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Cumming RT, Le Tirant S, Linde JB, Solan ME, Foley EM, Eulin NEC, Lavado R, Whiting MF, Bradler S, Bank S. On seven undescribed leaf insect species revealed within the recent "Tree of Leaves" (Phasmatodea, Phylliidae). Zookeys 2023; 1173:145-229. [PMID: 37577148 PMCID: PMC10416092 DOI: 10.3897/zookeys.1173.104413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
With the recent advance in molecular phylogenetics focused on the leaf insects (Phasmatodea, Phylliidae), gaps in knowledge are beginning to be filled. Yet, shortcomings are also being highlighted, for instance, the unveiling of numerous undescribed phylliid species. Here, some of these taxa are described, including Phylliumiyadaonsp. nov. from Mindoro Island, Philippines; Phylliumsamarensesp. nov. from Samar Island, Philippines; Phylliumortizisp. nov. from Mindanao Island, Philippines; Pulchriphylliumheraclessp. nov. from Vietnam; Pulchriphylliumdelisleisp. nov. from South Kalimantan, Indonesia; and Pulchriphylliumbhaskaraisp. nov. from Java, Indonesia. Several additional specimens of these species together with a seventh species described herein, Pulchriphylliumanangusp. nov. from southwestern India, were incorporated into a newly constructed phylogenetic tree. Additionally, two taxa that were originally described as species, but in recent decades have been treated as subspecies, are elevated back to species status to reflect their unique morphology and geographic isolation, creating the following new combinations: Pulchriphylliumscythe (Gray, 1843) stat. rev., comb. nov. from Bangladesh and northeastern India, and Pulchriphylliumcrurifolium (Audinet-Serville, 1838) stat. rev., comb. nov. from the Seychelles islands. Lectotype specimens are also designated for Pulchriphylliumscythe (Gray, 1843) stat. rev., comb. nov. and Pulchriphylliumcrurifolium (Audinet-Serville, 1838) stat. rev., comb. nov. from original type material.
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Affiliation(s)
- Royce T. Cumming
- Montreal Insectarium, 4581 rue Sherbrooke est, Montréal, H1X 2B2, Québec, CanadaMontreal InsectariumMontréalCanada
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USAAmerican Museum of Natural HistoryNew YorkUnited States of America
- Biology, Graduate Center, City University of New York, NY, USACity University of New YorkNew YorkUnited States of America
| | - Stéphane Le Tirant
- Montreal Insectarium, 4581 rue Sherbrooke est, Montréal, H1X 2B2, Québec, CanadaMontreal InsectariumMontréalCanada
| | - Jackson B. Linde
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, UT, USABrigham Young UniversityProvoUnited States of America
| | - Megan E. Solan
- Department of Environmental Science, Baylor University, Waco, TX, USABaylor UniversityWacoUnited States of America
| | | | - Norman Enrico C. Eulin
- Saint Michael Academy-Catarman, Northern Samar, 6400 PhilippinesSaint Michael Academy-CatarmanNorthern SamarPhilippines
| | - Ramon Lavado
- Department of Environmental Science, Baylor University, Waco, TX, USABaylor UniversityWacoUnited States of America
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, UT, USABrigham Young UniversityProvoUnited States of America
| | - Sven Bradler
- Department of Animal Evolution and Biodiversity, Johann- Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, GermanyUniversity of GöttingenGöttingenGermany
| | - Sarah Bank
- Department of Animal Evolution and Biodiversity, Johann- Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, GermanyUniversity of GöttingenGöttingenGermany
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2
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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3
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McKinnon LM, Miller JB, Whiting MF, Kauwe JSK, Ridge PG. A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates. Sci Rep 2021; 11:622. [PMID: 33436653 PMCID: PMC7803996 DOI: 10.1038/s41598-020-78803-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/23/2020] [Indexed: 01/24/2023] Open
Abstract
Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals.
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Affiliation(s)
- Lauren M McKinnon
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Monte L. Bean Museum, Brigham Young University, Provo, UT, 84602, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
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4
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Miller JB, McKinnon LM, Whiting MF, Kauwe JSK, Ridge PG. Codon Pairs are Phylogenetically Conserved: A comprehensive analysis of codon pairing conservation across the Tree of Life. PLoS One 2020; 15:e0232260. [PMID: 32401752 PMCID: PMC7219770 DOI: 10.1371/journal.pone.0232260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 04/10/2020] [Indexed: 11/27/2022] Open
Abstract
Identical codon pairing and co-tRNA codon pairing increase translational efficiency within genes when two codons that encode the same amino acid are translated by the same tRNA before it diffuses from the ribosome. We examine the phylogenetic signal in both identical and co-tRNA codon pairing across 23 428 species using alignment-free and parsimony methods. We determined that conserved codon pairing typically has a smaller window size than the length of a ribosome, and codon pairing tracks phylogenies across various taxonomic groups. We report a comprehensive analysis of codon pairing, including the extent to which each codon pairs. Our parsimony method generally recovers phylogenies that are more congruent with the established phylogenies than our alignment-free method. However, four of the ten taxonomic groups did not have sufficient orthologous codon pairings and were therefore analyzed using only the alignment-free methods. Since the recovered phylogenies using only codon pairing largely match phylogenies from the Open Tree of Life and the NCBI taxonomy, and are comparable to trees recovered by other algorithms, we propose that codon pairing biases are phylogenetically conserved and should be considered in conjunction with other phylogenomic techniques.
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Affiliation(s)
- Justin B. Miller
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Lauren M. McKinnon
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Michael F. Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States of America
- M.L. Bean Museum, Brigham Young University, Provo, UT, United States of America
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT, United States of America
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5
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Miller JB, McKinnon LM, Whiting MF, Ridge PG. Codon use and aversion is largely phylogenetically conserved across the tree of life. Mol Phylogenet Evol 2019; 144:106697. [PMID: 31805345 DOI: 10.1016/j.ympev.2019.106697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 04/10/2019] [Accepted: 11/29/2019] [Indexed: 01/11/2023]
Abstract
Using parsimony, we analyzed codon usages across 12,337 species and 25,727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890,814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codon's congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25,771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1109× more likely to be congruent with species relationships in the OTL than would be expected by random chance. Using the OTL as a reference, we show that codon usage is phylogenetically conserved within orthologous genes in archaea, bacteria, plants, mammals, and other vertebrates. We also show how to use our provided framework to test different tree hypotheses by confirming the placement of turtles as sister taxa to archosaurs.
