scholarly journals Molecular evolution of dengue virus types 1 and 4 in Korean travelers

2021 ◽  
Vol 166 (4) ◽  
pp. 1103-1112
Author(s):  
Eun-Ha Hwang ◽  
Green Kim ◽  
Hoyin Chung ◽  
Hanseul Oh ◽  
Jong-Hwan Park ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Positive Selection ◽  
Recent Common Ancestor ◽  
Coding Region ◽  
Genotype I ◽  
Most Recent Common Ancestor ◽  
Evolutionary Features ◽  
Molecular Phylogenetic ◽  
First Time ◽  
Global Travel

AbstractDengue virus (DV) is a mosquito-borne virus that is endemic to many tropical and subtropical areas. Recently, the annual incidence of DV infection has increased worldwide, including in Korea, due to global warming and increased global travel. We therefore sought to characterize the molecular and evolutionary features of DV-1 and DV-4 isolated from Korean overseas travelers. We used phylogenetic analysis based on the full coding region to classify isolates of DV-1 in Korea into genotype I (43251, KP406802), genotype IV (KP406803), and genotype V (KP406801). In addition, we found that strains of DV-4 belonged to genotype I (KP406806) and genotype II (43257). Evidence of positive selection in DV-1 strains was identified in the C, prM, NS2A, and NS5 proteins, whereas DV-4 showed positive selection only in the non-structural proteins NS2A, NS3, and NS5. The substitution rates per site per year were 5.58 × 10-4 and 6.72 × 10-4 for DV-1 and DV-4, respectively, and the time of the most recent common ancestor was determined using the Bayesian skyline coalescent method. In this study, the molecular, phylogenetic, and evolutionary characteristics of Korean DV-1 and DV-4 isolates were evaluated for the first time.

scholarly journals Phylogenetic and Phylogeographic Analysis of DENV-1 Genotype Ⅰ in Asian-Pacific Region

2020 ◽  
Vol 206 ◽  
pp. 01012
Author(s):  
Deyan Yang ◽  
Haiqi Wang ◽  
Bin Yan
Keyword(s):  
Dengue Virus ◽  
Common Ancestor ◽  
Asia Pacific ◽  
Recent Common Ancestor ◽  
Pacific Region ◽  
Asian Countries ◽  
Asia Pacific Region ◽  
Genotype I ◽  
Phylogeographic Analysis ◽  
Most Recent Common Ancestor

Objective: To clarify the evolutionary characteristics and transmission mode of DENV-1 genotype I dengue virus in the Asia-Pacific region. Methods: 200 DENV-1 genotype I dengue viruses in the Asia-Pacific region from 2010 to 2014 and 2015 to 2019 were used for phylogenetic analysis and bayesian phylogeographic analysis using a series of molecular biology software. Results: DENV-1 genotype I dengue virus spread frequently between coastal cities in China and Southeast Asian countries. The evolution rate of DENV-1 genotype I dengue virus during 2010-2014 was 5.73×104 (/site/year,95%CI) , and the time to the most recent common ancestor was 1970-09-14.And the evolution rate of virus during 2015-2019 was 5.25×104 (/site/year,95%CI) , and the time to the most recent common ancestor was 1978-10-30.The virus spatial diffusion pathways shows the phenomenon that the dengue virus of this genotype is widespread in the Asia-Pacific region, the spread of the dengue virus between the coastal provinces and some inland provinces of China, and Southeast Asian countries. The study results indicated that the monitoring and preventive measures should be strengthened to avoid the threat of personal safety caused by large-scale spread of DENV-1 in China.

