Setting the Molecular Phylogenetic Framework for the Dermaptera

2003 ◽  
Vol 34 (1) ◽  
pp. 65-79 ◽  
Author(s):  
◽  
◽  
Keyword(s):  
16S Rdna ◽  
18S Rdna ◽  
Sequence Data ◽  
Indirect Evidence ◽  
Sister Group ◽  
Bootstrap Support ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework ◽  
Insect Group ◽  
Basal Position

AbstractThe insect group Dermaptera is traditionally divided into the Forficulina, comprising the majority of the species, the African rodent commensals, Hemimerina, and the Indo-Malayan bat commensals, Arixeniina. Numerous contrasting classifications and phylogenies exist for the Dermaptera, based on morphological, molecular and biogeographic data. We have collected varying number of sequences from fifteen Forficulina and six outgroups to establish a molecular hypothesis of the group's phylogeny. Despite repeated attempts, we were unable to obtain sequence data for Arixeniina and Hemimerina. We obtained partial sequences for four taxa for cytochrome oxidase 1 (with two additional taxa from GenBank), twelve for 16S rDNA, fifteen for 28S rDNA expansion region 1, seven for expansion region 9-10, and nine for 18S rDNA (plus seven sequences from GenBank). In combined analyses, the root of the Dermaptera lies between Anisolabididae and other families. This position is not directly supported by bootstrap analyses. Indirect evidence for the basal position of Anisolabididae, Pygidicranidae and Apachyidae is however found in the association of the four other studied groups (Labiduridae, Spongiphoridae, Chelisochidae and Forficulidae) in a derived clade with significant bootstrap support. The division of Forficulina into Catadermaptera and Eudermaptera is not supported as the former is paraphyletic in the present analyses. Eudermaptera is monophyletic with bootstrap support but is sister group to Labiduridae, a taxon usually assigned to the Catadermaptera.

Homoplasy: from detecting pattern to determining process in evolution, but with a secondary role for morphology?

Zootaxa ◽  
2011 ◽  
Vol 2984 (1) ◽  
pp. 67 ◽  
Author(s):  
LEANDRO C. S. ASSIS ◽  
MARCELO R. DE CARVALHO ◽  
QUENTIN D. WHEELER
Keyword(s):  
Sequence Data ◽  
Morphological Characters ◽  
Flow Chart ◽  
Molecular Topology ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Secondary Role ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

David Wake and colleagues provided a thought-provoking review of the concept of homoplasy through the integration, within a phylogenetic framework, of genetic and developmental data (Wake et al. 2011). According to them (p. 1032) “Molecular sequence data have greatly increased our ability to identify homoplastic traits.” This is made clear, for example, in their flow chart for homoplasy detection (Figure 2, p. 1034), wherein homoplasy is discovered through the mapping of “traits of interest” onto a phylogram, a practice common in the molecular phylogenetic paradigm. The “mapping” is usually of morphological characters that are employed to support the chosen (molecular) topology, but which, as a consequence, do not themselves contribute to the formation of those topologies (Assis & Carvalho 2010).

Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure

2020 ◽  
Vol 190 (3) ◽  
pp. 1002-1019 ◽  
Author(s):  
Donald L J Quicke ◽  
Sergey A Belokobylskij ◽  
Yves Braet ◽  
Cornelis van Achterberg ◽  
Paul D N Hebert ◽  
...  
Keyword(s):  
Sequence Data ◽  
Elongation Factor ◽  
Sequence Divergence ◽  
Sister Group ◽  
Morphological Characters ◽  
Dna Sequence Data ◽  
Elongation Factor 1 Alpha ◽  
Molecular Phylogenetic ◽  
Molecular Dataset ◽  
First Time

Abstract A new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.

scholarly journals Urocystis cumminsii sp. nov., a smut fungus on Themidaceae from Arizona

Mycotaxon ◽  
2020 ◽  
Vol 134 (4) ◽  
pp. 591-599
Author(s):  
Kyryll G. Savchenko ◽  
Sylena R. Harper ◽  
Lori M. Carris ◽  
Lisa A. Castlebury
Keyword(s):  
United States ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
First Record ◽  
Smut Fungi ◽  
Its Sequence ◽  
Sequence Analyses ◽  
Molecular Phylogenetic ◽  
A New Species ◽  
Basal Position