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Affiliation(s)
- Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Lauren M McKinnon
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; M.L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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6
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Miller JB, McKinnon LM, Whiting MF, Ridge PG. CAM: an alignment-free method to recover phylogenies using codon aversion motifs. PeerJ 2019; 7:e6984. [PMID: 31198636 PMCID: PMC6555396 DOI: 10.7717/peerj.6984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Common phylogenomic approaches for recovering phylogenies are often time-consuming and require annotations for orthologous gene relationships that are not always available. In contrast, alignment-free phylogenomic approaches typically use structure and oligomer frequencies to calculate pairwise distances between species. We have developed an approach to quickly calculate distances between species based on codon aversion. METHODS Utilizing a novel alignment-free character state, we present CAM, an alignment-free approach to recover phylogenies by comparing differences in codon aversion motifs (i.e., the set of unused codons within each gene) across all genes within a species. Synonymous codon usage is non-random and differs between organisms, between genes, and even within a single gene, and many genes do not use all possible codons. We report a comprehensive analysis of codon aversion within 229,742,339 genes from 23,428 species across all kingdoms of life, and we provide an alignment-free framework for its use in a phylogenetic construct. For each species, we first construct a set of codon aversion motifs spanning all genes within that species. We define the pairwise distance between two species, A and B, as one minus the number of shared codon aversion motifs divided by the total codon aversion motifs of the species, A or B, containing the fewest motifs. This approach allows us to calculate pairwise distances even when substantial differences in the number of genes or a high rate of divergence between species exists. Finally, we use neighbor-joining to recover phylogenies. RESULTS Using the Open Tree of Life and NCBI Taxonomy Database as expected phylogenies, our approach compares well, recovering phylogenies that largely match expected trees and are comparable to trees recovered using maximum likelihood and other alignment-free approaches. Our technique is much faster than maximum likelihood and similar in accuracy to other alignment-free approaches. Therefore, we propose that codon aversion be considered a phylogenetically conserved character that may be used in future phylogenomic studies. AVAILABILITY CAM, documentation, and test files are freely available on GitHub at https://github.com/ridgelab/cam.
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Affiliation(s)
- Justin B. Miller
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Lauren M. McKinnon
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Michael F. Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States of America
- Brigham Young University, M.L. Bean Museum, Provo, UT, United States of America
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT, United States of America
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8
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Miller JB, Hippen AA, Belyeu JR, Whiting MF, Ridge PG. Missing something? Codon aversion as a new character system in phylogenetics. Cladistics 2017; 33:545-556. [PMID: 34706488 DOI: 10.1111/cla.12183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2016] [Indexed: 01/02/2023] Open
Abstract
Although many studies have documented codon usage bias in different species, the importance of codon usage in a phylogenetic framework remains largely unknown. We demonstrate that a phylogenetic signal is present in the codon usage and non-usage biases of 17 717 orthologues evaluated across 72 tetrapod species using a simple parsimony analysis of a binary matrix of codon characters. Phylogenies estimated using stop codons were more congruent with previous hypotheses than phylogenies based on any other single codon or a combination of codons. Although each codon is present in every species, specific genes have different codon preferences and may or may not use every possible codon. This observation allowed us to map the pattern of codon usage and non-usage across the topology. These results suggest that codon usage is phylogenetically conserved across shallow and deep levels within tetrapods.
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Affiliation(s)
- Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Ariel A Hippen
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Jonathon R Belyeu
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.,M.L. Bean Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
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Hastriter MW, Miller KB, Svenson GJ, Martin GJ, Whiting MF. New record of a phoretic flea associated with earwigs (Dermaptera, Arixeniidae) and a redescription of the bat flea Lagaropsylla signata (Siphonaptera, Ischnopsyllidae). Zookeys 2017:67-79. [PMID: 28331409 PMCID: PMC5345370 DOI: 10.3897/zookeys.657.11095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/06/2017] [Indexed: 11/26/2022] Open
Abstract
Lagaropsyllasignata (Wahlgren, 1903), previously known only from the Island of Java, Indonesia is redescribed and reported for the first time in Deer Cave, Gunung Mulu National Park, Sarawak, Malaysia (west coast of Borneo). Many were found clinging to the earwig Arixeniaesau Jordan, 1909. A similar account of a phoretic flea (Lagaropsyllaturba Smit, 1958) on the same species of cave-dwelling earwig has been reported in peninsular Malaysia in a well-documented association with the hairless naked bulldog bat, Cheiromelestorquatus Horsfield, 1824. The association of Lagaropsyllasignata with Arixeniaesau is parallel to the evolution and co-existence with bats in Deer Cave just as in the case of Lagaropsyllaturba, Arixeniaesau, and Cheiromelestorquatus. The evidence suggests that Lagaropsyllaturba and Lagaropsyllasignata are obligate phoretic parasites whose survival depends on Arixeniaesau to access a bat host. Arixeniaesau is reported for the first time in Deer Cave and the occurrence of Lagaropsyllasignata on the island of Borneo represented a new record, previously being found only on the island of Java. Images of Lagaropsyllasignata attached to Arixeniaesau are provided. Xeniariajacobsoni (Burr, 1912), often associated with Arixeniaesau in other geographical areas, was not present in the material examined from Deer Cave. The natural history of the earwig genera Arixenia Jordan, 1909 and Xeniaria Maa, 1974 are discussed and summarized relative to their associations with phoretic fleas and their bat hosts.
