scholarly journals A phylogenetic perspective on the association between ants (Hymenoptera: Formicidae) and black yeasts (Ascomycota: Chaetothyriales)

2017 ◽  
Vol 284 (1850) ◽  
pp. 20162519 ◽  
Author(s):  
Marie Vasse ◽  
Hermann Voglmayr ◽  
Veronika Mayer ◽  
Cécile Gueidan ◽  
Maximilian Nepel ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Internal Transcribed Spacer ◽  
Evolutionary History ◽  
Geographical Origin ◽  
Sequence Similarity ◽  
Black Yeasts ◽  
Symbiotic Associations ◽  
Operational Taxonomic Units ◽  
History Of ◽  
Phylogenetic Perspective

The frequency and the geographical extent of symbiotic associations between ants and fungi of the order Chaetothyriales have been highlighted only recently. Using a phylogenetic approach based on seven molecular markers, we showed that ant-associated Chaetothyriales are scattered through the phylogeny of this order. There was no clustering according to geographical origin or to the taxonomy of the ant host. However, strains tended to be clustered according to the type of association with ants: strains from ant-made carton and strains from plant cavities occupied by ants (‘domatia’) rarely clustered together. Defining molecular operational taxonomic units (MOTUs) with an internal transcribed spacer sequence similarity cut-off of 99% revealed that a single MOTU could be composed of strains collected from various ant species and from several continents. Some ant-associated MOTUs also contained strains isolated from habitats other than ant-associated structures. Altogether, our results suggest that the degree of specialization of the interactions between ants and their fungal partners is highly variable. A better knowledge of the ecology of these interactions and a more comprehensive sampling of the fungal order are needed to elucidate the evolutionary history of mutualistic symbioses between ants and Chaetothyriales.

scholarly journals Conservation analysis of SARS-CoV-2 spike suggests complicated viral adaptation history from bat to human

2020 ◽  
Vol 2020 (1) ◽  
pp. 290-303
Author(s):  
Kuan Cheok Lei ◽  
Xiaohua Douglas Zhang
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Mutation Analysis ◽  
Evolutionary History ◽  
Sequence Similarity ◽  
Similarity Analysis ◽  
Current Form ◽  
Conservation Analysis ◽  
Spike Sequences ◽  
History Of ◽  
Spike Sequence

Abstract Background The current coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome (SARS)-CoV-2, has become the most devastating public health emergency in the 21st century and one of the most influential plagues in history. Studies on the origin of SARS-CoV-2 have generally agreed that the virus probably comes from bat, closely related to a bat CoV named BCoV-RaTG13 taken from horseshoe bat (Rhinolophus affinis), with Malayan pangolin (Manis javanica) being a plausible intermediate host. However, due to the relatively low number of SARS-CoV-2-related strains available in public domain, the evolutionary history remains unclear. Methodology Nine hundred ninety-five coronavirus sequences from NCBI Genbank and GISAID were obtained and multiple sequence alignment was carried out to categorize SARS-CoV-2 related groups. Spike sequences were analyzed using similarity analysis and conservation analyses. Mutation analysis was used to identify variations within receptor-binding domain (RBD) in spike for SARS-CoV-2-related strains. Results We identified a family of SARS-CoV-2-related strains, including the closest relatives, bat CoV RaTG13 and pangolin CoV strains. Sequence similarity analysis and conservation analysis on spike sequence identified that N-terminal domain, RBD and S2 subunit display different degrees of conservation with several coronavirus strains. Mutation analysis on contact sites in SARS-CoV-2 RBD reveals that human-susceptibility probably emerges in pangolin. Conclusion and implication We conclude that the spike sequence of SARS-CoV-2 is the result of multiple recombination events during its transmission from bat to human, and we propose a framework of evolutionary history that resolve the relationship of BCoV-RaTG13 and pangolin coronaviruses with SARS-CoV-2. Lay Summary This study analyses whole-genome and spike sequences of coronavirus from NCBI using phylogenetic and conservation analyses to reconstruct the evolutionary history of severe acute respiratory syndrome (SARS)-CoV-2 and proposes an evolutionary history of spike in the progenitors of SARS-CoV-2 from bat to human through mammal hosts before they recombine into the current form.

scholarly journals Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 3511-3517
Author(s):  
Yanjun Shen ◽  
Na Yang ◽  
Zhihao Liu ◽  
Qiliang Chen ◽  
Yingwen Li
Keyword(s):  
Evolutionary History ◽  
History Of ◽  
Phylogenetic Perspective

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Alex Dornburg ◽  
Thomas J. Near
Keyword(s):  
Paradigm Shift ◽  
Evolutionary History ◽  
First Century ◽  
Evolutionary Relationships ◽  
Annual Review ◽  
Publication Date ◽  
Living Fossils ◽  
Actinopterygian Fishes ◽  
History Of ◽  
Phylogenetic Perspective

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

2007 ◽  
Vol 189 (21) ◽  
pp. 7932-7936 ◽  
Author(s):  
Tomoo Sawabe ◽  
Kumiko Kita-Tsukamoto ◽  
Fabiano L. Thompson
Keyword(s):  
Sequence Analysis ◽  
Evolutionary History ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Multilocus Sequence Analysis ◽  
Protein Coding ◽  
History Of

ABSTRACT We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br ).

scholarly journals The Evolutionary History of Beet necrotic yellow vein virus Deduced from Genetic Variation, Geographical Origin and Spread, and the Breaking of Host Resistance

2011 ◽  
Vol 24 (2) ◽  
pp. 207-218 ◽  
Author(s):  
Soutaro Chiba ◽  
Hideki Kondo ◽  
Masaki Miyanishi ◽  
Ida Bagus Andika ◽  
Chenggui Han ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Host Resistance ◽  
Evolutionary History ◽  
Sequence Variation ◽  
Geographical Origin ◽  
Geographical Location ◽  
Yellow Vein ◽  
Resistance Breaking ◽  
History Of ◽  
Report Analysis

Beet necrotic yellow vein virus (BNYVV) is an economically important pathogen of sugar beet and has been found worldwide, probably as the result of recent worldwide spread. The BNYVV genome consists of four or five RNA components. Here, we report analysis of sequence variation in the RNA3-p25, RNA4-p31, RNA2-CP, and RNA5-p26 genes of 73 worldwide isolates. The RNA3-p25 gene encodes virulence and avirulence factors. These four sets of gene sequences each fell into two to four groups, of which the three groups of p25 formed eight subgroups with different geographical distributions. Each of these subgroup isolates (strains) could have arisen from four original BNYVV population and their mixed infections. The genetic diversity for BNYVV was relatively small. Selection pressure varied greatly depending on the BNYVV gene and geographical location. Isolates of the Italy strain, in which p25 was subject to the strongest positive selection, were able to overcome the Rz1-host resistance gene to differing degrees, whereas other geographically limited strains could not. Resistance-breaking variants were generated by p25 amino acid changes at positions 67 and 68. Our studies suggest that BNYVV originally evolved in East Asia and has recently become a pathogen of cultivated sugar beet followed by the emergence of new resistance-breaking variants.

Disentangling the evolutionary history of three related shrub species using genome-wide molecular markers

2019 ◽  
Vol 20 (5) ◽  
pp. 1101-1112 ◽  
Author(s):  
Dona Kireta ◽  
Matthew J. Christmas ◽  
Andrew J. Lowe ◽  
Martin F. Breed
Keyword(s):  
Molecular Markers ◽  
Evolutionary History ◽  
Shrub Species ◽  
Genome Wide ◽  
History Of
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