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Benavides LR, Edgecombe GD, Giribet G. Re-evaluating and dating myriapod diversification with phylotranscriptomics under a regime of dense taxon sampling. Mol Phylogenet Evol 2023; 178:107621. [PMID: 36116731 DOI: 10.1016/j.ympev.2022.107621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Recent transcriptomic studies of myriapod phylogeny have been based on relatively small datasets with <40 myriapod terminals and variably supported or contradicted the traditional morphological groupings of Progoneata and Dignatha. Here we amassed a large dataset of 104 myriapod terminals, including multiple species for each of the four myriapod classes. Across the tree, most nodes are stable and well supported. Most analyses across a range of gene occupancy levels provide moderate to strong support for a deep split of Myriapoda into Symphyla + Pauropoda (=Edafopoda) and an uncontradicted grouping of Chilopoda + Diplopoda (=Pectinopoda nov.), as in other recent transcriptome-based analyses; no analysis recovers Progoneata or Dignatha as clades. As in all recent multi-locus and phylogenomic studies, chilopod interrelationships resolve with Craterostigmus excluded from Amalpighiata rather than uniting with other centipedes with maternal brood care in Phylactometria. Diplopod ordinal interrelationships are largely congruent with morphology-based classifications. Chilognathan clades that are not invariably advocated by morphologists include Glomerida + Glomeridesmida, such that the volvation-related characters of pill millipedes may be convergent, and Stemmiulida + Polydesmida more closely allied to Juliformia than to Callipodida + Chordeumatida. The latter relationship implies homoplasy in spinnerets and contradicts Nematophora. A time-tree with nodes calibrated by 25 myriapod and six outgroup fossil terminals recovers Cambrian-Ordovician divergences for the deepest splits in Myriapoda, Edafopoda and Pectinopoda, predating the terrestrial fossil record of myriapods as in other published chronograms, whereas age estimates within Chilopoda and Diplopoda overlap with or do not appreciably predate the calibration fossils. The grouping of Chilopoda and Diplopoda is recovered in all our analyses and is formalized as Pectinopoda nov., named for the shared presence of mandibular comb lamellae. New taxonomic proposals for Chilopoda based on uncontradicted clades are Tykhepoda nov. for the three blind families of Scolopendromorpha that share a "sieve-type" gizzard, and Taktikospina nov. for Scolopendromorpha to the exclusion of Mimopidae.
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Affiliation(s)
- Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | | | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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2
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A Rearrangement of the Mitochondrial Genes of Centipedes (Arthropoda, Myriapoda) with a Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13101787. [DOI: 10.3390/genes13101787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Due to the limitations of taxon sampling and differences in results from the available data, the phylogenetic relationships of the Myriapoda remain contentious. Therefore, we try to reconstruct and analyze the phylogenetic relationships within the Myriapoda by examining mitochondrial genomes (the mitogenome). In this study, typical circular mitogenomes of Mecistocephalus marmoratus and Scolopendra subspinipes were sequenced by Sanger sequencing; they were 15,279 bp and 14,637 bp in length, respectively, and a control region and 37 typical mitochondrial genes were annotated in the sequences. The results showed that all 13 PCGs started with ATN codons and ended with TAR codons or a single T; what is interesting is that the gene orders of M. marmoratus have been extensively rearranged compared with most Myriapoda. Thus, we propose a simple duplication/loss model to explain the extensively rearranged genes of M. marmoratus, hoping to provide insights into mitogenome rearrangement events in Myriapoda. In addition, our mitogenomic phylogenetic analyses showed that the main myriapod groups are monophyletic and supported the combination of the Pauropoda and Diplopoda to form the Dignatha. Within the Chilopoda, we suggest that Scutigeromorpha is a sister group to the Lithobiomorpha, Geophilomorpha, and Scolopendromorpha. We also identified a close relationship between the Lithobiomorpha and Geophilomorpha. The results also indicate that the mitogenome can be used as an effective mechanism to understand the phylogenetic relationships within Myriapoda.
