Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade
San SornSok TouchSovann LySareth RithNguyen TungAlain ViariLaurent GavotteDavun HollHeng SengNima Asgari‐JirhandehBeat RichnerDenis LaurentNora CheaVeasna DuongTetsuya ToyodaChadwick Y. YasudaPaul KitsutaniPaul ZhouBing SunVincent DeubelRubén O. DonisRoger FrutosPhilippe Buchy
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Zika virus (ZIKV) has caused explosive epidemics in the Pacific and the Americas, posing a serious threat to public health. Conventional opinion advocates that ZIKV evolved into two distinct lineages, namely, African and Asian. Descendants of this latter lineage dispersed globally causing major epidemics. However, based on shared amino acid replacements and phylogenetic analyses, it was recently contentiously proposed that the Asian lineage was a direct descendant of the African lineage. To address this contentious issue, we reconstructed a phylogenetic tree of ZIKV using the method based on shared amino acid replacements and found that ZIKV evolved into two distinct lineages. This supports the conventional phylogenetic divergence pattern of ZIKV. Evidence of recombination and sequencing errors was identified among the large collection of ZIKV. As such problematic sequences could confound the phylogenetic analyses, they were removed. Bayesian phylogenetic analyses using the improved sequence data enabled estimates for the divergence time in the past of the African and Asian lineages of ∼180 years ago. Moreover, we found that the Asian lineage viruses did not evolve at an elevated rate. Our findings provide additional support for the conventional opinion that the Asian lineage of ZIKV diverged from the African lineage.
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The genus Coelastrella was established by Chodat ( Bull. Soc. Bot. Geneve , 13 [1922] 66), and was characterized as being unicellular or in few‐celled aggregations with many longitudinal ribs on the cell wall. Many species of this genus showed strong ability to accumulate carotenoids and oils, so they have recently attracted much attention from researchers due to its potential applicability in the energy and food industries. In this study, a total of 23 strains of Coelastrella were sampled from China, and three new species and two new varieties were described: C. thermophila sp. nov., C. yingshanensis sp. nov., C. tenuitheca sp. nov., C. thermophila var. globulina var. nov., C. rubescens var. oocystiformis var. nov. Besides 18S rDNA and ITS 2 sequences, we have newly sequenced the tuf A gene marker for this taxon. Phylogenetic analysis combined with morphological studies revealed four morphotypes within the Coelastrella sensu lato clade, which contained the morphotype of original Coelastrella , original Scotiellopsis , Asterarcys , and morphotype of C. vacuolata and C. tenuitheca sp. nov. The relationships between morphological differences and phylogenic diversity based on different markers were discussed. Our results support that 18S rDNA was too conserved to be used a species‐specific or even a genus‐specific marker in this clade. The topology of tuf A gene‐based phylogenetic tree had a better match with the morphological findings.
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Evolution
Studies of phylogenetic relationships among species have been moving toward whole-genome analysis. Even with full genomes, the evolutionary history among some species, especially those that diverged rapidly, can be difficult to discern. This is especially true if there has been incomplete lineage sorting or hybridization among species. One clade for which it has been difficult to disentangle species relationships is the cat family. Examining the genomes of 27 cat species, Li et al. showed that the phylogenetic signal is not constant within genomes. However, relationships among cat clades can be identified in regions of low recombination, such as the X chromosome. These may explain the discrepancy between the fossil record and molecular estimates of species diversification in many clades.
Mol. Biol. Evol. 10.1093/molbev/msz139 (2019).
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To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family.We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia.Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses.Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character-state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.
Reticulate evolution
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The diversity, origin, and evolution of chromoviruses in Eukaryota were examined using the massive amount of genome sequence data for different eukaryotic lineages. A surprisingly large number of novel full-length chromoviral elements were found, greatly exceeding the number of the known chromoviruses. These new elements are mostly structurally intact and highly conserved. Chromoviruses in the key Amniota lineage, the reptiles, have been analyzed by PCR to explain their evolutionary dynamics in amniotes. Phylogenetic analyses provide evidence for a novel centromere-specific chromoviral clade that is widespread and highly conserved in all seed plants. Chromoviral diversity in plants, fungi, and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. The age of plant chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages, the green and the red algae. The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa. The evolutionary history and dynamics of chromoviruses can be explained simply by strict vertical transmission in plants, followed by more complex evolution in fungi and in Metazoa. The currently available data clearly show that chromoviruses indeed represent the oldest and the most widespread clade of Metaviridae.
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plant evolution
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Abstract Background The first case of SARS-CoV-2 in Basel, Switzerland, was detected on February 26 th 2020. We present a phylogenetic longitudinal study and explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26 th until March 23 rd . Methods We sequenced SARS-CoV-2 from naso-oropharyngeal swabs, generated 468 high quality genomes, and called variants with our COVID-19 Pipeline (COVGAP). We analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Findings The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected from March 2 nd , although the first lineage identified was B.1.1. Within B.1, a clade containing 68·2% of our samples, defined by the SNP C15324T, suggests local spreading events. We infer the geographic origin of this mutation to our tri-national region. The remaining genomes map broadly over the global phylogenetic tree, evidencing several events of introduction from and/or dissemination to other regions of the world. We also observe family transmission events. Interpretation A single lineage dominated the outbreak in the City of Basel while other lineages such as the first (B1.1) did not propagate. Thus spreading events seem to have contributed most to viral spread, while travel returners and family transmissions were better controlled by the recommended measures. This phylogenetic analysis enriches epidemiological and contact tracing data, allowing connection of seemingly unconnected events, and can inform public health interventions. Funding No dedicated funding was used for this work.
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Summary Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla , while distinguishing among sources of incongruence. We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla , and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches. All phylogenetic methods recovered the four major groups previously proposed for Lachemilla , but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera. Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.
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Phylogenomics
Coalescent theory
Taxonomic rank
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