scholarly journals Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

2012 ◽  
Vol 8 (6) ◽  
pp. 1043-1046 ◽  
Author(s):  
John J. Wiens ◽  
Carl R. Hutter ◽  
Daniel G. Mulcahy ◽  
Brice P. Noonan ◽  
Ted M. Townsend ◽  
...  
Keyword(s):  
Large Scale ◽  
Sister Group ◽  
Molecular Data ◽  
Base Pairs ◽  
Terrestrial Vertebrates ◽  
Squamate Reptiles ◽  
Tree Methods ◽  
Molecular Dataset ◽  
Diverse Groups ◽  
First Time

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.

scholarly journals Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

2017 ◽  
Vol 13 (9) ◽  
pp. 20170393 ◽  
Author(s):  
Jeffrey W. Streicher ◽  
John J. Wiens
Keyword(s):  
Strong Support ◽  
Sister Group ◽  
Species Tree ◽  
Sister Relationship ◽  
Weak Support ◽  
Terrestrial Vertebrates ◽  
Squamate Reptiles ◽  
Tree Methods ◽  
Nuclear Loci ◽  
Phylogenomic Analyses

Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.

Litter bugs exposed: phylogenetic relationships of Dipsocoromorpha (Hemiptera: Heteroptera) based on molecular data

2014 ◽  
Vol 45 (4) ◽  
pp. 351-370 ◽  
Author(s):  
Christiane Weirauch ◽  
Pavel Štys
Keyword(s):  
Phylogenetic Relationships ◽  
Sister Group ◽  
Molecular Data ◽  
Comprehensive Treatment ◽  
Species Discovery ◽  
True Bugs ◽  
Phylogenetic Framework ◽  
Molecular Dataset ◽  
First Time ◽  
Shed Light

Species in the heteropteran infraorder Dipsocoromorpha, or litter bugs, are small, cryptic, stunningly diverse and understudied. In addition to the vast amount of species discovery and morphological exploration that remain to be done in this group, phylogenetic relationships within the litter bugs are poorly understood. A phylogenetic framework will make Dipsocoromorpha more accessible for systematic studies at all levels and is therefore a first step towards a comprehensive treatment of the group. Using a molecular dataset (87 taxa of Hemiptera including 35 Dipsocoromorpha; two genes) and maximum likelihood and parsimony methods, we here aim to test, for the first time using cladistic methods and a comprehensive dataset, relationships within Dipsocoromorpha. We investigate if Dipsocoromorpha are monophyletic, shed light on the relationships among the three families included in this analysis, and study relationships within the largest family of Dipsocoromorpha, the Schizopteridae. Based on this dataset, we find that the monophyly of Dipsocoromorpha is strongly supported in all analyses and that Ceratocombidae and Dipsocoridae together are recovered as the sister group of Schizopteridae. Within Schizopteridae, Hypselosomatinae are treated as the sister group to a clade formed by the monophyletic Ogeriinae and monophyletic Schizopterinae. Within Schizopterinae, there is evidence for the monophyly of the Corixidea genus group, and we present additional infra-generic and genus-level hypotheses. We discuss these hypotheses in the light of current classifications and hypotheses on relationships and as the first contribution towards revealing the phylogenetic relationships of a remarkable and neglected clade of true bugs.

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.

Determining the position of Diomocoris, Micromimetus and Taylorilygus in the Lygus-complex based on molecular data and first records of Diomocoris and Micromimetus from Australia, including four new species (Insecta : Hemiptera : Miridae : Mirinae)

2021 ◽  
Author(s):  
Anna A. Namyatova ◽  
Michael D. Schwartz ◽  
Gerasimos Cassis
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Morphological Study ◽  
18S Rrna ◽  
Initial Step ◽  
Sister Group ◽  
Molecular Data ◽  
28S Rrna ◽  
Group Relationships ◽  
First Time