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3
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Zuo Q, Zhang Z, Shen Y. Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda. Ecol Evol 2022; 12:e8764. [PMID: 35356579 PMCID: PMC8948135 DOI: 10.1002/ece3.8764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/29/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: "TD (N\R) L + C" based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.
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Affiliation(s)
- Qing Zuo
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Zhisheng Zhang
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Yanjun Shen
- Chongqing Key Laboratory of Animal BiologySchool of Life SciencesChongqing Normal UniversityChongqingChina
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4
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Hilken G, Rosenberg J, Edgecombe GD, Blüml V, Hammel JU, Hasenberg A, Sombke A. The tracheal system of scutigeromorph centipedes and the evolution of respiratory systems of myriapods. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 60:101006. [PMID: 33246291 DOI: 10.1016/j.asd.2020.101006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
The tracheal system of scutigeromorph centipedes (Chilopoda) is special, as it consists of dorsally arranged unpaired spiracles. In this study, we investigate the tracheal systems of five different scutigeromorph species. They are strikingly similar to each other but depict unique characters compared to the tracheal systems of pleurostigmophoran centipedes, which has engendered an ongoing debate over a single versus independent origin of tracheal systems in Chilopoda. Up to now, only the respiratory system of Scutigera coleoptrata was investigated intensively using LM-, TEM-, and SEM-techniques. We supplement this with data for species from all three families of Scutigeromorpha. These reveal interspecific differences in atrial width and the shape and branching pattern of the tracheal tubules. Further, we investigated the tracheal system of Scutigera coleoptrata with three additional techniques: light sheet microscopy, microCT and synchrotron radiation based microCT analysis. This set of techniques allows a comparison between fresh versus fixed and dried material. The question of a unique vs. multiple origin of tracheal systems in centipedes and in Myriapoda as a whole is discussed with regard to their structural similarities and differences and the presence of hemocyanin as an oxygen carrier. We used morphological and molecular data and the fossil record to evaluate the alternative hypotheses.
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Affiliation(s)
- Gero Hilken
- Central Animal Laboratory, University Clinic, University Duisburg-Essen, Hufelandstraße 55, 45122, Essen, Germany.
| | | | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, London, SW7 5BD, United Kingdom
| | - Valentin Blüml
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Jörg U Hammel
- X-ray Imaging with Synchrotron Radiation, Helmholz-Zentrum Geesthacht, Institute of Materials Research, Max-Planck-Straße 1, 21502, Geesthacht, Germany
| | - Anja Hasenberg
- Institute for Experimental Immunology and Imaging, University Clinic, University Duisburg-Essen, Universitätsstraße 2, 45141, Essen, Germany
| | - Andy Sombke
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
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5
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Szucsich NU, Bartel D, Blanke A, Böhm A, Donath A, Fukui M, Grove S, Liu S, Macek O, Machida R, Misof B, Nakagaki Y, Podsiadlowski L, Sekiya K, Tomizuka S, Von Reumont BM, Waterhouse RM, Walzl M, Meng G, Zhou X, Pass G, Meusemann K. Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups. BMC Evol Biol 2020; 20:144. [PMID: 33148176 PMCID: PMC7640414 DOI: 10.1186/s12862-020-01699-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022] Open
Abstract
Background Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data. Results We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda. Conclusions Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.
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Affiliation(s)
- Nikolaus U Szucsich
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria. .,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria.
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Blanke
- Institute for Zoology, Biocenter, University of Cologne, D-50674, Cologne, Germany.,Institute of Evolutionary Biology and Animal Ecology, University of Bonn, D-53121, Bonn, Germany
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Makiko Fukui
- Department of Biology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Simon Grove
- Invertebrate Zoology, Collections and Research Facility, Tasmanian Museum and Art Gallery, Rosny, Tasmania, 7018, Australia
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Oliver Macek
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria.,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Yasutaka Nakagaki
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Kaoru Sekiya
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | | | - Björn M Von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Animal Venomics, Institute for Insect Biotechnology, University of Giessen, Heinrich Buff Ring 26-32, D-35394, Giessen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Manfred Walzl
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Guanliang Meng
- Centre of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Günther Pass
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany. .,Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, D-79104, Freiburg, Germany. .,Australian National Insect Collection, National Research Collections Australia, CSIRO, ACT, Canberra, 2601, Australia.
