scholarly journals The Opiliones Tree of Life: shedding light on harvestmen relationships through transcriptomics

2016 ◽  
Author(s):  
Rosa Fernándeza ◽  
Prashant Sharma ◽  
Ana L.M. Tourinho ◽  
Gonzalo Giribet
Keyword(s):  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Molecular Techniques ◽  
Evolutionary Patterns ◽  
Factors Affecting ◽  
Biogeographic Patterns ◽  
The Family ◽  
The Times ◽  
Phylogenomic Study ◽  
Data Matrices

AbstractOpiliones are iconic arachnids with a Paleozoic origin and a diversity that reflects ancient biogeographical patterns dating back at least to the times of Pangea. Due to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to systematics. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here we analyze a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing ca. 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families are precisely placed. Our dating analyses also using alternative calibration points, methods, and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as a general overview of the general biogeographic patterns of this ancient arthropod group.

scholarly journals The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics

2017 ◽  
Vol 284 (1849) ◽  
pp. 20162340 ◽  
Author(s):  
Rosa Fernández ◽  
Prashant P. Sharma ◽  
Ana Lúcia Tourinho ◽  
Gonzalo Giribet
Keyword(s):  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Molecular Techniques ◽  
Evolutionary Patterns ◽  
Factors Affecting ◽  
Biogeographic Patterns ◽  
The Family ◽  
The Times ◽  
Phylogenomic Study ◽  
Data Matrices

Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group.

Iridaceae 'Out of Australasia'? Phylogeny, Biogeography, and Divergence Time Based on Plastid DNA Sequences

2008 ◽  
Vol 33 (3) ◽  
pp. 495-508 ◽  
Author(s):  
Peter Goldblatt ◽  
Aaron Rodriguez ◽  
M. P. Powell ◽  
Jonathan T. Davies ◽  
John C. Manning ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Secondary Growth ◽  
Divergence Time ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Related Family ◽  
The Family

The current infrafamilial taxonomy of the Iridaceae recognizes four subfamilies; Isophysidoideae (1: 1); Nivenioideae (6: ca. 92), Iridoideae (29: 890), and Crocoideae (29: 1032). Phylogenetic analyses of sequences of five plastid DNA regions, rbcL, rps4, trnL–F, matK, and rps16, confirm most aspects of this classification and the evolutionary patterns that they imply, importantly the sisiter relationship of Isophysidoideae to the remainder of the family and the monophyly of Iridoideae. Subfamily Nivenioideae is, however, paraphyletic; Crocoideae is consistently found nested within it, sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia. This clade is sister to Aristea, which in turn is sister to the Madagascan Geosiris, and then to the Australasian Patersonia. We treat Aristea, Geosiris, and Patersonia as separate subfamilies, Aristeoideae and the new Geosiridaceae and Patersonioideae, rendering Nivenioideae and Crocoideae monophyletic. The alternative, uniting a widely circumscribed Nivenioideae and Crocoideae, seems undesirable because Nivenioideae have none of the numerous synapomorphies of Crocoideae, and that subfamily includes more than half the total species of Iridaceae. Main synapomorphies of Crocoideae are: pollen operculate; exine perforate; ovule campylotropous; root xylem vessels with simple perforations; rootstock a corm; inflorescence usually a spike; plants deciduous. Four more derived features of Crocoideae are shared only with core Nivenioideae: flowers long-lived; perianth tube well developed; flowers sessile; and septal nectaries present. The genera of the latter subfamily are evergreen shrubs, have monocot-type secondary growth, tangentially flattened seeds, and the inflorescence unit is a binate rhipidium. The latter feature unites core Nivenioideae with Aristea, Geosiris, and Patersonia, which have fugaceous flowers and, with few exceptions, a blue perianth. Molecular-based phylogenetic trees using sequences from five plastid DNA regions now show discrete generic clusters within Crocoideae and Iridoideae, the foundation for the tribal classification. The five tribe classification of Iridoideae, initially based on morphological characters and subsequently supported by a four plastid DNA region sequence analysis, continues to receive support using additional DNA sequences. Application of molecular clock techniques to our phylogeny indicates that the Iridaceae differentiated in the late Cretaceous and diverged from the next most closely related family, Doryanthaceae circa 82 mya, thus during the Campanian. The Tasmanian Isophysis is the only extant member of the clade sister to the remainder of the Iridaceae, from which it may have diverged 66 mya, in the Maastrichtian. The generic phylogeny shows the proximal clades of the family are all Australasian, which corroborates past hypotheses that the Iridaceae originated in Antarctica-Australasia, although its subsequent radiation occurred elsewhere, notably in southern Africa and temperate and highland South America at the end of the Eocene or later.

scholarly journals CHILDREN IN BESIKTAS DISTRICT OF ISTANBUL: THE TIME SPENT OUTSIDE

2021 ◽  
Vol 9 (57) ◽  
Keyword(s):  
City Center ◽  
Factors Affecting ◽  
Face To Face ◽  
The Family ◽  
The Face ◽  
Market Areas ◽  
The Times ◽  
The City ◽  
Lived Health ◽  
Made In

