scholarly journals Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

2021 ◽  
Vol 17 (7) ◽  
pp. e1009730
Author(s):  
Jialu Zheng ◽  
Jianhua Wang ◽  
Zhen Gong ◽  
Guan-Zhu Han
Keyword(s):  
Phylogenetic Analyses ◽  
Endogenous Retroviruses ◽  
Integration Time ◽  
Aquatic Environments ◽  
Ongoing Activity ◽  
Aquatic Life ◽  
Origin And Evolution ◽  
Molecular Fossils ◽  
Retroviral Infections

The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.

scholarly journals Origin and recent expansion of an endogenous gammaretroviral lineage in canids

2018 ◽  
Author(s):  
Julia V. Halo ◽  
Amanda L. Pendleton ◽  
Abigail S. Jarosz ◽  
Robert J. Gifford ◽  
Malika L. Day ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Sequence Variation ◽  
Sequence Data ◽  
Endogenous Retroviruses ◽  
Domestic Dog ◽  
Whole Genome Sequence ◽  
Canis Lupus Familiaris ◽  
Origin And Evolution ◽  
Mammalian Genomes ◽  
Retroviral Infections

AbstractMammalian genomes contain a fossilized record of ancient retroviral infections in the form of endogenous retroviruses (ERVs). We used whole genome sequence data to assess the origin and evolution of the recently active ERV-Fc gammaretroviral lineage based on the record of past infections retained in the genome of the domestic dog,Canis lupus familiaris.We identified 165 loci, including 58 insertions absent from the dog reference assembly, and characterized element polymorphism across 332 canids from nine species. Insertions were found throughout the dog genome including within and near gene models. Analysis of 19 proviral sequences identified shared disruptive mutations indicating defective proviruses were spread via complementation. The patterns of ERV polymorphism and sequence variation indicate multiple circulating viruses infected canid ancestors within the last 20 million to within 1.6 million years with a recent bust of germline invasion in the lineage leading to wolves and dogs.

scholarly journals Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses

2003 ◽  
Vol 77 (13) ◽  
pp. 7202-7213 ◽  
Author(s):  
Marco Salemi ◽  
Tulio De Oliveira ◽  
Valerie Courgnaud ◽  
Vincent Moulton ◽  
Barbara Holland ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Decomposition Analysis ◽  
Phylogeny Reconstruction ◽  
Origin And Evolution ◽  
Immunodeficiency Virus ◽  
Primate Lentiviruses ◽  
Recombinant Fragments ◽  
Clustering Patterns

ABSTRACT To clarify the origin and evolution of the primate lentiviruses (PLVs), which include human immunodeficiency virus types 1 and 2 as well as their simian relatives, simian immunodeficiency viruses (SIVs), isolated from several host species, we investigated the phylogenetic relationships among the six supposedly nonrecombinant PLV lineages for which the full genome sequences are available. Employing bootscanning as an exploratory tool, we located several regions in the PLV genome that seem to have uncertain or conflicting phylogenetic histories. Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns. Split decomposition analysis also shows that phylogenetic relationships among PLVs may be better represented by network-based graphs, such as the ones produced by SplitsTree. Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts.

scholarly journals Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
William E Diehl ◽  
Nirali Patel ◽  
Kate Halm ◽  
Welkin E Johnson
Keyword(s):  
Fossil Record ◽  
Viral Infections ◽  
Endogenous Retroviruses ◽  
Interspecies Transmission ◽  
Viral Spread ◽  
Protein Functions ◽  
History Of ◽  
Mammalian Genomes ◽  
Retroviral Infections

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections.

scholarly journals Mobilization of Endogenous Retroviruses in Mice after Infection with an Exogenous Retrovirus

2008 ◽  
Vol 83 (6) ◽  
pp. 2429-2435 ◽  
Author(s):  
Leonard H. Evans ◽  
A. S. M. Alamgir ◽  
Nick Owens ◽  
Nick Weber ◽  
Kimmo Virtaneva ◽  
...  
Keyword(s):  
Germ Line ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Gene Sequences ◽  
Endogenous Viruses ◽  
Mammalian Genomes ◽  
Leukemia Viruses ◽  
Retroviral Infections ◽  
Ecotropic Virus ◽  
Rna Transcript

