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Lis JA. Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea). Int J Mol Sci 2023; 24:ijms24097758. [PMID: 37175465 PMCID: PMC10178826 DOI: 10.3390/ijms24097758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The SSU nrDNA, a small subunit of the nuclear ribosomal DNA (coding 18S rRNA), is one of the most frequently sequenced genes in molecular studies in Hexapoda. In insects, including true bugs (Hemiptera: Heteroptera), only its primary structures (i.e., aligned sequences) are predominantly used in phylogenetic reconstructions. It is known that including RNA secondary structures in the alignment procedure is essential for improving accuracy and robustness in phylogenetic tree reconstruction. Moreover, local plasticity in rRNAs might impact their tertiary structures and corresponding functions. To determine the systematic position of Thaumastellidae within the superfamily Pentatomoidea, the secondary and-for the first time among all Hexapoda-tertiary structures of 18S rRNAs in twelve pentatomoid families were compared and analysed. Results indicate that the shapes of the secondary and tertiary structures of the length-variable regions (LVRs) in the 18S rRNA are phylogenetically highly informative. Based on these results, it is suggested that the Thaumastellidae is maintained as an independent family within the superfamily Pentatomoidea, rather than as a part of the family Cydnidae. Moreover, the analyses indicate a close relationship between Sehirinae and Parastrachiidae, expressed in morpho-molecular synapomorphies in the predicted secondary and tertiary structures of the length-variable region L (LVR L).
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Affiliation(s)
- Jerzy A Lis
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland
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2
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Palmisano JN, Farrell TM, Hazelrig CM, Brennan MN. Documenting Range Expansion of the Invasive Pentastome Parasite, Raillietiella orientalis, Using Southern Black Racer and Eastern Coachwhip Road Mortality. SOUTHEAST NAT 2023. [DOI: 10.1656/058.022.0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Hasegawa R, Katahira H, Koizumi I. Salmincola markewitschi or S. carpionis (Copepoda: Lernaeopodidae)? A requirement for taxonomic revision due to their high morphological variations. Folia Parasitol (Praha) 2022; 69. [DOI: 10.14411/fp.2022.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 07/15/2022] [Indexed: 11/06/2022]
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Swanepoel L, Loyola A, Flowers J, Lewbart GA, Garrett KB, Yabsley MJ. Infection with a novel pentastome (Raillietiella sp.) in a juvenile endangered Galápagos tortoise (Chelonoidis niger). Vet Parasitol Reg Stud Reports 2022; 35:100782. [PMID: 36184111 DOI: 10.1016/j.vprsr.2022.100782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Pentastomes are crustacean endoparasites in the lungs of herpetofauna and rarely mammals and birds. To date, the only pentastomes reported in chelonians, all aquatic turtles, are Diesingia megastomum from Brazil and Pelonia africana from South Africa. In March 2021, 185 juvenile tortoises (Chelonoidis niger) were confiscated after an attempted illegal exportation from the Galápagos. It is believed the tortoises were removed from nests on Santa Cruz Island. The young tortoises were individually wrapped in plastic and at seizure ten were dead and another 25 tortoises subsequently died. One of the tortoises, estimated to be 3 months old, had 11 pentastomes in the lungs. The pentastomes were identified as a Raillietiella sp. based on morphology. The specimens had a claviform body that tapers into a bifid tail, a 165.3 μm × 92.1 μm buccal cadre, and sharp tipped anterior and posterior hooks with the posterior hooks being larger than the anterior. The males have smooth copulatory spicules with a rounded, smooth base. All females were gravid. Molecular analysis confirmed that the parasites were a Raillietiella sp. Based on the COI gene, it was most similar (82.7% identical) to an undescribed Raillietiella species from a Caribbean anole (Anolis cristatellus) found in Florida followed by R. hebitihamata (81%), R. indica (80.7%), and R. orientalis (78.8-80.7%). Based on the 18S rRNA gene sequence (1799 bp), it was most similar (99.3% identical) to two undescribed Raillietiella species followed by R. aegypti from a berber skink (Eumeces schneideri) from Saudia Arabia. Phylogenetically, with both molecular targets, the Raillietiella sp. from the Galápagos tortoise grouped with other Raillietiella spp. and was basal within the group. Currently, the origin of this parasite (native to Galápagos or introduced) and the life cycle are unknown. Because some pentastome species, especially when in aberrant hosts, can be pathogenic, additional studies of parasites in native and introduced reptile and amphibian species in the Galápagos are needed to better understand the risk this parasite poses to Galápagos tortoises.
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Affiliation(s)
- Liandrie Swanepoel
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, Wildlife Health Building, 589 D.W, Brooks Dr, Athens, GA 30602, USA
| | - Andrea Loyola
- Dirección Parque Nacional Galápagos, Islas Galápagos, Ecuador
| | - James Flowers
- College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA
| | - Gregory A Lewbart
- College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA
| | - Kayla B Garrett
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, Wildlife Health Building, 589 D.W, Brooks Dr, Athens, GA 30602, USA; Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | - Michael J Yabsley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, Wildlife Health Building, 589 D.W, Brooks Dr, Athens, GA 30602, USA; Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA.
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Hasegawa R, Ayer CG, Umatani Y, Miura K, Ukumura M, Katahira H, Koizumi I. Potential negative effects and heterogeneous distribution of a parasitic copepod Salmincola edwardsii (Copepoda: Lernaeopodidae) on Southern Asian Dolly Varden Salvelinus curilus in Hokkaido, Japan. Parasitol Int 2021; 87:102529. [PMID: 34896616 DOI: 10.1016/j.parint.2021.102529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 08/19/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022]
Abstract
The genus Salmincola is an ectoparasitic copepod group commonly infesting the branchial and buccal cavities of salmonids. While negative impacts on hatchery fishes have been reported, their impacts on wild fish populations and distribution patterns are critically understudied. In the Shiretoko Peninsula, Hokkaido, Japan, we found parasites belonging to this genus on the branchial cavity of a stream salmonid, Southern Asian Dolly Varden Salvelinus curilus. All parasites recovered were identified as Salmincola edwardsii based on morphological characteristics and partial 28S rDNA sequences. Prevalence was highly heterogeneous even among neighboring streams (0-54.8%, < 10 km) with the mean intensity among streams being generally low (2.19 parasites/infeted fish). Despite the low intensity, quantile regression analysis showed negative trends between parasite intensity and host condition, suggesting that the infestation of S. edwardsii has a potential negative impact on the host salmonid. In addition, a single copepod was found from an anadromous fish, which could indicate some salinity tolerance of the copepods. It is important to evaluate the effects of Salmincola spp. on host species and determine the limiting factors on the parasite's distribution for proper management.
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Affiliation(s)
- Ryota Hasegawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.
| | - Christopher G Ayer
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoshiyuki Umatani
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0809, Japan
| | - Kazuki Miura
- Shiretoko Museum, Honmachi 49, Shari, Shari-gun, Hokkaido 099-4113, Japan
| | - Miyo Ukumura
- Sapporo Wild Salmon Project, 2-1 Makomanai Park, Minami-ku, Sapporo, Hokkaido 005-0017, Japan
| | - Hirotaka Katahira
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5201, Japan
| | - Itsuro Koizumi
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan; Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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Yu DN, Yu PP, Zhang LP, Storey KB, Gao XY, Zhang JY. Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations. PeerJ 2021; 9:e11402. [PMID: 34221707 PMCID: PMC8231340 DOI: 10.7717/peerj.11402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera. METHODS Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups. RESULTS Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.
