scholarly journals Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

The Auk ◽  
2021 ◽  
Author(s):  
Gustavo A Bravo ◽  
Bret M Whitney ◽  
Ricardo Belmonte-Lopes ◽  
Marcos R Bornschein ◽  
Natalia Aristizábal ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sensu Stricto ◽  
Monotypic Genus ◽  
The Family ◽  
Single Genus ◽  
Species Groups ◽  
Phylogenomic Analyses ◽  
Extinction Events ◽  
High Degree

Abstract The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements, with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus and Sakesphorus are not monophyletic. We resolve Herpsilochmus sellowi as a deep-branch sister to the monotypic genus Biatas and Sakesphorus cristatus as sister to a clade comprising Herpsilochmus sensu stricto and Dysithamnus. These results are consistent across loci, obtained via concatenation and coalescent-based analyses, and supported by likelihood-ratio tests of the distribution of our sampled coalescent histories. The phenotypic distinctiveness of both H. sellowi and Biatas argues against merging them into a single genus. Because no generic name is available for H. sellowi, we describe a monotypic genus. The polyphyly of Sakesphorus warrants recognition of the available generic name Sakesphoroides for the distinctive and monotypic S. cristatus. Furthermore, we recover 6 well-supported species groups within Herpsilochmus sensu stricto. Within the context of the family as a whole, the ubiquity of long terminal branches representing monotypic genera points to extinction events among ancestors of these lineages. We suggest that retention of ancestral characters or random genetic drift coupled with extensive extinction could explain the high degree of morphological and ecological similarity across these taxa, but we highlight the potential role of the environment in driving adaptive phenotypic convergence. Finally, our results send a cautionary message against the blind use of phylogenies containing imputed data based on taxonomy due to the increasingly frequent mismatches between traditional taxonomic classification and molecular phylogenies.

An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)

Zootaxa ◽  
2018 ◽  
Vol 4415 (1) ◽  
pp. 45 ◽  
Author(s):  
PIOTR GĄSIOREK ◽  
DANIEL STEC ◽  
WITOLD MOREK ◽  
ŁUKASZ MICHALCZYK
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Model Organism ◽  
Laboratory Strain ◽  
Sensu Stricto ◽  
Nominal Species ◽  
28S Rrna ◽  
The Family ◽  
The 19Th Century ◽  
Hypsibius Dujardini

A laboratory strain identified as “Hypsibius dujardini” is one of the best studied tardigrade strains: it is widely used as a model organism in a variety of research projects, ranging from developmental and evolutionary biology through physiology and anatomy to astrobiology. Hypsibius dujardini, originally described from the Île-de-France by Doyère in the first half of the 19th century, is now the nominal species for the superfamily Hypsibioidea. The species was traditionally considered cosmopolitan despite the fact that insufficient, old and sometimes contradictory descriptions and records prevented adequate delineations of similar Hypsibius species. As a consequence, H. dujardini appeared to occur globally, from Norway to Samoa. In this paper, we provide the first integrated taxonomic redescription of H. dujardini. In addition to classic imaging by light microscopy and a comprehensive morphometric dataset, we present scanning electron photomicrographs, and DNA sequences for three nuclear markers (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial marker (COI) that are characterised by various mutation rates. The results of our study reveal that a commercially available strain that is maintained in many laboratories throughout the world, and assumed to represent H. dujardini sensu stricto, represents, in fact, a new species: H. exemplaris sp. nov. Redescribing the nominal taxon for Hypsibiidae, we also redefine the family and amend the definitions of the subfamily Hypsibiinae and the genus Hypsibius. Moreover, we transfer H. arcticus (Murray, 1907) and Hypsibius conifer Mihelčič, 1938 to the genus Ramazzottius since the species exhibit claws and eggs of the Ramazzottius type. Finally, we designate H. fuhrmanni as subjectively invalid because the extremely poor description precludes identifying neotype material. 

INFLUENCE OF BACTRIO-CARRY IN THE FAMILY ON THE COURSE OF ATOPIC DERMATITIS IN A CHILD

2021 ◽  
pp. 114-119
Author(s):  
Vasileva E.A. ◽  
Kuyarov A.A. ◽  
Kuyarov A.V.
Keyword(s):  
Atopic Dermatitis ◽  
Secondary Infection ◽  
Family Members ◽  
Upper Respiratory Tract ◽  
Epidermal Barrier ◽  
The Family ◽  
Mucous Membranes ◽  
High Degree ◽  
Nose And Throat

