scholarly journals Analysis of the first complete genome sequence of an Old World monkey adenovirus reveals a lineage distinct from the six human adenovirus species

2004 ◽  
Vol 85 (10) ◽  
pp. 2799-2807 ◽  
Author(s):  
Gábor M. Kovács ◽  
Andrew J. Davison ◽  
Alexender N. Zakhartchouk ◽  
Balázs Harrach
Keyword(s):  
Common Ancestor ◽  
Early Stage ◽  
World Monkey ◽  
Phylogenetic Analyses ◽  
Human Adenovirus ◽  
Genomic Comparison ◽  
Old World ◽  
Simian Adenovirus ◽  
The Common

Simian adenovirus 3 (SAdV-3) is one of several adenoviruses that were isolated decades ago from Old World monkeys. Determination of the complete DNA sequence of SAdV-3 permitted the first full genomic comparison of a monkey adenovirus with adenoviruses of humans (HAdVs) and chimpanzees, which are recognized formally as constituting six of the species (HAdV-A to HAdV-F) within the genus Mastadenovirus. The SAdV-3 genome is 34 246 bp in size and has a G+C content of 55·3 mol%. It contains all the genes that are characteristic of the genus Mastadenovirus and has a single VA-RNA gene and six genes in each of the E3 and E4 regions. The genetic organization is the same as that of HAdV-12, a member of the HAdV-A species. Phylogenetic analyses showed that although SAdV-3 is related marginally more closely to HAdV-A and HAdV-F than to other species, it represents a unique lineage that branched at an early stage of primate adenovirus divergence. The results imply that the genetic layout in SAdV-3 and HAdV-12 may also have characterized the common ancestor of all sequenced primate adenoviruses.

scholarly journals Complete genome sequence of simian adenovirus 1: an Old World monkey adenovirus with two fiber genes

2005 ◽  
Vol 86 (6) ◽  
pp. 1681-1686 ◽  
Author(s):  
Gábor M. Kovács ◽  
Balázs Harrach ◽  
Alexander N. Zakhartchouk ◽  
Andrew J. Davison
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
World Monkey ◽  
Human Adenovirus ◽  
Vaccine Production ◽  
Old World ◽  
Old World Monkey ◽  
Poliomyelitis Vaccine ◽  
Simian Adenovirus ◽  
Six Genes

Simian adenovirus 1 (SAdV-1) is one of many adenovirus strains that were isolated from Old World monkey cells during poliomyelitis vaccine production several decades ago. Despite the availability of these viruses, knowledge of their genetic content and phylogeny is rudimentary. In the present study, the genome sequence of SAdV-1 (34 450 bp) was determined and analysed. In regions where genetic content varies between primate adenoviruses, SAdV-1 has a single virus-associated RNA gene, six genes in each of the E3 and E4 regions and two fiber genes. SAdV-1 clusters phylogenetically with HAdV-40, a member of human adenovirus species HAdV-F, which also has two fiber genes. However, based on phylogenetic distances and other taxonomic criteria, SAdV-1 is proposed to represent a novel adenovirus species.

scholarly journals SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 777-784
Author(s):  
Jürgen Schmitz ◽  
Martina Ohme ◽  
Hans Zischler
Keyword(s):  
New World ◽  
World Monkey ◽  
Old World ◽  
Alu Elements ◽  
Alu Sequences ◽  
Short Interspersed Elements ◽  
Divergence Point ◽  
Tarsius Bancanus ◽  
Cladistic Analyses ◽  
The Common

Abstract Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.

scholarly journals Placenta-Specific Protein 1 Is Conserved throughout the Placentalia under Purifying Selection

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Eric J. Devor
Keyword(s):  
Phylogenetic Analysis ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Purifying Selection ◽  
Specific Protein ◽  
Mammal Species ◽  
Crucial Component ◽  
Successful Group ◽  
The Common

Placental mammals (Placentalia) are a very successful group that, today, comprise 94% of all mammalian species. Recent phylogenetic analyses, coupled with new, quite complete fossils, suggest that the crown orders were all established rapidly from a common ancestor just after the Cretaceous/Tertiary (K/T) boundary 65 million years ago. Extensive molecular and morphologic evidence has led to a description of the common ancestor of all Placentalia in which a two-horned uterus and a hemochorial placenta are present. Thus, the process of placentation in which the placenta invades and anchors to the uterine epithelium was already established. One factor that has been suggested as a crucial component of this process is placenta-specific protein 1 (PLAC1). A phylogenetic analysis of the PLAC1 protein in 25 placental mammal species, representing nine of the sixteen crown orders of the Placentalia, suggests that this protein was present in the placental common ancestor in the form we see it today, that it evolved in the Placentalia and has been subject to the effects of purifying selection since its appearance.

