Creationism in Crisis - A New Endogenous Retrovirus Caught In The Act Of Invading a Genome

white-bellied mosaic-tailed rat Melomys leucogaster.
The species is being infected with the gibbon leukemia retrovirus.

Photo by Carlos Bocos

A rare recent case of retrovirus integration: An infectious gibbon ape leukemia virus is colonising a rodent’s genome in New Guinea - Leibniz Institute for Zoo and Wildlife Research

Researchers have discovered that a retrovirus is currently in the process of invading the genome of a rodent in New Guinea. This will add to the extensive list of known endogenous retroviruses. The virus, which appear to be harmless to the rodent - a mosaic tailed rat of the Melomys genus - is an infectious virus that causes leukemia in gibbons.

A retrovirus is an RNA virus that 'hides' in its host's DNA by inserting the DNA template for its RNA, using the enzyme reverse transcriptase that is coded for in its RNA. Once inserted it is replicated by every daughter cell. If it is inserted into the DNA of a germline cell, it can be passed on to the next generation.

Endogenous retroviruses (ERVs) are common in the genomes of all multicellular organisms and even some single-celled organisms, and as such constitute a large proportion of the non-coding or 'junk' DNA. A few may have been exapted for other purposes, but most are simply strands of viral DNA with a few mutations that broke them and rendered them harmless way back in our evolutionary history.

ERV's provide some of the most compelling evidence for common descent, especially since they appear at the same locus in the genomes of almost all members of a clade such as the vertebrates, including fish ancestors or the terrestrial vertebrates. The probability of the same ERV with the same mutations in in the same genetic locus to make it look like they form nested hierarchies, is vanishingly small, yet they do it over and over again.

The fact that they are present in all members of the same major clade tells us they must have been present in the last common ancestor of that clade, so they are a double embarrassment for creationists. They are both evidence of descent with modification and that there was no intelligence in the design of our genomes, because an intelligent designer would have no reason to include broken viral DNA which adds nothing by way of functionality yet must be replicated in every cell.

Tell me all about endogenous retroviruses; how they got into our genome and how they are evidence for evolution, please. Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that have become integrated into the genomes of their host organisms. Retroviruses are a type of RNA virus that can reverse transcribe their RNA genomes into DNA, which can then be integrated into the host cell's genome. When retroviruses infect germ cells (sperm or egg cells), the viral DNA can be passed on to subsequent generations, becoming a permanent part of the host's genetic material. Over time, these integrated viral sequences may accumulate mutations and become inactive, but they are still recognizable as remnants of past viral infections.

The presence of ERVs in the genomes of various species is strong evidence for evolution, supporting the theory of common descent. Here's how ERVs provide evidence for evolution:

1. Shared ERVs between related species: ERVs can be found in the genomes of diverse organisms, including humans, other mammals, birds, reptiles, and more. The presence of similar or identical ERVs in the genomes of closely related species provides evidence of common ancestry. For example, humans and other primates share many ERVs, indicating a common evolutionary ancestor.
2. ERVs at the same genomic locations: ERVs that are found at the same genomic locations in different species suggest that these sequences were present in the common ancestor of those species and were inherited through descent with modification. The likelihood of ERVs inserting into exactly the same genomic location independently in different species is extremely low, providing strong evidence for common ancestry. For instance, a specific ERV found at the same location in the genomes of humans and chimpanzees supports the hypothesis of a shared evolutionary history.
3. Functional remnants of ERVs: While many ERVs have accumulated mutations over time and are no longer functional, some ERVs retain functional elements that can influence gene regulation and expression. For example, certain ERVs contain regulatory sequences that control the expression of nearby genes. The presence of functional remnants of ERVs in the genomes of various species underscores their evolutionary significance and their potential to contribute to genetic diversity and adaptation.
4. Comparative genomics: Comparative genomic analyses, which involve comparing the genomes of different species, reveal patterns of ERV distribution and evolution that are consistent with the evolutionary relationships inferred from other types of data, such as morphological and molecular similarities. These analyses provide additional evidence supporting the evolutionary relatedness of different species.