The pathogenesis of atopic dermatitis (AD) is complex, and at present a unified concept of the development of the disease has not been formed. At the heart of pathogenesis, there is a complex interaction of numerous factors, such as genetic predisposition, dysfunction of the autonomic nervous system and the epidermal barrier. Previously, it has been proven that a high microbial contamination of the affected areas helps to maintain inflammation and aggravates skin dysfunction as a result of chronic inflammation, and favorable factors appear for the attachment of a secondary infection. However, little attention has been paid to dysfunctions of the epidermal barrier, the role of violations of the quantitative and qualitative composition of the microbiota in the development of AD, and this issue remains relevant at the present time. The aim of this study was to assess the effect of the carrier of bacteria on the mucous membranes of the upper respiratory tract in family members on the course of atopic dermatitis in a child. A bacteriological examination of the mucous membranes of the nose and throat was carried out in 34 children with AD and members of their families (74 people). When examining the mucous membranes of the nose and throat in family members of children with AD, it was found that the microflora isolated from family members in more than half of the cases has an increased potential for pathogenicity with a high degree of contamination (CFU lg 3), which forms an increased bacteriological load on the child. The tendency of bacterial carriage was revealed, contributing to the formation in the family of a permanent persistence of microflora with a high potential for pathogenicity. Asymptomatic carriage of bacteria forms an additional epidemiological load on the child, affects the severity of AD and is a risk factor in the development of secondary infection of the skin.

scholarly journals Self-concept and Family: A study on Greek secondary school students

2016 ◽  
Vol 10 (1) ◽  
Author(s):  
Dimitris Kiritsis
Keyword(s):  
Sampling Technique ◽  
Self Concept ◽  
School Students ◽  
The Family ◽  
Major Variation ◽  
Essential Contribution ◽  
The One ◽  
High Degree ◽  
The Relationship

The aim of the study is twofold. On the one hand it concerns the measurement and the examination of the subjects’ self-concept and on the other the detection and justification of the role of family in its configuration. The study analyzed the data collected from the answers to a research questionnaire of 1344 15-and 16-year-old school students in the Prefecture of Thessaloniki, Greece) with the use of a stratified random sampling technique. The first important finding concerned the high degree of the general self-concept of the adolescents. Among the seven specific sectors of the general self-concept a major variation was noted, with the higher average to be traced in the relationship that the students have configured with their peers and the lower one in the valuation of their academic competence. The second important finding was the ascertainment of the essential contribution of the family.

scholarly journals Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
José S. L. Patané ◽  
Joaquim Martins ◽  
Luiz Thiberio Rangel ◽  
José Belasque ◽  
Luciano A. Digiampietri ◽  
...  
Keyword(s):  
Citrus Canker ◽  
Xanthomonas Citri ◽  
The Family ◽  
Divergence Dating ◽  
Main Driver ◽  
Genomic Studies ◽  
History Of ◽  
Phylogenomic Analyses ◽  
High Degree ◽  
Blurring Effect

Abstract Background Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. Results Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. Conclusions Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.

Copepods (Cyclopoida) associated with ascidian hosts: Ascidicolidae, Buproridae, Botryllophilidae, and Enteropsidae, with descriptions of 84 new species

Zootaxa ◽  
2021 ◽  
Vol 4978 (1) ◽  
pp. 1-286
Author(s):  
IL-HOI KIM ◽  
GEOFF A. BOXSHALL
Keyword(s):  
New Species ◽  
Type Species ◽  
Valid Species ◽  
New Genera ◽  
Monotypic Genus ◽  
The Family ◽  
Taxonomic Research ◽  
Single Genus

The Monniot collection of copepods associated with ascidian hosts was built up over several decades of field collecting and taxonomic research on ascidians by Drs Claude & Françoise Monniot (MNHN, Paris). This paper describes a total of 84 new species of copepods collected from ascidian hosts and five new genera are established. Prior to this study the family Ascidicolidae comprised two genera accommodating five valid species; here we add two new genera, Hamistyelicola gen. nov. and Bathycopola gen. nov., and eight new species in total. The family Buproridae comprised a single genus consisting of three species; here we add a new monotypic genus, Buprorides gen. nov. The family Botryllophilidae comprised 68 valid species in seven genera and here we add 45 new species; 13 of Botryllophilus Hesse, 1864, nine of Schizoproctus Aurivillius, 1885, three of Haplostomides Chatton & Harant, 1924, 12 of Haplostoma Chatton & Harant, 1924, seven of Haplostomella Chatton & Harant, 1924 and a single new species of Haplosaccus Chatton & Harant, 1924. The Enteropsidae comprised 42 species in five genera and here we add two new genera, Monnioticopa gen. nov. and Periboia gen. nov., plus a total of 30 new species; 15 of Enterocola van Beneden, 1860, two of Enterocolides Chatton & Harant, 1922, five of Enteropsis C.W.S. Aurivillius, 1885, five of Monnioticopa gen. nov., two of Mychophilus Hesse, 1865, plus the type species of Periboia gen. nov. Generic diagnoses are provided for all genera represented in the collection. A further 13 known species are also reported and brief supplementary descriptive notes or full redescriptions are provided, as appropriate. 

