Phylogenetic roots of Alu-mediated rearrangements leading to cancer

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 160-167 ◽  
Author(s):  
Rosaleen Gibbons ◽  
Achilles Dugaiczyk
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Sequence Similarity ◽  
Dna Recombination ◽  
Splice Sites ◽  
Alu Repeats ◽  
Alu Sequence ◽  
History Of ◽  
High Level ◽  
Genomic Locations

There are over a million Alu repetitive elements dispersed throughout the human genome, and a high level of Alu-sequence similarity ensures a strong propensity for unequal crossover events, some of which have lead to deleterious oncogenic rearrangements. Furthermore, Alu insertions introduce consensus 3' splice sites, which potentially facilitate alternative splicing. Not surprisingly, Alu-mediated defective splicing has also been associated with cancer. To investigate a possible correlation between the expansion of Alu repeats associated with primate divergence and predisposition to cancer, 4 Alu-mediated rearrangements — known to be the basis of cancer — were selected for phylogenetic analysis of the necessary genotype. In these 4 cases, it was determined that the different phylogenetic age of the oncogenic recombination-prone genotype reflected the evolutionary history of Alu repeats spreading to new genomic sites. Our data implies that the evolutionary expansion of Alu repeats to new genomic locations establishes new predispositions to cancer in various primate species.Key words: Alu repeats, evolution, cancer, primates, splicing, DNA recombination.

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.

The amphibamiform Nanobamus macrorhinus from the early Permian of Texas

2019 ◽  
Vol 94 (2) ◽  
pp. 366-377 ◽  
Author(s):  
Bryan M. Gee ◽  
Robert R. Reisz
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Phylogenetic Position ◽  
Early Permian ◽  
Larval Form ◽  
Terrestrial Environments ◽  
History Of ◽  
Insight Into

AbstractNanobamus macrorhinus Schoch and Milner, 2014 is a small amphibamiform temnospondyl from the early Permian Arroyo Formation of Texas. It is most readily characterized by an elongate and partially subdivided naris. This condition is superficially reminiscent of that seen in the coeval trematopids, the group to which N. macrorhinus was originally referred to under an interpretation of the holotype as a larval form. This was discounted by later workers, but the amphibamiform affinities of the specimen were not formalized until recently. The specimen has never been described in the context of its amphibamiform affinities and remains poorly characterized, never having been sampled in a phylogenetic analysis. Here we present a complete, updated osteological description of N. macrorhinus, including an improved characterization of its unique mosaic of plesiomorphic and apomorphic features and clarification of the taxon's autapomorphies. Our analysis of the taxon's phylogenetic position within Amphibamiformes shows that N. macrorhinus was recovered as diverging after basal amphibamiforms, e.g., the micropholids, and before derived amphibamiforms, e.g., the amphibamids. This is supported by the unique mixture of retained plesiomorphies, e.g., nonforeshortened postparietals and an oval choana, and apomorphies, e.g., a narrow interorbital region and slender palatal rami of the pterygoid. These results reflect the complexity of terrestrial amphibamiform diversity and provide further insight into the evolutionary history of the lissamphibian stem in terrestrial environments.

scholarly journals Cretaceous diversity and disparity in a lacewing lineage of predators (Neuroptera: Mantispidae)

2020 ◽  
Vol 287 (1928) ◽  
pp. 20200629 ◽  
Author(s):  
Xiumei Lu ◽  
Bo Wang ◽  
Weiwei Zhang ◽  
Michael Ohl ◽  
Michael S. Engel ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Complete Loss ◽  
Remarkable Case ◽  
Predator Prey ◽  
Functional Convergence ◽  
The Family ◽  
High Species Diversity ◽  
History Of ◽  
Tropical Forest Ecosystem

Mantidflies (Mantispidae) are an unusual and charismatic group of predatory lacewings (Neuroptera), whereby the adults represent a remarkable case of morphological and functional convergence with praying mantises (Mantodea). The evolutionary history of mantidflies remains largely unknown due to a scarcity of fossils. Here, we report the discovery of a highly diverse palaeofauna of mantidflies from the mid-Cretaceous (lowermost Cenomanian) of Myanmar. The raptorial forelegs of these mantidflies possess highly divergent morphological modifications, some of which are unknown among modern mantidflies, e.g. the presence of forked basal profemoral spines or even the complete loss of foreleg spine-like structures. A phylogenetic analysis of Mantispidae reveals a pattern of raptorial foreleg evolution across the family. The high species diversity and disparate foreleg characters might have been driven by diverse niches of predator–prey interplay in the complex tropical forest ecosystem of the mid-Cretaceous.

scholarly journals Evolution of Larval Segment Position across 12DrosophilaSpecies

2019 ◽  
Author(s):  
Gizem Kalay ◽  
Joel Atallah ◽  
Noemie C. Sierra ◽  
Austin M. Tang ◽  
Amanda E. Crofton ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Local Control ◽  
Abdominal Segment ◽  
Evolutionary History ◽  
Phenotypic Change ◽  
Rates Of Change ◽  
First Instar ◽  
The Face ◽  
History Of ◽  
Developmental Traits