The morphology and phylogenetic relationships of a species of Urocystis on Dichelostemma capitatum (Themidaceae, Asparagales) collected in the Tucson Mountains in Arizona, United States, were studied using microscopy and ITS rDNA sequence analyses. This is a first record for smut fungi on hosts from Themidaceae. Molecular phylogenetic analyses based on ITS sequence data revealed its basal position in relation to species on Poaceae. As a result, the smut in leaves of Dichelostemma capitatum is described and illustrated here as a new species, Urocystis cumminsii.

scholarly journals Identifikasi Molekuler Bakteri Endofit Penghasil L-asparaginase yang Diisolasi dari Mangrove Buta-Buta (Excoecaria agallocha)

2019 ◽  
Vol 14 (1) ◽  
pp. 29
Author(s):  
Asep Awaludin Prihanto ◽  
Randy Fahrudin Ardiansyah ◽  
Ken Audia Pradarameswari
Keyword(s):  
16S Rdna ◽  
Molecular Identification ◽  
Endophytic Bacteria ◽  
Sequence Data ◽  
Enterobacter Cloacae ◽  
Selective Medium ◽  
Mangrove Plant ◽  
Excoecaria Agallocha ◽  
Molecular Phylogenetic ◽  
Phylogenetic Identification

AbstrakL-asparaginase (EC 3.5.1.1) adalah enzim yang menghidrolisis asam amino L-asparagin menjadi amonia dan asam aspartat. Enzim ini mempunyai manfaat utama dalam bidang farmasi dan industri pangan. Enzim L-asparaginase tersebar secara luas pada mikroorganisme. Mikroorganisme yang mempunyai potensi menghasilkan enzim ini adalah mikroorganisme endofit dari tumbuhan mangrove. Penelitian ini bertujuan untuk mengisolasi dan mengidentifikasi bakteri endofit penghasil L-asparaginase dari tumbuhan mangrove Buta-buta (E. agallocha). Skrining dilakukan dengan menggunakan medium selektif untuk mendapatkan bakteri penghasil enzim L-asparaginase. Identifikasi molekuler dilakukan dengan menggunakan analisis filogenetik berdasarkan data sekuen 16S rDNA. Dari hasil penelitian ini didapatkan lima isolat bakteri endofit penghasil enzim L-asparaginase, di mana isolat penghasil L-asparaginase tertinggi diidentifikasi secara molekuler. Hasil identifikasi filogenetik molekuler menunjukkan bahwa isolat kode D.104 teridentifikasi sebagai Enterobacter cloacae. Molecular Identification of L-asparaginase-Producing Endophytic Bacteria Isolated from Mangrove Buta-Buta (Excoecaria agallocha)AbstractL-asparaginase (EC 3.5.1.1) is an enzyme which hydrolyze amino acid L-asparagine to aspartate and ammonia. Two main applications of this enzyme are in the pharmaceutical and food industries. The enzyme is widely distributed on microorganism. A potential source of L-asparaginase-producing bacteria is an endophytic bacteria from mangrove plant. This study aimed to isolate and identify L-asparaginase-producing endophytic bacteria from a mangrove plant, E. agallocha (Buta-buta). A screening was carried out using a selective medium to obtain the L-asparaginase enzyme producing bacteria. Molecular identification was carried out using phylogenetic analysis based on 16S rDNA sequence data. In this study, five isolates of the L-asparaginase-producing endophytic bacteria were obtained. The molecular phylogenetic identification showed that the highest L-asparaginase-producing bacterial isolate (code D.104) was identified as Enterobacter cloacae.