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Affiliation(s)
- Michael W Hastriter
- Monte L. Bean Life Science Museum, Brigham Young University, 290 MLBM, P.O. Box 20200, Provo, Utah 84602-0200, USA
| | - Kelly B Miller
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Gavin J Svenson
- The Cleveland Museum of Natural History, 1 Wade Oval Drive, Cleveland, Ohio 44106, USA
| | - Gavin J Martin
- The Cleveland Museum of Natural History, 1 Wade Oval Drive, Cleveland, Ohio 44106, USA; Department of Biology, Brigham Young University, Provo, Utah 84606, USA
| | - Michael F Whiting
- Monte L. Bean Life Science Museum, Brigham Young University, 290 MLBM, P.O. Box 20200, Provo, Utah 84602-0200, USA; Department of Biology, Brigham Young University, Provo, Utah 84606, USA
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10
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Naegle MA, Mugleston JD, Bybee SM, Whiting MF. Reassessing the phylogenetic position of the epizoic earwigs (Insecta: Dermaptera). Mol Phylogenet Evol 2016; 100:382-390. [PMID: 27033951 DOI: 10.1016/j.ympev.2016.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 02/03/2016] [Accepted: 03/11/2016] [Indexed: 01/05/2023]
Abstract
Dermaptera is a relatively small order of free-living insects that typically feed on detritus and other plant material. However, two earwig lineages - Arixeniidae and Hemimeridae - are epizoic on Cheiromeles bats and Beamys and Cricetomys rats respectively. Both of these epizoic families are comprised of viviparous species. The monophyly of these epizoic lineages and their placement within dermapteran phylogeny has remained unclear. A phylogenetic analyses was performed on a diverse sample of 47 earwig taxa for five loci (18S rDNA, 28S rDNA, COI, Histone 3, and Tubulin Alpha I). Our results support two independent origins of the epizoic lifestyle within Dermaptera, with Hemimeridae and Arixeniidae each derived from a different lineage of Spongiphoridae. Our analyses places Marava, a genus of spongiphorids that includes free-living but viviparous earwigs, as sister group to Arixeniidae, suggesting that viviparity evolved prior to the shift to the epizoic lifestyle. Additionally, our results support the monophyly of Forficulidae and Chelisochidae and the paraphyly of Labiduridae, Pygidicranidae, Spongiphoridae, and Anisolabididae.
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Affiliation(s)
- Michael A Naegle
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA.
| | - Joseph D Mugleston
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
| | - Seth M Bybee
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
| | - Michael F Whiting
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
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11
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Manwaring KF, Whiting MF, Wilcox E, Bybee SM. A study of common scorpionfly (Mecoptera: Panorpidae) visual systems reveals the expression of a single opsin. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-015-0241-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Abstract
Recently, a set of publications described flea fossils from Jurassic and Early Cretaceous geological strata in northeastern China, which were suggested to have parasitized feathered dinosaurs, pterosaurs, and early birds or mammals. In support of these fossils being fleas, a recent publication in BMC Evolutionary Biology described the extended abdomen of a female fossil specimen as due to blood feeding.We here comment on these findings, and conclude that the current interpretation of the evolutionary trajectory and ecology of these putative dinosaur fleas is based on appeal to probability, rather than evidence. Hence, their taxonomic positioning as fleas, or stem fleas, as well as their ecological classification as ectoparasites and blood feeders is not supported by currently available data.
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Affiliation(s)
- Katharina Dittmar
- Department of Biological Sciences, University at Buffalo, Cooke 109, Buffalo, NY, 14260, USA.
- Graduate Program of Evolution, Ecology, and Behavior, University at Buffalo, State University of New York, 411 Cooke Hall, Buffalo, NY, 14260, USA.
| | - Qiyun Zhu
- Department of Biological Sciences, University at Buffalo, Cooke 109, Buffalo, NY, 14260, USA
| | - Michael W Hastriter
- Monte L. Bean Museum, Brigham Young University, 336 MLB, Provo, UT, 84602, USA
| | - Michael F Whiting
- Department of Biology and M. L. Bean Museum, Brigham Young University, 4142 LSB, Provo, UT, 84602, USA
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13
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Mugleston J, Naegle M, Song H, Bybee SM, Ingley S, Suvorov A, Whiting MF. Reinventing the leaf: multiple origins of leaf-like wings in katydids (Orthoptera : Tettigoniidae). INVERTEBR SYST 2016. [DOI: 10.1071/is15055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Insects have developed incredible means to avoid detection by predators. At least five insect orders have species that resemble leaves. Katydids (Orthoptera : Tettigoniidae) are the most diverse and wide-ranging of the leaf-like insects. At least 14 of the 20 extant katydid subfamilies contain species with leaf-like wings. Although it is undisputed that many katydids resemble leaves, methods for delineating the leaf-like from non-leaf-like forms have varied by author and in many cases are not explicitly stated. We provide a simple ratio method that can be used to differentiate the leaf-like and non-leaf-like forms. Geometric morphometrics were used to validate the ratio method. Leaf-like wings have been independently derived in at least 15 katydid lineages. Relative rates of speciation were found to be greater in the non-leaf-like forms, suggesting that leaf-like wings within Tettigoniidae are not a driver of diversification. Likewise, throughout Tettigoniidae, selection seems to be favouring the transition away from leaf-like wings. However, within the large Phaneropterinae subclade, relative speciation and transition rates between the leaf-like and non-leaf-like forms do not differ significantly.
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14
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Zhu Q, Hastriter MW, Whiting MF, Dittmar K. Fleas (Siphonaptera) are Cretaceous, and evolved with Theria. Mol Phylogenet Evol 2015; 90:129-39. [DOI: 10.1016/j.ympev.2015.04.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 03/16/2015] [Accepted: 04/28/2015] [Indexed: 10/23/2022]
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15
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Song H, Amédégnato C, Cigliano MM, Desutter‐Grandcolas L, Heads SW, Huang Y, Otte D, Whiting MF. 300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling. Cladistics 2015; 31:621-651. [DOI: 10.1111/cla.12116] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Hojun Song
- Department of Biology University of Central Florida Orlando FL USA
- Department of Entomology Texas A&M University College Station TX USA
| | - Christiane Amédégnato
- Département Systématique et Évolution Muséum National d ‘Histoire Naturelle’ ISYEB, UMR7205 CNRS MNHN UPMC EPHE Paris France
| | | | - Laure Desutter‐Grandcolas
- Département Systématique et Évolution Muséum National d ‘Histoire Naturelle’ ISYEB, UMR7205 CNRS MNHN UPMC EPHE Paris France
| | - Sam W. Heads
- Illinois Natural History Survey University of Illinois at Urbana‐Champaign Champaign IL USA
| | - Yuan Huang
- Institute of Zoology Shaanxi Normal University Xi'an China
| | - Daniel Otte
- Department of Biodiversity, Earth & Environmental Science Academy of Natural Sciences of Drexel University Philadelphia PA USA
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum Brigham Young University Provo UT USA
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Legendre F, Whiting MF, Grandcolas P. Phylogenetic analyses of termite post-embryonic sequences illuminate caste and developmental pathway evolution. Evol Dev 2014; 15:146-57. [PMID: 25098639 DOI: 10.1111/ede.12023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Termites are highly eusocial insects with a caste polyphenism (i.e., discontinuous morphological differences between castes) and elaborated behaviors. While the developmental pathways leading to caste occurrence are well-known in many species, the evolutionary origin of these pathways is still obscure. Recent molecular phylogenetic studies suggest multiple independent origins of sterile castes in termites, reviving a 30 years old debate. We demonstrate here that diploid sterile castes ("true" workers) evolved several times independently in this group and that this caste was lost at least once in a lineage with developmentally more flexible workers called pseudergates or "false" workers. We also infer that flexibility in post-embryonic development was acquired multiple times independently during termite evolution. We suggest that focusing on detailed developmental pathways in phylogenetic analyses is essential for elucidating the origin of caste polyphenism in termites.
