Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data

In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary rate of this virus. In addition, we proposed a simple Bayesian technique for the evaluation and visualization of ‘temporal signal dynamics’ along the phylogenetic tree. We showed that the evolutionary rate value of POWV is 3.3 × 10−5 nucleotide substitution per site per year (95% HPD, 2.0 × 10−5–4.7 × 10−5), which is lower than values reported in the previous studies. Divergence of the most recent common ancestor (MRCA) of POWV into two independent genetic lineages most likely occurred in the period between 2600 and 6030 years ago. We assume that the divergence of the virus lineages happened due to the melting of glaciers about 12,000 years ago, which led to the disappearance of the Bering Land Bridge between Eurasia and North America (the modern Alaskan territory) and spatial division of the viral areal into two parts. Genomic data provide evidence of the virus migrations between two continents. The mean migration rate detected from the Far East of Russia to North America was one event per 1750 years. The migration to the opposite direction occurred approximately once per 475 years.

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Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

World Journal of Pediatrics ◽

10.1007/s12519-021-00451-y ◽

2021 ◽

Author(s):

Ya-Fang Hu ◽

Li-Ping Jia ◽

Fang-Yuan Yu ◽

Li-Ying Liu ◽

Qin-Wei Song ◽

...

Keyword(s):

Molecular Epidemiology ◽

Evolutionary Rate ◽

Foot And Mouth Disease ◽

Recent Common Ancestor ◽

Rt Pcr ◽

Coxsackievirus A16 ◽

Most Recent Common Ancestor ◽

Etiological Agents ◽

High Level ◽

And Control

Abstract Background Coxsackievirus A16 (CVA16) is one of the major etiological agents of hand, foot and mouth disease (HFMD). This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16. Methods Throat swabs were collected from children with HFMD and suspected HFMD during 2010–2019. Enteroviruses (EVs) were detected and typed by real-time reverse transcription-polymerase chain reaction (RT-PCR) and RT-PCR. The genotype, evolutionary rate, the most recent common ancestor, population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene (VP1) by bioinformatics software. Results A total of 4709 throat swabs were screened. EVs were detected in 3180 samples and 814 were CVA16 positive. More than 81% of CVA16-positive children were under 5 years old. The prevalence of CVA16 showed obvious periodic fluctuations with a high level during 2010–2012 followed by an apparent decline during 2013–2017. However, the activities of CVA16 increased gradually during 2018–2019. All the Beijing CVA16 strains belonged to sub-genotype B1, and B1b was the dominant strain. One B1c strain was detected in Beijing for the first time in 2016. The estimated mean evolutionary rate of VP1 gene was 4.49 × 10–3 substitution/site/year. Methionine gradually fixed at site-23 of VP1 since 2012. Two sites were detected under episodic positive selection, one of which (site-223) located in neutralizing linear epitope PEP71. Conclusions The dominant strains of CVA16 belonged to clade B1b and evolved in a fast evolutionary rate during 2010–2019 in Beijing. To provide more favorable data for HFMD prevention and control, it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

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Huehuecanauhtlus tiquichensis, a new hadrosauroid dinosaur (Ornithischia: Ornithopoda) from the Santonian (Late Cretaceous) of Michoacán, Mexico

Canadian Journal of Earth Sciences ◽

10.1139/e11-062 ◽

2012 ◽

Vol 49 (2) ◽

pp. 379-395 ◽

Cited By ~ 10

Author(s):

Angel Alejandro Ramírez-Velasco ◽

Mouloud Benammi ◽

Albert Prieto-Márquez ◽

Jesús Alvarado Ortega ◽

René Hernández-Rivera

Keyword(s):