The first modern solitary Agariciidae (Anthozoa, Scleractinia) revealed by molecular and microstructural analysis

2012 ◽  
Vol 26 (3) ◽  
pp. 303 ◽  
Author(s):  
Marcelo V. Kitahara ◽  
Jaroslaw Stolarski ◽  
Stephen D. Cairns ◽  
Francesca Benzoni ◽  
Joel L. Stake ◽  
...  
Keyword(s):  
16S Rdna ◽  
Deep Water ◽  
Phylogenetic Analyses ◽  
Microstructural Analysis ◽  
Morphological Characteristics ◽  
28S Rdna ◽  
Fossil Species ◽  
Pacific Waters ◽  
Molecular Phylogenetic ◽  
Basal Position

Dactylotrochus cervicornis (= Tridacophyllia cervicornis Moseley, 1881), which occurs in Indo-Pacific waters between 73 and 852 m, was originally described as an astraeid but was later transferred to the Caryophylliidae. Assumed to be solitary, this species has no stolons and only one elongated fossa, and is unique among azooxanthellate scleractinians in often displaying extremely long thecal extensions that are septate and digitiform. Based on both molecular phylogenetic analyses (partial mitochondrial CO1 and 16S rDNA, and partial nuclear 28S rDNA) and morphological characteristics, we propose the transfer of D. cervicornis from the Caryophylliidae to the Agariciidae, making it the first extant representative of the latter family that is solitary and from deep water (azooxanthellate). The basal position of D. cervicornis within the agariciids implied by our analyses strengthens the case for inclusion of fossil species that were solitary, such as Trochoseris, in this family and suggests that the ancestor of this scleractinian family, extant members of which are predominantly colonial and zooxanthellate, may have been solitary and azooxanthellate.

scholarly journals Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

2003 ◽  
Vol 17 (4) ◽  
pp. 605 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Recent Common Ancestor ◽  
Bootstrap Support ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

scholarly journals Revision of the genus Emphylica Turner, 1913 based on morphology and molecular data (Lepidoptera, Crambidae, Pyraustinae)

ZooKeys ◽  
2019 ◽  
Vol 836 ◽  
pp. 113-133 ◽  
Author(s):  
Kai Chen ◽  
Qingming Liu ◽  
Jianhua Jin ◽  
Dandan Zhang
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Sequence Data ◽  
Southern China ◽  
Molecular Data ◽  
28S Rrna ◽  
New Combinations ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework ◽  
A New Species

Moths of the genus Emphylica Turner, 1913 resemble species of Achyra Guenée, 1849, Loxostege Hübner, 1825 and Sitochroa Hübner, 1825 in having a conical frons. In order to examine the monophyly of Emphylica, and its relationship to other genera with a conical frons, a molecular phylogenetic framework is reconstructed based on sequence data of COI, 16S rRNA, 28S rRNA, EF-1α and Wg gene regions. The results robustly support the monophyly of Emphylica. Achyra + (Loxostege + Sitochroa) is in a sister position to Emphylica. A new species, E.crassihamatasp. n., is described from Southern China and two new combinations, E.diaphana (Caradja & Meyrick, 1934), comb. n. and E.cruoralis (Warren, 1895), comb. n., are proposed. An identification key based on males is provided for all Emphylica species. The adult habitus and genitalia of all species are figured.

scholarly journals Pseudopolydora (Annelida: Spionidae) from the Arabian Gulf, Kuwait

2021 ◽  
Vol 773 ◽  
Author(s):  
Vasily I. Radashevsky ◽  
Manal Al-Kandari ◽  
Vasily V. Malyar ◽  
Victoria V. Pankova
Keyword(s):  
16S Rdna ◽  
Phylogenetic Relationships ◽  
18S Rdna ◽  
Sequence Data ◽  
Arabian Gulf ◽  
Morphological Features ◽  
Coralline Algae ◽  
Histone 3 ◽  
Species Complexes ◽  
Mitochondrial 16S Rdna