Overall, the presence of endogenous retroviruses in the genomes of diverse organisms, their shared distribution patterns, and their evolutionary implications provide compelling evidence for common descent and the evolutionary history of life on Earth.

Examples?

Certainly! Here are a few examples of endogenous retroviruses (ERVs) and their significance in providing evidence for evolution:

1. HERV-W and human evolution: Human endogenous retrovirus type W (HERV-W) is a family of ERVs found in the human genome. One particular HERV-W insertion, called ERVWE1 or Syncytin-1, has been co-opted for a functional role in human biology. Syncytin-1 is involved in placental development and is essential for the formation of the syncytiotrophoblast layer, which plays a crucial role in the exchange of nutrients between the mother and fetus during pregnancy. The presence of HERV-W elements in the human genome, including functional elements like Syncytin-1, provides evidence of past retroviral infections and their subsequent integration into the human lineage. This integration and subsequent co-option of viral elements for a beneficial function illustrate how ERVs can shape the evolution of their host organisms.
2. Fossil ERVs in the primate lineage: Comparative genomic analyses have revealed shared ERV insertions among various primate species, including humans, chimpanzees, gorillas, and orangutans. One notable example is the presence of a specific ERV insertion called HERV-K111 in the genomes of humans and African apes (chimpanzees, gorillas). This shared ERV insertion at the same genomic location provides strong evidence for a common evolutionary ancestor of humans and African apes. Additionally, the absence of this ERV insertion in the genomes of orangutans, which diverged from the human-chimpanzee lineage earlier, supports the evolutionary relatedness of humans and African apes.
3. ERV-derived regulatory elements in mammalian genomes: Some ERVs contain regulatory sequences that can influence the expression of nearby genes. For example, certain ERV-derived sequences act as enhancers or promoters, modulating the expression of adjacent genes during development or in response to environmental stimuli. The presence of these ERV-derived regulatory elements in the genomes of diverse mammalian species, with variations in their activity and effects on gene expression, provides evidence for their evolutionary conservation and functional significance across different lineages.

These examples highlight how the study of ERVs in the genomes of various organisms can shed light on their evolutionary history, including shared ancestry, genetic adaptation, and the co-option of viral elements for beneficial functions.

Not much comfort for creationists there. And it's about to get much worse, because we now have evidence of it occurring before our very eyes, exactly as evolutionary biologists and virologists have explained it and explain why it's such compelling evidence of common descent.

The research team led by the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) have just published their findings, in the journal, Proceedings of the National Academy of Sciences (PNAS), and describe their work in a Leibniz Institute for Zoo and Wildlife Research news release:

Retroviruses are viruses that multiply by incorporating their genes into the genome of a host cell. If the infected cell is a germ cell, the retrovirus can then be passed on to the next generation as an “endogenous” retrovirus (ERV) and spread as part of the host genome in that host species. In vertebrates, ERVs are ubiquitous and sometimes make up 10 per cent of the host genome. However, most retrovirus integrations are very old, already degraded and therefore inactive – their initial impact on host health has been minimised by millions of years of evolution. A research team led by the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) has now discovered a recent case of retrovirus colonisation in a rodent from New Guinea, the white-bellied mosaic-tailed rat. In a paper in the scientific journal "Proceedings of the National Academy of Sciences", they describe this new model of virus integration. The observations on this process will help to improve our understanding how retroviruses rewrite host genomes.

Retroviruses, such as the pathogen responsible for AIDS (HIV-1), integrate into the genome of the host cells they infect during their life cycle. When this happens in the germline (egg cells or cells that produce sperm) of the host, the retrovirus can actually become a gene of the host itself. This process is apparently common, as up to 10 percent of the genomes of most vertebrates consist of the remnants of such ancient infections. One of the best studied models of this process is the koala retrovirus (KoRV), which is currently colonising the koala genome.

What happens to the virus and the host during this process of genome colonisation we do not know, as most such events occurred millions of years ago and we only see the leftover ‘fossils’ of the retrovirus. Nor do we know what the host suffered health-wise during the infection process. The koala retrovirus (KoRV) is one of the few models of this process that occurs in real time and where we can observe the effects of genome colonisation on the host animal.