North America ◽

Late Cretaceous ◽

Common Ancestor ◽

Cladistic Analysis ◽

Lateral View ◽

Occlusal Plane ◽

Recent Common Ancestor ◽

Vicariant Event ◽

Most Recent Common Ancestor ◽

Caudal Vertebrae

Huehuecanauhtlus tiquichensis gen. et sp. nov. is the southernmost diagnostic basal hadrosauroid in the Americas. The holotype and referred material of this taxon came from Santonian strata in the Michoacán State, southwestern Mexico. Huehuecanauhtlus tiquichensis is diagnosed on the basis of a combination of dental, axial, and appendicular characters, including the following: at least two teeth exposed on the occlusal plane of the dentary and maxilla; seven sacral vertebrae; tall neural spines of caudal vertebrae; supraacetabular process long; and short and trapezoidal (in lateral view) postacetabular process. It differs from other hadrosauroids in having an ilium with extreme ventral deflection of the preacetabular process. Maximum parsimony cladistic analysis placed H. tiquichensis as a closely related outgroup to Hadrosauridae. The occurrence of H. tiquichensis in the Santonian of North America may be explained as a dispersal event from Asia to North America that occurred no later than the Albian or, alternatively, as a vicariant event of a most recent common ancestor widespread in both landmasses.

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Evolutionary dynamics of human and avian metapneumoviruses

Journal of General Virology ◽

10.1099/vir.0.2008/006957-0 ◽

2008 ◽

Vol 89 (12) ◽

pp. 2933-2942 ◽

Cited By ~ 67

Author(s):

Miranda de Graaf ◽

Albert D. M. E. Osterhaus ◽

Ron A. M. Fouchier ◽

Edward C. Holmes

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Recent Common Ancestor ◽

Human Populations ◽

Population Bottlenecks ◽

Genetic Lineages ◽

The Past ◽

Most Recent Common Ancestor ◽

Large Sets ◽

Respiratory Tract Illnesses

Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A–D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations – A1, A2, B1 and B2 – of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic diversity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The sampled genetic diversity of HMPV was found to have arisen within the past 119–133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic diversity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection.

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Genome Size Dynamics in Marine Ribbon Worms (Nemertea, Spiralia)

Genes ◽

10.3390/genes12091347 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1347

Author(s):

Juraj Paule ◽

Jörn von Döhren ◽

Christina Sagorny ◽

Maria A. Nilsson

Keyword(s):

Genome Size ◽

Evolutionary Rate ◽

Marine Species ◽

Recent Common Ancestor ◽

Future Studies ◽

Most Recent Common Ancestor ◽

Upper Intertidal ◽

Developmental Traits ◽

Important Basis ◽

Size Estimates

Nemertea is a phylum consisting of 1300 mostly marine species. Nemertea is distinguished by an eversible muscular proboscis, and most of the species are venomous. Genomic resources for this phylum are scarce despite their value in understanding biodiversity. Here, we present genome size estimates of Nemertea based on flow cytometry and their relationship to different morphological and developmental traits. Ancestral genome size estimations were done across the nemertean phylogeny. The results increase the available genome size estimates for Nemertea three-fold. Our analyses show that Nemertea has a narrow genome size range (0.43–3.89 pg) compared to other phyla in Lophotrochozoa. A relationship between genome size and evolutionary rate, developmental modes, and habitat was found. Trait analyses show that the highest evolutionary rate of genome size is found in upper intertidal, viviparous species with direct development. Despite previous findings, body size in nemerteans was not correlated with genome size. A relatively small genome (1.18 pg) is assumed for the most recent common ancestor of all extant nemerteans. The results provide an important basis for future studies in nemertean genomics, which will be instrumental to understanding the evolution of this enigmatic and often neglected phylum.

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Accuracy of demographic inferences from site frequency spectrum: the case of the yoruba population

10.1101/078618 ◽

2016 ◽

Author(s):

Marguerite Lapierre ◽

Amaury Lambert ◽

Guillaume Achaz

Keyword(s):