Early divergence of an Azorean endemic species in the moss genus Rhynchostegiella (Brachytheciaceae)

Phytotaxa ◽  
2015 ◽  
Vol 210 (1) ◽  
pp. 60 ◽  
Author(s):  
Alain Vanderpoorten ◽  
Jairo PatiÑo ◽  
Gerard Dirkse ◽  
TOM BLOCKEEL ◽  
Lars Hedenäs
Keyword(s):  
Endemic Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
Recent Common Ancestor ◽  
Width Ratio ◽  
Most Recent Common Ancestor ◽  
Molecular Phylogenetic ◽  
Variable Species ◽  
The One ◽  
A New Species

Using the moss genus Rhynchostegiella (Brachytheciaceae) as a model, we address the question of whether taxonomic shortcomings account for the extremely low rates of endemism reported in the Azorean bryophyte flora. Eight accessions initially assigned to three of the four previously reported species in the Azores were identified as a distinct species using the Generalized Mixed Yule Coalescent method in the context of a molecular phylogenetic analysis of the genus. Rhynchostegiella azorica sp. nov. is therefore described as a new species that is endemic to the Azores. Its morphological features intergrade with those observed in other species, with a seta that ranges from almost smooth to rough; a length to width ratio of the laminal cells that matches the one of the R. curviseta group; but a leaf apex that is typical of the R. tenella group. This suggests that previous reports of four Rhynchostegiella species from Azores are erroneous and that a single, morphologically variable species, R. azorica, occurs in the archipelago. Rhynchostegiella azorica is sister to the remainder of the species of the genus, whose most recent common ancestor was dated at 4–20 Ma. This points to a more ancient origin in comparison with other Macaronesian endemic species of the genus. The unexpected discovery of an Azorean endemic species in Rhynchostegiella suggests that patterns of endemicity in the Azorean bryophyte flora are not well estimated from traditional taxonomic knowledge and point to the necessity of an extensive integrative taxonomic revision.

scholarly journals Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica

2015 ◽  
Vol 112 (35) ◽  
pp. 10989-10994 ◽  
Author(s):  
Viviana D. Barreda ◽  
Luis Palazzesi ◽  
Maria C. Tellería ◽  
Eduardo B. Olivero ◽  
J. Ian Raine ◽  
...  
Keyword(s):  
Pollen Grains ◽  
Terrestrial Ecosystems ◽  
Flowering Plants ◽  
Flowering Plant ◽  
Recent Common Ancestor ◽  
Time Interval ◽  
Most Recent Common Ancestor ◽  
The Family ◽  
Dramatic Rise ◽  
Molecular Phylogenetic

The Asteraceae (sunflowers and daisies) are the most diverse family of flowering plants. Despite their prominent role in extant terrestrial ecosystems, the early evolutionary history of this family remains poorly understood. Here we report the discovery of a number of fossil pollen grains preserved in dinosaur-bearing deposits from the Late Cretaceous of Antarctica that drastically pushes back the timing of assumed origin of the family. Reliably dated to ∼76–66 Mya, these specimens are about 20 million years older than previously known records for the Asteraceae. Using a phylogenetic approach, we interpreted these fossil specimens as members of an extinct early diverging clade of the family, associated with subfamily Barnadesioideae. Based on a molecular phylogenetic tree calibrated using fossils, including the ones reported here, we estimated that the most recent common ancestor of the family lived at least 80 Mya in Gondwana, well before the thermal and biogeographical isolation of Antarctica. Most of the early diverging lineages of the family originated in a narrow time interval after the K/P boundary, 60–50 Mya, coinciding with a pronounced climatic warming during the Late Paleocene and Early Eocene, and the scene of a dramatic rise in flowering plant diversity. Our age estimates reduce earlier discrepancies between the age of the fossil record and previous molecular estimates for the origin of the family, bearing important implications in the evolution of flowering plants in general.

Towards uncovering evolution of lineage-specific calcium oxalate crystal patterns in Piperales

Botany ◽  
2015 ◽  
Vol 93 (3) ◽  
pp. 159-169 ◽  
Author(s):  
Harry T. Horner ◽  
Marie-Stéphanie Samain ◽  
Sarah T. Wagner ◽  
Stefan Wanke
Keyword(s):  
Calcium Oxalate ◽  
Recent Common Ancestor ◽  
Calcium Oxalate Crystal ◽  
Character Reconstruction ◽  
Most Recent Common Ancestor ◽  
Molecular Phylogenetic ◽  
Crystal Type ◽  
Phylogenetic Hypotheses ◽  
Crystal Sand ◽  
Ancestral Character Reconstruction

