1
|
Li X, Breinholt JW, Martinez JI, Keegan K, Ellis EA, Homziak NT, Zwick A, Storer CG, McKenna D, Kawahara AY. Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea). Cladistics 2024; 40:21-33. [PMID: 37787424 DOI: 10.1111/cla.12559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023] Open
Abstract
The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.
Collapse
Affiliation(s)
- Xuankun Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Jesse W Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Precision Genomics, Intermountain Healthcare, St George, UT, 84790, USA
| | - Jose I Martinez
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| | - Kevin Keegan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06268, USA
- Section of Invertebrate Zoology, Carnegie Museum of Natural History, 4400 Forbes Ave, Pittsburgh, PA, 15213-4080, USA
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Nicholas T Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Duane McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| |
Collapse
|
2
|
Encinas-Viso F, Bovill J, Albrecht DE, Florez-Fernandez J, Lessard B, Lumbers J, Rodriguez J, Schmidt-Lebuhn A, Zwick A, Milla L. Pollen DNA metabarcoding reveals cryptic diversity and high spatial turnover in alpine plant-pollinator networks. Mol Ecol 2023; 32:6377-6393. [PMID: 36065738 DOI: 10.1111/mec.16682] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022]
Abstract
Alpine plant-pollinator communities play an important role in the functioning of alpine ecosystems, which are highly threatened by climate change. However, we still have a poor understanding of how environmental factors and spatiotemporal variability shape these communities. Here, we investigate what drives structure and beta diversity in a plant-pollinator metacommunity from the Australian alpine region using two approaches: pollen DNA metabarcoding (MB) and observations. Individual pollinators often carry pollen from multiple plant species, and therefore we expected MB to reveal a more diverse and complex network structure. We used two gene regions (ITS2 and trnL) to identify plant species present in the pollen loads of 154 insect pollinator specimens from three alpine habitats and construct MB networks, and compared them to networks based on observations alone. We compared species and interaction turnover across space for both types of networks, and evaluated their differences for plant phylogenetic diversity and beta diversity. We found significant structural differences between the two types of networks; notably, MB networks were much less specialized but more diverse than observation networks, with MB detecting many cryptic plant species. Both approaches revealed that alpine pollination networks are very generalized, but we estimated a high spatial turnover of plant species (0.79) and interaction rewiring (0.6) as well as high plant phylogenetic diversity (0.68) driven by habitat differences based on the larger diversity of plant species and species interactions detected with MB. Overall, our findings show that habitat and microclimatic heterogeneity drives diversity and fine-scale spatial turnover of alpine plant-pollinator networks.
Collapse
Affiliation(s)
- Francisco Encinas-Viso
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Jessica Bovill
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - David E Albrecht
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Jaime Florez-Fernandez
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Bryan Lessard
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - James Lumbers
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Juanita Rodriguez
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Alexander Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Andreas Zwick
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Liz Milla
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| |
Collapse
|
3
|
Heikkilä M, Minet J, Zwick A, Hundsdoerfer A, Rougerie R, Kitching IJ. Critical re-examination of known purported fossil Bombycoidea (Lepidoptera). PeerJ 2023; 11:e16049. [PMID: 37965290 PMCID: PMC10642363 DOI: 10.7717/peerj.16049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/16/2023] [Indexed: 11/16/2023] Open
Abstract
We critically re-examine 17 records of fossils currently assigned to the lepidopteran superfamily Bombycoidea, which includes the silk moths, emperor moths and hawk moths. These records include subfossils, compression and impression fossils, permineralizations and ichnofossils. We assess whether observable morphological features warrant their confident assignment to the superfamily. None of the examined fossils displays characters that allow unequivocal identification as Sphingidae, but three fossils and a subfossil (Mioclanis shanwangiana Zhang, Sun and Zhang, 1994, two fossil larvae, and a proboscis in asphaltum) have combinations of diagnostic features that support placement in the family. The identification of a fossil pupa as Bunaeini (Saturniidae) is well supported. The other fossils that we evaluate lack definitive bombycoid and, in several cases, even lepidopteran characters. Some of these dubious fossils have been used as calibration points in earlier studies casting doubt on the resulting age estimates. All fossil specimens reliably assigned to Bombycoidea are relatively young, the earliest fossil evidence of the superfamily dating to the middle Miocene.
Collapse
Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, Luomus, University of Helsinki, Helsinki, Finland
| | - Joël Minet
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Anna Hundsdoerfer
- Molecular Laboratory, Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Rodolphe Rougerie
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | |
Collapse
|
4
|
Hsiao Y, Oberprieler RG, Zwick A, Zhou YL, Ślipiński A. Museomics unveil systematics, diversity and evolution of Australian cycad-pollinating weevils. Proc Biol Sci 2023; 290:20231385. [PMID: 37788699 PMCID: PMC10547556 DOI: 10.1098/rspb.2023.1385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023] Open
Abstract
Weevils have been shown to play significant roles in the obligate pollination of Australian cycads. In this study, we apply museomics to produce a first molecular phylogeny estimate of the Australian cycad weevils, allowing an assessment of their monophyly, placement and relationships. Divergence dating suggests that the Australian cycad weevils originated from the Late Oligocene to the Middle Miocene and that the main radiation of the cycad-pollinating groups occurred from the Middle to the Late Miocene, which is congruent with the diversification of the Australian cycads, thus refuting any notion of an ancient ciophilous system in Australia. Taxonomic studies reveal the existence of 19 Australian cycad weevil species and that their associations with their hosts are mostly non-species-specific. Co-speciation analysis shows no extensive co-speciation events having occurred in the ciophilous system of Australian cycads. The distribution pattern suggests that geographical factors, rather than diversifying coevolution, constitute the overriding process shaping the Australian cycad weevil diversity. The synchronous radiation of cycads and weevil pollinators is suggested to be a result of the post-Oligocene diversification common in Australian organisms.
Collapse
Affiliation(s)
- Yun Hsiao
- Australian National Insect Collection, CSIRO, Canberra, Australian Capital Territory 2601, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Rolf G. Oberprieler
- Australian National Insect Collection, CSIRO, Canberra, Australian Capital Territory 2601, Australia
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, Australian Capital Territory 2601, Australia
| | - Yu-Lingzi Zhou
- Australian National Insect Collection, CSIRO, Canberra, Australian Capital Territory 2601, Australia
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, Canberra, Australian Capital Territory 2601, Australia
| |
Collapse
|
5
|
Zwick P, Zwick A. Revision of the African Neoperla Needham, 1905 (Plecoptera: Perlidae: Perlinae) based on morphological and molecular data. Zootaxa 2023; 5316:1-194. [PMID: 37518401 DOI: 10.11646/zootaxa.5316.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Adults of the African species of the genus Neoperla Needham, 1905 (Plecoptera: Perlidae: Perlinae) are revised, and 82 valid species are recognised. Of the original 29 named species, 14 valid ones are redescribed from types, nine lectotypes are designated, and nine new synonymies are proposed. Sixty-two new species are named, and several additional new species only known from material insufficient for formal description are listed. There are one unavailable nomen nudum and three doubtful names. Diagnostic morphological traits of the recognised species are described and illustrated in detail where available of males, females, and eggs. Dichotomous keys to all species are provided. Mitochondrial DNA-data of 71 species-group taxa are available, which permits reliable association of sexes and minimises the risk of synonymies between species known from only one sex. Importantly, this includes DNA sequences from 50 holotypes. The DNA-data will also permit future monitoring with eDNA sequencing and identification of nymphs, which are probably important but so far unidentifiable bioindicators in streams. The genus Neoperla occurs largely in the northern hemisphere and in Africa, where it is restricted to the Ethiopian region south of the Sahara but unknown from Madagascar. A single specimen not clearly distinct from a widespread mainland species was taken on Comoro Island. All African species are endemic, but one African species group has a few outlying members in Asia. The Asian N. montivaga-group is not known from Africa. The following new species are described and named: N. aethiopica n. sp., N. amoena n. sp., N. angolana n. sp., N. bareensis n. sp., N. bella n. sp., N. benti n. sp., N. beta n. sp., N. bipolaris n. sp., N. biserrata n. sp., N. brachyphallus n. sp., N. caeleps n. sp., N. cataractae n. sp., N. claviger n. sp., N. coffea n. sp., N. costata n. sp., N. crenulata n. sp., N. crustata n. sp., N. decorata n. sp., N. dianae n. sp., N. dolium n. sp., N. dundoana n. sp., N. duodeviginti n. sp., N. erinaceus n. sp., N. excavata n. sp., N. filamentosa n. sp., N. funiculata n. sp., N. gibbosa n. sp., N. gordius n. sp., N. heideae n. sp., N. ivanloebli n. sp., N. juxtadidita n. sp., N. kalengonis n. sp., N. larvata n. sp., N. lineata n. sp., N. luhohonis n. sp., N. massevensis n. sp., N. multiserrata n. sp., N. muyukae n. sp., N. nichollsi n. sp., N. occulta n. sp., N. orthonema n. sp., N. pallidogigas n. sp., N. panafricana n. sp., N. pickeri n. sp., N. pilulifera n. sp., N. pirus n. sp., N. planidorsum n. sp., N. plicata n. sp., N. proxima n. sp., N. pusilla n. sp., N. rostrata n. sp., N. sambarua n. sp., N. sassandrae n. sp., N. schuelei n. sp., N. serrula n. sp., N. simplex n. sp., N. socia n. sp., N. sorella n. sp., N. spaghetti n. sp., N. spectabilis n. sp., N. spironema n. sp., N. tangana n. sp., N. tansanica n. sp., N. usambara n. sp., and N. vicina n. sp..
