ka/Ks, nad4L and nad6 are regarded as potential markers for future phylogenetic analyses, population genetics, and species delimitations in Mecoptera. The phylogenetic relationships were reconstructed for four families of Mecoptera based on all six available mitogenomes using Bayesian inference and maximum likelihood methods. The phylogeny is presented as Boreidae + (Nannochoristidae + (Bittacidae + Panorpidae)).
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Affiliation(s)
- Ning Li
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gui-Lin Hu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bao-Zhen Hua
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Bascompte J, García MB, Ortega R, Rezende EL, Pironon S. Mutualistic interactions reshuffle the effects of climate change on plants across the tree of life. SCIENCE ADVANCES 2019; 5:eaav2539. [PMID: 31106269 PMCID: PMC6520021 DOI: 10.1126/sciadv.aav2539] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/11/2019] [Indexed: 05/27/2023]
Abstract
Climatically induced local species extinctions may trigger coextinction cascades, thus driving many more species to extinction than originally predicted by species distribution models. Using seven pollination networks across Europe that include the phylogeny and life history traits of plants, we show a substantial variability across networks in climatically predicted plant extinction-and particularly the subsequent coextinction-rates, with much higher values in Mediterranean than Eurosiberian networks. While geographic location best predicts the probability of a plant species to be driven to extinction by climate change, subsequent coextinctions are best predicted by the local network of interactions. These coextinctions not only increase the total number of plant species being driven to extinction but also add a bias in the way the major taxonomic and functional groups are pruned.
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Affiliation(s)
- Jordi Bascompte
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - María B. García
- Instituto Pirenaico de Ecología (IPE-CSIC), Apartado 13034, E-50080 Zaragoza, Spain
| | - Raúl Ortega
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Enrico L. Rezende
- Department of Life Sciences, University of Roehampton, Holybourne Avenue, London SW15 4JD, UK
| | - Samuel Pironon
- Instituto Pirenaico de Ecología (IPE-CSIC), Apartado 13034, E-50080 Zaragoza, Spain
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27
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Tröger D, Beutel RG, Pohl H. The abdomen of a free-living female of Strepsiptera and the evolution of the birth organs. J Morphol 2019; 280:739-755. [PMID: 30892750 DOI: 10.1002/jmor.20981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 02/01/2023]
Abstract
Mengenillidae is a small, basal family of Strepsiptera, mainly characterized by free-living females in contrast to the endoparasitic females of Stylopidia. Here, we describe external and internal structures of the female abdomen of Eoxenos laboulbenei (Mengenillidae). The external morphology was examined and documented using microphotography. Internal structures were reconstructed three-dimensionally using a μCT-data set. The morphologically simplified abdomen comprises 10 segments. The integument is weakly sclerotized and flexible. Spiracles are present dorsolaterally on segments I-VII. Segment VII bears the posteroventral birth opening and the small abdominal segment X carries the anus at its apex. Numerous eggs float freely in the hemolymph. The musculature of segments I-IV is composed of ventral and dorsal longitudinal muscle bundles, strongly developed paramedial dorsoventral muscles and a complex meshwork of small pleural muscles, with minimal differences between the segments. Segments V-X contain more than 50 individual muscles, even though the musculature as a whole is weakly developed. Even though it is not involved in processing food, the digestive tract is well-developed. Its postabdominal section comprises a part of the midgut and the short hindgut. The midgut fills a large part of the postabdominal lumen. The lumina of the midgut and hindgut are not connected. Five or six nodular Malpighian tubules open into the digestive tract at the border region between the midgut and hindgut. The birth organ below the midgut releases the primary larvae after hatching via the birth opening at segment VII. It is likely derived from primary female genital ducts. The presence of six additional birth organs of segments I-VI are de novo formations and a groundplan apomorphy of Stylopidia, the large strepsipteran subgroup with endoparasitic females. The loss of the primary birth organ of segment VII is an apomorphy of Stylopiformia (Stylopidia excl. Corioxenidae).
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Affiliation(s)
- Daniel Tröger
- Entomology Group, Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Rolf G Beutel
- Entomology Group, Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Hans Pohl
- Entomology Group, Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
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Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A. Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. Int J Mol Sci 2019; 20:E1072. [PMID: 30832228 PMCID: PMC6429444 DOI: 10.3390/ijms20051072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 11/30/2022] Open
Abstract
Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.