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Affiliation(s)
- Dan-Na Yu
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Pan-Pan Yu
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Le-Ping Zhang
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Xin-Yan Gao
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jia-Yong Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
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Garibian PG, Karabanov DP, Neretina AN, Taylor DJ, Kotov AA. Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 2021; 9:e11310. [PMID: 33981506 PMCID: PMC8074845 DOI: 10.7717/peerj.11310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
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Affiliation(s)
- Petr G. Garibian
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Fish Ecology, I.D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Anna N. Neretina
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Derek J. Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, New York, United States
| | - Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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Vecchioni L, Arculeo M, Cottarelli V, Marrone F. Range‐wide phylogeography and taxonomy of the marine rock pools dweller
Tigriopus fulvus
(Fischer, 1860) (Copepoda, Harpacticoida). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Vecchioni
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF) University of Palermo Palermo Italy
| | - Marco Arculeo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF) University of Palermo Palermo Italy
| | - Vezio Cottarelli
- Department for Innovation in Biological Agro‐Food and Forest Systems Tuscia University Viterbo Italy
| | - Federico Marrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF) University of Palermo Palermo Italy
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Sun X, Yu D, Xie Z, Dong J, Ding Y, Yao H, Greenslade P. Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection. PLoS One 2020; 15:e0230827. [PMID: 32282807 PMCID: PMC7153868 DOI: 10.1371/journal.pone.0230827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 12/20/2022] Open
Abstract
Collembola are a basal group of Hexapoda renowned for both unique morphological characters and significant ecological roles. However, a robust and plausible phylogenetic relationship between its deeply divergent lineages has yet to be achieved. We carried out a mitophylogenomic study based on a so far the most comprehensive mitochondrial genome dataset. Our data matrix contained mitogenomes of 31 species from almost all major families of all four orders, with 16 mitogenomes newly sequenced and annotated. We compared the linear arrangements of genes along mitochondria across species. Then we conducted 13 analyses each under a different combination of character coding, partitioning scheme and heterotachy models, and assessed their performance in phylogenetic inference. Several hypothetical tree topologies were also tested. Mitogenomic structure comparison revealed that most species share the same gene order of putative ancestral pancrustacean pattern, while seven species from Onychiuridae, Poduridae and Symphypleona bear different levels of gene rearrangements, indicating phylogenetic signals. Tomoceroidea was robustly recovered for the first time in the presence of all its families and subfamilies. Monophyly of Onychiuroidea was supported using unpartitioned models alleviating LBA. Paronellidae was revealed polyphyletic with two subfamilies inserted independently into Entomobryidae. Although Entomobryomorpha has not been well supported, more than half of the analyses obtained convincing topologies by placing Tomoceroidea within or near remaining Entomobryomorpha. The relationship between elongate-shaped and spherical-shaped collembolans still remained ambiguous, but Neelipleona tend to occupy the basal position in most trees. This study showed that mitochondrial genomes could provide important information for reconstructing the relationships among Collembola when suitable analytical approaches are implemented. Of all the data refining and model selecting schemes used in this study, the combination of nucleotide sequences, partitioning model and exclusion of third codon positions performed better in generating more reliable tree topology and higher node supports than others.
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Affiliation(s)
- Xin Sun
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- * E-mail: ,
| | - Zhijing Xie
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Dong
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yinhuan Ding
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Haifeng Yao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Penelope Greenslade
- Environmental Management, School of Applied and Biomedical Science, Federation University, Ballarat, Victoria, Australia
- Division of Biology, Australian National University, Australian Capital Territory, Australia
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10
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Manni M, Simao FA, Robertson HM, Gabaglio MA, Waterhouse RM, Misof B, Niehuis O, Szucsich NU, Zdobnov EM. The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations. Genome Biol Evol 2020; 12:3534-3549. [PMID: 31778187 PMCID: PMC6938034 DOI: 10.1093/gbe/evz260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.
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Affiliation(s)
- Mosè Manni
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Felipe A Simao
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Marco A Gabaglio
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Switzerland
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Albert Ludwig University, Institute of Biology I (Zoology), Freiburg, Germany
| | | | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
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Song N, Li X, Yin X, Li X, Yin J, Pan P. The mitochondrial genomes of palaeopteran insects and insights into the early insect relationships. Sci Rep 2019; 9:17765. [PMID: 31780743 PMCID: PMC6883079 DOI: 10.1038/s41598-019-54391-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/13/2019] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic relationships of basal insects remain a matter of discussion. In particular, the relationships among Ephemeroptera, Odonata and Neoptera are the focus of debate. In this study, we used a next-generation sequencing approach to reconstruct new mitochondrial genomes (mitogenomes) from 18 species of basal insects, including six representatives of Ephemeroptera and 11 of Odonata, plus one species belonging to Zygentoma. We then compared the structures of the newly sequenced mitogenomes. A tRNA gene cluster of IMQM was found in three ephemeropteran species, which may serve as a potential synapomorphy for the family Heptageniidae. Combined with published insect mitogenome sequences, we constructed a data matrix with all 37 mitochondrial genes of 85 taxa, which had a sampling concentrating on the palaeopteran lineages. Phylogenetic analyses were performed based on various data coding schemes, using maximum likelihood and Bayesian inferences under different models of sequence evolution. Our results generally recovered Zygentoma as a monophyletic group, which formed a sister group to Pterygota. This confirmed the relatively primitive position of Zygentoma to Ephemeroptera, Odonata and Neoptera. Analyses using site-heterogeneous CAT-GTR model strongly supported the Palaeoptera clade, with the monophyletic Ephemeroptera being sister to the monophyletic Odonata. In addition, a sister group relationship between Palaeoptera and Neoptera was supported by the current mitogenomic data.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xinxin Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinghao Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jian Yin
- Xinyang Agriculture and Forestry University, Xinyang, 464001, China
| | - Pengliang Pan
- Xinyang Agriculture and Forestry University, Xinyang, 464001, China
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12
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Mitochondrial Genome Diversity in Collembola: Phylogeny, Dating and Gene Order. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090169] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Collembola (springtails) are an early diverging class of apterygotes, and mark the first substantial radiation of hexapods on land. Despite extensive work, the relationships between major collembolan lineages are still debated and, apart from the Early Devonian fossil Rhyniella praecursor, which demonstrates their antiquity, the time frame of springtail evolution is unknown. In this study, we sequence two new mitochondrial genomes and reanalyze all known Collembola mt-genomes, including selected metagenomic data, to produce an improved phylogenetic hypothesis for the group, develop a tentative time frame for their differentiation, and provide a comprehensive overview of gene order diversity. Our analyses support most taxonomically recognized entities. We find support for an Entomobryomorpha + Symphypleona clade, while the position of Neelipleona could not be assessed with confidence. A Silurian time frame for their basal diversification is recovered, with an indication that divergence times may be fairly old overall. The distribution of mitochondrial gene order indicates the pancrustacean arrangement as plesiomorphic and dominant in the group, with the exception of the family Onychiuridae. We distinguished multiple instances of different arrangements in individual genomes or small clusters. We further discuss the opportunities and drawbacks associated with the inclusion of metagenomic data in a classic study on mitochondrial genome diversity.