Collapse
Affiliation(s)
| | - Andreas Zwick
- Australian National Insect Collection; National Research Collections Australia; CSIRO; Canberra; ACT 2601; Australia.
| |
Collapse
|
6
|
Mohr T, Zwick A, Hans M, Bley I, Braun F, Khalmurzaev O, Matveev V, Loertzer P, Pryalukhin A, Hartmann A, Loertzer H, Geppert C, Wunderlich H, Naumann C, Kalthoff H, Junker K, Smola S, Lohse S. The prominent role of the Calprotectin-CD147-neutrophil axis in the progression of penile cancer. EUR UROL SUPPL 2022. [DOI: 10.1016/s2666-1683(22)01965-6] [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: 11/07/2022] Open
|
7
|
Jin M, Shin S, Ashman LG, Leschen RAB, Zwick A, de Keyzer R, McKenna DD, Ślipiński A. Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles. Mol Phylogenet Evol 2022; 172:107486. [PMID: 35469917 DOI: 10.1016/j.ympev.2022.107486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/12/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022]
Abstract
Cerambycinae is the second-largest subfamily of longhorn beetles in the Southern Hemisphere. The phylogeny of Cerambycinae is poorly known, resulting in a highly artificial tribal-level classification and a largely speculative evolutionary history. We reconstructed the phylogenetic relationships of Cerambycinae at the generic level using anchored hybrid enrichment data from hundreds of nuclear genes, with a primary focus on the extraordinarily diverse faunas of Australia and New Zealand. We also estimated divergence times by incorporating fossil calibrations in our analyses. We identified two main clades within Cerambycinae, which can also be separated morphologically by a distinct type of antennal foramen. We recovered a Late Jurassic origin of crown Cerambycinae. Dorcasominae, which was newly found to have representatives in Australia, was notably derived from within Cerambycinae. We recovered two independent origins of Australian Cerambycinae: one clade originated in the Early Cretaceous and is likely endemic to the Southern Hemisphere, while the other clade appears to have immigrated to Australia, perhaps from the Northern Hemisphere. Within the Australian lineages were multiple independent origins of New Zealand taxa, all of which are relative host-plant generalists. Tribal relationships and assignments are discussed, and based on our results, the following major nomenclatural acts were made: Dorcasominae Lacordaire, 1868 is downgraded to a tribe Dorcasomini of Cerambycinae Latreille, 1804; Neostenini Lacordaire, 1868syn. nov. is treated as a junior synonym of Uracanthini Blanchard, 1851.
Collapse
Affiliation(s)
- Mengjie Jin
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia; State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN, U.S.A; Center for Biodiversity Research, University of Memphis, Memphis, TN, USA; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Lauren G Ashman
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia; Research School of Biology, Australian National University, Canberra 2601, Australia
| | - Richard A B Leschen
- New Zealand Arthropod Collection, Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia
| | - Roger de Keyzer
- Research Associate, Entomology, Australian Museum, Sydney, New South Wales, Australia
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, U.S.A; Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia
| |
Collapse
|
8
|
Ashman LG, Hartley D, Jin M, Rowell DM, Teasdale L, Ślipiński A, Zwick A. Rhytiphora: a phylogenetic and morphological study of Australia’s largest longhorn beetle genus (Coleoptera: Cerambycidae). INVERTEBR SYST 2022. [DOI: 10.1071/is21071] [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: 11/23/2022]
|
9
|
Li X, St Laurent R, Earl C, Doorenweerd C, van Nieukerken EJ, Davis DR, Johns CA, Kawakita A, Kobayashi S, Zwick A, Lopez-Vaamonde C, Ohshima I, Kawahara AY. Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data. Cladistics 2021; 38:277-300. [PMID: 34710244 DOI: 10.1111/cla.12490] [Citation(s) in RCA: 5] [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] [Accepted: 07/28/2021] [Indexed: 11/27/2022] Open
Abstract
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.
Collapse
Affiliation(s)
- Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Camiel Doorenweerd
- Department of Plant and Environmental Protection Services, University of Hawaii, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | | | - Donald R Davis
- Department of Entomology, NHB 105, Smithsonian Institution, Washington, DC, USA
| | - Chris A Johns
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Kawakita
- The Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, 112-0001, Japan
| | - Shigeki Kobayashi
- Entomological Laboratory, Graduate School of life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Andreas Zwick
- Australian National Insect Collection, National Research Collections Australia, CSIRO, Canberra, ACT, 2601, Australia
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orléans, France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France
| | - Issei Ohshima
- Department of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan.,Center for Frontier Natural History, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| |
Collapse
|
10
|
Stringer DN, Bertozzi T, Meusemann K, Delean S, Guzik MT, Tierney SM, Mayer C, Cooper SJB, Javidkar M, Zwick A, Austin AD. Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus). PLoS One 2021; 16:e0256861. [PMID: 34534224 PMCID: PMC8448321 DOI: 10.1371/journal.pone.0256861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/17/2021] [Indexed: 12/02/2022] Open
Abstract
Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (<100 bp) and longer (>300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.
Collapse
Affiliation(s)
- Danielle N. Stringer
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Museum, Adelaide, South Australia, Australia
- * E-mail:
| | - Terry Bertozzi
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Museum, Adelaide, South Australia, Australia
| | - Karen Meusemann
- Evolutionary Biology and Ecology, Institute for Biology I, University of Freiburg, Freiburg, Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia, Acton, Australian Capital Territory, Australia
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Steven Delean
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Michelle T. Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Simon M. Tierney
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Steven J. B. Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Museum, Adelaide, South Australia, Australia
| | - Mohammad Javidkar
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Acton, Australian Capital Territory, Australia
| | - Andrew D. Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- South Australian Museum, Adelaide, South Australia, Australia
| |
Collapse
|
11
|
Li X, Teasdale LC, Bayless KM, Ellis AG, Wiegmann BM, Lamas CJE, Lambkin CL, Evenhuis NL, Nicholls JA, Hartley D, Shin S, Trautwein M, Zwick A, Lessard BD, Yeates DK. Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae). Cladistics 2021; 37:276-297. [PMID: 34478201 DOI: 10.1111/cla.12436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the main lineages in our AHE tree to build a data set with more genes (550 loci versus 216 loci) and higher support levels. Our overall results show strong congruence with the current classification of the family, with 11 out of 14 included subfamilies recovered as monophyletic. Heterotropinae and Mythicomyiinae are successive sister groups to the remainder of the family. We examined the evolution of key morphological characters through our phylogenetic hypotheses and show that neither the "sand chamber subfamilies" nor the "Tomophthalmae" are monophyletic in our phylogenomic analyses. Based on our results, we reinstate two tribes at the subfamily level (Phthiriinae stat. rev. and Ecliminae stat. rev.) and we include the genus Sericosoma Macquart (previously incertae sedis) in the subfamily Oniromyiinae, bringing the total number of bee fly subfamilies to 19. Our dating analyses indicate a Jurassic origin of the family (165-194 Ma), with the sand chamber evolving early in bee fly evolution, in the late Jurassic or mid-Cretaceous (100-165 Ma). We hypothesize that the angiosperm radiation and the hothouse climate established during the late Cretaceous accelerated the diversification of bee flies, by providing an expanded range of resources for the parasitoid larvae and nectarivorous adults.
