Genotypic diversity and dynamic nomenclature of Parechovirus A

AbstractHuman parechoviruses (PeV-A) can cause severe sepsis and neurological syndromes in neonates and children and are currently classified into 19 genotypes based on genetic divergence in the VP1 gene. However, the genotyping system has notable limitations including an arbitrary distance threshold and reliance on insufficiently robust phylogenetic reconstruction approaches leading to inconsistent genotype definitions. In order to improve the genotyping system, we investigated the molecular epidemiology of human parechoviruses, including the evolutionary history of the different PeV-A lineages as far as is possible. We found that PeV-A lineages suffer from severe substitution saturation in the VP1 gene which limit the inference of deep evolutionary timescales among the extant PeV-A and suggest that the degree of evolutionary divergence among current PeV-A lineages has been substantially underestimated, further confounding the current genotyping system. We propose an alternative nomenclature system based on robust, amino-acid level phylogenetic reconstruction and clustering with the PhyCLIP algorithm which delineates highly divergent currently designated genotypes more informatively. We also describe a dynamic nomenclature framework that combines PhyCLIP’s progressive clustering with phylogenetic placement for genotype assignment.

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Identification and Characterization of a Novel clcn7 Variant Associated With Osteopetrosis

10.20944/preprints202009.0543.v1 ◽

2020 ◽

Author(s):

Dmitrii S. Bug ◽

Ildar M. Barkhatov ◽

Yana V. Gudozhnikova ◽

Artem V. Tishkov ◽

Natalia V. Petukhova ◽

...

Keyword(s):

Structure Analysis ◽

Evolutionary History ◽

Hot Spot ◽

Phylogenetic Reconstruction ◽

Novel Variant ◽

Uncertain Significance ◽

Precise Diagnosis ◽

History Of ◽

Identification And Characterization

Osteopetrosis is a group of rare inheritable disorders of the skeleton characterized by increased bone density. The disease is remarkably heterogeneous in clinical presentation and often misdiagnosed. Therefore, genetic testing and molecular pathogenicity analysis are essential for precise diagnosis and new targets for preventive pharmacotherapy. Mutations in the CLCN7 gene give rise to the complete spectrum of osteopetrosis phenotypes and are responsible for about 75% of cases of autosomal dominant osteopetrosis. In this study, we report the identification of a novel variant in the CLCN7 gene in a patient diagnosed with osteopetrosis and provide evidence for its significance (likely deleterious) based on extensive comparative genomics, protein sequence and structure analysis. A set of automated bioinformatics tools used to predict consequences of this variant identified it as deleterious or pathogenic. Structure analysis revealed that the variant is located at the same “hot spot” as the most common CLCN7 mutations causing osteopetrosis. Deep phylogenetic reconstruction showed that not only Leu614Arg, but any non-aliphatic substitutions in this position are evolutionarily intolerant, further supporting the deleterious nature of the variant. The present study provides further evidence that reconstructing a precise evolutionary history of a gene helps predicting phenotypical consequences of variants of uncertain significance.

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DOMINO EFFECT: BORIS YELTSIN'S DECREE ON THE DE-PARTIZATION IN THE CHAIN OF THE COLLAPSE OF THE USSR

Central Russian Journal of Social Sciences ◽

10.22394/2071-2367-2021-16-5-69-80 ◽

2021 ◽

Vol 16 (5) ◽

pp. 69-80

Author(s):

D.G. SELTSER ◽

Keyword(s):

Scientific Literature ◽

Political Process ◽

The Political ◽

Direct Connection ◽

Domino Effect ◽

Nomenclature System ◽

Political Actors ◽

Political Consequences ◽

History Of

The purpose of the article is to clarify the place and role of the decree in the general course of the political process and highlight its direct consequences for the fate of the CPSU and the USSR. The scientific literature on the topic is analyzed. It is concluded that scientists draw a direct connection between the final events of the history of the USSR – Yeltsin's decree about departisation, degradation of the CPSU, resistance to the Emergency Committee and the liquidation of the CPSU / USSR. The author describes the stages of the personnel actions of Gorbachev and Yeltsin. In his opinion, the nomenclature system was expected: «construction» of the elite (1985–1987), elections in the party (1988–1990), elections in the state (1989–1990), decree about departisation (1991). The decree is seen as the final stage in the denationalization of the party. The CPSU, having lost power and property, ceased to be a state. The content of the decree, the behavior of political actors in connection with its adoption and the political consequences of the decree are considered. In conclusion, it is concluded that the decree was a domino effect, a provocation to the instant collapse of the USSR.

