scholarly journals The Canine Morbillivirus Strain Associated with An Epizootic in Caspian Seals Provides New Insights into the Evolutionary History of this Virus

Viruses ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 894 ◽  
Author(s):  
Wendy K. Jo ◽  
Martin Peters ◽  
Aidyn Kydyrmanov ◽  
Marco W. G. van de Bildt ◽  
Thijs Kuiken ◽  
...  
Keyword(s):  
Caspian Sea ◽  
Evolutionary History ◽  
Animal Species ◽  
Phylogenetic Analyses ◽  
Domestic Animal ◽  
Wild Type ◽  
The Caspian Sea ◽  
History Of ◽  
Sporadic Cases ◽  
Generation Sequencing

Canine morbillivirus (canine distemper virus; CDV) is a worldwide distributed morbillivirus that causes sporadic cases and recurrent epizootics among an increasing number of wild, feral, and domestic animal species. We investigated the evolutionary history of CDV strains involved in the 1988 Lake Baikal (CDVPS88) and the 2000 Caspian Sea (CDVPC00) seal die-offs by recovery of full-length sequences from archived material using next-generation sequencing. Bayesian phylogenetic analyses indicated that CDVPC00 constitutes a novel strain in a separate clade (tentatively termed “Caspian”) from the America-1 clade, which is comprised of older vaccine strains. The America-1/Caspian monophyletic group is positioned most basally with respect to other clades and is estimated to have separated from other CDV clades around 1832. Our results indicate that CDVPC00 recovered from the epizootic in the Caspian Sea in 2000 belongs to a previously undetected novel clade and constitutes the most ancestral wild-type CDV clade.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

scholarly journals Legal Status Of The Caspian Sea: History And Present

2012 ◽  
Vol 6 ◽  
Author(s):  
Ardak Kapyshev
Keyword(s):  
Caspian Sea ◽  
Legal Status ◽  
Oil Fields ◽  
Present Stage ◽  
The Caspian Sea ◽  
Interstate Relations ◽  
The Usa ◽  
History Of ◽  
The Right ◽  
Near Future

At  the  present  stage  one  of  the  unsolved   problems in  interstate relations of  Caspian bordering countries is defining international­legal status of the Caspian Sea. It is noted in the article that this problem is not a new one at all. The history of “division” of the Caspian Sea begins in the ancient age, namely in VIII century. It is underlined that the basic stumbling block  is the position of Iran on the right to use the Caspian Sea, and also occurrence of extra regional players, such as  the USA, China, etc. First of  all, it is connected with rich oil fields and other minerals, and also with convenient geopolitical and geostrategic position. The only way to worry out the international­legal delimitation of the Caspian Sea problem is a negotiating process. By now, despite of  certain disagreements on  legal status of  the Caspian Sea, five Caspian bordering countries managed to achieve certain progress, admitting the possibility of applying the principle of sectorial sectioning on the Caspian Sea.  Clear proof  of  it is the agreements on  division of ground on the northern part of Caspian Sea signed between Kazakhstan, Russia and Azerbaijan. It is important that Kazakhstan, Russia, Azerbaijan and Turkmenistan clearly stated their positions and agreed to make a compromise in their official statements. More than likely, in the near future Iran will soften its position, considering its present  situation and   strained relations with the USA. It has been alleged that the constructive  dialog  already  started; everything depends on  the mobility,  concurrency and rationality of actions of all Caspian bordering countries.

Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

2021 ◽  
Author(s):  
Keerthic Aswin ◽  
Srinivasan Ramachandran ◽  
Vivek T Natarajan
Keyword(s):  
Convergent Evolution ◽  
Genome Stability ◽  
Evolutionary History ◽  
Rna Binding ◽  
Phylogenetic Analyses ◽  
Comparative Genome Analysis ◽  
The Family ◽  
History Of ◽  
Key Residues

AbstractEvolutionary history of coronaviruses holds the key to understand mutational behavior and prepare for possible future outbreaks. By performing comparative genome analysis of nidovirales that contain the family of coronaviruses, we traced the origin of proofreading, surprisingly to the eukaryotic antiviral component ZNFX1. This common recent ancestor contributes two zinc finger (ZnF) motifs that are unique to viral exonuclease, segregating them from DNA proof-readers. Phylogenetic analyses indicate that following acquisition, genomes of coronaviruses retained and further fine-tuned proofreading exonuclease, whereas related families harbor substitution of key residues in ZnF1 motif concomitant to a reduction in their genome sizes. Structural modelling followed by simulation suggests the role of ZnF in RNA binding. Key ZnF residues strongly coevolve with replicase, and the helicase involved in duplex RNA unwinding. Hence, fidelity of replication in coronaviruses is a result of convergent evolution, that enables maintenance of genome stability akin to cellular proofreading systems.

scholarly journals Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182929 ◽  
Author(s):  
Elena A. Ritschard ◽  
Robert R. Fitak ◽  
Oleg Simakov ◽  
Sönke Johnsen
Keyword(s):  
Signal Transduction ◽  
Positive Selection ◽  
G Protein ◽  
Evolutionary History ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Genomic Signatures ◽  
History Of ◽  
G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

Evolutionary relationships of the Sparidae (Teleostei: Percoidei): integrating fossil and Recent data

2002 ◽  
Vol 93 (4) ◽  
pp. 333-353 ◽  
Author(s):  
Julia J. Day
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Successive Approximations ◽  
Feeding Strategies ◽  
New Genera ◽  
Minimum Age ◽  
Character Weighting ◽  
History Of ◽  
London Clay ◽  
Fossil Data

ABSTRACTThe Eocene sparid fauna (Teleostei: Percoidei) from Monte Bolca, Italy and from the London Clay, U.K. is revised based on re-examination of the type material and phylogenetic analyses of primarily osteological data. Two phylogenetic analyses, one of the Eocene taxa and a combined analysis of fossil and extant taxa, were performed. The addition of fossils to the extant data greatly increased numbers of most parsimonious trees, destabilising and obscuring basal relationships within the Sparidae. Combination of the data from fossil and extant data also affected relationships among the fossil taxa, changing some from those recovered using fossil data alone and destabilising others. Successive approximations character weighting supported the inclusion of the Eocene taxa within a monophyletic Sparidae. The genus Sparnodus, as previously conceived, is paraphyletic and is partitioned to remove the paraphyly. Five monotypic genera are recognised, including three new genera, Abromasta, Ellaserrata and Pseudosparnodus. Inclusion of the fossils in the phylogenetic analysis implies a minimum age of origin for the Sparidae of 55 Ma with most Recent sparid fauna in place no later than the Miocene, and provides further evidence that the diversification of feeding strategies occurred early on in the evolutionary history of the group.

scholarly journals Nuclear and mtDNA phylogenetic analyses clarify the evolutionary history of two species of native Hawaiian bats and the taxonomy of Lasiurini (Mammalia: Chiroptera)

PLoS ONE ◽  
2017 ◽  
Vol 12 (10) ◽  
pp. e0186085 ◽  
Author(s):  
Amy B. Baird ◽  
Janet K. Braun ◽  
Mark D. Engstrom ◽  
Ashlyn C. Holbert ◽  
Maritza G. Huerta ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Native Hawaiian ◽  
Phylogenetic Analyses ◽  
History Of

The Convention on the Legal Status of the Caspian Sea: The Final Answer or an Interim Solution to the Caspian Question?