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Affiliation(s)
- Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
- Department of Entomology, China Agricultural University, Beijing 100193, China.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China.
| | - Liming Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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Sequence and structural properties of circular RNAs in the brain of nurse and forager honeybees (Apis mellifera). BMC Genomics 2019; 20:88. [PMID: 30683059 PMCID: PMC6347836 DOI: 10.1186/s12864-018-5402-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022] Open
Abstract
Background The honeybee (Apis mellifera) represents a model organism for social insects displaying behavioral plasticity. This is reflected by an age-dependent task allocation. The most protruding tasks are performed by young nurse bees and older forager bees that take care of the brood inside the hive and collect food from outside the hive, respectively. The molecular mechanism leading to the transition from nurse bees to foragers is currently under intense research. Circular RNAs, however, were not considered in this context so far. As of today, this group of non-coding RNAs was only known to exist in two other insects, Drosophila melanogaster and Bombyx mori. Here we complement the state of circular RNA research with the first characterization in a social insect. Results We identified numerous circular RNAs in the brain of A. mellifera nurse bees and forager bees using RNA-Seq with exonuclease enrichment. Presence and circularity were verified for the most abundant representatives. Back-splicing in honeybee occurs further towards the end of transcripts and in transcripts with a high number of exons. The occurrence of circularized exons is correlated with length and CpG-content of their flanking introns. The latter coincides with increased DNA-methylation in the respective loci. For two prominent circular RNAs the abundance in worker bee brains was quantified in TaqMan assays. In line with previous findings of circular RNAs in Drosophila, circAmrsmep2 accumulates with increasing age of the insect. In contrast, the levels of circAmrad appear age-independent and correlate with the bee’s task. Its parental gene is related to amnesia-resistant memory. Conclusions We provide the first characterization of circRNAs in a social insect. Many of the RNAs identified here show homologies to circular RNAs found in Drosophila and Bombyx, indicating that circular RNAs are a common feature among insects. We find that exon circularization is correlated to DNA-methylation at the flanking introns. The levels of circAmrad suggest a task-dependent abundance that is decoupled from age. Moreover, a GO term analysis shows an enrichment of task-related functions. We conclude that circular RNAs could be relevant for task allocation in honeybee and should be investigated further in this context. Electronic supplementary material The online version of this article (10.1186/s12864-018-5402-6) contains supplementary material, which is available to authorized users.
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Pohl H, Beutel RG. Effects of miniaturization in primary larvae of Strepsiptera (Insecta). ARTHROPOD STRUCTURE & DEVELOPMENT 2019; 48:49-55. [PMID: 30500422 DOI: 10.1016/j.asd.2018.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
In this review the presently available morphological data on primary larvae of Strepsiptera are interpreted with respect to effects of miniaturization, but also their possible functional or phylogenetic background. The morphology of the 1st instars is mainly affected by functional constraints linked with parasitism but also by very distinct effects of miniaturization. The latter include modifications of the cephalic cuticle, the extremely limited free space in the body lumen, the shift of origins of cephalic muscles to the thorax, a reduced number of cephalic and thoracic muscles, extensions of muscles with cell bodies and other organelles, and an extreme concentration of the entire central nervous system in the middle region of the body. Pad-like adhesive structures on the distal leg segment and the abdominal jumping apparatus are clearly linked with the necessity to attach to a potential host but would not function in distinctly larger organisms.
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Affiliation(s)
- Hans Pohl
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany.
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
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31
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Pers D, Lynch JA. Ankyrin domain encoding genes from an ancient horizontal transfer are functionally integrated into Nasonia developmental gene regulatory networks. Genome Biol 2018; 19:148. [PMID: 30266092 PMCID: PMC6161386 DOI: 10.1186/s13059-018-1526-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND How regulatory networks incorporate additional components and how novel genes are functionally integrated into well-established developmental processes are two important and intertwined questions whose answers have major implications for understanding the evolution of development. We recently discovered a set of lineage-restricted genes with strong and specific expression patterns along the dorsal-ventral (DV) axis of the embryo of the wasp Nasonia that may serve as a powerful system for addressing these questions. We sought to both understand the evolutionary history of these genes and to determine their functions in the Nasonia DV patterning system. RESULTS We have found that the novel DV genes are part of a large family of rapidly duplicating and diverging ankyrin domain-encoding genes that originated most likely by horizontal transfer from a prokaryote in a common ancestor of the wasp superfamily Chalcidoidea. We tested the function of those ankyrin-encoding genes expressed along the DV axis and found that they participate in early embryonic DV patterning. We also developed a new wasp model system (Melittobia) and found that some functional integration of ankyrin genes have been preserved for over 90 million years. CONCLUSIONS Our results indicate that regulatory networks can incorporate novel genes that then become necessary for stable and repeatable outputs. Even a modest role in developmental networks may be enough to allow novel or duplicate genes to be maintained in the genome and become fully integrated network components.