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6
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7
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Moritz L, Wesener T, Koch M. An apparently non-swinging tentorium in the Diplopoda (Myriapoda): comparative morphology of the tentorial complex in giant pill-millipedes (Sphaerotheriida). Zookeys 2018; 741:77-91. [PMID: 29706773 PMCID: PMC5904393 DOI: 10.3897/zookeys.741.21909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/20/2017] [Indexed: 11/12/2022] Open
Abstract
The presence of a swinging tentorium is a key apomorphy of Myriapoda, but this character has been studied in detail in only few species. Here the tentorium, i.e., the peristomatic skeleton of the preoral chamber, is comparatively studied in three species of the millipede order Sphaerotheriida Brandt, 1833. Since dissections of the fragile tentorial components proved to be difficult, despite the large head size, they were analysed mainly in situ via micro-computed tomography. Our results confirm previous observations of large differences in the tentorial construction in the giant pill-millipedes compared to chilognathan diplopods. The tentorium of Sphaerotheriida consists of a curved, plate-like epipharyngeal bar with distal projections, an elongate and thin hypopharyngeal bar, and a plate-like triangular posterior process; a transverse bar is absent. Only seven muscles attach at the tentorium in giant pill-millipedes, including two antennal muscles and two muscles of the gnathochilarium. Within the order Sphaerotheriida, the composition of the tentorium and its muscular equipment seems to be conserved, except for some variability in the shape of the epipharyngeal bar. As the transverse bar has been considered essential for the mobility of the tentorium in myriapods, its absence in Sphaerotheriida may indicate that their tentorium is not capable of performing a swing. Loss of tentorial mobility may also pertain to the order Glomerida Brandt, 1833, inferred here from the absence of a posterior process. An apparently immobile tentorium in Glomerida and Sphaerotheriida can straightforwardly be correlated with transformations of the head related to their ability of volvation. The different transformations of the tentorium, here hypothesised to cause immobility, may support current assumptions that the ability of volvation evolved convergently in Glomerida and Sphaerotheriida. This conclusion, however, still requires more detailed studies of the head anatomy in Glomerida and Glomeridesmida Cook, 1895.
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Affiliation(s)
- Leif Moritz
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Section Myriapoda, Adenauerallee 160, 53113 Bonn, Germany
| | - Thomas Wesener
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Section Myriapoda, Adenauerallee 160, 53113 Bonn, Germany
| | - Markus Koch
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
- Senckenberg Gesellschaft für Naturforschung, Dept. Information Technology and Biodiversity Informatics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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8
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Fernández R, Edgecombe GD, Giribet G. Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. Sci Rep 2018; 8:83. [PMID: 29311682 PMCID: PMC5758774 DOI: 10.1038/s41598-017-18562-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/14/2017] [Indexed: 11/30/2022] Open
Abstract
The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda-Pauropoda grouping (named Dignatha), often recovering a Symphyla-Pauropoda group (named Edafopoda). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids.
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Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., 02138, Cambridge, MA, USA.
- Bioinformatics & Genomics, Centre for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Gonzalo Giribet
- Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., 02138, Cambridge, MA, USA
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9
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Dong Y, Zhu L, Bai Y, Ou Y, Wang C. Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida). Zookeys 2017:1-20. [PMID: 28138271 PMCID: PMC5240118 DOI: 10.3897/zookeys.637.9909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/17/2016] [Indexed: 11/30/2022] Open
Abstract
A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorphacoarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of Asiomorphacoarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.