Collapse
Affiliation(s)
- Xuankun Li
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia.,Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Luisa C Teasdale
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Allan G Ellis
- Botany and Zoology Department, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Carlos José E Lamas
- Museu de Zoologia da Universidade de São Paulo. Avenida Nazaré, 481 Ipiranga 04263-000, São Paulo, SP, Brazil
| | | | - Neal L Evenhuis
- J. Linsley Gressitt Center for Research in Entomology, Bishop Museum, 1525 Bernice Street, Honolulu, HI, 96817, USA
| | - James A Nicholls
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Diana Hartley
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA.,School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Bryan D Lessard
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| |
Collapse
|
12
|
Li HS, Tang XF, Huang YH, Xu ZY, Chen ML, Du XY, Qiu BY, Chen PT, Zhang W, Ślipiński A, Escalona HE, Waterhouse RM, Zwick A, Pang H. Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles. BMC Biol 2021; 19:7. [PMID: 33446206 PMCID: PMC7807722 DOI: 10.1186/s12915-020-00945-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has been documented in many herbivorous insects, conferring the ability to digest plant material and promoting their remarkable ecological diversification. Previous reports suggest HGT of antibacterial enzymes may have contributed to the insect immune response and limit bacterial growth. Carnivorous insects also display many evolutionary successful lineages, but in contrast to the plant feeders, the potential role of HGTs has been less well-studied. RESULTS Using genomic and transcriptomic data from 38 species of ladybird beetles, we identified a set of bacterial cell wall hydrolase (cwh) genes acquired by this group of beetles. Infection with Bacillus subtilis led to upregulated expression of these ladybird cwh genes, and their recombinantly produced proteins limited bacterial proliferation. Moreover, RNAi-mediated cwh knockdown led to downregulation of other antibacterial genes, indicating a role in antibacterial immune defense. cwh genes are rare in eukaryotes, but have been maintained in all tested Coccinellinae species, suggesting that this putative immune-related HGT event played a role in the evolution of this speciose subfamily of predominant predatory ladybirds. CONCLUSION Our work demonstrates that, in a manner analogous to HGT-facilitated plant feeding, enhanced immunity through HGT might have played a key role in the prey adaptation and niche expansion that promoted the diversification of carnivorous beetle lineages. We believe that this represents the first example of immune-related HGT in carnivorous insects with an association with a subsequent successful species radiation.
Collapse
Affiliation(s)
- Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xue-Fei Tang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ze-Yu Xu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mei-Lan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- School of Environment and Life Science, Nanning Normal University, Nanning, 530001, China
| | - Xue-Yong Du
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bo-Yuan Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pei-Tao Chen
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hermes E Escalona
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Life Sciences / School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
13
|
Hamilton CA, St Laurent RA, Dexter K, Kitching IJ, Breinholt JW, Zwick A, Timmermans MJTN, Barber JR, Kawahara AY. Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives. BMC Evol Biol 2019; 19:182. [PMID: 31533606 PMCID: PMC6751749 DOI: 10.1186/s12862-019-1505-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/29/2019] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. RESULTS The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). CONCLUSIONS Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
Collapse
Affiliation(s)
- C A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID, 83844, USA.
| | - R A St Laurent
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - K Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - I J Kitching
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - J W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- RAPiD Genomics, 747 SW 2nd Avenue #314, Gainesville, FL, 32601, USA
| | - A Zwick
- Australian National Insect Collection, CSIRO, Clunies Ross St, Acton, ACT, Canberra, 2601, Australia
| | - M J T N Timmermans
- Department of Natural Sciences, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - J R Barber
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - A Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| |
Collapse
|
14
|
Walsh TK, Perera O, Anderson C, Gordon K, Czepak C, McGaughran A, Zwick A, Hackett D, Tay WT. Mitochondrial DNA genomes of five major Helicoverpa pest species from the Old and New Worlds (Lepidoptera: Noctuidae). Ecol Evol 2019; 9:2933-2944. [PMID: 30891227 PMCID: PMC6405535 DOI: 10.1002/ece3.4971] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 05/24/2018] [Revised: 10/18/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022] Open
Abstract
Five species of noctuid moths, Helicoverpa armigera, H. punctigera, H. assulta, H. zea, and H. gelotopoeon, are major agricultural pests inhabiting various and often overlapping global distributions. Visual identification of these species requires a great deal of expertise and misidentification can have repercussions for pest management and agricultural biosecurity. Here, we report on the complete mitochondrial genomes of H. assulta assulta and H. assulta afra, H. gelotopoeon, H. punctigera, H. zea, and H. armigera armigera and H. armigera conferta' assembled from high-throughput sequencing data. This study significantly increases the mitogenome resources for these five agricultural pests with sequences assembled from across different continents, including an H. armigera individual collected from an invasive population in Brazil. We infer the phylogenetic relationships of these five Helicoverpa species based on the 13 mitochondrial DNA protein-coding genes (PCG's) and show that two publicly available mitogenomes of H. assulta (KP015198 and KR149448) have been misidentified or incorrectly assembled. We further consolidate existing PCR-RFLP methods to cover all five Helicoverpa pest species, providing an updated method that will contribute to species differentiation and to future monitoring efforts of Helicoverpa pest species across different continents. We discuss the value of Helicoverpa mitogenomes to assist with species identification in view of the context of the rapid spread of H. armigera in the New World. With this work, we provide the molecular resources necessary for future studies of the evolutionary history and ecology of these species.
Collapse
Affiliation(s)
- Tom K. Walsh
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | - Omaththage Perera
- USDA‐ARS Southern Insect Management Research UnitStonevilleMississippi
| | - Craig Anderson
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Western General HospitalUniversity of EdinburghEdinburghUK
| | - Karl Gordon
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | - Cecilia Czepak
- Escola de AgronomiaUniversidade Federal de GoiásGoiâniaBrazil
| | - Angela McGaughran
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
- Division of Ecology and Evolution, Research School of BiologyAustralian National UniversityCanberraACTAustralia
| | - Andreas Zwick
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| | | | - Wee Tek Tay
- CSIROBlack Mountain LaboratoriesCanberraACTAustralia
| |
Collapse
|
15
|
Kitching IJ, Rougerie R, Zwick A, Hamilton CA, St Laurent RA, Naumann S, Ballesteros Mejia L, Kawahara AY. A global checklist of the Bombycoidea (Insecta: Lepidoptera). Biodivers Data J 2018:e22236. [PMID: 29674935 PMCID: PMC5904559 DOI: 10.3897/bdj.6.e22236] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/08/2018] [Indexed: 12/02/2022] Open
Abstract
Background Bombycoidea is an ecologically diverse and speciose superfamily of Lepidoptera. The superfamily includes many model organisms, but the taxonomy and classification of the superfamily has remained largely in disarray. Here we present a global checklist of Bombycoidea. Following Zwick (2008) and Zwick et al. (2011), ten families are recognized: Anthelidae, Apatelodidae, Bombycidae, Brahmaeidae, Carthaeidae, Endromidae, Eupterotidae, Phiditiidae, Saturniidae and Sphingidae. The former families Lemoniidae and Mirinidae are included within Brahmaeidae and Endromidae respectively. The former bombycid subfamilies Oberthueriinae and Prismostictinae are also treated as synonyms of Endromidae, and the former bombycine subfamilies Apatelodinae and Phitditiinae are treated as families. New information This checklist represents the first effort to synthesize the current taxonomic treatment of the entire superfamily. It includes 12,159 names and references to their authors, and it accounts for the recent burst in species and subspecies descriptions within family Saturniidae (ca. 1,500 within the past 10 years) and to a lesser extent in Sphingidae (ca. 250 species over the same period). The changes to the higher classification of Saturniidae proposed by Nässig et al. (2015) are rejected as premature and unnecessary. The new tribes, subtribes and genera described by Cooper (2002) are here treated as junior synonyms. We also present a new higher classification of Sphingidae, based on Kawahara et al. (2009), Barber and Kawahara (2013) and a more recent phylogenomic study by Breinholt et al. (2017), as well as a reviewed genus and species level classification, as documented by Kitching (2018).