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13
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Ding S, Li W, Wang Y, Cameron SL, Murányi D, Yang D. The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes. Mol Phylogenet Evol 2019; 135:123-135. [PMID: 30876966 DOI: 10.1016/j.ympev.2019.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
Phylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae + Diamphipnoidae and Austroperlidae + Gripopterygidae; consistent with relationships proposed based on morphology. The largely northern hemisphere suborder Arctoperlaria also divided into two groups, Euholognatha and Systellognatha, each composed of the five families traditionally assigned to each infraorder (the placement Scopuridae by mt genome data remains untested at this time). Within Euholognatha, strong support for the clade Nemouridae + Notonemouridae confirmed the northern origin of the currently southern hemisphere restricted Notonemouridae. Other family level relationships within the Arctoperlaria differ from those recovered by previous morphology and molecular based analyses. A fossil-calibrated divergence estimation suggests the formation of two suborders dates back to the Jurassic (181 Ma), with subsequent diversification of most stonefly families during the Cretaceous. This result confirms the hypothesis that initial divergence between the suborders was driven by the breakup of the supercontinent Pangaea into Laurasia and Gondwanaland (commencing 200 Ma and complete by 150 Ma).
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Affiliation(s)
- Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China; Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Dávid Murányi
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Herman Ottó út 15, Budapest H-1022, Hungary; Department of Zoology, Hungarian Natural History Museum, Baross u. 13, Budapest H-1088, Hungary
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China.
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15
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Simon S, Blanke A, Meusemann K. Reanalyzing the Palaeoptera problem - The origin of insect flight remains obscure. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:328-338. [PMID: 29763650 DOI: 10.1016/j.asd.2018.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
The phylogenetic relationships of the winged insect lineages - mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) - are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
| | - Alexander Blanke
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany; Medical and Biological Engineering Research Group, School of Engineering and Computer Science, University of Hull, Cottingham Road, HU6 7RX, Hull, UK
| | - Karen Meusemann
- Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg (Brsg.), Germany; Center of Molecular Biodiversity Research (ZMB), Zoological Research Museum A. Koenig (ZFMK), Adenauerallee 160, D-53113 Bonn, Germany.
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Yeom J, Nikitin MA, Ivanenko VN, Lee W. A new minute ectosymbiotic harpacticoid copepod living on the sea cucumber Eupentacta fraudatrixin the East/Japan Sea. PeerJ 2018; 6:e4979. [PMID: 29915699 PMCID: PMC6004304 DOI: 10.7717/peerj.4979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/16/2018] [Indexed: 11/20/2022] Open
Abstract
The ectosymbiotic copepods,Vostoklaophonte eupentagen. & sp. nov. associated with the sea cucumberEupentacta fraudatrix, was found in the subtidal zone of Peter the Great Bay, East/Japan Sea. The new genus,Vostoklaophonte, is similar toMicrocheloniain the flattened body form, reduced mandible, maxillule and maxilla, but with well-developed prehensile maxilliped, and in the reduced segmentation and setation of legs 1–5. Most appendages of the new genus are more primitive than those ofMicrochelonia. The inclusion of the symbiotic generaMicrocheloniaandVostoklaophontegen. nov. in Laophontidae, as well as their close phylogenetic relationships, are supported by morphological observations and molecular data. This is the third record of laophontid harpacticoid copepods living in symbiosis with sea cucumbers recorded from the Korean and Californian coasts.
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Affiliation(s)
- Jisu Yeom
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Mikhail A. Nikitin
- A.N. Belozersky Institute of Physico-chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Viatcheslav N. Ivanenko
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Wonchoel Lee
- Department of Life Science, Hanyang University, Seoul, South Korea
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Bekker EI, Karabanov DP, Galimov YR, Haag CR, Neretina TV, Kotov AA. Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages. PLoS One 2018; 13:e0194045. [PMID: 29543844 PMCID: PMC5854346 DOI: 10.1371/journal.pone.0194045] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/25/2018] [Indexed: 11/30/2022] Open
Abstract
Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.
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Affiliation(s)
- Eugeniya I. Bekker
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Fish Ecology, I. D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Yan R. Galimov
- Laboratory of Experimental Embryology, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Christoph R. Haag
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Tatiana V. Neretina
- N.A.Pertsov White Sea Biological Station, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
- Kazan Federal University, Kazan, Russia
- * E-mail:
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Crustacean olfactory systems: A comparative review and a crustacean perspective on olfaction in insects. Prog Neurobiol 2017; 161:23-60. [PMID: 29197652 DOI: 10.1016/j.pneurobio.2017.11.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 11/10/2017] [Accepted: 11/28/2017] [Indexed: 12/20/2022]
Abstract
Malacostracan crustaceans display a large diversity of sizes, morphs and life styles. However, only a few representatives of decapod taxa have served as models for analyzing crustacean olfaction, such as crayfish and spiny lobsters. Crustaceans bear multiple parallel chemosensory pathways represented by different populations of unimodal chemosensory and bimodal chemo- and mechanosensory sensilla on the mouthparts, the walking limbs and primarily on their two pairs of antennae. Here, we focus on the olfactory pathway associated with the unimodal chemosensory sensilla on the first antennal pair, the aesthetascs. We explore the diverse arrangement of these sensilla across malacostracan taxa and point out evolutionary transformations which occurred in the central olfactory pathway. We discuss the evolution of chemoreceptor proteins, comparative aspects of active chemoreception and the temporal resolution of crustacean olfactory system. Viewing the evolution of crustacean brains in light of energetic constraints can help us understand their functional morphology and suggests that in various crustacean lineages, the brains were simplified convergently because of metabolic limitations. Comparing the wiring of afferents, interneurons and output neurons within the olfactory glomeruli suggests a deep homology of insect and crustacean olfactory systems. However, both taxa followed distinct lineages during the evolutionary elaboration of their olfactory systems. A comparison with insects suggests their olfactory systems ö especially that of the vinegar fly ö to be superb examples for "economy of design". Such a comparison also inspires new thoughts about olfactory coding and the functioning of malacostracan olfactory systems in general.
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Khodami S, McArthur JV, Blanco-Bercial L, Martinez Arbizu P. Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda). Sci Rep 2017; 7:9164. [PMID: 28831035 PMCID: PMC5567239 DOI: 10.1038/s41598-017-06656-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/16/2017] [Indexed: 11/10/2022] Open
Abstract
For the first time, the phylogenetic relationships between representatives of all 10 copepod orders have been investigated using 28S and 18S rRNA, Histone H3 protein and COI mtDNA. The monophyly of Copepoda (including Platycopioida Fosshagen, 1985) is demonstrated for the first time using molecular data. Maxillopoda is rejected, as it is a polyphyletic group. The monophyly of the major subgroups of Copepoda, including Progymnoplea Lang, 1948 (=Platycopioida); Neocopepoda Huys and Boxshall, 1991; Gymnoplea Giesbrecht, 1892 (=Calanoida Sars, 1903); and Podoplea Giesbrecht, 1892, are supported in this study. Seven copepod orders are monophyletic, including Platycopioida, Calanoida, Misophrioida Gurney, 1933; Monstrilloida Sars, 1901; Siphonostomatoida Burmeister, 1834; Gelyelloida Huys, 1988; and Mormonilloida Boxshall, 1979. Misophrioida (=Propodoplea Lang, 1948) is the most basal Podoplean order. The order Cyclopoida Burmeister, 1835, is paraphyletic and now encompasses Poecilostomatoida Thorell, 1859, as a sister to the family Schminkepinellidae Martinez Arbizu, 2006. Within Harpacticoida Sars, 1903, both sections, Polyarthra Lang, 1948, and Oligoarthra Lang, 1948, are monophyletic, but not sister groups. The order Canuelloida is proposed while maintaining the order Harpacticoida s. str. (Oligoarthra). Cyclopoida, Harpacticoida and Cyclopinidae are redefined, while Canuelloida ordo. nov., Smirnovipinidae fam. nov. and Cyclopicinidae fam. nov are proposed as new taxa.