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Affiliation(s)
- Yan Dong
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Lixin Zhu
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Yu Bai
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Yongyue Ou
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Changbao Wang
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
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10
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Robertson HE, Lapraz F, Rhodes AC, Telford MJ. The complete mitochondrial genome of the geophilomorph centipede Strigamia maritima. PLoS One 2015; 10:e0121369. [PMID: 25794168 PMCID: PMC4368715 DOI: 10.1371/journal.pone.0121369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/31/2015] [Indexed: 12/05/2022] Open
Abstract
Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard ‘cloverleaf’ secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to Strigamia.
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Affiliation(s)
- Helen E. Robertson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, United Kingdom
| | - François Lapraz
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, United Kingdom
| | - Adelaide C. Rhodes
- Center for Genome Research and Biocomputing, 2750 SW Campus Way, Oregon State University, Corvallis, Oregon, United States of America
| | - Maximilian J. Telford
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, United Kingdom
- * E-mail:
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11
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Rehm P, Meusemann K, Borner J, Misof B, Burmester T. Phylogenetic position of Myriapoda revealed by 454 transcriptome sequencing. Mol Phylogenet Evol 2014; 77:25-33. [PMID: 24732681 DOI: 10.1016/j.ympev.2014.04.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 02/02/2023]
Abstract
Myriapods had been considered closely allied to hexapods (insects and relatives). However, analyses of molecular sequence data have consistently placed Myriapoda either as a sister group of Pancrustacea, comprising crustaceans and hexapods, and thereby supporting the monophyly of Mandibulata, or retrieved Myriapoda as a sister group of Chelicerata (spiders, ticks, mites and allies). In addition, the relationships among the four myriapod groups (Pauropoda, Symphyla, Diplopoda, Chilopoda) are unclear. To resolve the phylogeny of myriapods and their relationship to other main arthropod groups, we collected transcriptome data from the symphylan Symphylella vulgaris, the centipedes Lithobius forficatus and Scolopendra dehaani, and the millipedes Polyxenus lagurus, Glomeris pustulata and Polydesmus angustus by 454 sequencing. We concatenated a multiple sequence alignment that contained 1550 orthologous single copy genes (1,109,847 amino acid positions) from 55 euarthropod and 14 outgroup taxa. The final selected alignment included 181 genes and 37,425 amino acid positions from 55 taxa, with eight myriapods and 33 other euarthropods. Bayesian analyses robustly recovered monophyletic Mandibulata, Pancrustacea and Myriapoda. Most analyses support a sister group relationship of Symphyla in respect to a clade comprising Chilopoda and Diplopoda. Inclusion of additional sequence data from nine myriapod species resulted in an alignment with poor data density, but broader taxon average. With this dataset we inferred Diplopoda+Pauropoda as closest relatives (i.e., Dignatha) and recovered monophyletic Helminthomorpha. Molecular clock calculations suggest an early Cambrian emergence of Myriapoda ∼513 million years ago and a late Cambrian divergence of myriapod classes. This implies a marine origin of the myriapods and independent terrestrialization events during myriapod evolution.
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Affiliation(s)
- Peter Rehm
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Karen Meusemann
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany; CSIRO Ecosystem Sciences, Australian National Insect Collection, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Janus Borner
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, D-53113 Bonn, Germany
| | - Thorsten Burmester
- Zoologisches Institut & Museum, Biozentrum Grindel, Martin-Luther-King Platz 3, D-20146 Hamburg, Germany.