Collapse
Affiliation(s)
| | - Rodolphe Rougerie
- Muséum national d'Histoire naturelle, Sorbonne Université, Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Paris, France
| | - Andreas Zwick
- CSIRO - Australian National Insect Collection, Canberra, Australia
| | - Chris A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, United States of America
| | - Ryan A St Laurent
- Florida Museum of Natural History, University of Florida, Gainesville, United States of America
| | | | - Liliana Ballesteros Mejia
- Muséum national d'Histoire naturelle, Sorbonne Université, Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Paris, France.,CESAB, Centre de Synthèse et d'Analyse sur la Biodiversité, Aix-en-Provence, France
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, United States of America
| |
Collapse
|
16
|
Fagua G, Condamine FL, Horak M, Zwick A, Sperling FAH. Diversification shifts in leafroller moths linked to continental colonization and the rise of angiosperms. Cladistics 2017; 33:449-466. [PMID: 34724755 DOI: 10.1111/cla.12185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2016] [Indexed: 11/28/2022] Open
Abstract
Tectonic dynamics and niche availability play intertwined roles in determining patterns of diversification. Such drivers explain the current distribution of many clades, whereas events such as the rise of angiosperms can have more specific impacts, such as on the diversification rates of herbivores. The Tortricidae, a diverse group of phytophagous moths, are ideal for testing the effects of these determinants on the diversification of herbivorous clades. To estimate ancestral areas and diversification patterns in Tortricidae, a complete tribal-level dated tree was inferred using molecular markers (one mitochondrial and five nuclear) and calibrated using fossil constraints. We found that Tortricidae diverged from their sister group c. 120 Myr ago (Ma) and diversified c. 97 Ma, a timeframe synchronous with the rise of angiosperms in the Early-mid Cretaceous. Ancestral areas analysis, based on updated Wallace's biogeographical regions, supports the hypothesis of a Gondwanan origin of Tortricidae in the South American plate. We also detected an increase in speciation rate that coincided with the peak of angiosperm diversification in the Cretaceous. This in turn probably was further heightened by continental colonization of the Palaeotropics when angiosperms became dominant by the end of the Late Cretaceous.
Collapse
Affiliation(s)
- Giovanny Fagua
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.,Department of Biology, Pontificia Universidad Javeriana, Carrera 7 No. 40-62, Bogotá, D.C., Colombia
| | - Fabien L Condamine
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.,CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095, Montpellier, France
| | - Marianne Horak
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| |
Collapse
|
17
|
Escalona HE, Zwick A, Li HS, Li J, Wang X, Pang H, Hartley D, Jermiin LS, Nedvěd O, Misof B, Niehuis O, Ślipiński A, Tomaszewska W. Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini). BMC Evol Biol 2017. [PMID: 28651535 PMCID: PMC5485688 DOI: 10.1186/s12862-017-1002-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tribe Coccinellini is a group of relatively large ladybird beetles that exhibits remarkable morphological and biological diversity. Many species are aphidophagous, feeding as larvae and adults on aphids, but some species also feed on other hemipterous insects (i.e., heteropterans, psyllids, whiteflies), beetle and moth larvae, pollen, fungal spores, and even plant tissue. Several species are biological control agents or widespread invasive species (e.g., Harmonia axyridis (Pallas)). Despite the ecological importance of this tribe, relatively little is known about the phylogenetic relationships within it. The generic concepts within the tribe Coccinellini are unstable and do not reflect a natural classification, being largely based on regional revisions. This impedes the phylogenetic study of important traits of Coccinellidae at a global scale (e.g. the evolution of food preferences and biogeography). RESULTS We present the most comprehensive phylogenetic analysis of Coccinellini to date, based on three nuclear and one mitochondrial gene sequences of 38 taxa, which represent all major Coccinellini lineages. The phylogenetic reconstruction supports the monophyly of Coccinellini and its sister group relationship to Chilocorini. Within Coccinellini, three major clades were recovered that do not correspond to any previously recognised divisions, questioning the traditional differentiation between Halyziini, Discotomini, Tytthaspidini, and Singhikaliini. Ancestral state reconstructions of food preferences and morphological characters support the idea of aphidophagy being the ancestral state in Coccinellini. This indicates a transition from putative obligate scale feeders, as seen in the closely related Chilocorini, to more agile general predators. CONCLUSIONS Our results suggest that the classification of Coccinellini has been misled by convergence in morphological traits. The evolutionary history of Coccinellini has been very dynamic in respect to changes in host preferences, involving multiple independent host switches from different insect orders to fungal spores and plants tissues. General predation on ephemeral aphids might have created an opportunity to easily adapt to mixed or specialised diets (e.g. obligate mycophagy, herbivory, predation on various hemipteroids or larvae of leaf beetles (Chrysomelidae)). The generally long-lived adults of Coccinellini can consume pollen and floral nectars, thereby surviving periods of low prey frequency. This capacity might have played a central role in the diversification history of Coccinellini.
Collapse
Affiliation(s)
- Hermes E Escalona
- Centre for Molecular Biodiversity Research (ZMB), Museum Alexander Koenig, Adenauerallee, 53113, Bonn, Germany.,Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Hao-Sen Li
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institute, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiahui Li
- College of Environment and Plant Protection, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, China
| | - Xingmin Wang
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province, Guangzhou, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institute, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Diana Hartley
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Lars S Jermiin
- Centre for Biodiversity Analysis, Australian National University, ACT, Acton, 2601, Australia
| | - Oldřich Nedvěd
- Institute of Entomology, Biology Centre, Branišovská 31, -37005, České Budějovice, CZ, Czech Republic.,University of South Bohemia, Branišovská, 31, České Budějovice, Czech Republic
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research (ZMB), Museum Alexander Koenig, Adenauerallee, 53113, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology) Albert Ludwig University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Wioletta Tomaszewska
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warszawa, Poland.
| |
Collapse
|
18
|
Palau A, Zwick A, Diesch J, Garz A, Valero V, Malinverni R, Navarro T, Goetze K, Buschbeck M. Polycomb Protein RING1A Limits Differentiation in Myelodysplastic Syndromes. Leuk Res 2017. [DOI: 10.1016/s0145-2126(17)30258-8] [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: 10/19/2022]
|
19
|
Yeates DK, Zwick A, Mikheyev AS. Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections. Curr Opin Insect Sci 2016; 18:83-88. [PMID: 27939715 DOI: 10.1016/j.cois.2016.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/23/2016] [Indexed: 05/25/2023]
Abstract
Museums and herbaria represent vast repositories of biological material. Until recently, working with these collections has been difficult, due to the poor condition of historical DNA. However, recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option. Here we describe the unique technical challenges of working with collection specimens, and innovative molecular methods developed to tackle them. We also highlight possible applications of collection specimens, for taxonomy, ecology and evolution. The application of next-generation sequencing methods to museum and herbaria collections is still in its infancy. However, by giving researchers access to billions of specimens across time and space, it holds considerable promise for generating future discoveries across many fields.
Collapse
Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia.