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Affiliation(s)
- Sahar Khodami
- Senckenberg am Meer, German Center for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany.
| | | | | | - Pedro Martinez Arbizu
- Senckenberg am Meer, German Center for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany
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20
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Ruiz CF, Rash JM, Besler DA, Roberts JR, Warren MB, Arias CR, Bullard SA. Exotic “Gill Lice” Species (Copepoda: Lernaeopodidae:SalmincolaSPP.) Infect Rainbow Trout (Oncorhynchus mykiss) and Brook Trout (Salvelinus fontinalis) in the Southeastern United States. J Parasitol 2017; 103:377-389. [DOI: 10.1645/16-165] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Carlos F. Ruiz
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Southeastern Cooperative Fish Parasite and Disease Project (SCFPDL), Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Jacob M. Rash
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Southeastern Cooperative Fish Parasite and Disease Project (SCFPDL), Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Doug A. Besler
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Southeastern Cooperative Fish Parasite and Disease Project (SCFPDL), Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Jackson R. Roberts
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Southeastern Cooperative Fish Parasite and Disease Project (SCFPDL), Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Micah B. Warren
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Southeastern Cooperative Fish Parasite and Disease Project (SCFPDL), Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Cova R. Arias
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Southeastern Cooperative Fish Parasite and Disease Project (SCFPDL), Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Stephen A. Bullard
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Southeastern Cooperative Fish Parasite and Disease Project (SCFPDL), Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
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Abstract
Background Classical cadherins are a metazoan-specific family of homophilic cell-cell adhesion molecules that regulate morphogenesis. Type I and type IV cadherins in this family function at adherens junctions in the major epithelial tissues of vertebrates and insects, respectively, but they have distinct, relatively simple domain organizations that are thought to have evolved by independent reductive changes from an ancestral type III cadherin, which is larger than derived paralogs and has a complicated domain organization. Although both type III and type IV cadherins have been identified in hexapods and branchiopods, the process by which the type IV cadherin evolved is still largely unclear. Results Through an analysis of arthropod genome sequences, we found that the only classical cadherin encoded in chelicerate genomes was the type III cadherin and that the two type III cadherin genes found in the spider Parasteatoda tepidariorum genome exhibited a complex yet ancestral exon-intron organization in arthropods. Genomic and transcriptomic data from branchiopod, copepod, isopod, amphipod, and decapod crustaceans led us to redefine the type IV cadherin category, which we separated into type IVa and type IVb, which displayed a similar domain organization, except type IVb cadherins have a larger number of extracellular cadherin (EC) domains than do type IVa cadherins (nine versus seven). We also showed that type IVa cadherin genes occurred in the hexapod, branchiopod, and copepod genomes whereas only type IVb cadherin genes were present in malacostracans. Furthermore, comparative characterization of the type IVb cadherins suggested that the presence of two extra EC domains in their N-terminal regions represented primitive characteristics. In addition, we identified an evolutionary loss of two highly conserved cysteine residues among the type IVa cadherins of insects. Conclusions We provide a genomic perspective of the evolution of classical cadherins among bilaterians, with a focus on the Arthropoda, and suggest that following the divergence of early arthropods, the precursor of the insect type IV cadherin evolved through stepwise reductive changes from the ancestral type III state. In addition, the complementary distributions of polarized genomic characters related to type IVa/IVb cadherins may have implications for our interpretations of pancrustacean phylogeny. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0991-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mizuki Sasaki
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, 569-1125, Osaka, Japan.,Current address: Department of Parasitology, Asahikawa Medical University, 2-1-1-1 Midorigaoka-higashi, Asahikawa, 078-8510, Hokkaido, Japan
| | - Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, 569-1125, Osaka, Japan.,Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, 569-1125, Osaka, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
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ESLAMI G, KHALATBARI-LIMAKI S, EHRAMPOUSH MH, GHOLAMREZAEI M, HAJIMOHAMMADI B, ORYAN A. Comparison of Three Different DNA Extraction Methods for Linguatula serrata as a Food Born Pathogen. IRANIAN JOURNAL OF PARASITOLOGY 2017; 12:236-242. [PMID: 28761484 PMCID: PMC5527034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/12/2016] [Indexed: 10/25/2022]
Abstract
BACKGROUND One of the most important items in molecular characterization of food-borne pathogens is high quality genomic DNA. In this study, we investigated three protocols and compared their simplicity, duration and costs for extracting genomic DNA from Linguatula serrata. METHODS The larvae were collected from the sheep's visceral organs from the Yazd Slaughterhouse during May 2013. DNA extraction was done in three different methods, including commercial DNA extraction kit, Phenol Chloroform Isoamylalcohol (PCI), and salting out. Extracted DNA in each method was assessed for quantity and quality using spectrophotometery and agarose gel electrophoresis, respectively. RESULTS The less duration was regarding to commercial DNA extraction kit and then salting out protocol. The cost benefit one was salting out and then PCI method. The best quantity was regarding to PCI with 72.20±29.20 ng/μl, and purity of OD260/OD280 in 1.76±0.947. Agarose gel electrophoresis for assessing the quality found all the same. CONCLUSION Salting out is introduced as the best method for DNA extraction from L. seratta as a food-borne pathogen with the least costand appropriate purity. Although, the best purity was regarding to PCI but PCI is not safe as salting out. In addition, the duration of salting out was less than PCI. The least duration was seen in commercial DNA extraction kit, but it is expensive and therefore is not recommended for developing countries where consumption of offal is common.
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Affiliation(s)
- Gilda ESLAMI
- Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Dept. of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sepideh KHALATBARI-LIMAKI
- Dept. of Food Hygiene and Safety, Faculty of Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Hasan EHRAMPOUSH
- Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Dept. of Environmental Health, Faculty of Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mostafa GHOLAMREZAEI
- Dept. of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Bahador HAJIMOHAMMADI
- Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Dept. of Food Hygiene and Safety, Faculty of Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ahmad ORYAN
- Dept. of Pathology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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Hiruta SF, Kobayashi N, Katoh T, Kajihara H. Molecular Phylogeny of Cypridoid Freshwater Ostracods (Crustacea: Ostracoda), Inferred from 18S and 28S rDNA Sequences. Zoolog Sci 2016; 33:179-85. [PMID: 27032683 DOI: 10.2108/zs150103] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
With the aim of exploring phylogenetic relationships within Cypridoidea, the most species-rich superfamily among the podocopidan ostracods, we sequenced nearly the entire 18S rRNA gene (18S) and part of the 28S rRNA gene (28S) for 22 species in the order Podocopida, with representatives from all the major cypridoid families. We conducted phylogenetic analyses using the methods of maximum likelihood, minimum evolution, and Bayesian analysis. Our analyses showed monophyly for Cyprididae, one of the four families currently recognized in Cypridoidea. Candonidae turned out to be paraphyletic, and included three clades corresponding to the subfamilies Candoninae, Paracypridinae, and Cyclocypridinae. We propose restricting the name Candonidae s. str. to comprise what is now Candoninae, and raising Paracypridinae and Cyclocyprininae to family rank within the superfamily Cypridoidea.
