scholarly journals Phylogenetic and ecological reevaluation of the order Onygenales

2021 ◽  
Author(s):  
Hazal Kandemir ◽  
Karolina Dukik ◽  
Marcus de Melo Teixeria ◽  
J. Benjamin Stielow ◽  
Fatima Zohra Delma ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Cellulose Degradation ◽  
Habitat Preferences ◽  
Divergence Time ◽  
Time Analysis ◽  
Multiple Gene ◽  
Number Of Species ◽  
Causative Agents ◽  
Taxonomic Groups ◽  
Systemic Infections

Abstract The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous, and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by abilities of keratin- and cellulose-degradation. The present study aimed to investigate whether the ecological trends of the members of the Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigaceae were accepted in the Onygenales, and two new families, Auxarthraceae and Neogymnomycetaceae were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of the Onygenales, supported by multilocus analyses of ITS, LSU, TUB , TEF1 , TEF3 , RPB1 , RPB2, and ribosomal protein 60S L10 (L1) ( RP60S ) sequences, combined with available data on ecology, physiology, morphology, and genomics.

scholarly journals Kinetics of Targeted Phage Rescue in a Mouse Model of SystemicEscherichia coliK1

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
György Schneider ◽  
Nikolett Szentes ◽  
Marianna Horváth ◽  
Ágnes Dorn ◽  
Alysia Cox ◽  
...  
Keyword(s):  
Capsular Polysaccharide ◽  
Protective Efficacy ◽  
Lytic Bacteriophage ◽  
E Coli ◽  
Causative Agents ◽  
High Level ◽  
Systemic Infections ◽  
Kinetics Of

Escherichia (E.) coliK1 strains remain common causative agents of neonatal sepsis and meningitis. We have isolated a lytic bacteriophage (ΦIK1) againstE. colistrain IHE3034 and tested its specificityin vitro, as well as distribution and protective efficacyin vivo. The phage was shown to be specific to the K1 capsular polysaccharide. In the lethal murine model, a high level of protection was afforded by the phage with strict kinetics. A single dose of 1 x 108phage particles administered 10 and 60 minutes following the bacterial challenge elicited 100 % and 95 % survival, respectively. No mice could be rescued if phage administration occurred 3 hours postinfection. Tissue distribution surveys in the surviving mice revealed that the spleen was the primary organ in which accumulation of active ΦIK1 phages could be detected two weeks after phage administration. These results suggest that bacteriophages have potential as therapeutic agents in the control of systemic infections.

Antiviral Activity of Cholesteryl Esters of Cinnamic Acid Derivatives

1998 ◽  
Vol 53 (9-10) ◽  
pp. 883-887 ◽  
Author(s):  
Angel S. Galabov ◽  
Lubomira Nikolaeva ◽  
Daniela Todorova ◽  
Tsenka Milkova
Keyword(s):  
Antiviral Activity ◽  
Cinnamic Acid ◽  
Cholesteryl Esters ◽  
Cinnamic Acid Derivatives ◽  
Steryl Esters ◽  
Causative Agents ◽  
Marked Activity ◽  
Taxonomic Groups

Cholesteryl 3”,4”-dimethoxycinnamate (7) and a new synthesized o-coumaroyl ester of 3β- (2’-hydroxyethoxy)-cholest-5-en (13) exhibited a marked activity against poliovirus type 1 (Mahoney). Compound 7 showed an approximately 20-fold greater selectivity in its antiviral activity than compound 13. These compounds were selected from thirteen steryl esters of cinnamic acid derivatives through an in vitro antiviral screening against viruses belonging to taxonomic groups with causative agents of important human infectious diseases to which chemotherapy is indicated, i.e. Picornaviridae, Orthomyxoviridae, Paramyxoviridae and Herpesviridae.

Weak genetic divergence between the two South American toad-headed turtles Mesoclemmys dahli and M. zuliae (Testudines: Pleurodira: Chelidae)

2012 ◽  
Vol 33 (3-4) ◽  
pp. 373-385 ◽  
Author(s):  
Mario Vargas-Ramírez ◽  
Jan Michels ◽  
Olga Victoria Castaño-Mora ◽  
Gladys Cárdenas-Arevalo ◽  
Natalia Gallego-García ◽  
...  
Keyword(s):  
Habitat Preferences ◽  
Divergence Time ◽  
South American ◽  
Mitochondrial Cytochrome ◽  
Closely Related Species ◽  
Turtle Species ◽  
American Toad ◽  
Distribution Ranges ◽  
Mountain Chain ◽  
Relaxed Molecular Clock