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Affiliation(s)
- Daniel Pers
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Ave, Chicago, IL, 60607, USA.
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Freitas L, Mello B, Schrago CG. Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda. J Evol Biol 2018; 31:1623-1631. [PMID: 30058265 DOI: 10.1111/jeb.13355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
The multispecies coalescent (MSC) has been increasingly used in phylogenomic analyses due to the accommodation of gene tree topological heterogeneity by taking into account population-level processes, such as incomplete lineage sorting. In this sense, the phylogeny of insect species, which are characterized by their large effective population sizes, is suitable for a coalescent-based analysis. Furthermore, studies so far recovered short internal branches at early divergences of the insect tree of life, indicating fast evolutionary radiations that increase the probability of incomplete lineage sorting in deep time. Here, we investigated the performance of the MSC for a phylogenomic data set of hexapods compiled by Misof et al. (2014, Science 346:763). Our analysis recovered the monophyly of most insect orders, and major phylogenetic relationships were in agreement with current insect systematics. We identified, however, some evolutionary associations that were consistently problematic. Most noticeable, Hexapod monophyly was disrupted by the sister group relationship between the remiped crustacean and Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea were found to be phylogenetically unstable. We show that these controversial phylogenetic arrangements were also poorly supported by previous analyses, and therefore, we evaluated their robustness to stochastic errors from sampling sites and terminals, confirming standing problems in hexapod phylogeny in the genomics age.
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Affiliation(s)
- Lucas Freitas
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Beatriz Mello
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos G Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Sayyari E, Whitfield JB, Mirarab S. Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction. Mol Biol Evol 2018; 34:3279-3291. [PMID: 29029241 DOI: 10.1093/molbev/msx261] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Species tree reconstruction from genome-wide data is increasingly being attempted, in most cases using a two-step approach of first estimating individual gene trees and then summarizing them to obtain a species tree. The accuracy of this approach, which promises to account for gene tree discordance, depends on the quality of the inferred gene trees. At the same time, phylogenomic and phylotranscriptomic analyses typically use involved bioinformatics pipelines for data preparation. Errors and shortcomings resulting from these preprocessing steps may impact the species tree analyses at the other end of the pipeline. In this article, we first show that the presence of fragmentary data for some species in a gene alignment, as often seen on real data, can result in substantial deterioration of gene trees, and as a result, the species tree. We then investigate a simple filtering strategy where individual fragmentary sequences are removed from individual genes but the rest of the gene is retained. Both in simulations and by reanalyzing a large insect phylotranscriptomic data set, we show the effectiveness of this simple filtering strategy.