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, PO Box 1700, Canberra, ACT 2601, Australia
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun 904-0412, Japan
| |
Collapse
|
20
|
Yeates DK, Meusemann K, Trautwein M, Wiegmann B, Zwick A. Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution. Curr Opin Insect Sci 2016; 13:16-23. [PMID: 27436549 DOI: 10.1016/j.cois.2015.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/08/2015] [Accepted: 10/18/2015] [Indexed: 06/06/2023]
Abstract
Our understanding on the phylogenetic relationships of insects has been revolutionised in the last decade by the proliferation of next generation sequencing technologies (NGS). NGS has allowed insect systematists to assemble very large molecular datasets that include both model and non-model organisms. Such datasets often include a large proportion of the total number of protein coding sequences available for phylogenetic comparison. We review some early entomological phylogenomic studies that employ a range of different data sampling protocols and analyses strategies, illustrating a fundamental renaissance in our understanding of insect evolution all driven by the genomic revolution. The analysis of phylogenomic datasets is challenging because of their size and complexity, and it is obvious that the increasing size alone does not ensure that phylogenetic signal overcomes systematic biases in the data. Biases can be due to various factors such as the method of data generation and assembly, or intrinsic biological feature of the data per se, such as similarities due to saturation or compositional heterogeneity. Such biases often cause violations in the underlying assumptions of phylogenetic models. We review some of the bioinformatics tools available and being developed to detect and minimise systematic biases in phylogenomic datasets. Phylogenomic-scale data coupled with sophisticated analyses will revolutionise our understanding of insect functional genomics. This will illuminate the relationship between the vast range of insect phenotypic diversity and underlying genetic diversity. In combination with rapidly developing methods to estimate divergence times, these analyses will also provide a compelling view of the rates and patterns of lineagenesis (birth of lineages) over the half billion years of insect evolution.
Collapse
Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia.
| | - Karen Meusemann
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Michelle Trautwein
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Brian Wiegmann
- Department of Entomology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| |
Collapse
|
21
|
Braby MF, Zwick A. Taxonomic revision of the Taractrocera ilia (Waterhouse) complex (Lepidoptera : Hesperiidae) from north-western Australia and mainland New Guinea based on morphological and molecular data. INVERTEBR SYST 2015. [DOI: 10.1071/is15028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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 taxonomy of the Taractrocera ilia complex is revised based on evidence from multiple sources, including phenotypic characters (wing colour pattern elements, morphology of adult and immature stages), ecology and molecular data. Three species are recognised in the complex: T. psammopetra Braby, sp. nov. is restricted to north-western Australia where it has a disjunct distribution (Kimberley and the central Arnhem Land plateau); T. ilia (Waterhouse, 1932) sensu stricto is endemic to the central Arnhem Land plateau where it is narrowly sympatric with T. psammopetra; while T. beta Evans, 1934, stat. nov. is allopatric and endemic to mainland New Guinea. Each species is illustrated and diagnosed based on comparative morphology of the adult stage, including androconia and male and female genitalia, and information on type material, biology, distribution and habitat is summarised and discussed. A phylogenetic hypothesis of the Australian species of Taractrocera based on combined analysis of molecular data (2.6 kb: mitochondrial COI and nuclear CAD, MDH, wingless) revealed that T. psammopetra is monophyletic and sister to T. ilia, with an overall mean divergence of 3.4% between the two species; the genus Taractrocera, however, emerged as polyphyletic. For T. psammopetra and T. ilia, the life history, including details of larval food plant specialisation and morphology of the immature stages, is described for the first time. Larvae of T. psammopetra and T. ilia specialise on ‘resurrection’ grasses, Micraira spp. (Poaceae), which typically grow as moss-like, mat-forming pioneer plants on shallow rock surfaces comprising open sandstone pavements or on rock ledges and under rock overhangs of sandstone cliffs. These food plants, together with the butterflies that they support, are a characteristic element of the sandstone plateaux of the Kimberley and central Arnhem Land, and they exemplify patterns of diversification, endemism and adaptation to these unique environments within the Australian monsoon tropics. Facultative larval diapause is recorded for both T. psammopetra and T. ilia in which larvae (all instars, but particularly the final instar) may suspend feeding for up to six months during the dry season when the food plants typically dehydrate. It is hypothesised that larval diapause may be the most flexible strategy to ameliorate seasonal adversity of the dry season and the onset, duration and inter-annual cycle of monsoon rainfall during the wet season, which is highly variable and unpredictable, given that Micraira can revive rapidly from a desiccated state after rainfall. http://zoobank.org/urn:lsid:zoobank.org:pub:51438A5E-048C-4C72-AD22-3FD176ECBA55
Collapse
|
22
|
Balke M, Schmidt S, Hausmann A, Toussaint EF, Bergsten J, Buffington M, Häuser CL, Kroupa A, Hagedorn G, Riedel A, Polaszek A, Ubaidillah R, Krogmann L, Zwick A, Fikáček M, Hájek J, Michat MC, Dietrich C, La Salle J, Mantle B, Ng PK, Hobern D. Biodiversity into your hands - A call for a virtual global natural history 'metacollection'. Front Zool 2013; 10:55. [PMID: 24044698 PMCID: PMC3848749 DOI: 10.1186/1742-9994-10-55] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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: 03/05/2013] [Accepted: 09/02/2013] [Indexed: 12/04/2022] Open
Abstract
Background Many scientific disciplines rely on correct taxon delineations and identifications. So does a great part of the general public as well as decision makers. Researchers, students and enthusiastic amateurs often feel frustrated because information about species remains scattered, difficult to access, or difficult to decipher. Together, this affects almost anyone who wishes to identify species or verify identifications. Many remedies have been proposed, but we argue that the role of natural history collections remains insufficiently appreciated. We suggest using state-of-the-art mass imaging technology and to join forces to create a global natural history metacollection on the internet, providing access to the morphology of tens of millions of specimens and making them available for automated digital image analysis. Discussion Robotic high-resolution imaging technology and fast (high performance) computer-based image stitching make it now feasible to digitize entire collection drawers typically used for arthropod collections, or trays or containers used for other objects. Resolutions of 500 megapixels and much higher are already utilized to capture the contents of 40x50 cm collection drawers, providing amazing detail of specimens. Flanked by metadata entry, this helps to create access to tens of thousands of specimens in days. By setting priorities and combining the holdings of the most comprehensive collections for certain taxa, drawer digitizing offers the unique opportunity to create a global, virtual metacollection. The taxonomic and geographic coverage of such a collection could never be achieved by a single institution or individual. We argue that by joining forces, many new impulses will emerge for systematic biology, related fields and understanding of biodiversity in general. Digitizing drawers containing unidentified, little-curated specimens is a contribution towards the beginning of a new era of online curation. It also will help taxonomists and curators to discover and process the millions of “gems” of undescribed species hidden in museum accessions. Summary Our proposal suggests creating virtual, high-resolution image resources that will, for the first time in history, provide access for expert scientists as well as students and the general public to the enormous wealth of the world’s natural history collections. We foresee that this will contribute to a better understanding, appreciation and increased use of biodiversity resources and the natural history collections serving this cause.
Collapse
Affiliation(s)
- Michael Balke
- Zoologische Staatssammlung, Münchhausenstr, 21, 81247 Munich, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, Kawahara AY, Sohn JC, Zwickl DJ, Cho S, Davis DR, Baixeras J, Brown J, Parr C, Weller S, Lees DC, Mitter KT. A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLoS One 2013; 8:e58568. [PMID: 23554903 PMCID: PMC3595289 DOI: 10.1371/journal.pone.0058568] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [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: 12/20/2012] [Accepted: 02/05/2013] [Indexed: 01/22/2023] Open
Abstract
Background Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies. Methodology / Principal Findings 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity. Conclusions / Significance Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.