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Affiliation(s)
- Frédéric Legendre
- UMR 7205 CNRS, Origine, Structure et Evolution de la Biodiversité, Département Systématique et Evolution, Muséum national d'Histoire naturelle, CP 50, 45, rue Buffon, 75005, Paris, France
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Abstract
Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.
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Affiliation(s)
- Hojun Song
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Matthew J. Moulton
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
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Chen H, Lin G, Ma J, Su J, Wang Z, Whiting MF, Zhang T, Zhao F. Genomic Resources Notes accepted 1 February 2014 - 31 March 2014. Mol Ecol Resour 2014; 14:882. [DOI: 10.1111/1755-0998.12263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Hongjian Chen
- Qinghai Institute for Endemic Disease Prevention and Control; Xining 811602 China
| | - Gonghua Lin
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810008 China
| | - Junying Ma
- Qinghai Institute for Endemic Disease Prevention and Control; Xining 811602 China
| | - Jianping Su
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810008 China
| | - Zuyun Wang
- Qinghai Institute for Endemic Disease Prevention and Control; Xining 811602 China
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum; Brigham Young University; Provo UT 84602 USA
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810008 China
| | - Fang Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810008 China
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19
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Legendre F, D'Haese CA, Deleporte P, Pellens R, Whiting MF, Schliep K, Grandcolas P. The evolution of social behaviour in Blaberid cockroaches with diverse habitats and social systems: phylogenetic analysis of behavioural sequences. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frédéric Legendre
- Origine, Structure et Evolution de la Biodiversité; Département Systématique et Evolution; Muséum national d'Histoire naturelle; UMR 7205 CNRS CP 50 45, rue Buffon 75005 Paris France
| | - Cyrille A. D'Haese
- Origine, Structure et Evolution de la Biodiversité; Département Systématique et Evolution; Muséum national d'Histoire naturelle; UMR 7205 CNRS CP 50 45, rue Buffon 75005 Paris France
| | - Pierre Deleporte
- Station Biologique; Université de Rennes 1; UMR 6552 CNRS F-35380 Paimpont France
| | - Roseli Pellens
- Origine, Structure et Evolution de la Biodiversité; Département Systématique et Evolution; Muséum national d'Histoire naturelle; UMR 7205 CNRS CP 50 45, rue Buffon 75005 Paris France
| | - Michael F. Whiting
- Department of Biology; Brigham Young University; 693 Widtsoe Building Provo UT 84602 USA
| | - Klaus Schliep
- Département Systématique et Evolution; Muséum national d'Histoire naturelle; Systématique, Adaptation, Evolution, Université Paris VI; UMR 7138 CNRS 9 quai St Bernard 75005 Paris France
| | - Philippe Grandcolas
- Origine, Structure et Evolution de la Biodiversité; Département Systématique et Evolution; Muséum national d'Histoire naturelle; UMR 7205 CNRS CP 50 45, rue Buffon 75005 Paris France
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Leavitt JR, Hiatt KD, Whiting MF, Song H. Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: A phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study. Mol Phylogenet Evol 2013; 67:494-508. [DOI: 10.1016/j.ympev.2013.02.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 02/10/2013] [Accepted: 02/15/2013] [Indexed: 11/24/2022]
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21
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Song H, Moulton MJ, Hiatt KD, Whiting MF. Uncovering historical signature of mitochondrial DNA hidden in the nuclear genome: the biogeography ofSchistocercarevisited. Cladistics 2013; 29:643-662. [DOI: 10.1111/cla.12013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Hojun Song
- Department of Biology; University of Central Florida; Orlando FL 32816 USA
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Matthew J. Moulton
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Kevin D. Hiatt
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
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22
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Nelson LA, Lambkin CL, Batterham P, Wallman JF, Dowton M, Whiting MF, Yeates DK, Cameron SL. Beyond barcoding: a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae). Gene 2012; 511:131-42. [PMID: 23043935 DOI: 10.1016/j.gene.2012.09.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 09/21/2012] [Accepted: 09/29/2012] [Indexed: 11/28/2022]
Abstract
Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117-200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.