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Species Delimitation and evolutionary history of tree frogs in the Hyla chinensis-group (Hylidae, Amphibian)

10.21203/rs.2.14113/v1 ◽

2019 ◽

Author(s):

Tao Pan ◽

Guiyou Wu ◽

Xing Kang ◽

Peng Yan ◽

Izaz Ali ◽

...

Keyword(s):

Species Delimitation ◽

Divergence Time ◽

Distinct Species ◽

Species Group ◽

Early Miocene ◽

Evolutionary Divergence ◽

Dabie Mountains ◽

Ancestral Area ◽

Ancestral Area Reconstruction ◽

History Of

Abstract Background Species are the cornerstone in many domains of biology research, which made the accurate species delimitation became critically important. In this study, the systematics and biogeography of the Hyla chinensis -group were analyzed based on phylogeny, species delimitation and ancestral area reconstruction methods.Results The phylogenetic results showed six specific clusters existed in the H. chinensis- group. BPP analysis indicated that six distinct species exist due to the high probability values (>0.95), which were also supported by the BF analysis. The divergence time of the H. chinensis -group is estimated to date back to 18.84 Mya in the early Miocene. Combining the results of ancestral area reconstruction, the H. chinensis -group might have originated from Guangxi-Hainan, then spread eastwardly and reached Nanling mountains, Wuyi mountains, Huangshan mountains and Taiwan. In rightabout colonization, it is gradually extended to the Yunnan-Guizhou Plateau, Sichuan basin, Qinling mountains and Dabie mountains. Considering the geological movement from early Miocene to Pliocene, the colonization pattern of the H. chinensis -group maybe closely related to the progressive uplift of Qinghai-Tibetan Plateau (QTP) and historical climate change.Conclusions Our study provides evidence for species delimitation and speciation process within the H. chinensis -group. Our study supports the hypothesis that the evolutionary divergence in this species group was a consequence of the progressive uplift of QTP and environmental change.

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Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates

Evolutionary Bioinformatics ◽

10.1177/1176934320903735 ◽

2020 ◽

Vol 16 ◽

pp. 117693432090373 ◽

Cited By ~ 4

Author(s):

Katherine E Noah ◽

Jiasheng Hao ◽

Luyan Li ◽

Xiaoyan Sun ◽

Brian Foley ◽

...

Keyword(s):

Codon Position ◽

Amino Acid Level ◽

Phylogenetic Reconstruction ◽

Original Data ◽

Data Sets ◽

Multiple Sequence ◽

Protein Coding ◽

Individual Gene ◽

The Third ◽

New Hypothesis

Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such “big data” sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new “principled” codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.

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The muricid gastropod subfamily Rapaninae: phylogeny and ecological history

Paleobiology ◽

10.1666/0094-8373(2000)026<0019:tmgsrp>2.0.co;2 ◽

2000 ◽

Vol 26 (1) ◽

pp. 19-46 ◽

Cited By ~ 73

Author(s):

Geerat J. Vermeij ◽

Sandra J. Carlson

Keyword(s):

Biological Diversity ◽

Phylogenetic Reconstruction ◽

Early Miocene ◽

Morphological Evidence ◽

West Pacific ◽

Ecological Diversification ◽

Ecological History ◽

History Of ◽

Paraphyletic Group ◽

Anatomical Characters

Members of the neogastropod muricid subfamily Rapaninae are abundant, shallow-water predators whose phylogeny was previously investigated by Kool (1993b), who used mainly anatomical characters. In order to deepen understanding of the evolution of this important clade and to incorporate functional, ecological fossil evidence, we performed a phylogenetic analysis based on 34 shell characters in 45 genus-level taxa, including five muricid outgroups. Cladograms based on shell characters alone differed from those founded on anatomical features these analyses differed from the phylogenetic reconstruction combining all available morphological evidence. The preferred cladogram incorporates all evidence and reveals a “Thais group” and an “Ergalatax clade” that both emerge from the derived portion of a more primitive, paraphyletic group of other rapanines. The Ocenebrinae, the other four outgroup taxa three ergalataxine taxa all lie outside the rapanine clade that includes the remaining ergalataxines as a derived subclade.We used the phylogenetic results to probe aspects of the ecological history of the Rapaninae. Our data imply that antipredatory shell defenses (elongated aperture, denticles on the inner side of the outer lip robust external spines and tubercles) evolved multiple times, mainly in post–early Miocene clades in the Indo–West Pacific region. These results support earlier nonphylogenetic inferences.We compared known prey types and methods of predation of living rapanines with their distribution on our phylogenetic tree. The plesiomorphic mode of feeding in the Rapaninae is drilling of hard-shelled prey. Feeding by other means and on such soft-bodied prey as sipunculan and polychaete worms evolved several times independently among post–early Miocene rapanines in the Indo–West Pacific. Methods of predation on hard-shelled prey that involve edge-drilling or attack by way of the aperture also evolved independently several times, but did so throughout the geographical range of the subfamily.Specialization for life on the upper shore occurred in at least eight lineages, all but two of which are confined to the Indo–West Pacific. Ecological diversification of the Rapaninae was therefore most common in the tropical Indo–West Pacific during and after early Miocene time. This diversification occurred in a setting of already high biological diversity and intense competition and predation.