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12
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Pick C, Scherbaum S, Hegedüs E, Meyer A, Saur M, Neumann R, Markl J, Burmester T. Structure, diversity and evolution of myriapod hemocyanins. FEBS J 2014; 281:1818-33. [DOI: 10.1111/febs.12742] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/23/2014] [Accepted: 02/06/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Pick
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Samantha Scherbaum
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Elöd Hegedüs
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Andreas Meyer
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
| | - Michael Saur
- Institute of Zoology; Johannes Gutenberg University of Mainz; Germany
| | - Ruben Neumann
- Institute of Zoology; Johannes Gutenberg University of Mainz; Germany
| | - Jürgen Markl
- Institute of Zoology; Johannes Gutenberg University of Mainz; Germany
| | - Thorsten Burmester
- Institute of Zoology and Zoological Museum; University of Hamburg; Germany
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13
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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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14
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Zwick A, Regier JC, Zwickl DJ. Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models. PLoS One 2012; 7:e47450. [PMID: 23185239 PMCID: PMC3502419 DOI: 10.1371/journal.pone.0047450] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 09/17/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND In a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy. METHODOLOGY/PRINCIPAL FINDINGS The hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY) in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2) are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neither compositional heterogeneity at the level of nucleotides nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately coded amino acids) is a major source of non-phylogenetic signal. CONCLUSIONS The incongruity in support between amino-acid and nucleotide analyses of the forementioned arthropod data set is resolved by showing that "standard" 20-amino-acid analyses yield lower node support specifically when serine provides crucial signal. Separate coding of Ser1 and Ser2 residues yields support commensurate with that found by degenerated nucleotides, without introducing phylogenetic artifacts. While exclusion of all serine data leads to reduced support for serine-sensitive nodes, these nodes are still recovered in the ML topology, indicating that the enhanced signal from Ser1 and Ser2 is not qualitatively different from that of the other amino acids.
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Affiliation(s)
- Andreas Zwick
- Department of Entomology, State Museum of Natural History, Stuttgart, Germany
| | - Jerome C. Regier
- Institute for Bioscience and Biotechnology Research and Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Derrick J. Zwickl
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
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Dong Y, Sun H, Guo H, Pan D, Qian C, Hao S, Zhou K. The complete mitochondrial genome of Pauropus longiramus (Myriapoda: Pauropoda): implications on early diversification of the myriapods revealed from comparative analysis. Gene 2012; 505:57-65. [PMID: 22659693 DOI: 10.1016/j.gene.2012.05.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 05/17/2012] [Accepted: 05/22/2012] [Indexed: 10/28/2022]
Abstract
Myriapods are among the earliest arthropods and may have evolved to become part of the terrestrial biota more than 400 million years ago. A noticeable lack of mitochondrial genome data from Pauropoda hampers phylogenetic and evolutionary studies within the subphylum Myriapoda. We sequenced the first complete mitochondrial genome of a microscopic pauropod, Pauropus longiramus (Arthropoda: Myriapoda), and conducted comprehensive mitogenomic analyses across the Myriapoda. The pauropod mitochondrial genome is a circular molecule of 14,487 bp long and contains the entire set of thirty-seven genes. Frequent intergenic overlaps occurred between adjacent tRNAs, and between tRNA and protein-coding genes. This is the first example of a mitochondrial genome with multiple intergenic overlaps and reveals a strategy for arthropods to effectively compact the mitochondrial genome by overlapping and truncating tRNA genes with neighbor genes, instead of only truncating tRNAs. Phylogenetic analyses based on protein-coding genes provide strong evidence that the sister group of Pauropoda is Symphyla. Additionally, approximately unbiased (AU) tests strongly support the Progoneata and confirm the basal position of Chilopoda in Myriapoda. This study provides an estimation of myriapod origins around 555 Ma (95% CI: 444-704 Ma) and this date is comparable with that of the Cambrian explosion and candidate myriapod-like fossils. A new time-scale suggests that deep radiations during early myriapod diversification occurred at least three times, not once as previously proposed. A Carboniferous origin of pauropods is congruent with the idea that these taxa are derived, rather than basal, progoneatans.