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Affiliation(s)
- Leigh A Nelson
- Australian National Insect Collection, CSIRO Ecosystem Sciences, Canberra, ACT, 2601, Australia
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23
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Ingley SJ, Bybee SM, Tennessen KJ, Whiting MF, Branham MA. Life on the fly: phylogenetics and evolution of the helicopter damselflies (Odonata, Pseudostigmatidae). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00555.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Bybee SM, Johnson KK, Gering EJ, Whiting MF, Crandall KA. All the better to see you with: a review of odonate color vision with transcriptomic insight into the odonate eye. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0090-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Cameron SL, Yoshizawa K, Mizukoshi A, Whiting MF, Johnson KP. Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera). BMC Genomics 2011; 12:394. [PMID: 21813020 PMCID: PMC3199782 DOI: 10.1186/1471-2164-12-394] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 08/04/2011] [Indexed: 01/16/2023] Open
Abstract
Background The gene composition, gene order and structure of the mitochondrial genome are remarkably stable across bilaterian animals. Lice (Insecta: Phthiraptera) are a major exception to this genomic stability in that the canonical single chromosome with 37 genes found in almost all other bilaterians has been lost in multiple lineages in favour of multiple, minicircular chromosomes with less than 37 genes on each chromosome. Results Minicircular mt genomes are found in six of the ten louse species examined to date and three types of minicircles were identified: heteroplasmic minicircles which coexist with full sized mt genomes (type 1); multigene chromosomes with short, simple control regions, we infer that the genome consists of several such chromosomes (type 2); and multiple, single to three gene chromosomes with large, complex control regions (type 3). Mapping minicircle types onto a phylogenetic tree of lice fails to show a pattern of their occurrence consistent with an evolutionary series of minicircle types. Analysis of the nuclear-encoded, mitochondrially-targetted genes inferred from the body louse, Pediculus, suggests that the loss of mitochondrial single-stranded binding protein (mtSSB) may be responsible for the presence of minicircles in at least species with the most derived type 3 minicircles (Pediculus, Damalinia). Conclusions Minicircular mt genomes are common in lice and appear to have arisen multiple times within the group. Life history adaptive explanations which attribute minicircular mt genomes in lice to the adoption of blood-feeding in the Anoplura are not supported by this expanded data set as minicircles are found in multiple non-blood feeding louse groups but are not found in the blood-feeding genus Heterodoxus. In contrast, a mechanist explanation based on the loss of mtSSB suggests that minicircles may be selectively favoured due to the incapacity of the mt replisome to synthesize long replicative products without mtSSB and thus the loss of this gene lead to the formation of minicircles in lice.
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Affiliation(s)
- Stephen L Cameron
- Discipline of Biogeosciences, Faculty of Science & Technology, Queensland University of Technology, Brisbane, QLD 4001, Australia.
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26
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Gontijo AM, Miguela V, Whiting MF, Woodruff RC, Dominguez M. Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein. Nat Commun 2011; 2:323. [PMID: 21610726 PMCID: PMC3113295 DOI: 10.1038/ncomms1328] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 04/27/2011] [Indexed: 11/09/2022] Open
Abstract
Genomes can encode a variety of proteins with unrelated architectures and activities. It is known that protein-coding genes of de novo origin have significantly contributed to this diversity. However, the molecular mechanisms and evolutionary processes behind these originations are still poorly understood. Here we show that the last 102 codons of a novel gene, Noble, assembled directly from non-coding DNA following an intronic deletion that induced alternative intron retention at the Drosophila melanogaster Rieske Iron Sulphur Protein (RFeSP) locus. A systematic analysis of the evolutionary processes behind the origin of Noble showed that its emergence was strongly biased by natural selection on and around the RFeSP locus. Noble mRNA is shown to encode a bona fide protein that lacks an iron sulphur domain and localizes to mitochondria. Together, these results demonstrate the generation of a novel protein at a naturally selected site.
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Affiliation(s)
- Alisson M Gontijo
- Instituto de Neurociencias de Alicante, CSIC-UMH, Sant Joan d'Alacant, Alicante 03550, Spain.
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27
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Beutel RG, Friedrich F, Hörnschemeyer T, Pohl H, Hünefeld F, Beckmann F, Meier R, Misof B, Whiting MF, Vilhelmsen L. Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola. Cladistics 2010; 27:341-355. [DOI: 10.1111/j.1096-0031.2010.00338.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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29
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Gullipalli D, Arif A, Aparoy P, Svenson GJ, Whiting MF, Reddanna P, Dutta-Gupta A. Identification of a developmentally and hormonally regulated Delta-Class glutathione S-transferase in rice moth Corcyra cephalonica. Comp Biochem Physiol B Biochem Mol Biol 2010; 156:33-9. [PMID: 20138238 DOI: 10.1016/j.cbpb.2010.01.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 01/29/2010] [Accepted: 01/30/2010] [Indexed: 10/19/2022]
Abstract
Glutathione S-transferases (GSTs) are a large family of multifunctional enzymes, known for their role in cellular detoxification. Here we report a cytosolic GST with optimal activity at alkaline pH (8.3) from the visceral fat body of late-last instar (LLI) larvae of a lepidopteran insect rice moth Corcyra cephalonica. All previously known GSTs are active between pH 6.0 to 6.5. Purification and characterization revealed the Corcyra cephalonica GST (CcGST) as a 23-kDa protein. HPLC and 2D analysis showed a single isoform of the protein in the LLI visceral fat body. Degenerate primer based method identified a 701-nucleotide cDNA and the longest open reading frame contained 216 amino acids. Multiple sequence and structural alignment showed close similarity with delta-class GSTs. CcGST is present mainly in the fat body with highest activity at the late-last instar larval stage. Juvenile hormone (JH) negatively inhibits the CcGST activity both ex vivo and in vivo. We speculate that high expression and activity of CcGST in the fat body of the late-last instar larvae, when endogenous JH titer is low may have role in the insect post-embryonic development unrelated to their previously known function.