scholarly journals The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-18 ◽  
Author(s):  
Patrick Forterre
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Critical Role ◽  
Last Common Ancestor ◽  
Dna Viruses ◽  
The Common ◽  
Basic Features ◽  
Origin Of Eukaryotes ◽  
Archaeal Ancestor ◽  
Selection Of

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

scholarly journals The molecular evolution of Dabie bandavirus (Phenuiviridae: Bandavirus: Dabie bandavirus), the agent of severe fever with thrombocytopenia syndrome

2022 ◽  
Vol 66 (6) ◽  
pp. 409-416
Author(s):  
T. E. Sizikova ◽  
V. N. Lebedev ◽  
S. V. Borisevich
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Virus Transmission ◽  
Infectious Agent ◽  
Global Public Health ◽  
The Common ◽  
Epidemiological Characteristics ◽  
Severe Fever

Since the Dabie bandavirus (DBV; former SFTS virus, SFTSV) was identified, the epidemics of severe fever with thrombocytopenic syndrome (SFTS) caused by this virus have occurred in several countries in East Asia. The rapid increase in incidence indicates that this infectious agent has a pandemic potential and poses an imminent global public health threat.The analysis of molecular evolution of SFTS agent that includes its variants isolated in China, Japan and South Korea was performed in this review. The evolution rate of DBV and the estimated dates of existence of the common ancestor were ascertained, and the possibility of reassortation was demonstrated.The evolutionary rates of DBV genome segments were estimated to be 2.28 × 10-4 nucleotides/site/year for S-segment, 2.42 × 10-4 for M-segment, and 1.19 × 10-4 for L-segment. The positions of positive selection were detected in the viral genome.Phylogenetic analyses showed that virus may be divided into two clades, containing six different genotypes. The structures of phylogenetic trees for S-, M- and L-segments showed that all genotypes originate from the common ancestor.Data of sequence analysis suggest that DBV use several mechanisms to maintain the high level of its genetic diversity. Understanding the phylogenetic factors that determine the virus transmission is important for assessing the epidemiological characteristics of the disease and predicting its possible outbreaks.

scholarly journals The Remarkable Conservation of Corticotropin-Releasing Hormone (CRH)-Binding Protein in the Honeybee (Apis mellifera) Dates the CRH System to a Common Ancestor of Insects and Vertebrates

Endocrinology ◽  
2005 ◽  
Vol 146 (5) ◽  
pp. 2165-2170 ◽  
Author(s):  
Mark O. Huising ◽  
Gert Flik
Keyword(s):  
Apis Mellifera ◽  
Common Ancestor ◽  
Binding Protein ◽  
Phylogenetic Analyses ◽  
Gene Organization ◽  
G Protein Coupled Receptors ◽  
Key Factor ◽  
The Common ◽  
G Protein Coupled ◽  
Crh Receptors

Abstract CRH-binding protein (CRH-BP) is a key factor in the regulation of CRH signaling; it modulates the bioactivity and bioavailability of CRH and its related peptides. The conservation of CRH-BP throughout vertebrates was only recently demonstrated. Here we report the presence of CRH-BP in the honeybee (Apis mellifera) and other insects. Honeybee CRH-BP resembles previously characterized vertebrate CRH-BP sequences with respect to conserved cysteine residues, gene organization, and overall sequence identity. Phylogenetic analyses confirm the unambiguous orthology of insect and vertebrate CRH-BP sequences. Soon after their discovery, it was noted that insect diuretic hormone-I (DH-I) and its receptor share similarities with the vertebrate CRH family and their receptors. Despite these similarities, demonstration of common ancestry of DH-I and the vertebrate CRH family is still speculative: the mature neuropeptides are short, and their genes differ substantially with regard to the number of coding exons. Moreover, DH and CRH receptors belong to the much larger family of G protein-coupled receptors. In contrast, the unique and conspicuous features of CRH-BP greatly facilitate the establishment of orthology over much larger evolutionary distances. The identification of CRH-BP in insects clearly indicates that this gene predates vertebrates by at least several hundred million years. Moreover, our findings imply that a CRH system is shared by insects and vertebrates alike and, consequently, that it has been present at least since the common ancestor to both phylogenetic lines of proto- and deuterostomians.

scholarly journals Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Hyeon-Mu Cho ◽  
Sang-Je Park ◽  
Se-Hee Choe ◽  
Ja-Rang Lee ◽  
Sun-Uk Kim ◽  
...  
Keyword(s):  
Splice Site ◽  
Common Ancestor ◽  
World Monkey ◽  
Sequence Divergence ◽  
New World Monkeys ◽  
Old World ◽  
Multifunctional Protein ◽  
Cooperative Evolution ◽  
Dna And Rna ◽  
Lysosome Related Organelles