Piperales is among the largest and most diverse angiosperm orders (>4000 species), occurring broadly in tropical and temperate habitats. Twenty-four of the species from 12 genera, representing all lineages of Piperales, except the holoparasitic Hydnoraceae, display a mixture of leaf calcium oxalate crystal types found in previous studies of the two genera of Piperaceae subfamily Piperoideae (Peperomia Ruiz & Pav. and Piper L.). Crystal macropatterns, a result of varying leaf anatomies and diverse habitats, are investigated in a comparative way by using clearings and recent molecular phylogenetic hypotheses to trace crystal types and macropattern evolution. Ancestral character reconstruction reveals that the most recent common ancestor of Piperales had either crystal sand or druses or both and that prisms, raphides, and styloids are derived from the ancestral crystal type(s). These results are also recovered for both the ancestors of the perianth-less and the perianth-bearing Piperales. Raphides or druses are found in the two other subfamilies of Piperaceae (Verhuellioideae and Zippelioideae). Asaraceae and Lactoridaceae display crystal sand, whereas Aristolochia L. (Aristolochiaceae) species display mainly druses. Our crystal investigation, combined with ancestral character reconstruction, suggests that styloids, raphides, and prisms are derived within Piperales from crystal sand or druses.

scholarly journals First phylogenetic analysis of dengue virus serotype 4 circulating in Espírito Santo state, Brazil, in 2013 and 2014

2017 ◽  
Vol 146 (1) ◽  
pp. 100-106 ◽  
Author(s):  
C. R. VICENTE ◽  
C. S. PANNUTI ◽  
P. R. URBANO ◽  
A. C. FELIX ◽  
C. CERUTTI JUNIOR ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Recent Common Ancestor ◽  
Phylogenetic Study ◽  
Envelope Gene ◽  
Mato Grosso ◽  
Espírito Santo ◽  
Most Recent Common Ancestor ◽  
Virus Serotype ◽  
Espirito Santo ◽  
Genotype Ii

SUMMARYThe purpose of the present study was to reconstruct the phylogeny of dengue virus serotype 4 (DENV-4) that was circulating in Espírito Santo state, Brazil, in 2013 and 2014, and to discuss the epidemiological implications associated with this evolutionary hypothesis. Partial envelope gene of eight DENV-4 samples from Espírito Santo state were sequenced and aligned with 72 worldwide DENV-4 reference sequences from GenBank. A phylogenetic tree was reconstructed through Bayesian Inference and the Time of the Most Recent Common Ancestor was estimated. The study detected the circulation of DENV-4 genotype II in Espírito Santo state, which was closely related to strains from the states of Mato Grosso collected in 2012 and of São Paulo sampled in 2015. This cluster emerged around 2011, approximately 4 years after the entry of the genotype II in Brazil through its northern states, possibly imported from Venezuela and Colombia. This is so far the first phylogenetic study of the DENV-4 circulating in Espírito Santo state and shows the importance of an internal route of dengue viral circulation in Brazil to the introduction of the virus into this state.

scholarly journals Intercity Spread of Echovirus 6 in Shandong Province, China: Application of Environmental Surveillance in Tracing Circulating Enteroviruses

2012 ◽  
Vol 78 (19) ◽  
pp. 6946-6953 ◽  
Author(s):  
Zexin Tao ◽  
Yanyan Song ◽  
Haiyan Wang ◽  
Yong Zhang ◽  
Hiromu Yoshida ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Gene Diversity ◽  
Likelihood Method ◽  
Recent Common Ancestor ◽  
Environmental Surveillance ◽  
Coding Region ◽  
Most Recent Common Ancestor ◽  
Two Cities ◽  
Echovirus 6 ◽  
Transmission Pathways