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Affiliation(s)
- Shimpei F Hiruta
- 1 Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | | | - Toru Katoh
- 1 Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroshi Kajihara
- 1 Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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Kjer KM, Simon C, Yavorskaya M, Beutel RG. Progress, pitfalls and parallel universes: a history of insect phylogenetics. J R Soc Interface 2016; 13:20160363. [PMID: 27558853 PMCID: PMC5014063 DOI: 10.1098/rsif.2016.0363] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.
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Affiliation(s)
- Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Margarita Yavorskaya
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
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25
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Yu D, Zhang F, Stevens MI, Yan Q, Liu M, Hu F. New insight into the systematics of Tomoceridae (Hexapoda, Collembola) by integrating molecular and morphological evidence. ZOOL SCR 2015. [DOI: 10.1111/zsc.12149] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences; Nanjing Agricultural University; Nanjing 210095 China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Mark I. Stevens
- South Australian Museum; GPO Box 234 Adelaide SA Australia
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide SA Australia
| | - Qibao Yan
- Department of Entomology, College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences; Nanjing Agricultural University; Nanjing 210095 China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences; Nanjing Agricultural University; Nanjing 210095 China
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Pepato AR, Klimov PB. Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment. BMC Evol Biol 2015; 15:178. [PMID: 26330076 PMCID: PMC4557820 DOI: 10.1186/s12862-015-0458-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites. RESULTS Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98-100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona. CONCLUSIONS Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates test.
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Affiliation(s)
- A R Pepato
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, Brazil.
| | - P B Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA.
- Tyumen State University, 10 Semakova St, Tyumen, 625003, Russia.
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Wu S, Xiong J, Yu Y. Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda. PLoS One 2015; 10:e0131498. [PMID: 26107258 PMCID: PMC4479608 DOI: 10.1371/journal.pone.0131498] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/01/2015] [Indexed: 01/20/2023] Open
Abstract
Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.
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Affiliation(s)
- Shu Wu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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Banerjee A, Manna S, Saha SK. A histological evaluation of development and axis formation in freshwater fish ectoparasite Argulus bengalensis Ramakrishna, 1951 (Crustacea: Branchiura). Parasitol Res 2015; 114:2199-212. [PMID: 25821935 DOI: 10.1007/s00436-015-4411-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022]
Abstract
The present investigation was carried out to underscore the developmental events of a crustacean ectoparasite of fish, Argulus bengalensis. Serial histological sections of the embryo were made at lateral, sagittal and longitudinal planes to explain its cleavage, gastrulation and axis specification. The centrolecithal egg of A. bengalensis underwent meroblastic superficial cleavage. The cleavage initiated at the future dorsal side of the egg within 5 h to 5 h and 30 min of incubation. Consequently, a small mass of energids appeared superficially at the future dorsal side within 6 h. Later, energids were found at the future ventral and lateral sides. A syncytial blastoderm was formed around the centrally placed yolk material which was transformed into a cellular blastoderm within 30 h of incubation. In the blastoderm, two cell masses were formed at the dorsal and ventral part which initially extended towards each other and later spread out though future anterior-posterior direction. The pressure exerted by the cell flow displaced the entire yolk material at the future postero-ventral side. At the time of egg laying, a prototype of the embryonic axes is determined. The substratum side of the egg formed the dorsal part, whilst the side facing water turned to the ventral part. The broader end of the egg formed the anterior side and the narrow end formed the posterior side of the embryo. The anterior-posterior axis formation was initiated within 72 to 96 h of incubation when the blastodermal cells displaced the yolk material at the future posterior end. Within 120 h of incubation, the germ layers of the embryo were determined. The study reveals that the cleavage pattern of A. bengalensis shows close similarities with that of the Malacostraca amongst the crustaceans and dipteran and hymenopteran amongst the insects.
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Affiliation(s)
- Anirban Banerjee
- Fish Biology Research Unit, Department of Zoology, School of Life Sciences, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
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Misof B, Meusemann K, von Reumont BM, Kück P, Prohaska SJ, Stadler PF. A priori assessment of data quality in molecular phylogenetics. Algorithms Mol Biol 2014. [DOI: 10.1186/s13015-014-0022-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Jaglarz MK, Kubrakiewicz J, Bilinski SM. The ovary structure and oogenesis in the basal crustaceans and hexapods. Possible phylogenetic significance. ARTHROPOD STRUCTURE & DEVELOPMENT 2014; 43:349-360. [PMID: 24858464 DOI: 10.1016/j.asd.2014.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 05/12/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
Recent large-scale phylogenetic analyses of exclusively molecular or combined molecular and morphological characters support a close relationship between Crustacea and Hexapoda. The growing consensus on this phylogenetic link is reflected in uniting both taxa under the name Pancrustacea or Tetraconata. Several recent molecular phylogenies have also indicated that the monophyletic hexapods should be nested within paraphyletic crustaceans. However, it is still contentious exactly which crustacean taxon is the sister group to Hexapoda. Among the favored candidates are Branchiopoda, Malacostraca, Remipedia and Xenocarida (Remipedia + Cephalocarida). In this context, we review morphological and ultrastructural features of the ovary architecture and oogenesis in these crustacean groups in search of traits potentially suitable for phylogenetic considerations. We have identified a suite of morphological characters which may prove useful in further comparative studies.
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Affiliation(s)
- Mariusz K Jaglarz
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland.
| | - Janusz Kubrakiewicz
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland
| | - Szczepan M Bilinski
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
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Legg DA, Sutton MD, Edgecombe GD. Arthropod fossil data increase congruence of morphological and molecular phylogenies. Nat Commun 2014; 4:2485. [PMID: 24077329 DOI: 10.1038/ncomms3485] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 08/21/2013] [Indexed: 12/11/2022] Open
Abstract
The relationships of major arthropod clades have long been contentious, but refinements in molecular phylogenetics underpin an emerging consensus. Nevertheless, molecular phylogenies have recovered topologies that morphological phylogenies have not, including the placement of hexapods within a paraphyletic Crustacea, and an alliance between myriapods and chelicerates. Here we show enhanced congruence between molecular and morphological phylogenies based on 753 morphological characters for 309 fossil and Recent panarthropods. We resolve hexapods within Crustacea, with remipedes as their closest extant relatives, and show that the traditionally close relationship between myriapods and hexapods is an artefact of convergent character acquisition during terrestrialisation. The inclusion of fossil morphology mitigates long-branch artefacts as exemplified by pycnogonids: when fossils are included, they resolve with euchelicerates rather than as a sister taxon to all other euarthropods.