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Miller KB, Bergsten J, Whiting MF. Phylogeny and classification of the tribe Hydaticini (Coleoptera: Dytiscidae): partition choice for Bayesian analysis with multiple nuclear and mitochondrial protein-coding genes. ZOOL SCR 2009. [DOI: 10.1111/j.1463-6409.2009.00393.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Cameron SL, Sullivan J, Song H, Miller KB, Whiting MF. A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders. ZOOL SCR 2009. [DOI: 10.1111/j.1463-6409.2009.00392.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Svenson GJ, Whiting MF. Reconstructing the origins of praying mantises (Dictyoptera, Mantodea): the roles of Gondwanan vicariance and morphological convergence. Cladistics 2009; 25:468-514. [DOI: 10.1111/j.1096-0031.2009.00263.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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33
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Dowton M, Cameron SL, Austin AD, Whiting MF. Phylogenetic approaches for the analysis of mitochondrial genome sequence data in the Hymenoptera – A lineage with both rapidly and slowly evolving mitochondrial genomes. Mol Phylogenet Evol 2009; 52:512-9. [DOI: 10.1016/j.ympev.2009.04.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 04/01/2009] [Accepted: 04/05/2009] [Indexed: 10/20/2022]
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Dittmar K, Dick CW, Patterson BD, Whiting MF, Gruwell ME. Pupal deposition and ecology of bat flies (Diptera: Streblidae): Trichobius sp. (caecus group) in a Mexican cave habitat. J Parasitol 2009; 95:308-14. [PMID: 18684039 DOI: 10.1645/ge-1664.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 08/06/2008] [Indexed: 11/10/2022] Open
Abstract
We studied the deposition of pupae of the winged bat fly Trichobius sp. (caecus group; Diptera), an ectoparasite of Natalus stramineus (Chiroptera, Natalidae), in a natural cave in Tamaulipas, Mexico. For the first time, we show a strong spatial segregation of populations of a streblid bat fly at different stages of development. Using molecular techniques we were able to match developmental stages to adults. Only 5 pupae were present in the main bat roosts. The overwhelming majority occurred exclusively in the bat flyway passages at a considerable distance from roosting bats. Pupal density corresponded positively with the average flight height of bats in the cave passage. Taken together, observations suggest that these ectoparasites must actively seek out their hosts by moving onto passing or roosting bats. The scarceness of pupae in the main roost may be dictated by environmental constraints for their development. The estimated population of viable pupae far exceeds the population of imagoes on the bats, and predation on adults by spiders is common.
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Affiliation(s)
- Katharina Dittmar
- SUNY at Buffalo, Department of Biological Sciences, Buffalo, New York 14260, USA.
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35
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Sheffield NC, Song H, Cameron SL, Whiting MF. Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics. Syst Biol 2009; 58:381-94. [DOI: 10.1093/sysbio/syp037] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nathan C. Sheffield
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Program in Computational Biology & Bioinformatics, Institute for Genome Sciences and Policy, Duke University, Box 90090, Durham, NC 27708, USA
| | - Hojun Song
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Stephen L. Cameron
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation, Entomology, PO Box 1700, Canberra, Australian Capital Territory, 2601, Australia
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Jensen D, Svenson GJ, Song H, Whiting MF. Phylogeny and evolution of male genitalia within the praying mantis genus Tenodera (Mantodea:Mantidae). INVERTEBR SYST 2009. [DOI: 10.1071/is09004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mantis genus Tenodera is composed of several species distributed across Africa, Asia and Australasia, along with recent human introductions to North America. Species of the genus are morphologically similar and utilise equivalent habitats across their distribution. Relationships among these species and the morphological characters used to diagnose them have never been formally tested, leaving authors to disagree as to the species composition of Tenodera. With DNA sequence data from five molecular loci and morphological characters from male genitalia, we reconstructed the phylogeny of Tenodera using multiple optimality criteria. All included species were found to be monophyletic in analyses of the combined data. Tenodera sinensis and T. bokiana were both supported as distinct species recovered in separate clades, resolving confusion as to their placement and classification. Our analysis identified a previously undescribed species of Tenodera collected in India, recovered as sister to T. aridifolia and T. sinensis, and exhibiting distinct male genital morphology. In light of the phylogeny, we characterise for the first time, and investigate the evolution of, the male genitalia, which allowed us to discover several transitions in structural forms. We also consider the connection of these transitions to sexual cannibalism and how this behaviour may have led to rapid evolution of the male genitalia.
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37
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Sheffield NC, Song H, Cameron SL, Whiting MF. A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol Biol Evol 2008; 25:2499-509. [PMID: 18779259 PMCID: PMC2568038 DOI: 10.1093/molbev/msn198] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2008] [Indexed: 11/14/2022] Open
Abstract
Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.
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Affiliation(s)
- N C Sheffield
- Department of Biology, Brigham Young University, USA.
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38
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Cameron SL, Dowton M, Castro LR, Ruberu K, Whiting MF, Austin AD, Diement K, Stevens J. Mitochondrial genome organization and phylogeny of two vespid wasps. Genome 2008; 51:800-8. [DOI: 10.1139/g08-066] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We sequenced the entire mitochondrial genome of Abispa ephippium (Hymenoptera: Vespoidea: Vespidae: Eumeninae) and most of the mitochondrial genome of Polistes humilis synoecus (Hymenoptera: Vespoidea: Vespidae: Polistinae). The arrangement of genes differed between the two genomes and also differed slightly from that inferred to be ancestral for the Hymenoptera. The genome organization for both vespids is different from that of all other mitochondrial genomes previously reported. A number of tRNA gene rearrangements were identified that represent potential synapomorphies for a subset of the Vespidae. Analysis of all available hymenopteran mitochondrial genome sequences recovered an uncontroversial phylogeny, one consistent with analyses of other types of data.