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Affiliation(s)
- Yan Dong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
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16
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Mokso R, Quaroni L, Marone F, Irvine S, Vila-Comamala J, Blanke A, Stampanoni M. X-ray mosaic nanotomography of large microorganisms. J Struct Biol 2011; 177:233-8. [PMID: 22227096 DOI: 10.1016/j.jsb.2011.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 12/14/2011] [Accepted: 12/19/2011] [Indexed: 11/18/2022]
Abstract
Full-field X-ray microscopy is a valuable tool for 3D observation of biological systems. In the soft X-ray domain organelles can be visualized in individual cells while hard X-ray microscopes excel in imaging of larger complex biological tissue. The field of view of these instruments is typically 10(3) times the spatial resolution. We exploit the assets of the hard X-ray sub-micrometer imaging and extend the standard approach by widening the effective field of view to match the size of the sample. We show that global tomography of biological systems exceeding several times the field of view is feasible also at the nanoscale with moderate radiation dose. We address the performance issues and limitations of the TOMCAT full-field microscope and more generally for Zernike phase contrast imaging. Two biologically relevant systems were investigated. The first being the largest known bacteria (Thiomargarita namibiensis), the second is a small myriapod species (Pauropoda sp.). Both examples illustrate the capacity of the unique, structured condenser based broad-band full-field microscope to access the 3D structural details of biological systems at the nanoscale while avoiding complicated sample preparation, or even keeping the sample environment close to the natural state.
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Affiliation(s)
- R Mokso
- Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland.
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17
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Andrew DR. A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics. ARTHROPOD STRUCTURE & DEVELOPMENT 2011; 40:289-302. [PMID: 21315832 DOI: 10.1016/j.asd.2011.02.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/20/2010] [Accepted: 02/01/2011] [Indexed: 05/30/2023]
Abstract
The enormous diversity of Arthropoda has complicated attempts by systematists to deduce the history of this group in terms of phylogenetic relationships and phenotypic change. Traditional hypotheses regarding the relationships of the major arthropod groups (Chelicerata, Myriapoda, Crustacea, and Hexapoda) focus on suites of morphological characters, whereas phylogenomics relies on large amounts of molecular sequence data to infer evolutionary relationships. The present discussion is based on expressed sequence tags (ESTs) that provide large numbers of short molecular sequences and so provide an abundant source of sequence data for phylogenetic inference. This study presents well-supported phylogenies of diverse arthropod and metazoan outgroup taxa obtained from publicly-available databases. An in-house bioinformatics pipeline has been used to compile and align conserved orthologs from each taxon for maximum likelihood inferences. This approach resolves many currently accepted hypotheses regarding internal relationships between the major groups of Arthropoda, including monophyletic Hexapoda, Tetraconata (Crustacea + Hexapoda), Myriapoda, and Chelicerata sensu lato (Pycnogonida + Euchelicerata). "Crustacea" is a paraphyletic group with some taxa more closely related to the monophyletic Hexapoda. These results support studies that have utilized more restricted EST data for phylogenetic inference, yet they differ in important regards from recently published phylogenies employing nuclear protein-coding sequences. The present results do not, however, depart from other phylogenies that resolve Branchiopoda as the crustacean sister group of Hexapoda. Like other molecular phylogenies, EST-derived phylogenies alone are unable to resolve morphological convergences or evolved reversals and thus omit what may be crucial events in the history of life. For example, molecular data are unable to resolve whether a Hexapod-Branchiopod sister relationship infers a branchiopod-like ancestry of the Hexapoda, or whether this assemblage originates from a malacostracan-like ancestor, with the morphologically simpler Branchiopoda being highly derived. Whereas this study supports many internal arthropod relationships obtained by other sources of molecular data, other approaches are required to resolve such evolutionary scenarios. The approach presented here turns out to be essential: integrating results of molecular phylogenetics and neural cladistics to infer that Branchiopoda evolved simplification from a more elaborate ancestor. Whereas the phenomenon of evolved simplification may be widespread, it is largely invisible to molecular techniques unless these are performed in conjunction with morphology-based strategies.
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Affiliation(s)
- David R Andrew
- Department of Neuroscience, University of Arizona, 1040 E. 4th St., Gould-Simpson Bldg. #611, Tucson, AZ 85721, USA.