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Patterns of genotypic diversity suggest a long history of clonality and population isolation in the Australian arid zone shrub Acacia carneorum

Plant Ecology ◽

10.1007/s11258-013-0278-7 ◽

2013 ◽

Vol 215 (1) ◽

pp. 55-71 ◽

Cited By ~ 11

Author(s):

Eleanor K. O’Brien ◽

Andrew J. Denham ◽

David J. Ayre

Keyword(s):

Arid Zone ◽

Genotypic Diversity ◽

Population Isolation ◽

History Of

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Host Switching in Lyssavirus History from the Chiroptera to the Carnivora Orders

Journal of Virology ◽

10.1128/jvi.75.17.8096-8104.2001 ◽

2001 ◽

Vol 75 (17) ◽

pp. 8096-8104 ◽

Cited By ~ 243

Author(s):

Hassan Badrane ◽

Noël Tordo

Keyword(s):

Average Rate ◽

Relative Rate ◽

Phylogenetic Reconstruction ◽

Surface Glycoprotein ◽

Host Switching ◽

Virulence Determinants ◽

Rates Of Evolution ◽

Tests Of Neutrality ◽

Genes Encoding ◽

History Of

ABSTRACT Lyssaviruses are unsegmented RNA viruses causing rabies. Their vectors belong to the Carnivora and Chiroptera orders. We studied 36 carnivoran and 17 chiropteran lyssaviruses representing the main genotypes and variants. We compared their genes encoding the surface glycoprotein, which is responsible for receptor recognition and membrane fusion. The glycoprotein is the main protecting antigen and bears virulence determinants. Point mutation is the main force in lyssavirus evolution, as Sawyer's test and phylogenetic analysis showed no evidence of recombination. Tests of neutrality indicated a neutral model of evolution, also supported by globally high ratios of synonymous substitutions (dS ) to nonsynonymous substitutions (dN ) (>7). Relative-rate tests suggested similar rates of evolution for all lyssavirus lineages. Therefore, the absence of recombination and similar evolutionary rates make phylogeny-based conclusions reliable. Phylogenetic reconstruction strongly supported the hypothesis that host switching occurred in the history of lyssaviruses. Indeed, lyssaviruses evolved in chiropters long before the emergence of carnivoran rabies, very likely following spillovers from bats. Using dated isolates, the average rate of evolution was estimated to be roughly 4.3 × 10−4 dS /site/year. Consequently, the emergence of carnivoran rabies from chiropteran lyssaviruses was determined to have occurred 888 to 1,459 years ago. Glycoprotein segments accumulating more dN than dS were distinctly detected in carnivoran and chiropteran lyssaviruses. They may have contributed to the adaptation of the virus to the two distinct mammal orders. In carnivoran lyssaviruses they overlapped the main antigenic sites, II and III, whereas in chiropteran lyssaviruses they were located in regions of unknown functions.

