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

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.

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Computational Inference of Selection Underlying the Evolution of the Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2

Journal of Virology ◽

10.1128/jvi.00411-20 ◽

2020 ◽

Vol 94 (12) ◽

Cited By ~ 45

Author(s):

Rachele Cagliani ◽

Diego Forni ◽

Mario Clerici ◽

Manuela Sironi

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Positive Selection ◽

Common Ancestor ◽

Purifying Selection ◽

Population Variation ◽

Binding Motif ◽

The Novel ◽

Species Barrier ◽

The Common ◽

Novel Coronavirus

ABSTRACT The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that recently emerged in China is thought to have a bat origin, as its closest known relative (BatCoV RaTG13) was described previously in horseshoe bats. We analyzed the selective events that accompanied the divergence of SARS-CoV-2 from BatCoV RaTG13. To this end, we applied a population genetics-phylogenetics approach, which leverages within-population variation and divergence from an outgroup. Results indicated that most sites in the viral open reading frames (ORFs) evolved under conditions of strong to moderate purifying selection. The most highly constrained sequences corresponded to some nonstructural proteins (nsps) and to the M protein. Conversely, nsp1 and accessory ORFs, particularly ORF8, had a nonnegligible proportion of codons evolving under conditions of very weak purifying selection or close to selective neutrality. Overall, limited evidence of positive selection was detected. The 6 bona fide positively selected sites were located in the N protein, in ORF8, and in nsp1. A signal of positive selection was also detected in the receptor-binding motif (RBM) of the spike protein but most likely resulted from a recombination event that involved the BatCoV RaTG13 sequence. In line with previous data, we suggest that the common ancestor of SARS-CoV-2 and BatCoV RaTG13 encoded/encodes an RBM similar to that observed in SARS-CoV-2 itself and in some pangolin viruses. It is presently unknown whether the common ancestor still exists and, if so, which animals it infects. Our data, however, indicate that divergence of SARS-CoV-2 from BatCoV RaTG13 was accompanied by limited episodes of positive selection, suggesting that the common ancestor of the two viruses was poised for human infection. IMPORTANCE Coronaviruses are dangerous zoonotic pathogens; in the last 2 decades, three coronaviruses have crossed the species barrier and caused human epidemics. One of these is the recently emerged SARS-CoV-2. We investigated how, since its divergence from a closely related bat virus, natural selection shaped the genome of SARS-CoV-2. We found that distinct coding regions in the SARS-CoV-2 genome evolved under conditions of different degrees of constraint and are consequently more or less prone to tolerate amino acid substitutions. In practical terms, the level of constraint provides indications about which proteins/protein regions are better suited as possible targets for the development of antivirals or vaccines. We also detected limited signals of positive selection in three viral ORFs. However, we warn that, in the absence of knowledge about the chain of events that determined the human spillover, these signals should not be necessarily interpreted as evidence of an adaptation to our species.

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Morphology-based phylogenetic analysis of the treehopper tribe Smiliini (Hemiptera: Membracidae: Smiliinae), with reinstatement of the tribe Telamonini

Zootaxa ◽

10.11646/zootaxa.3047.1.1 ◽

2011 ◽

Vol 3047 (1) ◽

pp. 1 ◽

Cited By ~ 6

Author(s):

MATTHEW S. WALLACE

Keyword(s):