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18
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Lukhtanov VA, Kuznetsova VG. What genes and chromosomes say about the origin and evolution of insects and other arthropods. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410090279] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Janssen R, Budd GE. Gene expression suggests conserved aspects of Hox gene regulation in arthropods and provides additional support for monophyletic Myriapoda. EvoDevo 2010; 1:4. [PMID: 20849647 PMCID: PMC2938723 DOI: 10.1186/2041-9139-1-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 07/05/2010] [Indexed: 01/28/2023] Open
Abstract
Antisense transcripts of Ultrabithorax (aUbx) in the millipede Glomeris and the centipede Lithobius are expressed in patterns complementary to that of the Ubx sense transcripts. A similar complementary expression pattern has been described for non-coding RNAs (ncRNAs) of the bithoraxoid (bxd) locus in Drosophila, in which the transcription of bxd ncRNAs represses Ubx via transcriptional interference. We discuss our findings in the context of possibly conserved mechanisms of Ubx regulation in myriapods and the fly. Bicistronic transcription of Ubx and Antennapedia (Antp) has been reported previously for a myriapod and a number of crustaceans. In this paper, we show that Ubx/Antp bicistronic transcripts also occur in Glomeris and an onychophoran, suggesting further conserved mechanisms of Hox gene regulation in arthropods. Myriapod monophyly is supported by the expression of aUbx in all investigated myriapods, whereas in other arthropod classes, including the Onychophora, aUbx is not expressed. Of the two splice variants of Ubx/Antp only one could be isolated from myriapods, representing a possible further synapomorphy of the Myriapoda.
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Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Villavägen 16, SE-75236 Uppsala, Sweden.
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20
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Mol Phylogenet Evol 2010; 55:1-17. [DOI: 10.1016/j.ympev.2009.09.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 08/28/2009] [Accepted: 09/22/2009] [Indexed: 10/20/2022]
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Shear WA, Edgecombe GD. The geological record and phylogeny of the Myriapoda. ARTHROPOD STRUCTURE & DEVELOPMENT 2010; 39:174-190. [PMID: 19944188 DOI: 10.1016/j.asd.2009.11.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 11/18/2009] [Indexed: 05/28/2023]
Abstract
We review issues of myriapod phylogeny, from the position of the Myriapoda amongst arthropods to the relationships of the orders of the classes Chilopoda and Diplopoda. The fossil record of each myriapod class is reviewed, with an emphasis on developments since 1997. We accept as working hypotheses that Myriapoda is monophyletic and belongs in Mandibulata, that the classes of Myriapoda are monophyletic, and that they are related as (Chilopoda (Symphyla (Diplopoda+Pauropoda))). The most pressing challenges to these hypotheses are some molecular and developmental evidence for an alliance between myriapods and chelicerates, and the attraction of symphylans to pauropods in some molecular analyses. While the phylogeny of the orders of Chilopoda appears settled, the relationships within Diplopoda remain unclear at several levels. Chilopoda and Diplopoda have a relatively sparse representation as fossils, and Symphyla and Pauropoda fossils are known only from Tertiary ambers. Fossils are difficult to place in trees based on living forms because many morphological characters are not very likely to be preserved in the fossils; as a consequence, most diplopod fossils have been placed in extinct higher taxa. Nevertheless, important information from diplopod fossils includes the first documented occurrence of air-breathing, and the first evidence for the use of a chemical defense. Stem-group myriapods are unknown, but evidence suggests the group must have arisen in the Early Cambrian, with a major period of cladogenesis in the Late Ordovician and early Silurian. Large terrestrial myriapods were on land at least by mid-Silurian.
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Affiliation(s)
- William A Shear
- Department of Biology, Hampden-Sydney College, 200 Via Sacra, Hampden-Sydney, VA 23943, USA.
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22
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Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 2010; 463:1079-83. [PMID: 20147900 DOI: 10.1038/nature08742] [Citation(s) in RCA: 609] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 12/10/2009] [Indexed: 11/09/2022]
Abstract
The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.
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Affiliation(s)
- Jerome C Regier
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
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23
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von Reumont BM, Meusemann K, Szucsich NU, Dell'Ampio E, Gowri-Shankar V, Bartel D, Simon S, Letsch HO, Stocsits RR, Luan YX, Wägele JW, Pass G, Hadrys H, Misof B. Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships. BMC Evol Biol 2009; 9:119. [PMID: 19473484 PMCID: PMC2695459 DOI: 10.1186/1471-2148-9-119] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 05/27/2009] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Whenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes. RESULTS We analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear. CONCLUSION Analyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.