Professor Alex Greenwood, corresponding author
Department of Wildlife Diseases
Leibniz Institute for Zoo and Wildlife Research
Berlin, Germany.

There is now some evidence that KoRV-related viruses are circulating in rodents and bats in Papua New Guinea and Indonesia. A group led by Greenwood and Dr Saba Mottaghinia, former PhD student in Greenwood’s department, analysed 278 samples from seven bat and one rodent family endemic to the Australo-Papua region (Australia and New Guinea). They discovered a retrovirus that is currently colonising the genome of an endemic rodent from New Guinea, the white-bellied mosaic-tailed rat (Melomys leucogaster). This is only the second example from the Australo-Papuan region, after KoRV, of a retrovirus that has colonised a genome while retaining a functional viral life cycle.

The gibbon ape leukaemia viruses (GALV), a group of viruses discovered in gibbons and woolly monkeys at a research facility in Thailand in the 1960s, are very closely related to KoRV. This is a curious and surprising relationship, as there is a geographical barrier, known as the Wallace lineage, which separates the fauna of Southeast Asia from Indonesia, Papua New Guinea and Australia's fauna. However, there is evidence that the gibbons and woolly monkeys at the research facility in Thailand have been infected with viruses from Papua New Guinea.

The discovery of GALV-like viruses in rodents and bats in Indonesian and Australian rodents and bats from New Guinea suggests that these viruses, and possibly also KoRV, originated in New Guinea.

There are hundreds of mammalian species from this region that have not yet been studied, suggesting that many more viruses and models exist in this region.

Professor Alex Greenwood.

The Leibniz-IZW team, together with scientists from the Charité, the Robert Koch Institute, the Max Delbrück Center, the University of Nicosia, California State University Fullerton, the South Australian Museum and Museum Victoria, examined 278 bat and rodent samples from Australia and New Guinea for KoRV and GALV-like viruses. They detected a GALV, the Woolly Monkey Virus (WMV) in a population of the white-bellied mosaic-tailed rat, an endemic rodent from New Guinea. In five of the rats from two New Guinea collection sites, WMV was integrated into the genome at the same location, indicating that it has spread as a gene and not by infection, i.e. it has become part of the genome. However, in other white-bellied mosaic-tailed rat populations the virus was absent – similar to KoRV in koalas, where all koalas in northern Australia have KoRV in their genome, whereas there are koalas in southern Australia that do not have intact KoRV. The virus, now called the “complete Melomys woolly monkey virus” (cMWMV), was able to infect cell lines, produce new viral progeny, was visible by electron microscopy as viral particles that detached from the cell membrane, and was even sensitive to the antiretroviral drug AZT.

The virus has all the characteristics of an exogenous infectious retrovirus, but is endogenous. It is probably a very recent colonisation event, much younger than KoRV./p>

Dr Saba Mottaghinia, lead author.
Department of Wildlife Diseases
Leibniz Institute for Zoo and Wildlife Research
Berlin, Germany.

The results suggest that cMWMV is a new model for retroviral colonisation of the host genome that occurs in real time, as in KoRV, and they also suggest that GALVs like WMV originated in the diverse fauna of New Guinea. The discoveries in New Guinea have certainly not been exhausted.

~ The authors dedicate the study to Ken P. Aplin of the South Australian Museum, who sadly passed away during the course of the project.

The team elaborate on their discovery in the statement of significance and the abstract to their research paper, the body of which, sadly, is behind an expensive paywall:

Significance

Retroviruses colonize vertebrate genomes forming endogenous retroviruses. With very few exceptions, these colonization events are ancient. After screening 278 samples representing seven bat and one rodent family endemic to the Australo-Papuan region (Australia and New Guinea), we report the discovery of genomically intact and infectious retroviruses currently colonizing the genome of a Melomys leucogaster in New Guinea. This represents the second example, after the koala retrovirus (KoRV), of a retrovirus that has colonized the genome but retains a functional viral life cycle identified in the Australo-Papuan region.