The Lygus-complex is one of the most taxonomically challenging groups of Miridae (Heteroptera), and its Australian fauna is poorly studied. Here we examine the Australian taxa of the Lygus-complex using morphological and molecular methods. After a detailed morphological study of the material collected throughout Australia, Taylorilygus nebulosus is transferred to Diomocoris, with the genus recorded for the first time in this country. Taylorilygus apicalis, also widely distributed in Australia, is redescribed on the basis of Australian material. The genus Micromimetus is recorded for the first time in Australia, with M. celiae, sp. nov., M. hannahae, sp. nov., M. nikolai, sp. nov. and M. shofneri, sp. nov. described as new to science. Micromimetus pictipes is redescribed and its distributional range is increased. The monophyly of the Lygus-complex and relationships within this group were tested using cytochrome c oxidase subunit I (COI), 16S rRNA, 18S rRNA and 28S rRNA markers. The Lygus-complex has been found to be non-monophyletic. Phylogeny confirmed the monophyly of Micromimetus, and it has shown that Taylorilygus apicalis is closer to Micromimetus species than to Diomocoris nebulosus. This study is the initial step in understanding the Lygus-complex phylogeny; analyses with more taxa, more genes and morphology are needed to reveal the interrelationships within this group, and sister-group relationships of Australian taxa. http://zoobank.org/urn:lsid:zoobank.org:pub:7393D96B-2BBA-438D-A134-D372EFE7FB9E

Scheming

2018 ◽  
Author(s):  
Seán Damer
Keyword(s):  
Social Class ◽  
Housing Policy ◽  
Large Scale ◽  
Class Structure ◽  
Local Council ◽  
Housing Scheme ◽  
Post War ◽  
First Time ◽  
The Voice ◽  
House Building

This book seeks to explain how the Corporation of Glasgow, in its large-scale council house-building programme in the inter- and post-war years, came to reproduce a hierarchical Victorian class structure. The three tiers of housing scheme which it constructed – Ordinary, Intermediate, and Slum-Clearance – effectively signified First, Second and Third Class. This came about because the Corporation uncritically reproduced the offensive and patriarchal attitudes of the Victorian bourgeoisie towards the working-class. The book shows how this worked out on the ground in Glasgow, and describes the attitudes of both authoritarian housing officials, and council tenants. This is the first time the voice of Glasgow’s council tenants has been heard. The conclusion is that local council housing policy was driven by unapologetic considerations of social class.

First description of the male of Cretaconiopteryx grandis Liu & Lu, 2017 (Neuroptera: Coniopterygidae) from the Cretaceous Burmese amber

Zootaxa ◽  
2019 ◽  
Vol 4674 (4) ◽  
pp. 482-490 ◽  
Author(s):  
HONGYU LI ◽  
BO WANG ◽  
XINGYUE LIU
Keyword(s):  
Male Genitalia ◽  
Upper Cretaceous ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Burmese Amber ◽  
Representative Species ◽  
First Time

The male of Cretaconiopteryx grandis Liu & Lu, 2017, which is the only representative species of the extinct dustywing subfamily Cretaconiopteryginae, is described for the first time from the Upper Cretaceous Burmese amber. The male genitalia, well preserved in the examined specimen, show a number of plesiomorphic characters, which support the sister group relationship between Coniopterygidae and the rest of extant lacewing families. 

scholarly journals Shell-crossing in a ΛCDM Universe

2020 ◽  
Vol 501 (1) ◽  
pp. L71-L75
Author(s):  
Cornelius Rampf ◽  
Oliver Hahn
Keyword(s):  
Dark Matter ◽  
Perturbation Theory ◽  
Large Scale ◽  
Cold Dark Matter ◽  
Three Dimensional ◽  
Random Initial Data ◽  
Recursion Relations ◽  
Indispensable Tool ◽  
First Time ◽  
Very High

ABSTRACT Perturbation theory is an indispensable tool for studying the cosmic large-scale structure, and establishing its limits is therefore of utmost importance. One crucial limitation of perturbation theory is shell-crossing, which is the instance when cold-dark-matter trajectories intersect for the first time. We investigate Lagrangian perturbation theory (LPT) at very high orders in the vicinity of the first shell-crossing for random initial data in a realistic three-dimensional Universe. For this, we have numerically implemented the all-order recursion relations for the matter trajectories, from which the convergence of the LPT series at shell-crossing is established. Convergence studies performed at large orders reveal the nature of the convergence-limiting singularities. These singularities are not the well-known density singularities at shell-crossing but occur at later times when LPT already ceased to provide physically meaningful results.