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Affiliation(s)
- Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
| | | | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
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Song N, Lin A, Zhao X. Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data. PLoS One 2018; 13:e0191826. [PMID: 29381758 PMCID: PMC5790268 DOI: 10.1371/journal.pone.0191826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/11/2018] [Indexed: 01/21/2023] Open
Abstract
It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Aili Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xincheng Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Li Y, Zhang R, Liu S, Donath A, Peters RS, Ware J, Misof B, Niehuis O, Pfrender ME, Zhou X. The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. BMC Evol Biol 2017; 17:269. [PMID: 29281964 PMCID: PMC5745899 DOI: 10.1186/s12862-017-1111-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 12/08/2017] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND The primary energy-producing pathway in eukaryotic cells, the oxidative phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and nuclear genes. To maintain the function of the OXPHOS system, the pattern of substitutions in mitochondrial and nuclear genes may not be completely independent. It has been suggested that slightly deleterious substitutions in mitochondrial genes are compensated by substitutions in the interacting nuclear genes due to positive selection. Among the four largest insect orders, Coleoptera (beetles), Hymenoptera (sawflies, wasps, ants, and bees), Diptera (midges, mosquitoes, and flies) and Lepidoptera (moths and butterflies), the mitochondrial genes of Hymenoptera exhibit an exceptionally high amino acid substitution rate while the evolution of nuclear OXPHOS genes is largely unknown. Therefore, Hymenoptera is an excellent model group for testing the hypothesis of positive selection driving the substitution rate of nuclear OXPHOS genes. In this study, we report the evolutionary rate of OXPHOS genes in Hymenoptera and test for evidence of positive selection in nuclear OXPHOS genes of Hymenoptera. RESULTS Our analyses revealed that the amino acid substitution rate of mitochondrial and nuclear OXPHOS genes in Hymenoptera is higher than that in other studied insect orders. In contrast, the amino acid substitution rate of non-OXPHOS genes in Hymenoptera is lower than the rate in other insect orders. Overall, we found the dN/dS ratio of the nuclear OXPHOS genes to be higher in Hymenoptera than in other insect orders. However, nuclear OXPHOS genes with high dN/dS ratio did not always exhibit a high amino acid substitution rate. Using branch-site and site model tests, we identified various codon sites that evolved under positive selection in nuclear OXPHOS genes. CONCLUSIONS Our results showed that nuclear OXPHOS genes in Hymenoptera are evolving faster than the genes in other three insect orders. The branch test suggested that while some nuclear OXPHOS genes in Hymenoptera show a signature of positive selection, the pattern is not consistent across all nuclear OXPHOS genes. As only few codon sites were under positive selection, we suggested that positive selection might not be the only factor contributing to the rapid evolution of nuclear OXPHOS genes in Hymenoptera.
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Affiliation(s)
- Yiyuan Li
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN USA
- Environmental Change Initiative, Notre Dame, IN USA
| | - Rui Zhang
- China National GeneBank, BGI-Shenzhen, Guangdong Province, Shenzhen, China
| | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Donath
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
| | - Ralph S. Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Bonn, Germany
| | - Jessica Ware
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102 USA
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Evolutionary Biology and Animal Ecology, Institute of Biology I (Zoology), Albert Ludwig University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
| | - Michael E. Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN USA
- Environmental Change Initiative, Notre Dame, IN USA
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193 China
- Department of Entomology, China Agricultural University, Beijing, 100193 China
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Perry M, Konstantinides N, Pinto-Teixeira F, Desplan C. Generation and Evolution of Neural Cell Types and Circuits: Insights from the Drosophila Visual System. Annu Rev Genet 2017; 51:501-527. [PMID: 28961025 DOI: 10.1146/annurev-genet-120215-035312] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Drosophila visual system has become a premier model for probing how neural diversity is generated during development. Recent work has provided deeper insight into the elaborate mechanisms that control the range of types and numbers of neurons produced, which neurons survive, and how they interact. These processes drive visual function and influence behavioral preferences. Other studies are beginning to provide insight into how neuronal diversity evolved in insects by adding new cell types and modifying neural circuits. Some of the most powerful comparisons have been those made to the Drosophila visual system, where a deeper understanding of molecular mechanisms allows for the generation of hypotheses about the evolution of neural anatomy and function. The evolution of new neural types contributes additional complexity to the brain and poses intriguing questions about how new neurons interact with existing circuitry. We explore how such individual changes in a variety of species might play a role over evolutionary timescales. Lessons learned from the fly visual system apply to other neural systems, including the fly central brain, where decisions are made and memories are stored.