Collapse
Affiliation(s)
- Jerome C. Regier
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (JCR); (CM)
| | - Charles Mitter
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (JCR); (CM)
| | - Andreas Zwick
- Entomology, State Museum of Natural History, Stuttgart, Germany
| | - Adam L. Bazinet
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Michael P. Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Akito Y. Kawahara
- Florida Museum of Natural History, Gainesville, Florida, United States of America
| | - Jae-Cheon Sohn
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Derrick J. Zwickl
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Soowon Cho
- Department of Plant Medicine, Chungbuk National University, Cheongju, Korea
| | - Donald R. Davis
- Department of Entomology, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Joaquin Baixeras
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - John Brown
- Systematic Entomology Lab, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Cynthia Parr
- Encyclopedia of Life, Smithsonian Institution, Washington, District of Columbia, United States of America
| | - Susan Weller
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - David C. Lees
- Department of Life Sciences, Natural History Museum, London, England
| | - Kim T. Mitter
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| |
Collapse
|
24
|
Sohn JC, Regier JC, Mitter C, Davis D, Landry JF, Zwick A, Cummings MP. A molecular phylogeny for yponomeutoidea (insecta, Lepidoptera, ditrysia) and its implications for classification, biogeography and the evolution of host plant use. PLoS One 2013; 8:e55066. [PMID: 23383061 PMCID: PMC3561450 DOI: 10.1371/journal.pone.0055066] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [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: 10/01/2012] [Accepted: 12/18/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Yponomeutoidea, one of the early-diverging lineages of ditrysian Lepidoptera, comprise about 1,800 species worldwide, including notable pests and insect-plant interaction models. Yponomeutoids were one of the earliest lepidopteran clades to evolve external feeding and to extensively colonize herbaceous angiosperms. Despite the group's economic importance, and its value for tracing early lepidopteran evolution, the biodiversity and phylogeny of Yponomeutoidea have been relatively little studied. METHODOLOGY/PRINCIPAL FINDINGS Eight nuclear genes (8 kb) were initially sequenced for 86 putative yponomeutoid species, spanning all previously recognized suprageneric groups, and 53 outgroups representing 22 families and 12 superfamilies. Eleven to 19 additional genes, yielding a total of 14.8 to 18.9 kb, were then sampled for a subset of taxa, including 28 yponomeutoids and 43 outgroups. Maximum likelihood analyses were conducted on data sets differing in numbers of genes, matrix completeness, inclusion/weighting of synonymous substitutions, and inclusion/exclusion of "rogue" taxa. Monophyly for Yponomeutoidea was supported very strongly when the 18 "rogue" taxa were excluded, and moderately otherwise. Results from different analyses are highly congruent and relationships within Yponomeutoidea are well supported overall. There is strong support overall for monophyly of families previously recognized on morphological grounds, including Yponomeutidae, Ypsolophidae, Plutellidae, Glyphipterigidae, Argyresthiidae, Attevidae, Praydidae, Heliodinidae, and Bedelliidae. We also assign family rank to Scythropiinae (Scythropiidae stat. rev.), which in our trees are strongly grouped with Bedelliidae, in contrast to all previous proposals. We present a working hypothesis of among-family relationships, and an informal higher classification. Host plant family associations of yponomeutoid subfamilies and families are non-random, but show no trends suggesting parallel phylogenesis. Our analyses suggest that previous characterizations of yponomeutoids as predominantly Holarctic were based on insufficient sampling. CONCLUSIONS/SIGNIFICANCE We provide the first robust molecular phylogeny for Yponomeutoidea, together with a revised classification and new insights into their life history evolution and biogeography.
Collapse
Affiliation(s)
- Jae-Cheon Sohn
- Department of Entomology, University of Maryland, College Park, MD, USA.
| | | | | | | | | | | | | |
Collapse
|
25
|
Zwick A, Regier JC, Zwickl DJ. Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models. PLoS One 2012; 7:e47450. [PMID: 23185239 PMCID: PMC3502419 DOI: 10.1371/journal.pone.0047450] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [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: 01/02/2012] [Accepted: 09/17/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND In a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy. METHODOLOGY/PRINCIPAL FINDINGS The hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY) in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2) are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neither compositional heterogeneity at the level of nucleotides nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately coded amino acids) is a major source of non-phylogenetic signal. CONCLUSIONS The incongruity in support between amino-acid and nucleotide analyses of the forementioned arthropod data set is resolved by showing that "standard" 20-amino-acid analyses yield lower node support specifically when serine provides crucial signal. Separate coding of Ser1 and Ser2 residues yields support commensurate with that found by degenerated nucleotides, without introducing phylogenetic artifacts. While exclusion of all serine data leads to reduced support for serine-sensitive nodes, these nodes are still recovered in the ML topology, indicating that the enhanced signal from Ser1 and Ser2 is not qualitatively different from that of the other amino acids.
Collapse
Affiliation(s)
- Andreas Zwick
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
| | - Jerome C. Regier
- Institute for Bioscience and Biotechnology Research and Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Derrick J. Zwickl
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| |
Collapse
|
26
|
Regier JC, Brown JW, Mitter C, Baixeras J, Cho S, Cummings MP, Zwick A. A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution. PLoS One 2012; 7:e35574. [PMID: 22536410 PMCID: PMC3334928 DOI: 10.1371/journal.pone.0035574] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [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: 10/31/2011] [Accepted: 03/20/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Tortricidae, one of the largest families of microlepidopterans, comprise about 10,000 described species worldwide, including important pests, biological control agents and experimental models. Understanding of tortricid phylogeny, the basis for a predictive classification, is currently provisional. We present the first detailed molecular estimate of relationships across the tribes and subfamilies of Tortricidae, assess its concordance with previous morphological evidence, and re-examine postulated evolutionary trends in host plant use and biogeography. METHODOLOGY/PRINCIPAL FINDINGS We sequenced up to five nuclear genes (6,633 bp) in each of 52 tortricids spanning all three subfamilies and 19 of the 22 tribes, plus up to 14 additional genes, for a total of 14,826 bp, in 29 of those taxa plus all 14 outgroup taxa. Maximum likelihood analyses yield trees that, within Tortricidae, differ little among data sets and character treatments and are nearly always strongly supported at all levels of divergence. Support for several nodes was greatly increased by the additional 14 genes sequenced in just 29 of 52 tortricids, with no evidence of phylogenetic artifacts from deliberately incomplete gene sampling. There is strong support for the monophyly of Tortricinae and of Olethreutinae, and for grouping of these to the exclusion of Chlidanotinae. Relationships among tribes are robustly resolved in Tortricinae and mostly so in Olethreutinae. Feeding habit (internal versus external) is strongly conserved on the phylogeny. Within Tortricinae, a clade characterized by eggs being deposited in large clusters, in contrast to singly or in small batches, has markedly elevated incidence of polyphagous species. The five earliest-branching tortricid lineages are all species-poor tribes with mainly southern/tropical distributions, consistent with a hypothesized Gondwanan origin for the family. CONCLUSIONS/SIGNIFICANCE We present the first robustly supported phylogeny for Tortricidae, and a revised classification in which all of the sampled tribes are now monophyletic.
Collapse
Affiliation(s)
- Jerome C. Regier
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
- Institute for Bioscience and Biotechnology Research, College Park, Maryland, United States of America
| | - John W. Brown
- Systematic Entomology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Charles Mitter
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
| | - Joaquín Baixeras
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Soowon Cho
- Department of Plant Medicine, Chungbuk National University, Cheongju, Korea
| | - Michael P. Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Andreas Zwick
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
| |
Collapse
|
27
|
Cho S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S, Davis DR, Baixeras J, Brown JW, Parr C. Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)? Syst Biol 2011; 60:782-96. [PMID: 21840842 PMCID: PMC3193767 DOI: 10.1093/sysbio/syr079] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 03/04/2010] [Accepted: 04/12/2011] [Indexed: 11/15/2022] Open
Abstract
This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa×26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.