Abstract Background The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our previous study, we identified an intriguing unreported transcript of the BLOC1S2 gene that has a novel exon derived from two transposable elements (TEs), MIR and AluSp. To investigate the evolutionary footprint and molecular mechanism of action of this transcript, we performed PCR and RT-PCR experiments and sequencing analyses using genomic DNA and RNA samples from humans and various non-human primates. Results The results showed that the MIR element had integrated into the genome of our common ancestor, specifically in the BLOC1S2 gene region, before the radiation of all primate lineages and that the AluSp element had integrated into the genome of our common ancestor, fortunately in the middle of the MIR sequences, after the divergence of Old World monkeys and New World monkeys. The combined MIR and AluSp sequences provide a 3′ splice site (AG) and 5′ splice site (GT), respectively, and generate the Old World monkey-specific transcripts. Moreover, branch point sequences for the intron removal process are provided by the MIR and AluSp combination. Conclusions We show for the first time that sequential integration into the same location and sequence divergence events of two different TEs generated lineage-specific transcripts through sequence collaboration during primate evolution.

scholarly journals Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts

2020 ◽  
Vol 7 (2) ◽  
pp. 191887 ◽  
Author(s):  
Hong Zou ◽  
Ivan Jakovlić ◽  
Dong Zhang ◽  
Cong-Jie Hua ◽  
Rong Chen ◽  
...  
Keyword(s):  
Gene Order ◽  
Replication Origin ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Taxon Sampling ◽  
Mitochondrial Genomes ◽  
Long Branch Attraction ◽  
Strand Asymmetry ◽  
Complete Exclusion ◽  
The Common

The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of Asotana magnifica (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.

scholarly journals Congruence, fossils and the evolutionary tree of rodents and lagomorphs

2019 ◽  
Vol 6 (7) ◽  
pp. 190387 ◽  
Author(s):  
Robert J. Asher ◽  
Martin R. Smith ◽  
Aime Rankin ◽  
Robert J. Emry
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Evolutionary Process ◽  
Morphological Characters ◽  
Evolutionary Tree ◽  
Locomotor Pattern ◽  
Living Species ◽  
The Common ◽  
Common Ancestors

Given an evolutionary process, we expect distinct categories of heritable data, sampled in ever larger amounts, to converge on a single tree of historical relationships. We tested this assertion by undertaking phylogenetic analyses of a new morphology-DNA dataset for mammals, focusing on Glires and including the oldest known skeletons of geomyoid and Ischyromys rodents. Our results support geomyoids in the mouse-related clade (Myomorpha) and a ricochetal locomotor pattern for the common ancestor of geomyoid rodents. They also support Ischyromys in the squirrel-related clade (Sciuromorpha) and the evolution of sciurids and Aplodontia from extinct, ‘protrogomorph’-grade rodents. Moreover, ever larger samples of characters from our dataset increased congruence with an independent, well-corroborated tree. Addition of morphology from fossils increased congruence to a greater extent than addition of morphology from extant taxa, consistent with fossils' temporal proximity to the common ancestors of living species, reflecting the historical, phylogenetic signal present in our data, particularly in morphological characters from fossils. Our results support the widely held but poorly tested intuition that fossils resemble the common ancestors shared by living species, and that fossilizable hard tissues (i.e. bones and teeth) help to reconstruct the evolutionary tree of life.

scholarly journals Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp.

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 702
Author(s):  
Tomáš Skalický ◽  
João M. P. Alves ◽  
Anderson C. Morais ◽  
Jana Režnarová ◽  
Anzhelika Butenko ◽  
...  
Keyword(s):  
Papua New Guinea ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
New Guinea ◽  
Bacterial Symbionts ◽  
Bacterial Genomes ◽  
Phylogenetic Relatedness ◽  
The Common ◽  
Multicellular Organisms

Trypanosomatids of the subfamily Strigomonadinae bear permanent intracellular bacterial symbionts acquired by the common ancestor of these flagellates. However, the cospeciation pattern inherent to such relationships was revealed to be broken upon the description of Angomonas ambiguus, which is sister to A. desouzai, but bears an endosymbiont genetically close to that of A. deanei. Based on phylogenetic inferences, it was proposed that the bacterium from A. deanei had been horizontally transferred to A. ambiguus. Here, we sequenced the bacterial genomes from two A. ambiguus isolates, including a new one from Papua New Guinea, and compared them with the published genome of the A. deanei endosymbiont, revealing differences below the interspecific level. Our phylogenetic analyses confirmed that the endosymbionts of A. ambiguus were obtained from A. deanei and, in addition, demonstrated that this occurred more than once. We propose that coinfection of the same blowfly host and the phylogenetic relatedness of the trypanosomatids facilitate such transitions, whereas the drastic difference in the occurrence of the two trypanosomatid species determines the observed direction of this process. This phenomenon is analogous to organelle (mitochondrion/plastid) capture described in multicellular organisms and, thereafter, we name it endosymbiont capture.

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