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The Evolution of Insect Metallothioneins

10.1101/2020.06.25.172213 ◽

2020 ◽

Author(s):

Mei Luo ◽

Cédric Finet ◽

Haosu Cong ◽

Hong-yi Wei ◽

Henry Chung

Keyword(s):

Metal Binding ◽

Phylogenetic Reconstruction ◽

Model Organism ◽

Low Complexity ◽

Toxic Heavy Metals ◽

Heavy Metal Detoxification ◽

History Of ◽

Cysteine Content ◽

Tandem Duplications ◽

Unique Dataset

ABSTRACTMetallothioneins (MTs) are a family of cysteine-rich metal-binding proteins that are important in the chelating and detoxification of toxic heavy metals. Until now, the short length and the low sequence complexity of MTs has hindered the possibility of any phylogenetic reconstruction, hampering the study of their evolution. To answer this longstanding question, we developed an iterative BLAST search pipeline that allowed us to build a unique dataset of more than 300 MT sequences in insects. By combining phylogenetics and synteny analysis, we reconstructed the evolutionary history of MTs in insects. We show that the MT content in insects has been shaped by lineage-specific tandem duplications from a single ancestral MT. Strikingly, we also uncovered a sixth MT, MtnF, in the model organism Drosophila melanogaster. MtnF evolves faster than other MTs and is characterized by a non-canonical length and higher cysteine content. Our methodological framework not only paves the way for future studies on heavy metal detoxification but also can allow us to identify other previously unidentified genes and other low complexity genomic features.

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Fast-evolving alignment sites are highly informative for reconstructions of deep Tree of Life phylogenies

10.1101/835504 ◽

2019 ◽

Author(s):

L. Thibério Rangel ◽

Gregory P. Fournier

Keyword(s):

Signal To Noise Ratio ◽

Phylogenetic Signal ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Tree Of Life ◽

Signal To Noise ◽

Fast Analysis ◽

Substantial Impact ◽

Substitution Saturation ◽

Noise Ratio

AbstractThe trimming of fast-evolving sites, often known as “slow-fast” analysis, is broadly used in microbial phylogenetic reconstruction under assumption that fast-evolving sites do not retain accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here we show that, contrary to this assumption, even the fastest evolving sites, present in conserved proteins often used in Tree of Life studies, contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site specific substitution-rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we additionally show that both slow-and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.Significance StatementIt is common practice among comprehensive microbial phylogenetic studies to trim fast-evolving sites from the source alignment in the expectation to increase the signal to noise ratio. Here we show that despite fast-evolving sites being more sensitive to parameter misspecifications than mid-rate evolving sites, such sensitivity is comparable, if not smaller, than what we observe among slow-evolving sites. Through the use of both empirical and simulated datasets we also show that, besides the lack of evidences regarding the noisy nature of fast-evolving sites, such sites are of core importance for the reliable the reconstruction of short-branched bipartitions. Such points are exemplified by the variations in the Eukarya+Archaea Tree of Life when subjective alignment trimming strategies are employed.

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Low-Coverage Whole Genomes Reveal the Higher Phylogeny of Green Lacewings

Insects ◽

10.3390/insects12100857 ◽

2021 ◽

Vol 12 (10) ◽

pp. 857

Author(s):

Yuyu Wang ◽

Ruyue Zhang ◽

Yunlong Ma ◽

Jing Li ◽

Fan Fan ◽

...

Keyword(s):

Phylogenetic Reconstruction ◽

Divergence Time ◽

Sister Group ◽

Data Matrix ◽

Limited Sampling ◽

Green Lacewings ◽

Whole Genomes ◽

History Of ◽

Low Coverage ◽

Cretaceous Period

Green lacewings are one of the largest families within Neuroptera and are widely distributed all over the world. Many species within this group are important natural predators that are widely used for the biological control of pests in agricultural ecosystems. Several proposed phylogenetic relationships among the three subfamilies of Chrysopidae have been extensively debated. To further understand the higher phylogeny as well as the evolutionary history of Chrysopidae, we newly sequenced and analyzed the low-coverage genomes of 5 species (Apochrysa matsumurae, Chrysopa pallens, Chrysoperla furcifera, Italochrysa pardalina, Nothochrysa sinica), representing 3 subfamilies of Chrysopidae. There are 2213 orthologs selected to reconstruct the phylogenetic tree. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches, based on different data matrices. All the results suggested that Chrysopinae were a monophyletic sister group to the branch Apochrysinae + Nothochrysinae. These results were completely supported, except by the concatenation analyses of the nt data matrix, which suggested that Apochrysinae were a sister group to Chrysopinae + Nothchrysinae. The different topology from the nt data matrix may have been caused by the limited sampling of Chrysopidae. The divergence time showed that Chrysopinae diverged from Apochrysinae + Nothochrysinae during the Early Cretaceous period (144–151 Ma), while Aporchrysinae diverged from Nothochrysinae around 117–133 Ma. These results will improve our understanding of the higher phylogeny of Chrysopidae and lay a foundation for the utilization of natural predators.

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