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Affiliation(s)
- Stephen L. Cameron
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
| | - Mark Dowton
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
| | - Lyda R. Castro
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
| | - Kalani Ruberu
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
| | - Michael F. Whiting
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
| | - Andy D. Austin
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
| | - Kieren Diement
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
| | - Julia Stevens
- Australian National Insect Collection and CSIRO Entomology, Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT 2601, Australia
- Centre for Medical Bioscience, School of Biological Sciences, University of Wollongong, Wollongong, NSW 2522, Australia
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
- Australian Center for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, SA 5005, Australia
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Beutel RG, Friedrich F, Whiting MF. Head morphology of Caurinus (Boreidae, Mecoptera) and its phylogenetic implications. Arthropod Struct Dev 2008; 37:418-433. [PMID: 18555961 DOI: 10.1016/j.asd.2008.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 02/13/2008] [Accepted: 02/15/2008] [Indexed: 05/26/2023]
Abstract
External and internal head structures of Caurinus dectes were examined and described in detail. The features are compared to conditions found in other groups of Antliophora. Caurinus is obviously crucial for the reconstruction of the mecopteran and antliophoran groundplan. It displays a remarkable series of plesiomorphic character states such as a complete clypeolabral suture, the presence of M. hypopharyngomandibularis (M. 13) and M. frontohypopharyngalis (M. 41), a subdivided clypeus, a short head without rostrum, a dorsal tentorial arm attached to the head capsule, the absence of a cranial dilator of the antenna, and large mandibles with a well developed apical tooth, two distinct subapical teeth, and a basal molar part. The first three plesiomorphic features render potential autapomorphies of Mecoptera in the traditional sense invalid. Autapomorphies of Caurinus are the distinctly flattened labrum, the absence of the labroepipharyngeal muscle, the very large size of M. 13, the strongly enlarged penultimate palpomeres, the partition of M. 41, the very strongly developed precerebral sucking chamber, strongly curved optic lobes, the presence of a large protocerebral extension in the genal region and deep posterior excavations of the protocerebrum. The maxillolabial plate, the absence of cardines as separate structures, the reduction of ocelli, and the origin of maxillary palp muscles on a median ridge or area of the maxillolabial plate are likely autapomorphies of Boreidae. Another potential autapomorphy of the family is the presence of longitudinal furrows on the mandibles. However, they are absent in Boreus. The thick strongly sclerotised, median ridge of the maxillolabial plate, the missing retractibility of the prementum, the absence of extrinsic labial muscles, and the presence of a median ridge on the prepharyngeal roof suggest a clade Boreus+Hesperoboreus. The origin of extrinsic maxillary muscles from the clypeus has probably evolved independently in Boreus and Hesperoboreus, and in Panorpa, respectively. The absence of M. craniolacinialis and the presence of a row of several subapical mandibular teeth are autapomorphies of Boreus. The presence of a specific intrinsic muscle of the salivary duct and a membranous galea enclosing the labrum and mandibular base are derived features shared by Boreidae and Pistillifera (galea absent in Nannochorista, Siphonaptera and Diptera). The loss of M. frontolabralis (M. 8) is a potential apomorphy of Mecoptera incl. Siphonaptera. A sister group relationship between Boreidae and Siphonaptera is not supported by characters of the adult head. Head structures of Siphonaptera are extremely modified in correlation with ectoparasitic habits.
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Affiliation(s)
- Rolf G Beutel
- Institut für Spezielle Zoologie and Evolutionsbiologie, FSU Jena, 07743 Jena, Germany.
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41
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Bybee SM, Ogden TH, Branham MA, Whiting MF. Molecules, morphology and fossils: a comprehensive approach to odonate phylogeny and the evolution of the odonate wing. Cladistics 2008; 24:477-514. [DOI: 10.1111/j.1096-0031.2007.00191.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Legendre F, Whiting MF, Bordereau C, Cancello EM, Evans TA, Grandcolas P. The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: Implications for the evolution of the worker and pseudergate castes, and foraging behaviors. Mol Phylogenet Evol 2008; 48:615-27. [PMID: 18502666 DOI: 10.1016/j.ympev.2008.04.017] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 03/25/2008] [Accepted: 04/09/2008] [Indexed: 10/22/2022]
Abstract
A phylogenetic hypothesis of termite relationships was inferred from DNA sequence data. Seven gene fragments (12S rDNA, 16S rDNA, 18S rDNA, 28S rDNA, cytochrome oxidase I, cytochrome oxidase II and cytochrome b) were sequenced for 40 termite exemplars, representing all termite families and 14 outgroups. Termites were found to be monophyletic with Mastotermes darwiniensis (Mastotermitidae) as sister group to the remainder of the termites. In this remainder, the family Kalotermitidae was sister group to other families. The families Kalotermitidae, Hodotermitidae and Termitidae were retrieved as monophyletic whereas the Termopsidae and Rhinotermitidae appeared paraphyletic. All of these results were very stable and supported with high bootstrap and Bremer values. The evolution of worker caste and foraging behavior were discussed according to the phylogenetic hypothesis. Our analyses suggested that both true workers and pseudergates ("false workers") were the result of at least two different origins. Our data support a traditional hypothesis of foraging behavior, in which the evolutionary transition from a one-piece type to a separate life type occurred through an intermediate behavioral form.
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Affiliation(s)
- Frédéric Legendre
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, UMR 5202, CNRS, CP 50 (Entomologie), 45 rue Buffon, 75005 Paris, France.
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Robertson JA, Whiting MF, McHugh JV. Searching for natural lineages within the Cerylonid Series (Coleoptera: Cucujoidea). Mol Phylogenet Evol 2008; 46:193-205. [DOI: 10.1016/j.ympev.2007.09.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 08/06/2007] [Accepted: 09/26/2007] [Indexed: 11/17/2022]
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Cameron SL, Whiting MF. The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 2007; 408:112-23. [PMID: 18065166 DOI: 10.1016/j.gene.2007.10.023] [Citation(s) in RCA: 263] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/07/2007] [Accepted: 10/22/2007] [Indexed: 11/18/2022]
Abstract
The entire mitochondrial genome of the tobacco hornworm, Manduca sexta (Lepidoptera: Spinghidae) was sequenced -- a circular molecular 15516 bp in size. The arrangement of the protein coding genes (PCGs) was the same as that found in the ancestral insect, however Manduca possessed the derived tRNA arrangement of CR-M-I-Q which has been found in all Lepidoptera sequenced to date. Additionally, Manduca, like all lepidopteran mt genomes, has numerous large intergenic spacer regions and microsatellite-like repeat regions. Nucleotide composition is highly A+T biased, and the lepidopterans have the second most biased nucleotide composition of the insect orders after Hymenoptera. Secondary structural features of the PCGs identified in other Lepidoptera were present but highly modified by the presence of microsatellite-like repeat regions which may significantly alter their function in the post-transcriptional modification of pre-mRNAs. Secondary structure models of the ribosomal RNA genes of Manduca are presented and are similar to those proposed for other insect orders. Conserved regions were identified within non-translated spacer regions which correspond to sites for the origin and termination of replication and transcription. Comparisons of gene variability across the order suggest that the mitochondrial genes most frequently used in phylogenetic analysis of the Lepidoptera, cox1 and cox2, are amongst the least variable genes in the genome and phylogenetic resolution could be improved by using alternative, higher variability genes such as nad2, nad3, nad4 and nad5.
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Affiliation(s)
- Stephen L Cameron
- Australian National Insect Collection & CSIRO Entomology, Black Mountain Laboratories, Canberra, ACT, Australia.