scholarly journals Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2861 ◽  
Author(s):  
Scott William Roy
Keyword(s):  
Dna Sequences ◽  
Molecular Mechanisms ◽  
Transcriptomic Data ◽  
Coding Regions ◽  
Evolutionary Origins ◽  
Helicase Gene ◽  
Trans Splicing ◽  
High Degree ◽  
Future Work

Background The mechanisms by which DNA sequences are expressed is the central preoccupation of molecular genetics. Recently, ourselves and others reported that in the diplomonad protist Giardia lamblia, the coding regions of several mRNAs are produced by ligation of independent RNA species expressed from distinct genomic loci. Such trans-splicing of introns was found to affect nearly as many genes in this organism as does classical cis-splicing of introns. These findings raised questions about the incidence of intron trans-splicing both across the G. lambliatranscriptome and across diplomonad diversity in general, however a dearth of transcriptomic data at the time prohibited systematic study of these questions. Methods I leverage newly available transcriptomic data from G. lamblia and the related diplomonad Spironucleus salmonicidato search for trans-spliced introns. My computational pipeline recovers all four previously reported trans-spliced introns in G. lamblia, suggesting good sensitivity. Results Scrutiny of thousands of potential cases revealed only a single additional trans-spliced intron in G. lamblia, in the p68 helicase gene, and no cases in S. salmonicida. The p68 intron differs from the previously reported trans-spliced introns in its high degree of streamlining: the core features of G. lamblia trans-spliced introns are closely packed together, revealing striking economy in the implementation of a seemingly inherently uneconomical molecular mechanism. Discussion These results serve to circumscribe the role of trans-splicing in diplomonads both in terms of the number of genes effected and taxonomically. Future work should focus on the molecular mechanisms, evolutionary origins and phenotypic implications of this intriguing phenomenon.

A revision of the family Syringogastridae (Diptera: Diopsoidea)

Zootaxa ◽  
2009 ◽  
Vol 1996 (1) ◽  
pp. 1-80 ◽  
Author(s):  
S. A. MARSHALL ◽  
M. BUCK ◽  
J. H. SKEVINGTON ◽  
D. GRIMALDI
Keyword(s):  
New Species ◽  
New World ◽  
Sister Group ◽  
South American ◽  
Fossil Species ◽  
Extant Species ◽  
The Family ◽  
Single Genus ◽  
Species Groups ◽  
Molecular Characters

The New World family Syringogastridae (Diptera, Acalyptratae) with the single genus Syringogaster is revised. Eleven new extant species are described in four newly recognized species groups to give a total of 20 extant species (S. brachypecta, S. apiculata and S. tenuipes in the rufa-group; S. atricalyx, S. figurata, S. plesioterga, and S. dactylopleura in the figurata-group; and S. nigrithorax, S. brunneina, S. sharkeyi and S. palenque in the brunnea-group; Marshall & Buck are the authors of all extant new species). The craigi-group includes two new fossil species, S. miocenecus Grimaldi and S. craigi Grimaldi, each described on the basis of a unique Miocene (ca. 17 myo) amber specimen from the Dominican Republic. Morphological and molecular characters are used to estimate phylogenetic relationships among species of Syringogastridae, and between Syringogastridae and related diopsids. The fossil species appear to form the sister group to the Central and South American figurata group, and reveal Antillean extinction of the family from earlier in the Tertiary.

Aliarcobacter, Halarcobacter, Malaciobacter, Pseudarcobacter and Poseidonibacter are later synonyms of Arcobacter: transfer of Poseidonibacter parvus, Poseidonibacter antarcticus, ‘Halarcobacter arenosus’, and ‘Aliarcobacter vitoriensis’ to Arcobacter as Arcobacter parvus comb. nov., Arcobacter antarcticus comb. nov., Arcobacter arenosus comb. nov. and Arcobacter vitoriensis comb. nov.