Abstract

Germline colonization by retroviruses results in the formation of endogenous retroviruses (ERVs). Most colonization’s occurred millions of years ago. However, in the Australo-Papuan region (Australia and New Guinea), several recent germline colonization events have been discovered. The Wallace Line separates much of Southeast Asia from the Australo-Papuan region restricting faunal and pathogen dispersion. West of the Wallace Line, gibbon ape leukemia viruses (GALVs) have been isolated from captive gibbons. Two microbat species from China appear to have been infected naturally. East of Wallace’s Line, the woolly monkey virus (a GALV) and the closely related koala retrovirus (KoRV) have been detected in eutherians and marsupials in the Australo-Papuan region, often vertically transmitted. The detected vertically transmitted GALV-like viruses in Australo-Papuan fauna compared to sporadic horizontal transmission in Southeast Asia and China suggest the GALV-KoRV clade originates in the former region and further models of early-stage genome colonization may be found. We screened 278 samples, seven bat and one rodent family endemic to the Australo-Papuan region and bat and rodent species found on both sides of the Wallace Line. We identified two rodents (Melomys) from Australia and Papua New Guinea and no bat species harboring GALV-like retroviruses. Melomys leucogaster from New Guinea harbored a genomically complete replication-competent retrovirus with a shared integration site among individuals. The integration was only present in some individuals of the species indicating this retrovirus is at the earliest stages of germline colonization of the Melomys genome, providing a new small wild mammal model of early-stage genome colonization.

Mottaghinia, Saba; Stenzel, Saskia; Tsangaras, Kyriakos; Nikolaidis, Nikolas; Laue, Michael; Müller, Karin; Hölscher, Henriette; Löber, Ulrike; McEwen, Gayle K.; Donnellan, Stephen C.; Rowe, Kevin C.; Aplin, Ken P.; Goffinet, Christine; Greenwood, Alex D.
A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea
Proceedings of the National Academy of Sciences (PNAS), 121(6) e2220392121; DOI:10.1073/pnas.2220392121

© 2024 PNAS.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Just to round off what is turning out to be another difficult week for those creationists with enough integrity to read the latest science even when it refutes their beliefs (are there any?) here is a little more about ERV's and how they provide such compelling evidence for common descent:

I understand there are ERVs common to fish and mammals, including humans; do you have any information on this? Yes, indeed! There are ERVs that are shared between fish and mammals, including humans. These shared ERVs provide fascinating insights into the evolutionary history of vertebrates and the ancient interactions between retroviruses and their hosts. Here are some key points about ERVs common to fish and mammals:

1. ERV families in fish and mammals: Studies have identified several families of ERVs that are conserved across vertebrate lineages, including fish (such as zebrafish) and mammals (including humans). These ERV families have been found to share sequence similarities and structural features, indicating their common ancestry and evolutionary conservation.
2. Shared ERVs in the same genomic locations: One striking aspect of these shared ERVs is their presence at orthologous genomic loci in different vertebrate species. Orthologous genomic loci are regions of the genome that are evolutionarily conserved between species due to their shared ancestry. The presence of ERVs at orthologous genomic loci in both fish and mammals suggests that these retroviral insertions occurred in the common ancestor of these vertebrate groups and have been inherited through descent with modification.
3. Functional implications: Some of these shared ERVs may retain functional elements that have been conserved across vertebrate evolution. For example, certain ERVs contain regulatory sequences that can influence the expression of nearby genes involved in various biological processes. The conservation of these functional elements across fish and mammals suggests their importance in vertebrate biology and evolution.
4. Evolutionary significance: The presence of shared ERVs between fish and mammals provides compelling evidence for the deep evolutionary relationships between these groups. These shared retroviral elements offer molecular markers that can be used to study the evolutionary divergence and relationships among different vertebrate lineages.
5. Transspecies transmission: It's also worth noting that retroviruses, including ERVs, have the potential to undergo transspecies transmission, where viral particles infect individuals of different species, leading to the integration of viral sequences into the genomes of new host species. Such events can contribute to the spread of ERVs across different vertebrate lineages and the sharing of retroviral sequences among distantly related species.

Overall, the presence of ERVs shared between fish and mammals underscores the evolutionary continuity and shared ancestry of vertebrates, highlighting the complex interplay between retroviruses and their host genomes over millions of years of evolution.

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