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Cameron SL, Whiting MF. Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae). Genome 2007; 50:188-202. [PMID: 17546084 DOI: 10.1139/g06-148] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Termites of the genus Reticulitermes are some of the most significant pests of structural timber and tree farming in the northern hemisphere, causing losses in the billions of dollars annually because of direct damage and termite control costs. This group has been frequently targeted for population genetic, phylogenetic, and species limit studies, most of which use mitochondrial (mt) genes; however, only a small fraction of the genome has been sequenced. The entire mt genome was sequenced for the eastern North American members of Reticulitermes: R. flavipes, R. santonensis, R. virginicus, and R. hageni. The mt genome has the same gene content and organization as that found in most insect species; however, the nucleotide composition and skew are highly biased (AT% low, strong A- and C-skew). Both the protein-coding and transfer RNA genes show high absolute levels of nucleotide substitution, suggesting that the high rates of mutation within Reticulitermes inferred from analyses of single mt genes are a general characteristic of the entire mt genome. The AT-rich or control region has a remarkable structure not previously observed in insect mt genomes. The majority of the control region is made up of 2 sets of repeat units, typically with 2 full and 1 partial copies of both the A (or small; 186 bp) and B (or large; 552 bp) repeats. The partial repeat units overlap by 36 bp. The size, location, and degree of overlap for the partial repeat units correspond to highly conserved stem/loop structures within the repeat units, suggesting that these structures are involved in the replication-mediated processes that govern repeat-unit evolution within mt genomes. Finally, molecular variation within the mt gene regions was compared with previous regions used in molecular diagnostics or phylogenetics of Reticulitermes. High numbers of single nucleotide polymorphisms were found in each of the mt genes, and some of the highest variability was found in gene regions that have not previously been investigated in this group. The whole mt genome sequence can thus be used to predict useful regions for future investigation.
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Affiliation(s)
- Stephen L Cameron
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA.
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46
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Fenn JD, Cameron SL, Whiting MF. The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Mol Biol 2007; 16:239-52. [PMID: 17316330 DOI: 10.1111/j.1365-2583.2006.00721.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The Anabrus simplex is a swarming plague orthopteran found in western North America. The genome is 15 766 bp in length and genome organization follows the ancestral insect gene arrangement. atp6 lacked any readily identifiable stop codon. Examination of mRNA secondary structure for this gene suggested a stem/loop-mediated mRNA post-transcriptional processing to liberate a mature atp6 mRNA with a complete stop codon produced by polyadenylation. Comparison of similar protein with protein gene boundaries in other insect species reveal a general mechanism for mRNA excision and provide further supporting evidence for post-transcriptional mRNA processing in mitochondrial genomes. The A + T-rich region, or control region, was sequenced for 55 A. simplex individuals from 12 different populations. Variance studies between these individuals show that the A + T-rich region contains significant phylogenetic signal to be used in population studies.
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Affiliation(s)
- J D Fenn
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA.
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47
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Miller KB, Bergsten J, Whiting MF. Phylogeny and classification of diving beetles in the tribe Cybistrini (Coleoptera, Dytiscidae, Dytiscinae). ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2006.00254.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jarvis KJ, Whiting MF. Phylogeny and biogeography of ice crawlers (Insecta: Grylloblattodea) based on six molecular loci: designating conservation status for Grylloblattodea species. Mol Phylogenet Evol 2006; 41:222-37. [PMID: 16798019 DOI: 10.1016/j.ympev.2006.04.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 04/04/2006] [Accepted: 04/13/2006] [Indexed: 11/22/2022]
Abstract
Ice crawlers (Insecta: Grylloblattodea) are rarely encountered insects that consist of five genera representing 26 species from North America and Asia. Asian grylloblattids are the most diverse, but North American ice crawlers (genus Grylloblatta) are known for their adaptation to cold conditions. Phylogenetic relationships among grylloblattid species and genera are not known. Six genes were sampled in 35 individuals for 18S rRNA, 28S rRNA, histone 3, 12S rRNA, 16S rRNA, and cytochrome oxidase II from 21 populations of Grylloblatta, three populations from Japan (genus Galloisiana), and three populations from Russia (genus Grylloblattina). Phylogenetic analysis of these data with two mantophasmid outgroups in POY supported monophyletic genera, with Grylloblatta as sister to Grylloblattina. Grylloblatta was shown to contain two major lineages: a clade in Northern California and Oregon and a clade in Washington and Oregon. One new species and six candidate species are proposed. IUCN Red List Conservation Criteria were implemented to designate conservation status for each lineage.
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Affiliation(s)
- Karl J Jarvis
- Brigham Young University, Integrative Biology, 1256 Locust Lane, Provo, UT 84604, USA.
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Cameron SL, Barker SC, Whiting MF. Mitochondrial genomics and the new insect order Mantophasmatodea. Mol Phylogenet Evol 2006; 38:274-9. [PMID: 16321547 DOI: 10.1016/j.ympev.2005.09.020] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 09/02/2005] [Accepted: 09/20/2005] [Indexed: 11/22/2022]
Affiliation(s)
- Stephen L Cameron
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA.
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Trowbridge RE, Dittmar K, Whiting MF. Identification and phylogenetic analysis of Arsenophonus- and Photorhabdus-type bacteria from adult Hippoboscidae and Streblidae (Hippoboscoidea). J Invertebr Pathol 2005; 91:64-8. [PMID: 16289111 DOI: 10.1016/j.jip.2005.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 08/15/2005] [Accepted: 08/17/2005] [Indexed: 11/15/2022]
Abstract
This is the first report of Arsenophonus- and Photorhabdus-type bacteria from Streblidae (bat flies) and Hippoboscidae (louse flies, keds). Strains were detected by means of polymerase chain reaction of 16S rDNA, and phylogenetic analysis determined the relationship of the obtained sequences to previously reported sequences in GenBank. Phylogenetic analysis by means of maximum parsimony revealed that all isolated Arsenophonus spp. 16S rDNA sequences formed a monophyletic sub-clade within other insect Arsenophonus spp., while the Photorhabdus spp. sequences are part of a monophyletic clade including Photorhabdus spp., Xenorhabdus spp. and Proteus spp.
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Affiliation(s)
- Richard E Trowbridge
- Department of Integrative Biology, Brigham Young University, Provo, UT 84602, USA
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