Collapse
Affiliation(s)
- Soowon Cho
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
- Present address: Department of Plant Medicine, Chungbuk National University, Cheongju, Korea
| | - Andreas Zwick
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, MD 20742, USA
| | - Jerome C. Regier
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, MD 20742, USA
| | - Charles Mitter
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Michael P. Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Jianxiu Yao
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, MD 20742, USA
- Present address: Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Zaile Du
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, MD 20742, USA
| | - Hong Zhao
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, MD 20742, USA
| | - Akito Y. Kawahara
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Susan Weller
- Department of Entomology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Donald R. Davis
- Department of Entomology, Smithsonian Institution, Washington, DC 20560, USA
| | - Joaquin Baixeras
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - John W. Brown
- Systematic Entomology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Cynthia Parr
- Encyclopedia of Life, Smithsonian Institution, Washington, DC 20560, USA
| |
Collapse
|
28
|
Abstract
BACKGROUND This study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions. METHODOLOGY/PRINCIPAL FINDINGS The current study analyzes DNA sequences from 68 gene segments of 62 distinct protein-coding nuclear genes for 80 species. Gene segments analyzed individually support numerous nodes recovered in combined-gene analyses, but few of the higher-level nodes of greatest current interest. However, neither is there support for conflicting alternatives to these higher-level nodes. Gene segments with higher rates of nonsynonymous change tend to be more informative overall, but those with lower rates tend to provide stronger support for deeper nodes. Higher-level nodes with bootstrap values in the 80% - 99% range for the complete data matrix are markedly more sensitive to substantial drops in their bootstrap percentages after character subsampling than those with 100% bootstrap, suggesting that these nodes are likely not to have been strongly supported with many fewer data than in the full matrix. Data set partitioning of total data by (mostly) synonymous and (mostly) nonsynonymous change improves overall node support, but the result remains much inferior to analysis of (unpartitioned) nonsynonymous change alone. Clusters of genes with similar nonsynonymous rate properties (e.g., faster vs. slower) show some distinct patterns of node support but few conflicts. Synonymous change is shown to contribute little, if any, phylogenetic signal to the support of higher-level nodes, but it does contribute nonphylogenetic signal, probably through its underlying heterogeneous nucleotide composition. Analysis of seemingly conservative indels does not prove useful. CONCLUSIONS Generating a robust molecular higher-level phylogeny of Arthropoda is currently possible with large amounts of data and an exclusive reliance on nonsynonymous change.
Collapse
Affiliation(s)
- Jerome C. Regier
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, United States of America
| | - Andreas Zwick
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, United States of America
- Entomology, State Museum of Natural History, Stuttgart, Germany
| |
Collapse
|
29
|
Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010; 463:1079-83. [PMID: 20147900 DOI: 10.1038/nature08742] [Citation(s) in RCA: 609] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 12/10/2009] [Indexed: 11/09/2022]
Abstract
The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.
Collapse
Affiliation(s)
- Jerome C Regier
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Regier JC, Zwick A, Cummings MP, Kawahara AY, Cho S, Weller S, Roe A, Baixeras J, Brown JW, Parr C, Davis DR, Epstein M, Hallwachs W, Hausmann A, Janzen DH, Kitching IJ, Solis MA, Yen SH, Bazinet AL, Mitter C. Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol Biol 2009; 9:280. [PMID: 19954545 PMCID: PMC2796670 DOI: 10.1186/1471-2148-9-280] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [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: 01/28/2009] [Accepted: 12/02/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis. RESULTS Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (P < 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (P < or = 0.005), and nearly so for the superfamily Drepanoidea as currently defined (P < 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data. CONCLUSION Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.
Collapse
Affiliation(s)
- Jerome C Regier
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
| | - Andreas Zwick
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
| | - Michael P Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Akito Y Kawahara
- Department of Entomology, University of Maryland, College Park, Maryland 20742, USA
| | - Soowon Cho
- Department of Entomology, University of Maryland, College Park, Maryland 20742, USA
- Department of Plant Medicine, Chungbuk National University, Cheongju 361-763, Korea
| | - Susan Weller
- Department of Entomology, University of Minnesota, St. Paul, Minnesota 55455, USA
| | - Amanda Roe
- Department of Entomology, University of Minnesota, St. Paul, Minnesota 55455, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Joaquin Baixeras
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Apartat de correus 2085, 46071 Valencia, Spain
| | - John W Brown
- Systematic Entomology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, USA
| | - Cynthia Parr
- Encyclopedia of Life, Smithsonian Institution, Washington, D.C. 20013-7012, USA
| | - Donald R Davis
- Department of Entomology, Smithsonian Institution, Washington, D.C. 20013-7012, USA
| | - Marc Epstein
- Plant Pest Diagnostics Branch, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, California 95832-1448, USA
| | - Winifred Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Axel Hausmann
- Bavarian State Collection of Zoology, Münchhausenstrasse 21, D-81247 München, Germany
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ian J Kitching
- Department of Entomology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - M Alma Solis
- Systematic Entomology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, USA
| | - Shen-Horn Yen
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Adam L Bazinet
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Charles Mitter
- Department of Entomology, University of Maryland, College Park, Maryland 20742, USA
| |
Collapse
|
31
|
Carles R, Farcău C, Bonafos C, Benassayag G, Pécassou B, Zwick A. The synthesis of single layers of Ag nanocrystals by ultra-low-energy ion implantation for large-scale plasmonic structures. Nanotechnology 2009; 20:355305. [PMID: 19671966 DOI: 10.1088/0957-4484/20/35/355305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Single layers of silver (Ag) nanoparticles embedded in silica (SiO2) have been fabricated by ultra-low-energy ion implantation. The distance between the Ag particles and the free SiO2 surface is controlled with nanometer precision. Raman scattering and reflectivity measurements strongly correlate to transmission electron microscopy analyses, allowing the use of these non-invasive techniques to monitor structural and dynamical properties. These results open up new opportunities to manipulate electromagnetic near-field interactions on wafer-scale plasmonic devices.
Collapse
Affiliation(s)
- R Carles
- Groupe Nanomat-CEMES-CNRS-Université de Toulouse, 29 rue Jeanne Marvig, Toulouse Cedex 4, France.
| | | | | | | | | | | |
Collapse
|
32
|
Carles R, Zwick A, Moura C, Djafari-Rouhani M. Density of vibrational states in highly disordered systems through Raman scattering and atomic-scale simulation. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/13642819808204967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- R. Carles
- a Laboratoire de Physique des Solides , Université Paul Sabatier , 31063, Toulouse , Cedex , 4 , France
| | - A. Zwick
- a Laboratoire de Physique des Solides , Université Paul Sabatier , 31063, Toulouse , Cedex , 4 , France
| | - C. Moura
- b Departamento de Fisica , Universidade do Minho , Largo do Paço, 4719 , Braga-Codex , Portugal
| | - M. Djafari-Rouhani
- b Departamento de Fisica , Universidade do Minho , Largo do Paço, 4719 , Braga-Codex , Portugal
| |
Collapse
|
33
|
Della-Justina HM, Winkler AM, Manczak T, de Oliveira PH, de Araújo DB, Neto AC, Zwick A, Gamba HR. Development of a Galvanic Vestibular Stimulator for fMRI exams. Neuroimage 2009. [DOI: 10.1016/s1053-8119(09)70930-9] [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: 12/01/2022] Open
|
34
|
Zwick A. The principal structure of male genital sclerites and muscles of bombycoid moths, with special reference to Anthelidae (Lepidoptera: Bombycoidea). Arthropod Struct Dev 2009; 38:147-161. [PMID: 18765298 DOI: 10.1016/j.asd.2008.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 07/22/2008] [Accepted: 07/24/2008] [Indexed: 05/26/2023]
Abstract
Male genital structures and muscles of bombycoid moths have repeatedly been misidentified in the literature. Furthermore, the genital structures of some bombycoid families, such as the poorly known Australo-New Guinean Anthelidae, have essentially remained unstudied. Based on comparative morphology, this study details the principal arrangements of male genital sclerites and muscles in all bombycoid families, with particular focus on basic structures and their modifications in Anthelidae. Emphasis is placed on the homology of and fusions between these structures and their function, providing a basis for the interpretation of modifications in future phylogenetic and taxonomic studies. This includes the unique fusion of gnathos and valvae in several bombycoid families, the arrangement and extent of the fused tegumen and vinculum, as well as the homology of the "transtilla". Further, a modification of the valve adductor muscle (the segment IX sternum to valva muscle, m4) widely regarded as a synapomorphy of Bombycoidea is demonstrated to be non-existent, as is the presumed presence of the valve abductor muscle (the segment IX tergum to valva muscle, m2) in Saturniidae.
Collapse
Affiliation(s)
- Andreas Zwick
- Australian National Insect Collection, CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia.
| |
Collapse
|
35
|
Regier JC, Shultz JW, Ganley ARD, Hussey A, Shi D, Ball B, Zwick A, Stajich JE, Cummings MP, Martin JW, Cunningham CW. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst Biol 2009; 57:920-38. [PMID: 19085333 DOI: 10.1080/10635150802570791] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations--first codon positions encoding leucine and arginine, which were also compositionally heterogeneous--yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned--fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase support of taxonomic relationships, sequence data from 49 additional taxa for three slow genes (i.e., EF-1 alpha, EF-2, and Pol II) were combined with the various 13-taxon data sets. The 62-taxon analyses supported the results of the 13-taxon analyses and provided increased support for additional pancrustacean clades found in an earlier analysis including only EF-1 alpha, EF-2, and Pol II.