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Stephen L. W. On ◽  
William G. Miller ◽  
Patrick J. Biggs ◽  
Angela J. Cornelius ◽  
Peter Vandamme
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Sensu Stricto ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Single Genus ◽  
Phylogenomic Analyses ◽  
High Level

This paper re-examines the taxonomic positions of recently described Poseidonibacter (P. parvum and P. antarcticus ), Aliarcobacter (‘Al. vitoriensis’), Halarcobacter (‘H. arenosus’) and Arcobacter ( A. caeni , A. lacus ) species, and other species proposed to represent novel genera highly related to the genus Arcobacter . Phylogenomic and several overall genome relatedness indices (OGRIs) were applied to a total of 118 representative genomes for this purpose. Phylogenomic analyses demonstrated the Arcobacter clade to be distinct from other Epsilonproteobacteria , clearly defined and containing closely related species. Aliarcobacter butzleri and Malaciobacter pacificus did not cluster with other members of these proposed genera, indicating incoherence of these genera. Every OGRI measure applied indicated a high level of relatedness among all Arcobacter clade species, including the recently described taxa studied here, and substantially lower between type species representatives for other Epsilonproteobacteria. Where published guidelines were available, OGRI values for Arcobacter clade species were either unsupportive of division into other genera or were at the lowest boundary range (for average amino acid identity). We propose that Aliarcobacter , Halarcobacter , Malaciobacter , Pseudarcobacter , Poseidonibacter and Arcobacter sensu stricto be considered members of a single genus, Arcobacter , and subsequently transfer P. parvum, P. antarcticus , ‘ Al. vitoriensis ’ and ‘H. arenosus’ to Arcobacter as Arcobacter parvum comb. nov., Arcobacter antarcticus comb. nov., Arcobacter vitoriensis comb. nov. and Arcobacter arenosus comb. nov.

scholarly journals The Role of Family in the Construction of Traditions among Second-Generation Chinese Immigrants in Hungary

2021 ◽  
Vol 13 (2021/1) ◽  
Author(s):  
Eszter Knyihár ◽  
Gergely Salát
Keyword(s):  
Second Generation ◽  
Country Of Origin ◽  
Chinese Immigrants ◽  
Host Society ◽  
Cultural Elements ◽  
The Family ◽  
Family Setting ◽  
And Control ◽  
High Degree

Previous research conducted in Hungary has shown that second generation Chinese immigrants construct a complex, multicultural identity which contains elements from the cultural environment created by the host society, the migrant diaspora, the family of the migrant and the country of origin as well. This paper presents the findings of an interview-based research project conducted in Hungary with the involvement of 20 second-generation Chinese immigrants and seeks to examine the complexity of their cultural identity, focussing especially the role of the family in the construction of traditions. According to our findings we argue that in the family setting, there is constant negotiation between generations regarding norms and traditions, which reveal different priorities. In this article I show that those areas where the most negotiations occur also overlap with the fields of increased parental interest and control, namely: education, dating/marriage, and language. I also discuss how holidays celebrated by the family show a high degree of flexibility and mixed solutions, involving cultural elements from both the host society and the country of origin.

scholarly journals Ultrastructure of antennal sensilla of Cistogaster globosa (Fabricius, 1775) и Cylindromyia interrupta (Meigen, 1824) (Diptera: Tachinidae)

2021 ◽  
Vol 10 (1) ◽  
pp. 14-19
Author(s):  
Evgeniy Vasilyevich Aksenenko ◽  
Mikhailovna Anna Kondratyeva
Keyword(s):  
Unit Area ◽  
Sensory System ◽  
Ultrastructural Organization ◽  
Antennal Sensilla ◽  
Sem Images ◽  
Main Site ◽  
The Family ◽  
Host Habitat ◽  
High Degree

The paper describes the ultrastructure of antennal sensilla among two species of tachinid flies (Diptera: Tachinidae). For this purpose, the antennae of the adult flies Cistogaster globosa (Fabricius, 1775) and Cylindromyia interrupta (Meigen, 1824) were examined using a scanning electron microscope (SEM). The choice of antennae as structures for studying the receptor organs is explained by the fact that among insects they are the main site of sensilla localization. There is also a high degree of oligomerization of the antenna segments, which determines the concentration of sensilla on the apical segment in the short-tied circular-seam Diptera (Brachycera-Cyclorrhapha), to which the family Tachinidae also belongs. Most of antennal sensilla are morphologically independent elementary sensory formations. Each type of such sensory formations is responsible for one or more functions. Three types of sensilla were identified (trichoid, basiconic and coeloconical) as a result of the analysis of two tachinid species antennae. Trichoid and basiconic sensilla were found among the tachinid fly Cistogaster globosa, and trichoid and coeloconical sensilla were found among Cylindromyia interrupta. A large number of microtrichia was also found on the antenna elements in both tachinid species. Original SEM-images of the ultrastructural organization of the tachinid sensory system are provided; their localization and number per unit area are shown. The obtained data expand our understanding of the role of these morphological structures in the orientation of tachinid fly in the implementation of the reproductive strategy: search for a sexual partner, search for a potential host habitat, and search for a host.

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