Seven species of Pseudopolydora are described and illustrated from the Arabian Gulf, Kuwait: P. achaeta Radashevsky & Hsieh, 2000, P. antennata (Claparède, 1868), P. arabica Radashevsky & Al-Kandari, 2020, P. auha sp. nov., P. kuwaiti sp. nov., P. melanopalpa sp. nov., and P. multispinosa sp. nov. The morphology of the developed planktonic larvae is described for P. antennata and P. kuwaiti sp. nov. Adults of all species live in tubes in soft sediments, while adults of P. kuwaiti sp. nov. also bore in shells of gastropods and dead corals encrusted by coralline algae. Pseudopolydora antennata and P. arabica form dense settlements up to 50 000 individuals per 1 m2, while other species are comparatively rare. The phylogenetic relationships between the examined species and other Pseudopolydora (18 species in total) were assessed in an analysis of sequence data of four gene fragments: mitochondrial 16S rDNA, nuclear 18S rDNA and 28S rDNA, and Histone 3 (2473 bp in total). Three species complexes are distinguished involving P. antennata, P. diopatra Hsieh, 1992 and P. paucibranchiata (Okuda, 1937). Sets of adult morphological features shared by species of each complex and an identification key to Pseudopolydora species from the Arabian Gulf are provided.

scholarly journals Iheyaspira bathycodon new species (Vetigastropoda: Trochoidea: Turbinidae: Skeneinae) from the Von Damm Vent Field, Mid-Cayman Spreading Centre, Caribbean

2012 ◽  
Vol 93 (4) ◽  
pp. 1017-1024 ◽  
Author(s):  
Verity Nye ◽  
Jon Copley ◽  
Katrin Linse ◽  
Sophie Plouviez
Keyword(s):  
New Species ◽  
16S Rdna ◽  
Hydrothermal Vent ◽  
18S Rdna ◽  
Hydrothermal Vents ◽  
Phylogenetic Position ◽  
Faunal Composition ◽  
Molecular Phylogenetic ◽  
Morphological Differences ◽  
Molecular Phylogenetic Data

Iheyaspira bathycodon sp. nov. is described from the Von Damm Vent Field on the world's deepest spreading centre, the Mid-Cayman Spreading Centre (MCSC), Caribbean, at 2300 m depth. The new species is defined and illustrated from 11 specimens, with brief notes on habitat and known distribution. Molecular phylogenetic data from partial COI mDNA, 16S rDNA and nuclear 18S rDNA regions are used to analyse the species’ phylogenetic position and its morphology is compared with previously described skeneid and vent taxa. The new species is distinguished from the most closely allied vent species, Iheyaspira lequios Okutani, Sasaki & Tsuchida, 2000 by morphological differences in radula diagnosis and appendage structure of the head-foot. Iheyaspira bathycodon sp. nov. is the tenth turbinid to be described from a hydrothermal-vent environment and the second species to be named from recently discovered hydrothermal vents on the MCSC. Determining the faunal composition of assemblages at the vent fields of the MCSC will help to elucidate the vent biogeography of the region.

scholarly journals Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)

2020 ◽  
Author(s):  
Joris A. M. Bertrand ◽  
Anaïs Gibert ◽  
Christel Llauro ◽  
Olivier Panaud
Keyword(s):  
Plastid Genome ◽  
Rapid Evolution ◽  
Genomic Data ◽  
Sister Group ◽  
Hybrid Assembly ◽  
Genome Sequences ◽  
Plastid Genomes ◽  
Molecular Phylogenetic ◽  
Phylogenetic Hypotheses ◽  
Basal Position

Some lineages of the Orchid genus Ophrys exhibit among the highest diversification rates reported so far. As a consequence of a such intense and rapid evolution, the systematics and the taxonomy of this genus remains unclear. A hybrid assembly approach based-on long- and short-read genomic data allowed us to outperform classical methods to successfully assemble whole plastid genomes for two new Ophrys species: O. aymoninii and O. lutea. Along with three other previously Ophrys plastid genome sequences, we then reconstructed the first whole plastome-based molecular phylogeny including representatives of the three mains recognized Ophrys lineages. Our results support the placement of the O. insectifera clade as sister group of ‘non-basal Ophrys’ rather than a basal position. Our findings corroborate recent results obtained from genomic data (RAD-seq and transcriptomes) but contrast with previous ones. These results therefore confirm that molecular phylogenetic hypotheses based on a limited number of loci (e.g. nrITS, matK, rbcL) may have provided a biased picture of phylogenetic relationships within Ophrys and possibly other plant taxa.

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