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Affiliation(s)
- Michael Perry
- Department of Biology, New York University, New York, NY 10003, USA;
| | | | - Filipe Pinto-Teixeira
- Department of Biology, New York University, New York, NY 10003, USA; .,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA; .,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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Che LH, Zhang SQ, Li Y, Liang D, Pang H, Ślipiński A, Zhang P. Genome-wide survey of nuclear protein-coding markers for beetle phylogenetics and their application in resolving both deep and shallow-level divergences. Mol Ecol Resour 2017; 17:1342-1358. [DOI: 10.1111/1755-0998.12664] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/09/2017] [Accepted: 02/14/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Li-Heng Che
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Shao-Qian Zhang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Yun Li
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Dan Liang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Hong Pang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
| | - Adam Ślipiński
- Australian National Insect Collection; CSIRO; GPO Box 1700 Canberra ACT 2601 Australia
| | - Peng Zhang
- State Key Laboratory of Biocontrol; College of Ecology and Evolution; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510006; Guangdong Province China
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Paulo DF, Azeredo-Espin AML, Canesin LEC, Vicentini R, Junqueira ACM. Identification and characterization of microRNAs in the screwworm flies Cochliomyia hominivorax and Cochliomyia macellaria (Diptera: Calliphoridae). INSECT MOLECULAR BIOLOGY 2017; 26:46-57. [PMID: 27775856 DOI: 10.1111/imb.12270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression through post-transcriptional regulation. Here, we report the identification and characterization of miRNAs in two closely related screwworm flies with different feeding habits: Cochliomyia hominivorax and Cochliomyia macellaria. The New World screwworm, C. hominivorax, is an obligatory parasite of warm-blooded vertebrates, whereas the secondary screwworm, C. macellaria, is a free-living organism that feeds on decaying organic matter. Here, the small RNA transcriptomes of adults and third-instar larvae of both species were sequenced. A total of 110 evolutionarily conserved miRNAs were identified, and 10 putative precursor miRNAs (pre-miRNAs) were predicted. The relative expression of six selected miRNAs was further investigated, including miRNAs that are related to reproduction and neural processes in other insects. Mature miRNAs were also characterized across an evolutionary time scale, suggesting that the majority of them have been conserved since the emergence of the Arthropoda [540 million years ago (Ma)], Hexapoda (488 Ma) and Brachycera (195 Ma) lineages. This study is the first report of miRNAs for screwworm flies. We also performed a comparative analysis with the hereby predicted miRNAs from the sheep blowfly, Lucilia cuprina. The results presented may advance our understanding of parasitic habits within Calliphoridae and assist further functional studies in blowflies.
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Affiliation(s)
- D F Paulo
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - A M L Azeredo-Espin
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - L E C Canesin
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - R Vicentini
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - A C M Junqueira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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Eyun SI. Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol Biol 2017; 17:23. [PMID: 28103796 PMCID: PMC5244711 DOI: 10.1186/s12862-017-0883-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 01/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level. RESULTS This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of Copepoda among five other crustacean groups (Anostraca, Cladocera, Sessilia, Amphipoda, and Decapoda) using 24 nuclear protein-coding genes. Phylogenomics has confirmed the monophyly of Copepoda and Podoplea. However, this study reveals surprising differences with the majority of the copepod phylogenies and unexpected similarities with postembryonic characters and earlier proposed morphological phylogenies; More precisely, Cyclopoida is more closely related to Siphonostomatoida than to Harpacticoida which is likely the most basally-branching group of Podoplea. Divergence time estimation suggests that the origin of Harpacticoida can be traced back to the Devonian, corresponding well with recently discovered fossil evidence. Copepoda has a close affinity to the clade of Malacostraca and Thecostraca but not to Branchiopoda. This result supports the hypothesis of the newly proposed clades, Communostraca, Multicrustacea, and Allotriocarida but further challenges the validity of Hexanauplia and Vericrustacea. CONCLUSIONS The first phylogenomic study of Copepoda provides new insights into taxonomic relationships and represents a valuable resource that improves our understanding of copepod evolution and their wide range of ecological adaptations.