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Affiliation(s)
| | - Karen Meusemann
- Molecular Lab, Zoologisches Forschungsmuseum A. Koenig, Bonn, Germany
| | | | | | | | - Daniela Bartel
- Department of Evolutionary Biology, University Vienna, Vienna, Austria
| | - Sabrina Simon
- ITZ, Ecology & Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
| | - Harald O Letsch
- Molecular Lab, Zoologisches Forschungsmuseum A. Koenig, Bonn, Germany
| | - Roman R Stocsits
- Molecular Lab, Zoologisches Forschungsmuseum A. Koenig, Bonn, Germany
| | - Yun-xia Luan
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | | | - Günther Pass
- Department of Evolutionary Biology, University Vienna, Vienna, Austria
| | - Heike Hadrys
- ITZ, Ecology & Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Bernhard Misof
- UHH Biozentrum Grindel und Zoologisches Museum, University of Hamburg, Hamburg, Germany
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Gai Y, Song D, Sun H, Yang Q, Zhou K. The complete mitochondrial genome of Symphylella sp. (Myriapoda: Symphyla): Extensive gene order rearrangement and evidence in favor of Progoneata. Mol Phylogenet Evol 2008; 49:574-85. [PMID: 18782622 DOI: 10.1016/j.ympev.2008.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 08/15/2008] [Accepted: 08/16/2008] [Indexed: 10/21/2022]
Abstract
We determined the complete 14,667bp mitochondrial DNA sequence of Symphylella sp., the first representative of the Scolopendrellidae (Arthropoda: Myriapoda: Symphyla). With respect to the ancestral arthropod mitochondrial gene order, two protein-coding genes, the rRNAs and 10 of the tRNAs appear to be rearranged. This rearrangement is novel in the arthropods and genes with identical transcriptional polarity are clustered except for trnE, trnN and putative control region (CR), resembling two previously reported diplopod genomes. A duplication/loss (random and non-random)-recombination model was proposed to account for the generation of the gene order in Symphylella sp. All phylogenetic analysis yielded strong support for a clade of Symphyla plus Diplopoda, i.e., Progoneata. However, the phylogenetic position of Myriapoda within Arthropoda remains unclear. The amino acid dataset gives strong support for an affinity to Pancrustacea, while the nucleotide dataset weakly supports Myriapoda grouped with Chelicerata.
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Affiliation(s)
- Yonghua Gai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; Nanjing Institute of Geology and Palaeontology, Chinese Academy of Science, Nanjing 210008, China
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Podsiadlowski L, Kohlhagen H, Koch M. The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla. Mol Phylogenet Evol 2007; 45:251-60. [PMID: 17764978 DOI: 10.1016/j.ympev.2007.07.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 07/10/2007] [Accepted: 07/16/2007] [Indexed: 11/30/2022]
Abstract
The first complete mitochondrial genome of a representative of the Symphyla, Scutigerella causeyae (Arthropoda: Myriapoda), was sequenced using a PCR-based approach. Its gene order shows different positions for three tRNA genes compared to the ancestral arthropod pattern. Presence of a pseudogene with partial sequence similarity to rrnS favours the duplication-random loss model as an explanation for at least one of the translocations. None of the genome rearrangements hypothesized for S. causeyae are shared by any of the other four myriapod mitochondrial genomes sequenced so far (two from Chilopoda and two from Diplopoda). Different rearrangement events must have occurred independently in the lineages leading to S. causeyae, Lithobius forficatus, Scutigera coleoptrata and Diplopoda. Phylogenetic analyses could not unequivocally elucidate the position of Symphyla among myriapods. While the nucleotide dataset of eleven protein-coding genes gives weak support for an affinity to Chilopoda, this is not recovered with the corresponding amino acid dataset.
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Affiliation(s)
- Lars Podsiadlowski
- AG Systematik und Evolution der Tiere, Institut für Biologie, Freie Universität Berlin, Germany.
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