AbstractMany developmental traits that are critical to the survival of the organism are also robust. These robust traits are resistant to phenotypic change in the face of variation. This presents a challenge to evolution. In this paper, we asked whether and how a well-established robust trait,Drosophilasegment patterning, changed over the evolutionary history of the genus. We compared segment position scaled to body length at the first-instar larval stage among 12Drosophilaspecies. We found that relative segment position has changed many times across the phylogeny. Changes were frequent, but primarily small in magnitude. Phylogenetic analysis demonstrated that rates of change in segment position are variable along theDrosophilaphylogenetic tree, and that these changes can occur in short evolutionary timescales. Correlation between position shifts of segments decreased as the distance between two segments increased, suggesting local control of segment position. The posterior-most abdominal segment showed the highest magnitude of change on average, had the highest rate of evolution between species, and appeared to be evolving more independently as compared to the rest of the segments. This segment was exceptionally elongated in the cactophilic species in our dataset, raising questions as to whether this change may be adaptive.

scholarly journals Phylogenetic analysis of the betacoronavirus S1 subunit

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1389
Author(s):  
Irina Zyrianova
Keyword(s):  
Phylogenetic Analysis ◽  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Evolutionary History ◽  
Protein Sequences ◽  
Cell Receptor ◽  
Receptor Binding Domain ◽  
Host Cell Receptor ◽  
History Of ◽  
The Many

The ongoing pandemic outbreak of coronavirus disease 2019 (COVID-19) has been caused by the new betacoronavirus (BetaCoV) severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Together with other epidemic outbreaks of BetaCoV infectious diseases (Severe Acute Respiratory Syndrome (SARS) in 2002-2003 in China and Middle East Respiratory Syndrome (MERS) in 2012 in the Middle East, which have been caused by SARS-CoV and MERS-CoV, respectively), these events have generated interest in the coronaviruses (CoVs). Although many phylogenetic analyzes have been reported at a gene or protein level, there is no study as yet encompassing the many sequences publicly available for BetaCoVs, including those that have been manipulated in the lab. In this study, the phylogenetic analysis of 679 different S1 protein sequences of BetaCoVs from a total of 1595, which are publicly available in GenBank from the beginning of the pandemic event to April 2020, has been carried out. The S1 subunit is one part of the S (spike) protein, one of three CoV envelope proteins. The S1 subunit contains a host cell receptor binding domain. This domain is essential in the initiation of the infectious process. Therefore, its phylogenetic analysis is very important for studying CoV evolution. The phylogenetic analysis of BetaCoV S1 protein presented herein shows the evolutionary history of BetaCoVs from bovine CoV to SARS-CoV-2.

New cyriacotheriid pantodonts (Mammalia, Pantodonta) from the Paleocene of Alberta, Canada, and the relationships of Cyriacotheriidae

2010 ◽  
Vol 84 (2) ◽  
pp. 197-215 ◽  
Author(s):  
Craig S. Scott
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Fossil Record ◽  
Evolutionary History ◽  
New Genus ◽  
The Family ◽  
Two New Species ◽  
Unusual Combination ◽  
Early Paleocene ◽  
History Of

Cyriacotheriidae are a family of unusual small-bodied pantodonts known from the Paleocene of the Western Interior of North America. Cyriacotheriids possess a suite of dental characters similar to that of pantodonts (e.g., molar dilambdodonty, lingual molar hypoconulids), as well as several divergent features (e.g., molarized premolars, strong molar conules) that have been interpreted as “dermopteran-like.” the unusual combination of pantodont and dermopteran-like characters, combined with a limited fossil record, has made attempts at understanding the broader relationships of Cyriacotheriidae difficult. This paper reports on a new genus and two new species of cyriacotheriids from the Paleocene of Alberta, Canada, with both species significantly older than those of the only previously described cyriacotheriid, Cyriacotherium. Collectively, the dentitions of these new taxa exhibit derived characters seen in Cyriacotherium (e.g., robust molar conules, strong molar dilambdodonty) in addition to a number of plesiomorphies seen in more basal pantodonts (e.g., conspicuous molar entoconids, deep premolar ectoflexus) and, importantly, posterior premolars that are weakly molariform and non-dilambdodont. A phylogenetic analysis of the new cyriacotheriid, basal pantodonts, dermopterans, and dermopteran-like eutherians resulted in Cyriacotheriidae nesting within a monophyletic Pantodonta. the results strengthen previous hypotheses regarding the pantodont affinities of the family, and suggest that the dermopteran-like features seen in the more derived Cyriacotherium were acquired convergently. Although the discovery of new cyriacotheriids sheds light on the evolutionary history of the family, it cannot resolve the ongoing questions of pantodont origins; nonetheless, their discovery in strata of early Paleocene age indicates that significant parts of the evolutionary history of Cyriacotheriidae, and North American pantodonts more generally, have yet to be discovered.