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Affiliation(s)
- Seong-Il Eyun
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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40
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Wang Y, Liu X, Garzón‐Orduña IJ, Winterton SL, Yan Y, Aspöck U, Aspöck H, Yang D. Mitochondrial phylogenomics illuminates the evolutionary history of Neuropterida. Cladistics 2016; 33:617-636. [DOI: 10.1111/cla.12186] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2016] [Indexed: 01/19/2023] Open
Affiliation(s)
- Yuyu Wang
- Department of Entomology China Agricultural University Beijing 100193 China
- Department of Biological Sciences Vanderbilt University Nashville TN 37235 USA
| | - Xingyue Liu
- Department of Entomology China Agricultural University Beijing 100193 China
| | - Ivonne J. Garzón‐Orduña
- California Department of Food & Agriculture California State Collection of Arthropods 3294 Meadowview Rd Sacramento CA USA
| | - Shaun L. Winterton
- California Department of Food & Agriculture California State Collection of Arthropods 3294 Meadowview Rd Sacramento CA USA
| | - Yan Yan
- Department of Entomology China Agricultural University Beijing 100193 China
| | - Ulrike Aspöck
- Department of Entomology Natural History Museum Vienna Burgring 7 Vienna A‐1010 Austria
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine Medical Parasitology Medical University of Vienna Kinderspitalgasse 15 Vienna A‐1090 Austria
| | - Ding Yang
- Department of Entomology China Agricultural University Beijing 100193 China
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James M, Nandamuri SP, Stahl A, Buschbeck EK. The unusual eyes of Xenos peckii (Strepsiptera: Xenidae) have green- and UV--sensitive photoreceptors. ACTA ACUST UNITED AC 2016; 219:3866-3874. [PMID: 27974533 DOI: 10.1242/jeb.148361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/29/2016] [Indexed: 11/20/2022]
Abstract
The highly specialized evolution of Strepsiptera has produced one of the most unusual eyes among mature insects, perhaps in line with their extremely complex and challenging life cycle. This relatively rare insect order is one of the few for which it has been unclear what spectral classes of photoreceptors any of its members may possess, an even more apt question given the nocturnal evolution of the group. To address this question, we performed electroretinograms on adult male Xenos peckii: we measured spectral responses to equi-quantal monochromatic light flashes of different wavelengths, and established VlogI relationships to calculate spectral sensitivities. Based on opsin template fits, we found maximal spectral sensitivity (λmax) in the green domain at 539 nm. Application of a green light to 'bleach' green receptors revealed that a UV peak was contributed to by an independent UV opsin with a λmax of 346 nm. Transcriptomics and a phylogenetic analysis including 50 other opsin sequences further confirmed the presence of these two opsin classes. While these findings do not necessarily indicate that these unorthodox insects have color vision, they raise the possibility that UV vision plays an important role in the ability of X. peckii males to find the very cryptic strepsipteran females that are situated within their wasp hosts.
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Affiliation(s)
- Marisano James
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Sri Pratima Nandamuri
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA
| | - Aaron Stahl
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA
| | - Elke K Buschbeck
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA
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Kjer K, Borowiec ML, Frandsen PB, Ware J, Wiegmann BM. Advances using molecular data in insect systematics. CURRENT OPINION IN INSECT SCIENCE 2016; 18:40-47. [PMID: 27939709 DOI: 10.1016/j.cois.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.
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Affiliation(s)
- Karl Kjer
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Marek L Borowiec
- University of Rochester, 226 Hutchison Hall, Rochester, NY 14627, USA
| | - Paul B Frandsen
- Smithsonian Institution, Office of Research Information Services, Office of the Chief Information Officer, Washington, D.C. 20024, USA
| | - Jessica Ware
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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Noble LM, Holland LM, McLauchlan AJ, Andrianopoulos A. A Plastic Vegetative Growth Threshold Governs Reproductive Capacity in Aspergillus nidulans. Genetics 2016; 204:1161-1175. [PMID: 27672092 PMCID: PMC5105849 DOI: 10.1534/genetics.116.191122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
Ontogenetic phases separating growth from reproduction are a common feature of cellular life. Long recognized for flowering plants and animals, early literature suggests this life-history component may also be prevalent among multicellular fungi. We establish the basis of developmental competence-the capacity to respond to induction of asexual development-in the filamentous saprotroph Aspergillus nidulans, describing environmental influences, including genotype-by-environment interactions among precocious mutants, gene expression associated with wild type and precocious competence acquisition, and the genetics of competence timing. Environmental effects are consistent with a threshold driven by metabolic rate and organism density, with pH playing a particularly strong role in determining competence timing. Gene expression diverges significantly over the competence window, despite a lack of overt morphological change, with differentiation in key metabolic, signaling, and cell trafficking processes. We identify five genes for which mutant alleles advance competence timing, including the conserved GTPase RasB (AN5832) and ambient pH sensor PalH (AN6886). In all cases examined, inheritance of competence timing is complex and non-Mendelian, with F1 progeny showing highly variable transgressive timing and dominant parental effects with a weak contribution from progeny genotype. Competence provides a new model for nutrient-limited life-cycle phases, and their elaboration from unicellular origins. Further work is required to establish the hormonal and bioenergetic basis of the trait across fungi, and underlying mechanisms of variable inheritance.