3.17% efficient Cu2ZnSnS4–BiVO4 integrated tandem cell for standalone overall solar water splitting

2021 ◽  
Author(s):  
Dingwang Huang ◽  
Kang Wang ◽  
Lintao Li ◽  
Kuang Feng ◽  
Na An ◽  
...  
Keyword(s):  
Water Splitting ◽  
Large Scale ◽  
Tandem Cell ◽  
Solar Water ◽  
Solar Water Splitting ◽  
First Time

3.17% efficient Cu2ZnSnS4–BiVO4 integrated tandem cell and a large scale 5 × 5 cm integrated CZTS–BiVO4 tandem device for standalone overall solar water splitting was assembled for the first time.

scholarly journals The SAMI Galaxy Survey: the third and final data release

2021 ◽  
Author(s):  
Scott M Croom ◽  
Matt S Owers ◽  
Nicholas Scott ◽  
Henry Poetrodjojo ◽  
Brent Groves ◽  
...  
Keyword(s):  
Large Scale ◽  
Resolving Power ◽  
Stellar Kinematics ◽  
New Era ◽  
Optical Wavelength ◽  
Astronomical Optics ◽  
Data Release ◽  
Gas Ionization ◽  
Release Data ◽  
First Time

Abstract We have entered a new era where integral-field spectroscopic surveys of galaxies are sufficiently large to adequately sample large-scale structure over a cosmologically significant volume. This was the primary design goal of the SAMI Galaxy Survey. Here, in Data Release 3 (DR3), we release data for the full sample of 3068 unique galaxies observed. This includes the SAMI cluster sample of 888 unique galaxies for the first time. For each galaxy, there are two primary spectral cubes covering the blue (370–570 nm) and red (630–740 nm) optical wavelength ranges at spectral resolving power of R = 1808 and 4304 respectively. For each primary cube, we also provide three spatially binned spectral cubes and a set of standardized aperture spectra. For each galaxy, we include complete 2D maps from parameterized fitting to the emission-line and absorption-line spectral data. These maps provide information on the gas ionization and kinematics, stellar kinematics and populations, and more. All data are available online through Australian Astronomical Optics (AAO) Data Central.

scholarly journals A Novel and Efficient High-Yield Method for Preparing Bacterial Ghosts

Toxins ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 420
Author(s):  
Yi Ma ◽  
Liu Cui ◽  
Meng Wang ◽  
Qiuli Sun ◽  
Kaisheng Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression System ◽  
High Yield ◽  
Wild Type ◽  
High Quality ◽  
Efficient Protection ◽  
Bacterial Ghosts ◽  
Cell Envelopes ◽  
Extracellular Structures ◽  
First Time

Bacterial ghosts (BGs) are empty cell envelopes possessing native extracellular structures without a cytoplasm and genetic materials. BGs are proposed to have significant prospects in biomedical research as vaccines or delivery carriers. The applications of BGs are often limited by inefficient bacterial lysis and a low yield. To solve these problems, we compared the lysis efficiency of the wild-type protein E (EW) from phage ΦX174 and the screened mutant protein E (EM) in the Escherichia coli BL21(DE3) strain. The results show that the lysis efficiency mediated by protein EM was improved. The implementation of the pLysS plasmid allowed nearly 100% lysis efficiency, with a high initial cell density as high as OD600 = 2.0, which was higher compared to the commonly used BG preparation method. The results of Western blot analysis and immunofluorescence indicate that the expression level of protein EM was significantly higher than that of the non-pLysS plasmid. High-quality BGs were observed by SEM and TEM. To verify the applicability of this method in other bacteria, the T7 RNA polymerase expression system was successfully constructed in Salmonella enterica (S. Enterica, SE). A pET vector containing EM and pLysS were introduced to obtain high-quality SE ghosts which could provide efficient protection for humans and animals. This paper describes a novel and commonly used method to produce high-quality BGs on a large scale for the first time.

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