Exploiting new genome data and Internet resources for the phylogenetic analysis of proteases, substrates and inhibitors

2007 ◽  
Vol 35 (3) ◽  
pp. 599-603 ◽  
Author(s):  
C. Southan
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Protease Gene ◽  
Endogenous Inhibitor ◽  
Genome Data ◽  
Catalytic Function ◽  
Internet Resources ◽  
Multiple Alignments ◽  
Interaction Partners ◽  
History Of

Multiple alignments and phylogenetic tree constructions are established techniques for examining the evolutionary history of protease sequences in organisms such as humans, mice, fruitflies, nematode worms and yeast. They also facilitate the mapping of those conserved positions that are important for structure and catalytic function. However, the continued increase in completed or draft genomes offers new opportunities for examining protease evolution across a broader (e.g. more mammals) and deeper (e.g. more invertebrates) phylogenetic range. In addition, the improving annotation not only of proteases, but also of their substrates, interaction partners in proteolytic complexes and endogenous inhibitor proteins now means that aspects of co-evolution can be addressed. The increasing phylogenetic coverage is also important for resolving orthology issues that arise from protease gene duplication or loss in different lineages. Selected sequences will be used to exemplify the utility of Internet resources and present results for these types of analysis.

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 Presence of Prokaryotic and Eukaryotic Species in All Subgroups of the PPi-Dependent Group II Phosphofructokinase Protein Family

2001 ◽  
Vol 183 (22) ◽  
pp. 6714-6716 ◽  
Author(s):  
Miklós Müller ◽  
Jennifer A. Lee ◽  
Paul Gordon ◽  
Terry Gaasterland ◽  
Christoph W. Sensen
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Sinorhizobium Meliloti ◽  
Propionibacterium Freudenreichii ◽  
Gene Products ◽  
Inorganic Pyrophosphate ◽  
Eukaryotic Species ◽  
History Of ◽  
Group Ii ◽  
Complex Evolutionary History

ABSTRACT Inorganic pyrophosphate-dependent phosphofructokinase (PPi-PFK) of the amitochondriate eukaryoteMastigamoeba balamuthi was sequenced and showed about 60% identity to PPi-PFKs from two eubacteria,Propionibacterium freudenreichii and Sinorhizobium meliloti. These gene products represent a newly recognized lineage of PFKs. All four lineages of group II PFKs, as defined by phylogenetic analysis, contained both prokaryotic and eukaryotic species, underlining the complex evolutionary history of this enzyme.

scholarly journals Persistence and invasiveness of high-level heteroplasmy through biparental transmission of a selfish mitochondrion in Drosophila

2020 ◽  
Author(s):  
Guilherme C. Baião ◽  
Anton Strunov ◽  
Eleanor Heyworth ◽  
Daniela I. Schneider ◽  
Julia Thoma ◽  
...  
Keyword(s):  
Species Complex ◽  
Evolutionary History ◽  
High Titer ◽  
Genomic Integrity ◽  
Male And Female ◽  
Low Level ◽  
Nuclear Background ◽  
History Of ◽  
High Level ◽  
Drosophila Paulistorum

ABSTRACTHeteroplasmy is the coexistence of more than one type of mitochondria in an organism. Although widespread sequencing has identified several cases of transient or low-level heteroplasmy that primarily occur through mutation or paternal leakage, stable, high-titer heteroplasmy remains rare in animals. In this study we present a unique, stable and high-level heteroplasmy in male and female flies belonging to the neotropical Drosophila paulistorum species complex. We show that mitochondria of D. paulistorum are polyphyletic and form two clades, α and β, with two subclades each. Mitochondria of the α2 subclade appear functional based on their genomic integrity but are exclusively found in heteroplasmic flies and never in homoplasmy, suggesting that they are a secondary mitotype with distinct functionality from the primary mitochondria. Using qPCR, we show that α2 titer do not respond to energetic demands of the cell and are generally higher in males than females. By crossing hetero- and homoplasmic flies, we find that α2 can be transmitted to their offspring via both parents and that levels are dependent on nuclear background. Following α2 mitotype levels during embryogenesis, we demonstrate that this secondary mitotype replicates rapidly just after fertilization of the egg in a period when primary mitochondria are dormant. This so-called “Replication precox” mitochondrial phenotype likely prevents the α2 mitotype from being outcompeted by the primary mitotype – and thereby secures its persistence and further spread as a selfish mitochondrion, we hereby designate “Spartacus”. Finally, we reconstruct the evolutionary history of mitochondria in the willistoni subgroup uncovering signs of multiple mitochondrial losses and introgressions. Our data indicate an α-like mitochondrial ancestor in the willistoni subgroup, with the β mitotype likely acquired via introgression from an unidentified donor. We hypothesize that the selfish characteristics of α2 might have emerged as a response to competition for inheritance with the introgressed β mitotype.

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