Frequency Spectrum ◽

Simulated Data ◽

Population Data ◽

Recent Common Ancestor ◽

Theoretical Issue ◽

Demographic Models ◽

Most Recent Common Ancestor ◽

Site Frequency Spectrum ◽

Demographic Inference ◽

And Migration

AbstractSome methods for demographic inference based on the observed genetic diversity of current populations rely on the use of summary statistics such as the Site Frequency Spectrum (SFS). Demographic models can be either model-constrained with numerous parameters such as growth rates, timing of demographic events and migration rates, or model-flexible, with an unbounded collection of piecewise constant sizes. It is still debated whether demographic histories can be accurately inferred based on the SFS. Here we illustrate this theoretical issue on an example of demographic inference for an African population. The SFS of the Yoruba population (data from the 1000 Genomes Project) is fit to a simple model of population growth described with a single parameter (e.g., founding time). We infer a time to the most recent common ancestor of 1.7 million years for this population. However, we show that the Yoruba SFS is not informative enough to discriminate between several different models of growth. We also show that for such simple demographies, the fit of one-parameter models outperforms the model-flexible method recently developed by Liu and Fu. The use of this method on simulated data suggests that it is biased by the noise intrinsically present in the data.

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Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography

Current HIV Research ◽

10.2174/1570162x17666190618155816 ◽

2019 ◽

Vol 17 (2) ◽

pp. 114-125 ◽

Cited By ~ 1

Author(s):

Dmitry Neshumaev ◽

Aleksey Lebedev ◽

Marina Malysheva ◽

Anatoly Boyko ◽

Sergey Skudarnov ◽

...

Keyword(s):

Genetic Diversity ◽

Temporal Dynamics ◽

Phylogenetic Reconstruction ◽

Viral Population ◽

Recent Common Ancestor ◽

Krasnoyarsk Region ◽

Most Recent Common Ancestor ◽

And Migration ◽

Viral Lineage ◽

Hiv 1

Background:The information about the dynamics of the viral population and migration events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size of the country and limited transport accessibility to certain territories may determine unique traits of the HIV-1 evolutionary history in different regions.Objective:The aim of this study was to explore the genetic diversity of HIV-1 in the Krasnoyarsk region and reconstruct spatial-temporal dynamics of the infection in the region.Methods:The demographic and virologic data from 281 HIV-infected individuals in Krasnoyarsk region collected during 2011-2016 were analyzed. The time to the most recent common ancestor, evolutionary rates, population growth, and ancestral geographic movements was estimated using Bayesian coalescent-based methods.Results:The study revealed moderate diversity of the HIV-1 subtypes found in the region, which included A6 (92.3%), CRF063_02A (4.3%), B (1.1%), and unique recombinants (2.5%). Phylogenetic reconstruction revealed that the A6 subtype was introduced into Krasnoyarsk region by one viral lineage, which arose around 1996.9 (1994.5-1999.5). The phylogeography analysis pointed to Krasnoyarsk city as the geographical center of the epidemic, which further spread to central neighboring districts of the region. At least two epidemic growth phases of subtype A6 were identified which included exponential growth in early-2000s followed by the decline in the mid/late 2010s.Conclusion:This study demonstrates a change in the genetic diversity of HIV-1 in the Krasnoyarsk region. At the beginning of the epidemic, subtype A6 prevailed, subtypes B and CRF063_02A appeared in the region later.

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Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

Journal of Virology ◽

10.1128/jvi.02353-15 ◽

2015 ◽

Vol 90 (3) ◽

pp. 1244-1258 ◽

Cited By ~ 10

Author(s):

Natalie N. Kinloch ◽

Daniel R. MacMillan ◽

Anh Q. Le ◽

Laura A. Cotton ◽

David R. Bangsberg ◽

...

Keyword(s):

North America ◽

North American ◽

Consensus Sequence ◽

Hla Class I ◽

Class I ◽

Recent Common Ancestor ◽

Most Recent Common Ancestor ◽

Subtype B ◽

Hiv 1 ◽

Over Time

ABSTRACTHuman leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989;n= 338) and modern (2001 to 2011;n= 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era.IMPORTANCEHLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many—though not all—HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era.

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Global phylogeography and evolution of chelonid fibropapilloma-associated herpesvirus

Journal of General Virology ◽

10.1099/vir.0.038950-0 ◽

2012 ◽

Vol 93 (5) ◽

pp. 1035-1045 ◽

Cited By ~ 30

Author(s):

A. R. Patrício ◽

L. H. Herbst ◽

A. Duarte ◽

X. Vélez-Zuazo ◽

N. Santos Loureiro ◽

...