Collapse
Affiliation(s)
- Jerome C Regier
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Schmickal T, Zwick A, Schinke B, Lederle K, Wentzensen A. Entwicklung eines elektronischen Steifigkeitsmesssystems mit permanenter Datenspeicherung. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s10039-007-1227-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
String S, Butler K, Grill D, Zwick A, Mangione K, Eastlack M. MUSCLE PERFORMANCE OF THE QUADRICEPS IN ELDERS AFTER HIP FRACTURE. J Geriatr Phys Ther 2005. [DOI: 10.1519/00139143-200512000-00016] [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: 11/08/2022]
|
38
|
Azéma L, Ladame S, Lapeyre C, Zwick A, Lakhdar-Ghazal F. Does phosphoryl protonation occurs in aqueous phosphoesters solutions. Spectrochim Acta A Mol Biomol Spectrosc 2005; 62:287-92. [PMID: 16257727 DOI: 10.1016/j.saa.2004.12.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Accepted: 12/20/2004] [Indexed: 05/05/2023]
Abstract
Ionisation of trimethylphosphate (TMP), dimethylphosphate (DMP) and diethylphosphate (DEP) is investigated by acidic titration in water by Raman (R), Fourier transform infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopies. The vibrational frequencies of the PO(2)(-) ionic form and the neutral form were found in accord with the literature. While increasing further H(+) concentration, the PO band disappears in the benefit of new ones. These results, together with deuteration experiments indicate the presence of a new ionic form positively charged with general formula R(1)R(2)R(3)P(OH)(+) or R(1)R(2)P(OH)(+)(2). The pK of this phosphonium entities is lying in the range -2, -4. These results were confirmed by (31)P NMR titration. The occurrence of such a phosphonium ion in aqueous solutions might be of crucial importance for biochemical reactions and interactions, owing to the large spread of phosphoryl group in biomolecules and keeping in mind that intracellular compartments are more likely concentrated media with little free water than real aqueous solutions. Furthermore, pK's can be shifted by physical-chemical parameters like dielectric constant and electric field. This may involve at least fractional positive charge apparition that might be important in biochemical regulation by charge-charge and charge-dipole interactions. This finding will gain to be further explored on more complex molecules like phospholipids, nucleic acids and proteins.
Collapse
Affiliation(s)
- L Azéma
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR-CNRS 5068, Université Paul Sabatier, 118 Route de Narbonne 31062 Toulouse Cedex 4, France
| | | | | | | | | |
Collapse
|
39
|
Moussa NO, Molnár G, Bonhommeau S, Zwick A, Mouri S, Tanaka K, Real JA, Bousseksou A. Selective photoswitching of the binuclear spin crossover compound {[Fe(bt)(NCS)2]2(bpm)} into two distinct macroscopic phases. Phys Rev Lett 2005; 94:107205. [PMID: 15783518 DOI: 10.1103/physrevlett.94.107205] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Indexed: 05/24/2023]
Abstract
The low-spin (LS-LS, S = 0) diamagnetic form of the binuclear spin crossover complex {[Fe(bt)(NCS)(2)](2)(bpm)} was selectively photoconverted into two distinct macroscopic phases at different excitation wavelengths (1342 or 647.1 nm). These long-lived metastable phases have been identified, respectively, as the symmetry-broken paramagnetic form (HS-LS, S = 2) and the antiferromagnetically coupled (HS-HS, S = 0) high-spin form of the compound. The selectivity may be explained by the strong coupling of the primary excited states to the paramagnetic state.
Collapse
Affiliation(s)
- N Ould Moussa
- Laboratoire de Chimie de Coordination, CNRS UPR-8241, 205 route de Narbonne, F-31077 Toulouse, France
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Torres CMS, Zwick A, Poinsotte F, Groenen J, Prunnila M, Ahopelto J, Mlayah A, Paillard V. Observations of confined acoustic phonons in silicon membranes. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/pssc.200405313] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
41
|
|
42
|
|
43
|
|
44
|
Nouvel G, Zwick A, Renucci MA, Lockwood DJ, Noel H. Magnetic ordering and Raman scattering from electronic excitations and phonons in uranium trichalcogenides. ACTA ACUST UNITED AC 2000. [DOI: 10.1088/0022-3719/20/12/016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
45
|
|
46
|
|
47
|
Zwick A, Munir M, Ryan CK, Gian J, Burt RW, Leppert M, Spirio L, Chey WY. Gastric adenocarcinoma and dysplasia in fundic gland polyps of a patient with attenuated adenomatous polyposis coli. Gastroenterology 1997; 113:659-63. [PMID: 9247488 DOI: 10.1053/gast.1997.v113.pm9247488] [Citation(s) in RCA: 129] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Gastric adenocarcinoma has been previously recognized as a potential complication of familial adenomatous polyposis coli (APC) and attenuated forms of APC (AAPC). This tumor has only been reported to originate from adenomatous polyps of the gastric mucosa in these clinical conditions. There have been no previous case reports of gastric adenocarcinoma arising from the more commonly found fundic gland polyps associated with AAPC or APC. We report the first definitive case of gastric adenocarcinoma arising from a hyperplastic polyp of the fundis of a patient with AAPC.
Collapse
Affiliation(s)
- A Zwick
- William B. and Shella Konar Center for Digestive and Liver Diseases, University of Rochester Medical Center, New York, USA
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Jünemann KP, Scheepe J, Persson-Jünemann C, Schmidt P, Abel K, Zwick A, Tschada R, Alken P. Basic experimental studies on corpus cavernosum electromyography and smooth-muscle electromyography of the urinary bladder. World J Urol 1994; 12:266-73. [PMID: 7866425 DOI: 10.1007/bf00191206] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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: 01/27/2023] Open
Abstract
In contrast to the extensive work on in vitro experiments for elucidation of the electrical properties of smooth musculature, the acquisition of knowledge on electrical signal behaviour from smooth-muscle cells in an in vivo situation remains very limited and rare. Smooth-muscle electromyographic recording from the smooth musculature of the genitourinary tract, in particular from the penile cavernous bodies and the urinary bladder, has recently become one of the most interesting issues in both impotence research as well as neurophysiological assessment of the urinary bladder. However, the inadequate available data on corpus cavernosum and EMG recordings remains controversial due to the significant discrepancy between basic physiology of the smooth musculature, technical prerequisites and the expected clinical impact from the smooth-muscle EMG of genitourinary organs. This article is an attempt to describe the fundamentals of smooth-muscle EMG signal behaviour and the technical prerequisites for data acquisition and analysis of electrical activity from smooth-muscle cells of the cavernous bodies and urinary bladder. A description is given of the technical aspects, including methodology and interpretation of the recorded data, and also of the possible interference by artefacts (endogeneous and exogeneous) that might limit the clinical relevance of this encouraging method. The advantages, pitfalls and limitations of online analogous data registration and the possibility of computer-assisted smooth-muscle electrical activity recording and analysis are demonstrated by basic in vivo studies on cavernous bodies and also the detrusor muscle.
Collapse
Affiliation(s)
- K P Jünemann
- Urologische Klinik, Fakultät für Klinische Medizin der Universität Heidelberg, Mannheim, Germany
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Chehaidar A, Zwick A, Carles R, Bandet J. Multiple-order Raman scattering and the density of vibrational states in a-GaAs. Phys Rev B Condens Matter 1994; 50:5345-5351. [PMID: 9976876 DOI: 10.1103/physrevb.50.5345] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
50
|
Castillo S, Favrot J, Bouissou T, Brazier J, Boisdon M, Zwick A. Assignment of the vibrational spectra of 2(1H)-pyridinone (2-pyridone) in the solid state, and in solution as centrosymmetrical dimer. Comparison with 1-methyl-2(1H)-pyridinone (N-methyl-2-pyridone). ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0584-8539(94)80035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|