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Affiliation(s)
- David A Legg
- 1] Department of Earth Sciences and Engineering, Royal School of Mines, Imperial College London, London SW7 2AZ, UK [2] Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK [3] Oxford University Museum of Natural History, Oxford OX1 3PW, UK
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Miyazawa H, Ueda C, Yahata K, Su ZH. Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development. Sci Rep 2014; 4:4127. [PMID: 24535281 PMCID: PMC3927213 DOI: 10.1038/srep04127] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/03/2014] [Indexed: 01/05/2023] Open
Abstract
Myriapoda, a subphylum of Arthropoda, comprises four classes, Chilopoda, Diplopoda, Pauropoda, and Symphyla. While recent molecular evidence has shown that Myriapoda is monophyletic, the internal phylogeny, which is pivotal for understanding the evolutionary history of myriapods, remains unresolved. Here we report the results of phylogenetic analyses and estimations of divergence time and ancestral state of myriapods. Phylogenetic analyses were performed based on three nuclear protein-coding genes determined from 19 myriapods representing the four classes (17 orders) and 11 outgroup species. The results revealed that Symphyla whose phylogenetic position has long been debated is the sister lineage to all other myriapods, and that the interordinal relationships within classes were consistent with traditional classifications. Ancestral state estimation based on the tree topology suggests that myriapods evolved from an ancestral state that was characterized by a hemianamorphic mode of post-embryonic development and had a relatively low number of body segments and legs.
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Affiliation(s)
- Hideyuki Miyazawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Chiaki Ueda
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kensuke Yahata
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhi-Hui Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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Dell’Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, Minh BQ, von Haeseler A, Ebersberger I, Pass G, Misof B. Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol 2014; 31:239-49. [PMID: 24140757 PMCID: PMC3879454 DOI: 10.1093/molbev/mst196] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.
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Affiliation(s)
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
- CSIRO Ecosystem Sciences, Australian National Insect Collection, Acton, ACT, Australia
| | | | - Ralph S. Peters
- Zoologisches Forschungsmuseum Alexander Koenig, Abteilung Arthropoda, Bonn, Germany
| | - Benjamin Meyer
- Institut für Systemische Neurowissenschaften, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Janus Borner
- Biozentrum Grindel & Zoologisches Museum, Universität Hamburg, Hamburg, Germany
| | - Malte Petersen
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
| | - Andre J. Aberer
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Heidelberg, Germany
| | - Alexandros Stamatakis
- Heidelberg Institute for Theoretical Studies (HITS), Scientific Computing Group, Heidelberg, Germany
- Karlsruher Institut für Technologie, Fakultät für Informatik, Karlsruhe, Germany
| | - Manfred G. Walzl
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Ingo Ebersberger
- Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Günther Pass
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Bonn, Germany
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Brenneis G, Stollewerk A, Scholtz G. Embryonic neurogenesis in Pseudopallene sp. (Arthropoda, Pycnogonida) includes two subsequent phases with similarities to different arthropod groups. EvoDevo 2013; 4:32. [PMID: 24289241 PMCID: PMC3879066 DOI: 10.1186/2041-9139-4-32] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/08/2013] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Studies on early neurogenesis have had considerable impact on the discussion of the phylogenetic relationships of arthropods, having revealed striking similarities and differences between the major lineages. In Hexapoda and crustaceans, neurogenesis involves the neuroblast, a type of neural stem cell. In each hemi-segment, a set of neuroblasts produces neural cells by repeated asymmetrical and interiorly directed divisions. In Euchelicerata and Myriapoda, neurogenesis lacks neural stem cells, featuring instead direct immigration of neural cell groups from fixed sites in the neuroectoderm. Accordingly, neural stem cells were hitherto assumed to be an evolutionary novelty of the Tetraconata (Hexapoda + crustaceans). To further test this hypothesis, we investigated neurogenesis in Pycnogonida, or sea spiders, a group of marine arthropods with close affinities to euchelicerates. RESULTS We studied neurogenesis during embryonic development of Pseudopallene sp. (Callipallenidae), using fluorescent histochemical staining and immunolabelling. Embryonic neurogenesis has two phases. The first phase shows notable similarities to euchelicerates and myriapods. These include i) the lack of morphologically different cell types in the neuroectoderm; ii) the formation of transiently identifiable, stereotypically arranged cell internalization sites; iii) immigration of predominantly post-mitotic ganglion cells; and iv) restriction of tangentially oriented cell proliferation to the apical cell layer. However, in the second phase, the formation of a central invagination in each hemi-neuromere is accompanied by the differentiation of apical neural stem cells. The latter grow in size, show high mitotic activity and an asymmetrical division mode. A marked increase of ganglion cell numbers follows their differentiation. Directly basal to the neural stem cells, an additional type of intermediate neural precursor is found. CONCLUSIONS Embryonic neurogenesis of Pseudopallene sp. combines features of central nervous system development that have been hitherto described separately in different arthropod taxa. The two-phase character of pycnogonid neurogenesis calls for a thorough reinvestigation of other non-model arthropods over the entire course of neurogenesis. With the currently available data, a common origin of pycnogonid neural stem cells and tetraconate neuroblasts remains unresolved. To acknowledge this, we present two possible scenarios on the evolution of arthropod neurogenesis, whereby Myriapoda play a key role in the resolution of this issue.
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Affiliation(s)
- Georg Brenneis
- Humboldt-Universität zu Berlin, Institut für Biologie/Vergleichende Zoologie, Philippstraße 13, Berlin 10115, Germany
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie/Vergleichende Zoologie, Philippstraße 13, Berlin 10115, Germany
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Simon S, Hadrys H. A comparative analysis of complete mitochondrial genomes among Hexapoda. Mol Phylogenet Evol 2013; 69:393-403. [DOI: 10.1016/j.ympev.2013.03.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 02/13/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
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Zieger E, Bräunig P, Harzsch S. A developmental study of serotonin-immunoreactive neurons in the embryonic brain of the marbled crayfish and the migratory locust: evidence for a homologous protocerebral group of neurons. ARTHROPOD STRUCTURE & DEVELOPMENT 2013; 42:507-520. [PMID: 24067539 DOI: 10.1016/j.asd.2013.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 08/19/2013] [Accepted: 08/23/2013] [Indexed: 06/02/2023]
Abstract
It is well established that the brains of adult malacostracan crustaceans and winged insects display distinct homologies down to the level of single neuropils such as the central complex and the optic neuropils. We wanted to know if developing insect and crustacean brains also share similarities and therefore have explored how neurotransmitter systems arise during arthropod embryogenesis. Previously, Sintoni et al. (2007) had already reported a homology of an individually identified cluster of neurons in the embryonic crayfish and insect brain, the secondary head spot cells that express the Engrailed protein. In the present study, we have documented the ontogeny of the serotonergic system in embryonic brains of the Marbled Crayfish in comparison to Migratory Locust embryos using immunohistochemical methods combined with confocal laser-scan microscopy. In both species, we found a cluster of early emerging serotonin-immunoreactive neurons in the protocerebrum with neurites that cross to the contralateral brain hemisphere in a characteristic commissure suggesting a homology of this cell cluster. Our study is a first step towards a phylogenetic analysis of neurotransmitter system development and shows that, as for the ventral nerve cord, traits related to neurogenesis in the brain can provide valuable hints for resolving the much debated question of arthropod phylogeny.