Mesoclemmys dahli and M. zuliae are two endangered, little-known toad-headed turtles with small distribution ranges in Colombia and Venezuela, respectively. Using the mitochondrial cytochrome b gene as a marker, we investigate their phylogeographic differentiation. Furthermore, based on 2341 bp of mtDNA and 2109 bp of nDNA of M. dahli, M. zuliae and allied chelid turtles, we infer their divergence time using a fossil-calibrated relaxed molecular clock approach. Mesoclemmys dahli and M. zuliae are closely related species, with an estimated mean divergence time of 10.6 million years. This estimate correlates with the uplift of the Serranía de Perijá, an Andean mountain chain separating their distribution ranges, suggesting that this event could have caused the evolution of the two species. Haplotype and nucleotide diversities of M. dahli are markedly higher than in Podocnemis lewyana, another endemic turtle species of Colombia. This pronounced dissimilarity may reflect differences in the phylogeographies and demographic histories of the two species, but also different habitat preferences.

scholarly journals Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

2021 ◽  
Author(s):  
Xiaojin Liu ◽  
Daping Xu ◽  
Zhou Hong ◽  
Ningnan Zhang ◽  
Zhiyi Cui
Keyword(s):  
Chloroplast Genome ◽  
Evolutionary Dynamics ◽  
Divergence Time ◽  
Major Type ◽  
Time Analysis ◽  
Chloroplast Genomes ◽  
Extant Species ◽  
History Of ◽  
Insight Into ◽  
Simple Sequence

Abstract Background Santalum (Santalaceae, sandalwood) is a hemiparasitic genus including approximately 15 extant species. It is known for its aromatic heartwood oil, which is used in incense and perfume. Demand for sandalwood-based products has led to drastic over-harvesting, and wild Santalum populations are now threatened. Knowledge of the phylogenetic relationships and genetic diversity will be critical for the conservation and proper management of this genus. Here, we sequenced the chloroplast genome of 11 Santalum species. The data were then used to investigate the chloroplast genome evolutionary dynamics and relationships and divergence time within Santalum and related species. Results The Santalum chloroplast genome contains the typical quadripartite structures, ranging from 143,291 to 144,263 bp. The chloroplast genome contains 124 genes. The whole set of ndh genes and the infA gene were found to lose their function. Between 17 and 31 SSRs were found in the Santalum chloroplast genome, and mononucleotide simple sequence repeats (SSRs) were the major type. The P-distance among the Santalum species was 0.0003 to 0.00828. Three mutation hotspot regions, 14 small inversions, and 460 indels events were discovered in the Santalum chloroplast genome. Our phylogenomic assessment provides improved resolution compared to past analyses. Our divergence time analysis shows that the crown age of Santalum was 8.46 Mya, the first divergence occurred around 6.97 Mya, and diversification was complete within approximately 1 Mya. Conclusions By sequencing the 12 chloroplast genomes of Santalum, we gain insight into the evolution of its chloroplast genomes. The chloroplast genome sequences had sufficient polymorphic information to elucidate the evolutionary history of Santalum.

Phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (Testudines: Testudinidae)

Zootaxa ◽  
2017 ◽  
Vol 4320 (3) ◽  
pp. 487
Author(s):  
JULIETA SÁNCHEZ ◽  
JUAN A. HOLLEY ◽  
SEBASTIÁN POLJAK ◽  
ALEJANDRO D. BOLZÁN ◽  
CLAUDIO M. BRAVI
Keyword(s):  
South America ◽  
Divergence Time ◽  
Geographic Range ◽  
Middle Pleistocene ◽  
Second Step ◽  
Cyt B ◽  
Time Analysis ◽  
Late Pliocene ◽  
Inference Methods ◽  
Time Of Origin

We present a phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (the southernmost tortoises of South America) within crown Testudinidae. We compiled a dataset of 1118 bp cytochrome b (cyt b) sequences derived from 111 individuals sampled across the known geographic range of the species, and performed a phylogenetic analysis employing Maximum Parsimony, Maximum Likelihood and Bayesian Inference methods. The resulting trees showed similar topologies and support values. The C. chilensis complex was always recovered as a monophyletic group composed by two major clades (i.e. haplogroups). The biogeographic distribution of one of these clades overlaps with the Dry Chaco eco–region, while the biogeographic distribution of the other overlaps with the Monte eco–region. In order to date the origin and diversification time of these two clades, we employed a previously published two-step molecular clock method. In the first step we dated the time of origin of C. chilensis as a clade within the Testudinidae family using new and previously published sequences, extinct testudinid taxa for age calibration and the Fossilized Birth-Death (FBD) model. In the second step we dated the divergence between the haplogroups of C. chilensis based on the time of origin estimated in the first step and a coalescent evolution model. Our results suggest that divergence between Dry Chaco and Monte tortoises may have occurred about 2.47 million of years ago. We interpret these results in the light of the environmental and geological changes that occurred during the late Pliocene to Middle Pleistocene of South America. 

scholarly journals Prediction of Signal Peptides in Proteins from Malaria Parasites