Keyword(s):

Puerto Rico ◽

Common Ancestor ◽

Evolutionary Rate ◽

Monte Carlo Analysis ◽

Sea Turtle ◽

Eastern Pacific ◽

Recent Common Ancestor ◽

Gulf Of Guinea ◽

Western Atlantic ◽

Most Recent Common Ancestor

A global phylogeny for chelonid fibropapilloma-associated herpesvirus (CFPHV), the most likely aetiological agent of fibropapillomatosis (FP) in sea turtles, was inferred, using dated sequences, through Bayesian Markov chain Monte Carlo analysis and used to estimate the virus evolutionary rate independent of the evolution of the host, and to resolve the phylogenetic positions of new haplotypes from Puerto Rico and the Gulf of Guinea. Four phylogeographical groups were identified: eastern Pacific, western Atlantic/eastern Caribbean, mid-west Pacific and Atlantic. The latter comprises the Gulf of Guinea and Puerto Rico, suggesting recent virus gene flow between these two regions. One virus haplotype from Florida remained elusive, representing either an independent lineage sharing a common ancestor with all other identified virus variants or an Atlantic representative of the lineage giving rise to the eastern Pacific group. The virus evolutionary rate ranged from 1.62×10−4 to 2.22×10−4 substitutions per site per year, which is much faster than what is expected for a herpesvirus. The mean time for the most recent common ancestor of the modern virus variants was estimated at 192.90–429.71 years ago, which, although more recent than previous estimates, still supports an interpretation that the global FP pandemic is not the result of a recent acquisition of a virulence mutation(s). The phylogeographical pattern obtained seems partially to reflect sea turtle movements, whereas altered environments appear to be implicated in current FP outbreaks and in the modern evolutionary history of CFPHV.

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Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

Invertebrate Systematics ◽

10.1071/is02046_co ◽

2003 ◽

Vol 17 (4) ◽

pp. 605 ◽

Cited By ~ 1

Author(s):

Philip S. Ward ◽

Seán G. Brady

Keyword(s):

Sequence Data ◽

Strong Support ◽

Sister Group ◽

Molecular Data ◽

Morphological Data ◽

Recent Common Ancestor ◽

Bootstrap Support ◽

Data Set ◽

Molecular Sequence Data ◽

Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

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Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes

Viruses ◽

10.3390/v13091790 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1790

Author(s):

Xuhua Xia

Keyword(s):

Common Ancestor ◽

Evolutionary Rate ◽

Pearson Correlation ◽

Sequence Divergence ◽

Full Length ◽

Recent Common Ancestor ◽

High Quality ◽

Most Recent Common Ancestor ◽

Large Tree ◽

Collection Time

All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence divergence of SARS-CoV-2 lineages. Here, I present dating results for the first time from a large phylogenetic tree with 86,582 high-quality full-length SARS-CoV-2 genomes. The tree contains 83,688 genomes with full specification of collection time. Such a large tree spanning a period of about 1.5 years offers an excellent opportunity for dating the MRCA of the sampled SARS-CoV-2 genomes. The MRCA is dated 16 August 2019, with the evolutionary rate estimated to be 0.05526 mutations/genome/day. The Pearson correlation coefficient (r) between the root-to-tip distance (D) and the collection time (T) is 0.86295. The NCBI tree also includes 10 SARS-CoV-2 genomes isolated from cats, collected over roughly the same time span as human COVID-19 infection. The MRCA from these cat-derived SARS-CoV-2 is dated 30 July 2019, with r = 0.98464. While the dating method is well known, I have included detailed illustrations so that anyone can repeat the analysis and obtain the same dating results. With 16 August 2019 as the date of the MRCA of sampled SARS-CoV-2 genomes, archived samples from respiratory or digestive tracts collected around or before 16 August 2019, or those that are not descendants of the existing SARS-CoV-2 lineages, should be particularly valuable for tracing the origin of SARS-CoV-2.

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