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Affiliation(s)
- Elisabeth Zieger
- Ernst Moritz Arndt Universität Greifswald, Fachbereich Biologie, Zoologisches Institut und Museum, AG Cytology und Evolutionsbiologie, Soldmannstrasse 23, D-17498 Greifswald, Germany.
| | - Peter Bräunig
- Unit for "Developmental Biology and Morphology of Animals", Institute for Biology II, RWTH Aachen University, Lukasstr. 1, D-52070 Aachen, Germany
| | - Steffen Harzsch
- Ernst Moritz Arndt Universität Greifswald, Fachbereich Biologie, Zoologisches Institut und Museum, AG Cytology und Evolutionsbiologie, Soldmannstrasse 23, D-17498 Greifswald, Germany
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Sasaki G, Ishiwata K, Machida R, Miyata T, Su ZH. Molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of Entognatha. BMC Evol Biol 2013; 13:236. [PMID: 24176097 PMCID: PMC4228403 DOI: 10.1186/1471-2148-13-236] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 10/29/2013] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Molecular phylogenetic analyses have revealed that Hexapoda and Crustacea form a common clade (the Pancrustacea), which is now widely accepted among zoologists; however, the origin of Hexapoda remains unresolved. The main problems are the unclear relationships among the basal hexapod lineages, Protura (proturans), Collembola (springtails), Diplura (diplurans), and Ectognatha (bristletails, silverfishes, and all winged insects). Mitogenomic analyses have challenged hexapod monophyly and suggested the reciprocal paraphyly of Hexapoda and Crustacea, whereas studies based on nuclear molecular data support the monophyletic origin of hexapods. Additionally, there are significant discrepancies with respect to these issues between the results of morphological and molecular studies. To investigate these problems, we performed phylogenetic analyses of Pancrustacea based on the protein sequences of three orthologous nuclear genes encoding the catalytic subunit of DNA polymerase delta and the largest and second largest subunits of RNA polymerase II from 64 species of arthropods, including representatives of all hexapod orders. RESULTS Phylogenetic analyses were conducted based on the inferred amino acid (aa) sequences (~3400 aa in total) of the three genes using the maximum likelihood (ML) method and Bayesian inference. Analyses were also performed with additional datasets generated by excluding long-branch taxa or by using different outgroups. These analyses all yielded essentially the same results. All hexapods were clustered into a common clade, with Branchiopoda as its sister lineage, whereas Crustacea was paraphyletic. Within Hexapoda, the lineages Ectognatha, Palaeoptera, Neoptera, Polyneoptera, and Holometabola were each confirmed to be monophyletic with robust support, but monophyly was not supported for Entognatha (Protura + Collembola + Diplura), Ellipura (Protura + Collembola), or Nonoculata (Protura + Diplura). Instead, our results showed that Protura is the sister lineage to all other hexapods and that Diplura or Diplura + Collembola is closely related to Ectognatha. CONCLUSION This is the first study to include all hexapod orders in a phylogenetic analysis using multiple nuclear protein-coding genes to investigate the phylogeny of Hexapoda, with an emphasis on Entognatha. The results strongly support the monophyletic origin of hexapods but reject the monophyly of Entognatha, Ellipura, and Nonoculata. Our results provided the first molecular evidence in support of Protura as the sister group to other hexapods. These findings are expected to provide additional insights into the origin of hexapods and the processes involved in the adaptation of insects to life on land.
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Affiliation(s)
- Go Sasaki
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569–1125, Japan
- Present address: School of Medicine, Kumamoto University, Kumamoto 860-8556, Japan
| | - Keisuke Ishiwata
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569–1125, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
- Present address: Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Ryuichiro Machida
- Sugadaira Montane Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Takashi Miyata
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569–1125, Japan
| | - Zhi-Hui Su
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569–1125, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
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Barnett AA, Thomas RH. The expression of limb gap genes in the mite Archegozetes longisetosus reveals differential patterning mechanisms in chelicerates. Evol Dev 2013; 15:280-92. [PMID: 23809702 DOI: 10.1111/ede.12038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The modular organization of arthropod limbs has lead to the evolution of a diversity of appendages within this phylum. A conserved trait within the arthropods is the utilization of a conserved set of regulatory genes that specify the appendage podomeres along the proximo-distal axis, termed the limb gap genes. These include extradenticle, homothorax, dachshund, and Distal-less. The deployment of these genes in the most basally branching arthropod group, the chelicerates, has only been studied in detail in two chelicerate groups, the harvestmen and spiders. Given the broad range of appendage diversity within the chelicerates, comparative studies of gap gene deployment in other chelicerates groups is needed. We therefore followed limb gap gene expression in a member of the largest chelicerate group, Acari, the oribatid mite Archegozetes longisetosus. We show that in contrast to many arthropod species, A. longisetosus expresses homothorax and extradenticle exclusively in the proximal portion of the appendages, which refutes the hypothesis of a sister-group relationship between chelicerates and myriapods. We also provide evidence that mites posses the ancestral chelicerate condition of possessing three-segmented chelicerae, which also express the gene dachshund. This adds support to the hypothesis that a cheliceral dachshund domain is ancestral to arachnids. Lastly, we provide evidence that the suppression of the fourth pair of walking legs, a putative synapomorphy for Acari, is accomplished by repressing the development of the medial and distal regions of the limb.
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Affiliation(s)
- Austen A Barnett
- Department of Zoology, Southern Illinois University, Carbondale, IL 62901, USA
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Petrunina AS, Neretina TV, Mugue NS, Kolbasov GA. Tantulocarida versus Thecostraca: inside or outside? First attempts to resolve phylogenetic position of Tantulocarida using gene sequences. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Tatyana V. Neretina
- Pertsov White Sea Biological Station; Lomonosov Moscow State University; Moscow Russia
| | - Nikolay S. Mugue
- Russian Federal Research Institute of Fisheries & Oceanography (VNIRO); Moscow Russia
| | - Gregory A. Kolbasov
- Pertsov White Sea Biological Station; Lomonosov Moscow State University; Moscow Russia
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40
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Wolfe JM, Hegna TA. Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages. Cladistics 2013; 30:366-390. [DOI: 10.1111/cla.12051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2013] [Indexed: 01/14/2023] Open
Affiliation(s)
- Joanna M. Wolfe
- Department of Geology and Geophysics; Yale University; 210 Whitney Avenue New Haven CT 06520 USA
- Division of Invertebrate Zoology & Sackler Institute of Comparative Genomics; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
| | - Thomas A. Hegna
- Department of Geology and Geophysics; Yale University; 210 Whitney Avenue New Haven CT 06520 USA
- Department of Geology; Western Illinois University; Tillman Hall 1 University Circle Macomb IL 61455 USA
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41
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Phylogenetic position of Linguatula arctica and Linguatula serrata (Pentastomida) as inferred from the nuclear 18S rRNA gene and the mitochondrial cytochrome c oxidase subunit I gene. Parasitol Res 2013; 112:3517-25. [DOI: 10.1007/s00436-013-3534-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 07/01/2013] [Indexed: 11/27/2022]
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Kocarek P, John V, Hulva P. When the body hides the ancestry: phylogeny of morphologically modified epizoic earwigs based on molecular evidence. PLoS One 2013; 8:e66900. [PMID: 23826171 PMCID: PMC3691250 DOI: 10.1371/journal.pone.0066900] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 05/14/2013] [Indexed: 11/19/2022] Open
Abstract
Here, we present a study regarding the phylogenetic positions of two enigmatic earwig lineages whose unique phenotypic traits evolved in connection with ectoparasitic relationships with mammals. Extant earwigs (Dermaptera) have traditionally been divided into three suborders: the Hemimerina, Arixeniina, and Forficulina. While the Forficulina are typical, well-known, free-living earwigs, the Hemimerina and Arixeniina are unusual epizoic groups living on molossid bats (Arixeniina) or murid rodents (Hemimerina). The monophyly of both epizoic lineages is well established, but their relationship to the remainder of the Dermaptera is controversial because of their extremely modified morphology with paedomorphic features. We present phylogenetic analyses that include molecular data (18S and 28S ribosomal DNA and histone-3) for both Arixeniina and Hemimerina for the first time. This data set enabled us to apply a rigorous cladistics approach and to test competing hypotheses that were previously scattered in the literature. Our results demonstrate that Arixeniidae and Hemimeridae belong in the dermapteran suborder Neodermaptera, infraorder Epidermaptera, and superfamily Forficuloidea. The results support the sister group relationships of Arixeniidae+Chelisochidae and Hemimeridae+Forficulidae. This study demonstrates the potential for rapid and substantial macroevolutionary changes at the morphological level as related to adaptive evolution, in this case linked to the utilization of a novel trophic niche based on an epizoic life strategy. Our results also indicate that the evolutionary consequences of the transition to an ectoparazitic mode of living, which is extremely rare in earwigs, have biased previous morphology-based hypotheses regarding the phylogeny of this insect group.