2018 ◽  
Vol 19 (12) ◽  
pp. 3709 ◽  
Author(s):  
Michał Burdukiewicz ◽  
Piotr Sobczyk ◽  
Jarosław Chilimoniuk ◽  
Przemysław Gagat ◽  
Paweł Mackiewicz
Keyword(s):  
Learning Systems ◽  
Proper Function ◽  
Signal Peptides ◽  
Endomembrane System ◽  
Malaria Parasites ◽  
Apicomplexan Parasites ◽  
Different Types ◽  
Causative Agents ◽  
Taxonomic Groups ◽  
Unique Amino Acid

Signal peptides are N-terminal presequences responsible for targeting proteins to the endomembrane system, and subsequent subcellular or extracellular compartments, and consequently condition their proper function. The significance of signal peptides stimulates development of new computational methods for their detection. These methods employ learning systems trained on datasets comprising signal peptides from different types of proteins and taxonomic groups. As a result, the accuracy of predictions are high in the case of signal peptides that are well-represented in databases, but might be low in other, atypical cases. Such atypical signal peptides are present in proteins found in apicomplexan parasites, causative agents of malaria and toxoplasmosis. Apicomplexan proteins have a unique amino acid composition due to their AT-biased genomes. Therefore, we designed a new, more flexible and universal probabilistic model for recognition of atypical eukaryotic signal peptides. Our approach called signalHsmm includes knowledge about the structure of signal peptides and physicochemical properties of amino acids. It is able to recognize signal peptides from the malaria parasites and related species more accurately than popular programs. Moreover, it is still universal enough to provide prediction of other signal peptides on par with the best preforming predictors.

MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees

2019 ◽  
Author(s):  
Mark N Puttick
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
R Package ◽  
Posterior Distributions ◽  
Time Analysis ◽  
Divergence Time Estimation ◽  
R Packages ◽  
Geological Timescale ◽  
Time Information ◽  
Age Estimates

Abstract Summary The fossil record is incomplete, so molecular divergence time analysis is a crucial tool in estimating evolutionary timescales. MCMCtree contained in the PAML software provides Bayesian methods to estimate divergence times of genomic-sized sequences. Here, I present MCMCtreeR, a flexible R package to prepare time priors for MCMCtree analysis and plot time-scaled phylogenies. The package provides functions to refine parameters and visualize time-calibrated node prior distributions so that these priors accurately reflect confidence in known, usually fossil, time information. After the parameters have been chosen, the package produces output files ready for MCMCtree analysis. Following analysis, the package has tools to compare prior and posterior calibrated node age distributions and produce plots of the time-scaled phylogenies. The plotting functions allow for the inclusion of age uncertainty on time-scaled phylogenies, including the display of full posterior distributions on nodes. Options also allow for the inclusion of the geological timescale, and these plotting functions are applicable with posterior age estimates from any Bayesian divergence time estimation software. Availability and implementation MCMCtreeR is an R package available on CRAN (https://CRAN.R-project.org/package=MCMCtreeR). MCMCtreeR depends on the R packages ape, sn and stats4.

scholarly journals An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

2019 ◽  
Vol 286 (1895) ◽  
pp. 20182076 ◽  
Author(s):  
Dominic A. Evangelista ◽  
Benjamin Wipfler ◽  
Olivier Béthoux ◽  
Alexander Donath ◽  
Mari Fujita ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Sister Group ◽  
Divergence Times ◽  
Sister Group Relationship ◽  
Time Analysis ◽  
The Social ◽  
History Of ◽  
Egg Care ◽  
Phylogenomic Study

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

scholarly journals Integrated phylogenomics and fossil data illuminate the evolution of beetles

2021 ◽  
Author(s):  
Chenyang Cai ◽  
Erik Tihelka ◽  
Mattia Giacomelli ◽  
John F. Lawrence ◽  
Adam Ślipiński ◽  
...  
Keyword(s):  
Divergence Time ◽  
Single Copy ◽  
Time Analysis ◽  
Rate Heterogeneity ◽  
Protein Coding ◽  
Morphological Studies ◽  
Divergence Dates ◽  
Cretaceous Terrestrial Revolution ◽  
Fossil Data

AbstractWith over 380,000 described species and possibly several million more yet unnamed, beetles represent the most biodiverse animal order. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here we use a dataset of 68 single-copy nuclear protein coding genes sampling 129 out of the 194 recognized extant families as well as the first comprehensive set of fully-justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov., and Staphyliniformia sensu nov., alongside changes below the superfamily level. The heterogeneous former superfamily Cucujoidea is divided into three monophyletic groups: Erotyloidea stat. nov., Nitiduloidea stat. nov., and Cucujoidea sensu nov. Our divergence time analysis recovered an evolutionary timescale congruent with the fossil record: a late Carboniferous origin of Coleoptera, a late Paleozoic origin of all modern beetle suborders, and a Triassic–Jurassic origin of most extant families. While fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution, many polyphagan superfamilies exhibited increases in richness with Cretaceous flowering plants.

Sign in / Sign up

Export Citation Format

Share Document