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Affiliation(s)
- Luke M Noble
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10012
| | - Linda M Holland
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, D04, Ireland
| | - Alisha J McLauchlan
- Genetics, Genomics and Development, School of BioSciences University of Melbourne, Victoria 3010, Australia
| | - Alex Andrianopoulos
- Genetics, Genomics and Development, School of BioSciences University of Melbourne, Victoria 3010, Australia
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44
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Tian Y, Kubatko LS. Expected pairwise congruence among gene trees under the coalescent model. Mol Phylogenet Evol 2016; 106:144-150. [PMID: 27693467 DOI: 10.1016/j.ympev.2016.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/07/2016] [Accepted: 09/23/2016] [Indexed: 12/24/2022]
Abstract
Although it is widely appreciated that gene trees may differ from the overall species tree and from one another due to various evolutionary processes (e.g., incomplete lineage sorting (ILS), horizontal gene transfer, etc.), the extent of this incongruence is rarely quantified and discussed. Here we consider the expected amount of incongruence arising from ILS, as modeled by the coalescent process. In particular, we compute the probability that two gene trees randomly sampled from the same species tree agree with one another as well as the distribution of the Robinson-Foulds distance between them, for species trees with three to eight taxa. We demonstrate that, as expected under the coalescent model, the amount of discordance is affected by species tree-specific factors such as speciation times and effective population sizes for the species under consideration. Our results highlight the fact that substantial discordance may occur, even when the number of species is very small, which has implications both for larger taxon samples and for any method that uses estimated gene trees as the basis for further statistical inference. The amount of incongruence is substantial enough that such methods may need to be modified to account for variability in the underlying gene trees.
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Affiliation(s)
- Yuan Tian
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, United States
| | - Laura S Kubatko
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, United States; Department of Statistics, The Ohio State University, United States.
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45
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Abstract
SUMMARYComplex life cycles are common in free-living and parasitic organisms alike. The adaptive decoupling hypothesis postulates that separate life cycle stages have a degree of developmental and genetic autonomy, allowing them to be independently optimized for dissimilar, competing tasks. That is, complex life cycles evolved to facilitate functional specialization. Here, I review the connections between the different stages in parasite life cycles. I first examine evolutionary connections between life stages, such as the genetic coupling of parasite performance in consecutive hosts, the interspecific correlations between traits expressed in different hosts, and the developmental and functional obstacles to stage loss. Then, I evaluate how environmental factors link life stages through carryover effects, where stressful larval conditions impact parasites even after transmission to a new host. There is evidence for both autonomy and integration across stages, so the relevant question becomes how integrated are parasite life cycles and through what mechanisms? By highlighting how genetics, development, selection and the environment can lead to interdependencies among successive life stages, I wish to promote a holistic approach to studying complex life cycle parasites and emphasize that what happens in one stage is potentially highly relevant for later stages.
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46
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Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles. PLoS One 2016; 11:e0163529. [PMID: 27668729 PMCID: PMC5036811 DOI: 10.1371/journal.pone.0163529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/10/2016] [Indexed: 11/19/2022] Open
Abstract
Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.
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47
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Pers D, Buchta T, Özüak O, Wolff S, Pietsch JM, Memon MB, Roth S, Lynch JA. Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network. BMC Biol 2016; 14:63. [PMID: 27480122 PMCID: PMC4968023 DOI: 10.1186/s12915-016-0285-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/18/2016] [Indexed: 01/23/2023] Open
Abstract
Background Gene regulatory networks (GRNs) underlie developmental patterning and morphogenetic processes, and changes in the interactions within the underlying GRNs are a major driver of evolutionary processes. In order to make meaningful comparisons that can provide significant insights into the evolution of regulatory networks, homologous networks from multiple taxa must be deeply characterized. One of the most thoroughly characterized GRNs is the dorsoventral (DV) patterning system of the Drosophila melanogaster embryo. We have developed the wasp Nasonia as a comparative DV patterning model because it has shown the convergent evolution of a mode of early embryonic patterning very similar to that of the fly, and it is of interest to know whether the similarity at the gross level also extends to the molecular level. Results We used RNAi to dorsalize and ventralize Nasonia embryos, RNAseq to quantify transcriptome-wide expression levels, and differential expression analysis to identify genes whose expression levels change in either RNAi case. This led to the identification of >100 genes differentially expressed and regulated along the DV axis. Only a handful of these genes are shared DV components in both fly and wasp. Many of those unique to Nasonia are cytoskeletal and adhesion molecules, which may be related to the divergent cell and tissue behavior observed at gastrulation. In addition, many transcription factors and signaling components are only DV regulated in Nasonia, likely reflecting the divergent upstream patterning mechanisms involved in producing the conserved pattern of cell fates observed at gastrulation. Finally, several genes that lack Drosophila orthologs show robust and distinct expression patterns. These include genes with vertebrate homologs that have been lost in the fly lineage, genes that are found only among Hymenoptera, and several genes that entered the Nasonia genome through lateral transfer from endosymbiotic bacteria. Conclusions Altogether, our results provide insights into how GRNs respond to new functional demands and how they can incorporate novel components. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0285-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Pers
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Avenue, Chicago, IL, 60402, USA
| | - Thomas Buchta
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Orhan Özüak
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Selma Wolff
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Jessica M Pietsch
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Mohammad Bilal Memon
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Avenue, Chicago, IL, 60402, USA
| | - Siegfried Roth
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Avenue, Chicago, IL, 60402, USA.