This paper aims to look at the factors affecting the time spend outside their homes for the preschool children aged 0-6 and their families in Istanbul metropole city center focusing on Besiktas district of Istanbul. Building new cities particularly with open areas and new facilities to encourage secure mobility and social interaction is a growing topic of discussion globally. The effects of environment on children and children’s free movement in the natural environment on their mental and physical development are also another growing topic of discussion among the scholars worldwide. Using the methods of observation made in various spaces in Besiktas District such as market areas, streets and data from the face-to-face indepth interviews conducted with 24 parents of 0-6 aged children in Besiktas; the research aims to present the main factors affecting the children’s interaction with the city, mainly the time spend outside together with their parents and alone. The paper will reveal that the number of people taking care of the child, the occupation of the parents, the age of the child, geography and facilities of the place lived, health problems and spacial closeness to the family relatives are prominent factors affecting the time spent outdoors for children. Related to the factors discussed in the paper the times spend outside with children and interaction with the city are mainly limited and not very qualified. The findings of the research can be of value for the further studies in the areas of sociology, education, architecture, and city planners.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

scholarly journals Molecular diversity and evolutionary trends of cysteine-rich peptides from the venom glands of Chinese spider Heteropoda venatoria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jie Luo ◽  
Yiying Ding ◽  
Zhihao Peng ◽  
Kezhi Chen ◽  
Xuewen Zhang ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Molecular Diversity ◽  
Insect Pests ◽  
Phylogenetic Analyses ◽  
Spider Venom ◽  
Evolutionary Trends ◽  
The Family ◽  
Venom Glands ◽  
Venom Evolution ◽  
Expressed Sequence

AbstractHeteropoda venatoria in the family Sparassidae is highly valued in pantropical countries because the species feed on domestic insect pests. Unlike most other species of Araneomorphae, H. venatoria uses the great speed and strong chelicerae (mouthparts) with toxin glands to capture the insects instead of its web. Therefore, H. venatoria provides unique opportunities for venom evolution research. The venom of H. venatoria was explored by matrix-assisted laser desorption/ionization tandem time-of-flight and analyzing expressed sequence tags. The 154 sequences coding cysteine-rich peptides (CRPs) revealed 24 families based on the phylogenetic analyses of precursors and cysteine frameworks in the putative mature regions. Intriguingly, four kinds of motifs are first described in spider venom. Furthermore, combining the diverse CRPs of H. venatoria with previous spider venom peptidomics data, the structures of precursors and the patterns of cysteine frameworks were analyzed. This work revealed the dynamic evolutionary trends of venom CRPs in H. venatoria: the precursor has evolved an extended mature peptide with more cysteines, and a diminished or even vanished propeptides between the signal and mature peptides; and the CRPs evolved by multiple duplications of an ancestral ICK gene as well as recruitments of non-toxin genes.

Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

2017 ◽  
Vol 74 (7) ◽  
pp. 1875-1884 ◽  
Author(s):  
Dmitry N. Kulagin ◽  
Tatiana V. Neretina
Keyword(s):  
Atlantic Ocean ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Maturity Stage ◽  
Congeneric Species ◽  
Morphological Examination ◽  
Posterior Teeth ◽  
Biogeographic Patterns ◽  
True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

scholarly journals Pathogenicity, Epidemiology and Virulence Factors of Salmonella species: A Review

2017 ◽  
Vol 9 (4) ◽  
pp. 460-466 ◽  
Author(s):  
Tamègnon Victorien DOUGNON ◽  
Boris LEGBA ◽  
Esther DEGUENON ◽  
Gildas HOUNMANOU ◽  
Jerrold AGBANKPE ◽  
...  
Keyword(s):  
Public Health ◽  
Virulence Factors ◽  
Meat Products ◽  
Health Problems ◽  
Molecular Techniques ◽  
Salmonella Spp ◽  
Salmonella Infections ◽  
The Family ◽  
The World ◽  
Salmonella Control

Salmonella infections are major public health problems worldwide. The hereby review aimed to establish an overview on the pathogenicity, epidemiology and virulence factors of Salmonella spp. in the world. A systematic search was conducted online using the keywords ‘Salmonella’, ‘Salmonella spp.’, ‘Salmonella spp. Epidemiology’, ‘virulence factors of Salmonella spp. in the world’, ‘bacteria responsible for the contamination of meat products’, ‘non-typhoid salmonella’. These keywords were entered into databases such as PubMed and Google Scholar using mainly French language. The obtained articles were included based on the reliability of their source, the study area (usually Benin and Africa) and the subject. The review revealed that Salmonella spp. is motile Gram-negative rod-shaped bacteria, of the family Enterobacteriaceae, currently counting more than 2,600 serovars. Human contamination occurs through the ingestion of contaminated water and food and can cause gastroenteritis or typhoid fever, which are two serious public health problems. A gene set constituting the pathogenicity islands determines the pathogenesis of Salmonella spp. The diagnosis is based on bacteriological, serological and molecular techniques. Salmonella infections are usually treated using antibiotics; however, emergence of antibiotic resistance in these microorganisms suggests that the anti-salmonella control should explore new sources such as medicinal plants

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