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 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 Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

2020 ◽  
Author(s):  
Rebecca M Varney ◽  
Bastian Brenzinger ◽  
Manuel António E. Malaquias ◽  
Christopher P. Meyer ◽  
Michael Schrödl ◽  
...  
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Taxonomic Revision ◽  
Land Snails ◽  
Current Understanding ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Small Subset ◽  
Weak Support

Abstract ● Background: Heterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the “lower heterobranchs.” Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia.● Results: To assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of “lower heterobranchs.” Phylogenetic analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference analysis with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny than maximum likelihood analyses using site-homogeneous models. Interestingly, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.● Conclusions: Mitochondrial genomes provide support for shallow nodes within Heterobranchia, but despite a relatively conserved gene order and recovery of a topology largely consistent with the current understanding of heterobranch phylogeny, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for resolving deeper splits within this clade.

The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order

Genome ◽  
2009 ◽  
Vol 52 (5) ◽  
pp. 456-466 ◽  
Author(s):  
Kathrin Fahrein ◽  
Susan E. Masta ◽  
Lars Podsiadlowski
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Large Data ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Data Set ◽  
Weak Support ◽  
Genome Data

Amblypygi (whip spiders) are terrestrial chelicerates inhabiting the subtropics and tropics. In morphological and rRNA-based phylogenetic analyses, Amblypygi cluster with Uropygi (whip scorpions) and Araneae (spiders) to form the taxon Tetrapulmonata, but there is controversy regarding the interrelationship of these three taxa. Mitochondrial genomes provide an additional large data set of phylogenetic information (sequences, gene order, RNA secondary structure), but in arachnids, mitochondrial genome data are missing for some of the major orders. In the course of an ongoing project concerning arachnid mitochondrial genomics, we present the first two complete mitochondrial genomes from Amblypygi. Both genomes were found to be typical circular duplex DNA molecules with all 37 genes usually present in bilaterian mitochondrial genomes. In both species, gene order is identical to that of Limulus polyphemus (Xiphosura), which is assumed to reflect the putative arthropod ground pattern. All tRNA gene sequences have the potential to fold into structures that are typical of metazoan mitochondrial tRNAs, except for tRNA-Ala, which lacks the D arm in both amblypygids, suggesting the loss of this feature early in amblypygid evolution. Phylogenetic analysis resulted in weak support for Uropygi being the sister group of Amblypygi.

scholarly journals Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration

2021 ◽  
Vol 13 (9) ◽  
Author(s):  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Tomasz Strzała ◽  
Grzegorz Zaniewicz ◽  
Marcin Kurkowski ◽  
...  
Keyword(s):  
Control Region ◽  
Gene Order ◽  
Concerted Evolution ◽  
Common Ancestor ◽  
Gallus Gallus ◽  
Pandion Haliaetus ◽  
The Common ◽  
Control Regions

Abstract The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus, as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately.

scholarly journals Evolution, Diversification, and Biogeography of Grasshoppers (Orthoptera: Acrididae)

2018 ◽  
Vol 2 (4) ◽  
Author(s):  
Hojun Song ◽  
Ricardo Mariño-Pérez ◽  
Derek A Woller ◽  
Maria Marta Cigliano
Keyword(s):  
South America ◽  
Common Ancestor ◽  
Taxonomic Revision ◽  
Valid Species ◽  
Mitochondrial Genomes ◽  
Behavioral Diversity ◽  
The Family ◽  
The Common ◽  
Biogeographical Analysis ◽  
Forest Habitats

Abstract The grasshopper family Acrididae is one of the most diverse lineages within Orthoptera, including more than 6,700 valid species distributed worldwide. Grasshoppers are dominant herbivores, which have diversified into grassland, desert, semi-aquatic, alpine, and tropical forest habitats, and exhibit a wide array of morphological, ecological, and behavioral diversity. Nevertheless, the phylogeny of Acrididae as a whole has never been proposed. In this study, we present the first comprehensive phylogeny of Acrididae based on mitochondrial genomes and nuclear genes to test monophyly of the family and different subfamilies as well as to understand the evolutionary relationships among them. We recovered the monophyletic Acrididae and identified four major clades as well as several well-characterized subfamilies, but we also found that paraphyly is rampant across many subfamilies, highlighting the need for a taxonomic revision of the family. We found that Acrididae originated in the Paleocene of the Cenozoic period (59.3 million years ago) and, because the separation of South America and Africa predates the origin of the family, we hypothesize that the current cosmopolitan distribution of Acrididae was largely achieved by dispersal. We also inferred that the common ancestor of modern grasshoppers originated in South America, contrary to a popular belief that they originated in Africa, based on a biogeographical analysis. We estimate that there have been a number of colonization and recolonization events between the New World and the Old World throughout the diversification of Acrididae, and, thus, the current diversity in any given region is a reflection of this complex history.

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 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 Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids

2020 ◽  
Author(s):  
Ryo Harada ◽  
Yuji Inagaki
Keyword(s):  
Dna Replication ◽  
Common Ancestor ◽  
Dna Polymerases ◽  
Mitochondrial Genomes ◽  
Large Contribution ◽  
Evolutionary Trend ◽  
Evolutionary Origins ◽  
Dna Replication And Repair ◽  
Specific Affinity ◽  
The Common

AbstractMitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as “PolIBCD+”) have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via non-vertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.

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