ABSTRACT Mammalian genomes harbor a large number of retroviral elements acquired as germ line insertions during evolution. Although many of the endogenous retroviruses are defective, several contain one or more intact viral genes that are expressed under certain physiological or pathological conditions. This is true of the endogenous polytropic retroviruses that generate recombinant polytropic murine leukemia viruses (MuLVs). In these recombinants the env gene sequences of exogenous ecotropic MuLVs are replaced with env gene sequences from an endogenous polytropic retrovirus. Although replication-competent endogenous polytropic retroviruses have not been observed, the recombinant polytropic viruses are capable of replicating in numerous species. Recombination occurs during reverse transcription of a virion RNA heterodimer comprised of an RNA transcript from an endogenous polytropic virus and an RNA transcript from an exogenous ecotropic MuLV RNA. It is possible that homodimers corresponding to two full-length endogenous RNA genomes are also packaged. Thus, infection by an exogenous virus may result not only in recombination with endogenous sequences, but also in the mobilization of complete endogenous retrovirus genomes via pseudotyping within exogenous retroviral virions. We report that the infection of mice with an ecotropic virus results in pseudotyping of intact endogenous viruses that have not undergone recombination. The endogenous retroviruses infect and are integrated into target cell genomes and subsequently replicate and spread as pseudotyped viruses. The mobilization of endogenous retroviruses upon infection with an exogenous retrovirus may represent a major interaction of exogenous retroviruses with endogenous retroviruses and may have profound effects on the pathogenicity of retroviral infections.

scholarly journals Ancestral Mutations Acquired in Refrex-1, a Restriction Factor against Feline Retroviruses, during its Cooption and Domestication

2015 ◽  
Vol 90 (3) ◽  
pp. 1470-1485 ◽  
Author(s):  
Jumpei Ito ◽  
Takuya Baba ◽  
Junna Kawasaki ◽  
Kazuo Nishigaki
Keyword(s):  
Field Model ◽  
Leukemia Virus ◽  
Endogenous Retroviruses ◽  
Chimeric Virus ◽  
Feline Leukemia Virus ◽  
Domestic Cats ◽  
Terminal Domain ◽  
Viral Particles ◽  
Triangular Relationships ◽  
Retroviral Infections

ABSTRACTEndogenous retroviruses (ERVs) are remnants of ancestral retroviral infections of germ cells. Retroviral endogenization is an adaptation process for the host genome, and ERVs are gradually attenuated or inactivated by mutation. However, some ERVs that have been “domesticated” by their hosts eventually gain physiological functions, such as placentation or viral resistance. We previously reported the discovery of Refrex-1, a soluble antiretroviral factor in domestic cats that specifically inhibits infection by feline leukemia virus subgroup D (FeLV-D), a chimeric virus of FeLV, and a feline ERV, ERV-DC. Refrex-1 is a truncated envelope protein (Env) encoded by both ERV-DC7 and ERV-DC16 proviral loci. Here, we reconstituted ancestral and functional Env from ERV-DC7 and ERV-DC16 envelope genes (env) by inducing reverse mutations. Unexpectedly, ERV-DC7 and ERV-DC16 full-length Env (ERV-DC7 fl and ERV-DC16 fl), reconstructed by removing stop codons, did not produce infectious viral particles. ERV-DC7 fl and ERV-DC16 fl were highly expressed in cells but were not cleaved into surface subunits (SU) and transmembrane subunits, nor were they incorporated into virions. G407R/N427I-A429T and Y431D substitutions within the SU C-terminal domain of ERV-DC7 fl and ERV-DC16 fl, respectively, caused these dysfunctions. The residues glycine 407 and tyrosine 431 are relatively conserved among infectious gammaretroviruses, and their substitution causes the same dysfunctions as the tested retroviruses. Our results reveal that specific mutations within the SU C-terminal domain suppressed Env cleavage and incorporation into virions and indicate that these mutations contributed to the domestication of Refrex-1 through multistep events that occurred in the postintegration period.IMPORTANCEDomestic cats are colonized with various exogenous retroviruses (exRVs), such as feline leukemia virus (FeLV), and their genomes contain numerous ERVs, some of which are replication-competent proviruses. The feline hosts, exRVs, and ERVs have complicated genetic interactions and provide an interesting field model for triangular relationships: recombination between FeLV and ERV-DC, which is a feline ERV, generated FeLV-D, a chimeric virus, and FeLV-D is restricted by Refrex-1, an antiretroviral factor corresponding to truncated Env of ERV-DC7 and ERV-DC16. Here, we reconstructed ancestral, functional Env from ERV-DC7 and ERV-DC16envby inducing reverse mutations to elucidate how Refrex-1 was generated from its ancestor. Our results reveal that they were repeatedly inactivated by mutations preventing Env maturation. Our results provide insights into how ERVs were “domesticated” by their hosts and identify the mutations that mediated these evolutions. Notably, experiments that restore inactivated ERVs might uncover previously unrecognized features or properties of retroviruses.