Phylogenetic Analysis ◽

Common Ancestor ◽

Hind Wing ◽

Morphological Characters ◽

Dorsal Margin ◽

Incertae Sedis ◽

Plant Associations ◽

Original Dataset ◽

The Common ◽

Morphological Differences

Members of the Smiliini, the nominotypical tribe of the large New World subfamily Smiliinae, are predominately Nearctic in distribution. This tribe included 169 mostly tree-feeding species in 23 genera. A parsimony-based phylogenetic analysis of an original dataset comprising 89 traditional and newly discovered morphological characters for 69 species, including representatives of 22 of the 23 described genera of Smiliini and five other previously recognized tribes of the subfamily, resulted in a single most parsimonious tree with three major clades. The broad recent concept of Smiliini (including Telamonini as a junior synonym) was not recovered as monophyletic by the analysis. Instead, the analysis supported narrower definitions of both Telamonini, here reinstated from synonymy, and Smiliini. A key and diagnoses are given to define these tribes, along with discussions of their phylogeny, biogeography, and host plant associations. The genera Antianthe Fowler, Hemicardiacus Plummer, Smilirhexia McKamey, and Tropidarnis Fowler are placed as Smiliinae, incertae sedis. Based on the phylogeny, several genera from both tribes including Atymna Stål, Cyrtolobus Goding, Heliria Stål, and Telamona Fitch are not monophyletic. Diagnostic characters emphasizing the morphological differences between the Smiliini and Telamonini include the dorsal margin of the head, the shape of the pronotum, the size of the pronotal humeral angles, the presence or absence of pronotal longitudinal rugae, the size of forewing cells, variations in the fusion of veins R and M apically in both the foreand hind wing, and the shape of the apex of the female second valvulae. Mapping geographic distribution onto the phylogeny suggests that the common ancestor of the ingroup (all three clades) occurred in Central America and Mexico, with multiple dispersals to temperate North America. Many Smiliini and Telamonini feed on various species of oak (Quercus) and the close evolutionary association between these insects and their hosts is discussed.

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Phylogenetic Analysis and Karyotype Evolution in Two Species of Core Gruiformes: Aramides cajaneus and Psophia viridis

Genes ◽

10.3390/genes11030307 ◽

2020 ◽

Vol 11 (3) ◽

pp. 307 ◽

Cited By ~ 1

Author(s):

Ivanete de Oliveira Furo ◽

Rafael Kretschmer ◽

Patrícia C. M. O’Brien ◽

Jorge C. Pereira ◽

Malcolm A. Ferguson-Smith ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genomic Dna ◽

Common Ancestor ◽

Karyotype Evolution ◽

Molecular Cytogenetics ◽

Ancestral Karyotype ◽

The Core ◽

Fulica Atra ◽

The Common ◽

Different Origins

Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by conventional staining or molecular cytogenetics. Due to this, this study aimed to analyze the karyotype of two species (Aramides cajaneus and Psophia viridis) belonging to families Rallidae and Psopiidae, respectively, by comparative chromosome painting. The results show that some chromosome rearrangements in this group have different origins, such as the association of GGA5/GGA7 in A. cajaneus, as well as the fission of GGA4p and association GGA6/GGA7, which place P. viridis close to Fulica atra and Gallinula chloropus. In addition, we conclude that the common ancestor of the core Gruiformes maintained the original syntenic groups found in the putative avian ancestral karyotype.

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The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

Archaea ◽

10.1155/2013/372396 ◽

2013 ◽

Vol 2013 ◽

pp. 1-18 ◽

Cited By ~ 64

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.

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Origin and Isoform Specific Functions of Exchange Proteins Directly Activated by cAMP: A Phylogenetic Analysis

Cells ◽

10.3390/cells10102750 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2750

Author(s):

Zhuofu Ni ◽

Xiaodong Cheng

Keyword(s):

Phylogenetic Analysis ◽

Common Ancestor ◽

Phylogenetic Analyses ◽

Sequence Diversity ◽

Sequence Motifs ◽

Nucleotide Exchange ◽

Animal Kingdom ◽

Specific Sequence ◽

Guanine Nucleotide Exchange ◽

The Individual

Exchange proteins directly activated by cAMP (EPAC1 and EPAC2) are one of the several families of cellular effectors of the prototypical second messenger cAMP. To understand the origin and molecular evolution of EPAC proteins, we performed a comprehensive phylogenetic analysis of EPAC1 and EPAC2. Our study demonstrates that unlike its cousin PKA, EPAC proteins are only present in multicellular Metazoa. Within the EPAC family, EPAC1 is only associated with chordates, while EPAC2 spans the entire animal kingdom. Despite a much more contemporary origin, EPAC1 proteins show much more sequence diversity among species, suggesting that EPAC1 has undergone more selection and evolved faster than EPAC2. Phylogenetic analyses of the individual cAMP binding domain (CBD) and guanine nucleotide exchange (GEF) domain of EPACs, two most conserved regions between the two isoforms, further reveal that EPAC1 and EPAC2 are closely clustered together within both the larger cyclic nucleotide receptor and RAPGEF families. These results support the notion that EPAC1 and EPAC2 share a common ancestor resulting from a fusion between the CBD of PKA and the GEF from RAPGEF1. On the other hand, the two terminal extremities and the RAS-association (RA) domains show the most sequence diversity between the two isoforms. Sequence diversities within these regions contribute significantly to the isoform-specific functions of EPACs. Importantly, unique isoform-specific sequence motifs within the RA domain have been identified.

