Evolutionary history of orangutan plasmodia revealed by phylogenetic analysis of complete mtDNA genomes and new biogeographical divergence dating calibration models

2021 ◽  
Author(s):  
Michael J. C. Reid ◽  
William M. Switzer ◽  
Sabrina K. Alonso ◽  
Carl A. Lowenberger ◽  
Michael A. Schillaci
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Calibration Models ◽  
Divergence Dating ◽  
History Of ◽  
Complete Mtdna

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 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 Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae

2013 ◽  
Vol 94 (4) ◽  
pp. 738-748 ◽  
Author(s):  
Ying Tao ◽  
Mang Shi ◽  
Christina Conrardy ◽  
Ivan V. Kuzmin ◽  
Sergio Recuenco ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Evolutionary Rate ◽  
Mammalian Species ◽  
Evolutionary Analysis ◽  
Viral Pathogens ◽  
Genomic Features ◽  
Wide Range ◽  
History Of ◽  
Multiple Species

Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus–host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.

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