ABSTRACTEnvironmental surveillance is an effective approach in investigating circulating enteroviruses and had been conducted in the cities of Jinan and Linyi since February 2008 and April 2010, respectively. This study analyzed 46 sewage samples collected in the two cities in 2011 and found that echovirus 6 (E6) was the predominant serotype, with 134 isolates (65 in Jinan and 69 in Linyi) from 23 (50%) samples. This differs from the 2010 data that found 29 E6 isolates in Jinan and only 3 in Linyi. Phylogenetic analysis of the VP1 coding region showed that all environmental E6 samples from 2008 to 2011 (n= 167) segregated into two lineages and revealed an increase in VP1 gene diversity in 2011, suggesting that the increased number of E6 detections reflects a real epidemic in the two cities. Most Linyi isolates (n= 61, or 88%) in 2011 segregated into sublineage 1a, together with 18 Jinan isolates in 2011. Interestingly, the ancestral VP1 sequence of sublineage 1a inferred using the maximum-likelihood method had 100% identity with the sequence of one environmental isolate from Jinan in August 2010, suggesting an intercity spread from Jinan to Linyi. By Bayesian phylodynamic methods, the most recent common ancestor of Linyi isolates in sublineage 1a dated back to 24 December 2010, revealing that this sublineage was likely imported into Linyi from August to December in 2010. This study demonstrates that environmental surveillance is a sensitive method in tracing transmission pathways of circulating enteroviruses among different regions and reveals that E6-associated aseptic meningitis is an emerging concern in China.

scholarly journals Genomic and Micro-Evolutionary Features of Mammalian 2 orthobornavirus (Variegated Squirrel Bornavirus 1, VSBV-1)

2021 ◽  
Vol 9 (6) ◽  
pp. 1141
Author(s):  
Dániel Cadar ◽  
Jonas Schmidt-Chanasit ◽  
Dennis Tappe
Keyword(s):  
Evolutionary Dynamics ◽  
Animal Husbandry ◽  
Purifying Selection ◽  
Recent Common Ancestor ◽  
Positive Pressure ◽  
Evolutionary Mechanisms ◽  
Time Resolved ◽  
Viral Pathogen ◽  
Most Recent Common Ancestor ◽  
Evolutionary Features

Mammalian 2 orthobornavirus (VSBV-1) is an emerging zoonotic pathogen discovered in several exotic squirrel species and associated with fatal human encephalitis. The dynamics of VSBV-1 spread and evolution in its presumed natural hosts are unknown. Here, we present the phylogeny, micro-evolution, cross-species transmission and spread of VSBV-1 at a temporal and spatial resolution within the limits of animal husbandry. The results showed that VSBV-1 can be classified into six distinct groups and that the most recent common ancestor of the known German strains emerged at least 20 years ago. We here demonstrate that the genetic diversity of the VSBV-1 groups is shaped primarily by in situ evolution and most of the amino acid changes are deleterious polymorphisms removed by purifying selection. Evidence of adaptive evolution has been found in the G and L genes which might have an influence on transmission fitness. Furthermore, there was also evidence for some form of adaptive changes in the glycoprotein which suggests that many sites might be subjected to positive pressure evolving under episodic directional selection, indicating past occurrence of positive selection. Host switching events were detected as dominant evolutionary mechanisms driving the virus-host associations. Virus spread by animal trade followed by subsequent local micro-evolution in zoos and holdings is responsible for diversifying strains. Time-resolved phylogeny indicated that Prevost’s squirrels might be the original squirrel species carrying and seeding the virus in Germany. This study provides the first insight into the ecology and micro-evolutionary dynamics of this novel viral pathogen in the captive exotic squirrel population under artificial ecological conditions (zoos and animal husbandry) and co-housing of different squirrel species.

scholarly journals Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10234 ◽  
Author(s):  
Alejandro Berrio ◽  
Valerie Gartner ◽  
Gregory A. Wray
Keyword(s):  
Protein Structure ◽  
Positive Selection ◽  
Protein Function ◽  
Rna Stability ◽  
Spike Protein ◽  
Recent Common Ancestor ◽  
Molecular Processes ◽  
Gene Encoding ◽  
Rna Molecules ◽  
Most Recent Common Ancestor

Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.