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48
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Kjer KM, Simon C, Yavorskaya M, Beutel RG. Progress, pitfalls and parallel universes: a history of insect phylogenetics. J R Soc Interface 2016; 13:20160363. [PMID: 27558853 PMCID: PMC5014063 DOI: 10.1098/rsif.2016.0363] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.
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Affiliation(s)
- Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Margarita Yavorskaya
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
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49
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Wang M, Rasnitsyn AP, Li H, Shih C, Sharkey MJ, Ren D. Phylogenetic analyses elucidate the inter-relationships of Pamphilioidea (Hymenoptera, Symphyta). Cladistics 2016; 32:239-260. [PMID: 34736302 DOI: 10.1111/cla.12129] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 11/29/2022] Open
Abstract
The phylogeny of the superfamily Pamphilioidea is reconstructed using morphology and DNA sequence data of living and fossil taxa by employing two phylogenetic methods (maximum parsimony and Bayesian inference). Based on our results, the monophyly of Pamphilioidea and Pamphiliidae are corroborated, whereas two extinct families, Xyelydidae and Praesiricidae, are not monophyletic. Because members of Praesiricidae together with Megalodontes form a monophyletic group, we propose that the paraphyletic Praesiricidae is synonymized under Megalodontesidae (syn. nov.). The origin of Pamphilioidea is hypothesized to be as early as the Early Jurassic. To better understand morphological evolution in the early lineages of Pamphilioidea, ancestral states of the first flagellomere and the first and second abdominal terga are reconstructed on the morphology-based tree. In addition, three new genera (Medilyda, Brevilyda, Strenolyda) with five new species (Medilyda procera, M. distorta, Brevilyda provecta, Strenolyda marginalis and S. retrorsa) are described based on well-preserved xyelydid fossils from the Middle Jurassic Jiulongshan Formation of north-eastern China.
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Affiliation(s)
- Mei Wang
- College of Life Sciences, Capital Normal University, 105 Xisanhuanbeilu, Haidian District, Beijing, 100048, China.,Department of Entomology, University of Kentucky, S225 Agricultural Science Center North, Lexington, KY, 40546-0091, USA
| | - Alexandr P Rasnitsyn
- Palaeontological Institute, Russian Academy of Sciences, 123 Profsoyuznayaul., Moscow, 117997, Russia.,Department of Palaeontology, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Hu Li
- Department of Entomology, University of Kentucky, S225 Agricultural Science Center North, Lexington, KY, 40546-0091, USA.,Department of Entomology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Chungkun Shih
- College of Life Sciences, Capital Normal University, 105 Xisanhuanbeilu, Haidian District, Beijing, 100048, China
| | - Michael J Sharkey
- Department of Entomology, University of Kentucky, S225 Agricultural Science Center North, Lexington, KY, 40546-0091, USA
| | - Dong Ren
- College of Life Sciences, Capital Normal University, 105 Xisanhuanbeilu, Haidian District, Beijing, 100048, China
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50
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Song F, Li H, Jiang P, Zhou X, Liu J, Sun C, Vogler AP, Cai W. Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models. Genome Biol Evol 2016; 8:1411-26. [PMID: 27189999 PMCID: PMC4898802 DOI: 10.1093/gbe/evw086] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
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Affiliation(s)
- Fan Song
- Department of Entomology, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Pei Jiang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington
| | - Jinpeng Liu
- Markey Cancer Center, University of Kentucky, Lexington
| | - Changhai Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alfried P Vogler
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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