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

Voprosy Virusologii ◽

10.36233/0507-4088-68 ◽

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.

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Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses

Open Biology ◽

10.1098/rsob.130219 ◽

2014 ◽

Vol 4 (4) ◽

pp. 130219 ◽

Cited By ~ 25

Author(s):

Daniel J. Macqueen ◽

Alexander H. Wilcox

Keyword(s):

Selective Pressure ◽

Phylogenetic Analyses ◽

Single Gene ◽

Purifying Selection ◽

Tissue Expression ◽

Cartilaginous Fish ◽

Research Attention ◽

Evolutionary Origins ◽

The Common

The calpains are a superfamily of proteases with extensive relevance to human health and welfare. Vast research attention is given to the vertebrate ‘classical’ subfamily, making it surprising that the evolutionary origins, distribution and relationships of these genes is poorly characterized. Consequently, there exists uncertainty about the conservation of gene family structure, function and expression that has been principally defined from work with mammals. Here, more than 200 vertebrate classical calpains were incorporated in phylogenetic analyses spanning an unprecedented range of taxa, including jawless and cartilaginous fish. We demonstrate that the common vertebrate ancestor had at least six classical calpains, including a single gene that gave rise to CAPN11 , 1 , 2 and 8 in the early jawed fish lineage, plus CAPN3 , 9 , 12 , 13 and a novel calpain gene, hereafter named CAPN17 . We reveal that while all vertebrate classical calpains have been subject to persistent purifying selection during evolution, the degree and nature of selective pressure has often been lineage-dependent. The tissue expression of the complete classic calpain family was assessed in representative teleost fish, amphibians, reptiles and mammals. This highlighted systematic divergence in expression across vertebrate taxa, with most classic calpain genes from fish and amphibians having more extensive tissue distribution than in amniotes. Our data suggest that classical calpain functions have frequently diverged during vertebrate evolution and challenge the ongoing value of the established system of classifying calpains by expression.

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A phylogenetic analysis of the New World tribe Phanaeini (Coleoptera: Scarabaeidae: Scarabaeinae): Hypotheses on relationships and origins

Insect Systematics & Evolution ◽

10.1163/187631204788964664 ◽

2004 ◽

Vol 35 (1) ◽

pp. 43-63 ◽

Cited By ~ 22

Author(s):

◽

T. Keith Philips ◽

Clarke Scholtz

Keyword(s):

Phylogenetic Analysis ◽

South America ◽

New World ◽

Common Ancestor ◽

Morphological Characters ◽

Monophyletic Clade ◽

Close Relationship ◽

Ball Surface ◽

Species Groups ◽

The Common

AbstractA phylogenetic analysis of Phanaeini based on 137 morphological characters supports the hypothesis that the nine included genera, Coprophanaeus, Dendropaemon, Diabroctis, Homalotarsus, Megatharsis, Oxysternon, Phanaeus, Sulcophanaeus and Tetrameira, form a monophyletic clade. Monophyly is unaffected by the inclusion of Gromphas, Oruscatus, and Bolbites and these should also be considered phanaeines. The sister lineage is Ennearabdus (Eucraniini) and both evolved from ancestral Dichotomiini within South America. There is no support for a close relationship with the Onitini or any other remaining tribe. All phanaeine genera appear to be monophyletic except Sulcophanaeus, of which two species groups appear as sister taxa while the remaining three form an independent paraphyletic clade. Ancestral phanaeines were coprophagous with necrophagy evolving at least twice. Myrmecophily is also derived and most likely evolved only once in the common ancestor of Dendropaemon, Homalotarsus, Megatharsis and Tetramereia. Bare dung ball construction for larval development is also the most likely ancestral condition with a soil covering on the exterior ball surface and parental cooperation evolving in the more derived lineages.

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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 ◽

10.1210/en.2004-1514 ◽

2005 ◽

Vol 146 (5) ◽

pp. 2165-2170 ◽

Cited By ~ 52

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.

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

Journal of General Virology ◽

10.1099/vir.0.80225-0 ◽

2004 ◽

Vol 85 (10) ◽

pp. 2799-2807 ◽

Cited By ~ 25

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.

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