2020 ◽  
Vol 35 (2) ◽  
pp. 232-263
Author(s):  
Elena Karataeva
Keyword(s):  
Caspian Sea ◽  
Legal Status ◽  
Complete Solution ◽  
The Caspian Sea ◽  
New Developments ◽  
History Of ◽  
Final Answer

Abstract This article analyses new developments in the question of the Caspian Sea legal status, namely the signing of the Convention on the Legal Status of the Caspian Sea on 12 August 2018 in Kazakhstan, after twenty-six years in the making. First, the article provides an overview of the history of the Caspian Sea ownership and examines the legal status question from the collapse of the USSR to the present day. Then, the text of the newly signed Convention is examined to determine whether it provides the final answers to the issues of the legal status and delimitation of the sea. It is contended that despite this seminal breakthrough, the convention does not provide a complete solution. Specifically, while it establishes Caspian Sea zones and their limits, it fails to clarify some key contentious aspects, including delimitation principles between the opposite and adjacent Caspian States, which remain to be determined bilaterally.

Geostrategic Features of Interaction between Kazakhstan and Iran in the Regional and World Aspect: Analysis and Evaluation

2019 ◽  
Vol 10 (7) ◽  
pp. 2133
Author(s):  
Akmaral U. TYULYUBAYEVA ◽  
Madina M. ABISHEVA ◽  
Aikerim A. TURUNTAYEVA ◽  
Saltanat T. JAKUBAYEVA
Keyword(s):  
Caspian Sea ◽  
International Level ◽  
Analysis Method ◽  
Islamic Republic ◽  
The Caspian Sea ◽  
Analysis And Evaluation ◽  
Bilateral Relations ◽  
History Of ◽  
Islamic Republic Of Iran ◽  
Bilateral Cooperation

Kazakhstan and the Islamic Republic of Iran are two states that have common sea borders through the Caspian Sea, two friendly neighbors, successfully developing both bilateral cooperation and cooperation at the regional and international level. The relevance of this study is that today it is advisable to study the foreign policy of not only world powers, but also ‘non-knowing’ countries in order to determine the scenario for the development of relations between the two countries. The purpose of the article is to analyze and evaluate the geostrategic features of the interaction of Kazakhstan and Iran in the regional and global aspects. The leading approach to the study of this problem is the analysis method, which allowed to study the history of relations between Kazakhstan and Iran at different stages. This article attempts to determine the geostrategic features of the interaction between Kazakhstan and Iran in the regional and world aspect analyze and evaluate their bilateral relations.  

Morphology, songs and genetics identify two new cicada species from Morocco: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. (Hemiptera: Cicadettini)

Zootaxa ◽  
2017 ◽  
Vol 4237 (3) ◽  
pp. 517
Author(s):  
GONÇALO JOÃO COSTA ◽  
VERA L. NUNES ◽  
EDUARDO MARABUTO ◽  
RAQUEL MENDES ◽  
TELMA G. LAURENTINO ◽  
...  
Keyword(s):  
Evolutionary History ◽  
New Genus ◽  
Acoustic Analysis ◽  
Phylogenetic Analyses ◽  
Habitat Preferences ◽  
Dna Barcode ◽  
Genetic Data ◽  
North African ◽  
History Of ◽  
The Subject

Morocco has been the subject of very few expeditions on the last century with the objective of studying small cicadas. In the summer of 2014 an expedition was carried out to Morocco to update our knowledge with acoustic recordings and genetic data of these poorly known species. We describe here two new small-sized cicadas that could not be directly assigned to any species of North African cicadas: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. In respect to T. afroamissa it is the first species of the genus to be found outside Europe and we frame this taxon within the evolutionary history of the genus. Acoustic analysis of this species allows us to confidently separate T. afroamissa from its congeners. With B. dimelodica, a small species showing a remarkable calling song characterized by an abrupt frequency modulation, a new genus had to be erected. Bayesian inference and maximum likelihood phylogenetic analyses with DNA-barcode sequences of Cytochrome C Oxidase 1 support the monophyly of both species, their distinctness and revealed genetic structure within B. dimelodica. Alongside the descriptions we also provide GPS coordinates of collection points, distributions and habitat preferences. 

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