A Review of Emerging Contaminants in Water

2020 ◽  
pp. 177-202
Author(s):  
Alexandros I. Stefanakis ◽  
Julie A. Becker
Keyword(s):  
Human Health ◽  
Emerging Contaminants ◽  
Aquatic Environments ◽  
Contaminants Of Emerging Concern ◽  
Aquatic Life ◽  
Introduction Pathways ◽  
Analytical Instrumentation ◽  
Surface And Groundwater

Contaminants of emerging concern or, simply, emerging contaminants represent a newly discovered group of chemicals present in surface and groundwater. It was only the improvements in analytical instrumentation that allowed for the detection of these contaminants even at trace levels. The continuous detection of new chemicals with time raises questions concerning their source pathways, their fate, transport, transformations and impact on aquatic environments. The scope of this chapter is to present an overview of the contaminants classified as “emerging”, their sources and introduction pathways to the environment and the related risks to human health and aquatic life.

A Review of Emerging Contaminants in Water

2015 ◽  
pp. 55-80 ◽  
Author(s):  
Alexandros I. Stefanakis ◽  
Julie A. Becker
Keyword(s):  
Human Health ◽  
Emerging Contaminants ◽  
Aquatic Environments ◽  
Contaminants Of Emerging Concern ◽  
Aquatic Life ◽  
Introduction Pathways ◽  
Analytical Instrumentation ◽  
Surface And Groundwater

Contaminants of emerging concern or, simply, emerging contaminants represent a newly discovered group of chemicals present in surface and groundwater. It was only the improvements in analytical instrumentation that allowed for the detection of these contaminants even at trace levels. The continuous detection of new chemicals with time raises questions concerning their source pathways, their fate, transport, transformations and impact on aquatic environments. The scope of this chapter is to present an overview of the contaminants classified as “emerging”, their sources and introduction pathways to the environment and the related risks to human health and aquatic life.

scholarly journals Physical trade-offs shape the evolution of buoyancy control in sharks

2017 ◽  
Vol 284 (1866) ◽  
pp. 20171345 ◽  
Author(s):  
Adrian C. Gleiss ◽  
Jean Potvin ◽  
Jeremy A. Goldbogen
Keyword(s):  
Phylogenetic Analyses ◽  
Liver Volume ◽  
The Body ◽  
Fundamental Aspect ◽  
Shark Species ◽  
Lean Tissue ◽  
Aquatic Life ◽  
Positive Allometry ◽  
Trade Offs ◽  
Buoyancy Control

Buoyancy control is a fundamental aspect of aquatic life that has major implications for locomotor performance and ecological niche. Unlike terrestrial animals, the densities of aquatic animals are similar to the supporting fluid, thus even small changes in body density may have profound effects on locomotion. Here, we analysed the body composition (lipid versus lean tissue) of 32 shark species to study the evolution of buoyancy. Our comparative phylogenetic analyses indicate that although lean tissue displays minor positive allometry, liver volume exhibits pronounced positive allometry, suggesting that larger sharks evolved bulkier body compositions by adding lipid tissue to lean tissue rather than substituting lean for lipid tissue, particularly in the liver. We revealed a continuum of buoyancy control strategies that ranged from more buoyant sharks with larger livers in deeper ecosystems to relatively denser sharks with small livers in epipelagic habitats. Across this eco-morphological spectrum, our hydrodynamic modelling suggests that neutral buoyancy yields lower drag and more efficient steady swimming, whereas negative buoyancy may be more efficient during accelerated movements. The evolution of buoyancy control in sharks suggests that ecological and physiological factors mediate the selective pressures acting on these traits along two major gradients, body size and habitat depth.

Design and Analysis of Small Scale Horizontal Archimedean Screw for Electric Power Generation

2017 ◽  
Author(s):  
Paul E. Slaboch ◽  
Jillian Coday
Keyword(s):  
Power Generation ◽  
Electric Power ◽  
Environmentally Friendly ◽  
Small Scale ◽  
Aquatic Environments ◽  
Efficient Design ◽  
Electric Power Generation ◽  
Aquatic Life ◽  
Overall Efficiency ◽  
Pass Through

A small scale horizontal Archimedean screw was designed, built, and tested for small-scale electric power generation. The small-scale device is suitable for deployment in shallow waterways and rivers. The design of the screw is environmentally friendly and allows for fish and other aquatic life to pass through harmlessly. A series of horizontal screws were designed over a range of blade pitch and tip conditions to determine the most efficient configuration of the device. The tip conditions included straight, flanged, and open. The device was placed both inside and outside of a duct to control tip conditions. The flanged condition added material to the tip of the device to simulate a partially ducted screw. Preliminary studies have shown that the straight bladed screw is the most efficient design. Preliminary data also show that the addition of a duct reduced the overall efficiency of the device. The flange feature on the screw was shown to be ineffective as well. However, the design was environmentally friendly and would provide electric power on a small scale without harm to local aquatic environments.

scholarly journals High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 633 ◽  
Author(s):  
Maria Paola Pisano ◽  
Nicole Grandi ◽  
Enzo Tramontano
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Large Fraction ◽  
Expression Patterns ◽  
Cell Types ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses ◽  
Retroviral Infections ◽  
The Impact

Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.

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