Arnebolagus, the oldest eulagomorph, and phylogenetic relationships within the Eocene Eulagomorpha new clade (Mammalia, Duplicidentata)

2020 ◽  
pp. 1-12
Author(s):  
Alexey V. Lopatin ◽  
Alexander O. Averianov
Keyword(s):  
Phylogenetic Relationships ◽  
Common Ancestor ◽  
Morphological Characters ◽  
Recent Common Ancestor ◽  
Early Eocene ◽  
Modern Aspect ◽  
Most Recent Common Ancestor ◽  
Single Tooth ◽  
Land Mammal ◽  
First Time

Abstract Arnebolagus leporinus Lopatin and Averianov, 2008, known previously from a single tooth (P3) from the early Eocene Bumban Member of Naran Bulak Formation at Tsagan-Khushu locality in Mongolia, is redescribed based on additional specimens from the type locality. Phylogenetic relationships of Eocene stem lagomorphs from Asia and North America are reconstructed for the first time based on a parsimony analysis of 54 morphological characters and 32 taxa. Two new node-based clades are proposed, stemming from the most-recent common ancestor of Lepus Linnaeus, 1758 and Dawsonolagus Li, Meng, and Wang, 2007 (Eulagomorpha new clade, ‘lagomorphs of the modern aspect’) and from the most-recent common ancestor of Lepus and Gobiolagus Burke, 1941 (Epilagomorpha new clade). Arnebolagus Lopatin and Averianov, 2008 is geologically oldest and the most plesiomorphic eulagomorph, similar to Dawsonolagus from the early Eocene Arshanto Formation of China in its weakly pronounced, unilateral hypsodonty of the upper cheek teeth and its brachyodont lower cheek teeth with separate roots. Arnebolagus is more plesiomorphic than Dawsonolagus in having two roots of P4. Arnebolagus is the oldest known eulagomorph, the only taxon known from the earliest Eocene Bumbanian Asiatic Land Mammal Age (ALMA). The other Asiatic early Eocene eulagomorphs (Dawsonolagus, Aktashmys Averianov, 1994, and Romanolagus Shevyreva, 1995) come from the Arshantan ALMA.

scholarly journals Human DNA Sequence Variation in a 6.6-kb Region Containing the Melanocortin 1 Receptor Promoter

Genetics ◽  
2001 ◽  
Vol 158 (3) ◽  
pp. 1253-1268 ◽  
Author(s):  
Kateryna D Makova ◽  
Michele Ramsay ◽  
Trefor Jenkins ◽  
Wen-Hsiung Li
Keyword(s):  
Sequence Variation ◽  
Population Expansion ◽  
Purifying Selection ◽  
Phylogenetic Footprinting ◽  
Recent Common Ancestor ◽  
Coding Region ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Most Recent Common Ancestor ◽  
Dna Sequence Variation

AbstractAn ∼6.6-kb region located upstream from the melanocortin 1 receptor (MC1R) gene and containing its promoter was sequenced in 54 humans (18 Africans, 18 Asians, and 18 Europeans) and in one chimpanzee, gorilla, and orangutan. Seventy-six polymorphic sites were found among the human sequences and the average nucleotide diversity (π) was 0.141%, one of the highest among all studies of nuclear sequence variation in humans. Opposite to the pattern observed in the MC1R coding region, in the present region π is highest in Africans (0.136%) compared to Asians (0.116%) and Europeans (0.122%). The distributions of π, θ, and Fu and Li's F-statistic are nonuniform along the sequence and among continents. The pattern of genetic variation is consistent with a population expansion in Africans. We also suggest a possible phase of population size reduction in non-Africans and purifying selection acting in the middle subregion and parts of the 5′ subregion in Africans. We hypothesize diversifying selection acting on some sites in the 5′ and 3′ subregions or in the MC1R coding region in Asians and Europeans, though we cannot reject the possibility of relaxation of functional constraints in the MC1R gene in Asians and Europeans. The mutation rate in the sequenced region is 1.65 × 10—9 per site per year. The age of the most recent common ancestor for this region is similar to that for the other long noncoding regions studied to date, providing evidence for ancient gene genealogies. Our population screening and phylogenetic footprinting suggest potentially important sites for the MC1R promoter function.

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