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Affiliation(s)
- Petr Kocarek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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43
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Kenning M, Müller C, Wirkner CS, Harzsch S. The Malacostraca (Crustacea) from a neurophylogenetic perspective: New insights from brain architecture in Nebalia herbstii Leach, 1814 (Leptostraca, Phyllocarida). ZOOL ANZ 2013. [DOI: 10.1016/j.jcz.2012.09.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Thomas JA, Trueman JWH, Rambaut A, Welch JJ. Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny. Syst Biol 2013; 62:285-97. [DOI: 10.1093/sysbio/sys093] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jessica A. Thomas
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - John W. H. Trueman
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Andrew Rambaut
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - John J. Welch
- Department of Biology, University of York, York YO10 5DD, UK; 2Research School of Biology, Australian National University, Canberra ACT 0200, Australia; 3Institute for Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK; and 4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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Wang Y, Engel MS, Rafael JA, Dang K, Wu H, Wang Y, Xie Q, Bu W. A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera. PLoS One 2013; 8:e53679. [PMID: 23301099 PMCID: PMC3536744 DOI: 10.1371/journal.pone.0053679] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/03/2012] [Indexed: 01/30/2023] Open
Abstract
The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.
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Affiliation(s)
- Yanhui Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Michael S. Engel
- Division of Entomology (Paleoentomology), Natural History Museum, London, England
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Jose A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Haoyang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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Altshuler I, Vaillant JJ, Xu S, Cristescu ME. The evolutionary history of sarco(endo)plasmic calcium ATPase (SERCA). PLoS One 2012; 7:e52617. [PMID: 23285113 PMCID: PMC3527596 DOI: 10.1371/journal.pone.0052617] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 11/20/2012] [Indexed: 12/18/2022] Open
Abstract
Investigating the phylogenetic relationships within physiologically essential gene families across a broad range of taxa can reveal the key gene duplication events underlying their family expansion and is thus important to functional genomics studies. P-Type II ATPases represent a large family of ATP powered transporters that move ions across cellular membranes and includes Na+/K+ transporters, H+/K+ transporters, and plasma membrane Ca2+ pumps. Here, we examine the evolutionary history of one such transporter, the Sarco(endo)plasmic reticulum calcium ATPase (SERCA), which maintains calcium homeostasis in the cell by actively pumping Ca2+ into the sarco(endo)plasmic reticulum. Our protein-based phylogenetic analyses across Eukaryotes revealed two monophyletic clades of SERCA proteins, one containing animals, fungi, and plants, and the other consisting of plants and protists. Our analyses suggest that the three known SERCA proteins in vertebrates arose through two major gene duplication events after the divergence from tunicates, but before the separation of fishes and tetrapods. In plants, we recovered two SERCA clades, one being the sister group to Metazoa and the other to Apicomplexa clade, suggesting an ancient duplication in an early eukaryotic ancestor, followed by subsequent loss of one copy in Opisthokonta, the other in protists, and retention of both in plants. We also report relatively recent and independent gene duplication events within invertebrate taxa including tunicates and the leech Helobdella robusta. Thus, it appears that both ancient and recent gene duplication events have played an important role in the evolution of this ubiquitous gene family across the eukaryotic domain.
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Affiliation(s)
- Ianina Altshuler
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.
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47
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48
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Sharma PP, Schwager EE, Extavour CG, Giribet G. Evolution of the chelicera: adachshunddomain is retained in the deutocerebral appendage of Opiliones (Arthropoda, Chelicerata). Evol Dev 2012; 14:522-33. [DOI: 10.1111/ede.12005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Evelyn E. Schwager
- Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street; Cambridge; MA 02138; USA
| | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street; Cambridge; MA 02138; USA
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49
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Böhm A, Szucsich NU, Pass G. Brain anatomy in Diplura (Hexapoda). Front Zool 2012; 9:26. [PMID: 23050723 PMCID: PMC3585824 DOI: 10.1186/1742-9994-9-26] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 10/03/2012] [Indexed: 01/27/2023] Open
Abstract
Background In the past decade neuroanatomy has proved to be a valuable source of character systems that provide insights into arthropod relationships. Since the most detailed description of dipluran brain anatomy dates back to Hanström (1940) we re-investigated the brains of Campodea augens and Catajapyx aquilonaris with modern neuroanatomical techniques. The analyses are based on antibody staining and 3D reconstruction of the major neuropils and tracts from semi-thin section series. Results Remarkable features of the investigated dipluran brains are a large central body, which is organized in nine columns and three layers, and well developed mushroom bodies with calyces receiving input from spheroidal olfactory glomeruli in the deutocerebrum. Antibody staining against a catalytic subunit of protein kinase A (DC0) was used to further characterize the mushroom bodies. The japygid Catajapyx aquilonaris possesses mushroom bodies which are connected across the midline, a unique condition within hexapods. Conclusions Mushroom body and central body structure shows a high correspondence between japygids and campodeids. Some unique features indicate that neuroanatomy further supports the monophyly of Diplura. In a broader phylogenetic context, however, the polarization of brain characters becomes ambiguous. The mushroom bodies and the central body of Diplura in several aspects resemble those of Dicondylia, suggesting homology. In contrast, Archaeognatha completely lack mushroom bodies and exhibit a central body organization reminiscent of certain malacostracan crustaceans. Several hypotheses of brain evolution at the base of the hexapod tree are discussed.
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Affiliation(s)
- Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
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50
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Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK. Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny. Mol Biol Evol 2012; 30:215-33. [DOI: 10.1093/molbev/mss216] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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