Rosa Rubicondior: Refuting Creationism - Ancient Viruses Hidden in Bird Genomes Reveal Evolution in Action

Phylogenomics Unveils the Complex Evolution of Retroviruses in Birds | Molecular Biology and Evolution | Oxford Academic

Information about endogenous retroviruses is normally unwelcome news for creationists because they form phylogenies which exactly map onto the evolution of different species from common ancestry. This is no less true of a new research paper published by four researchers from the College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China, published in Molecular Biology & Evolution.

Endogenous retroviruses for part of the 'junk' (non-coding/non-regulatory) DNA, but some of it have been exapted for other functions over the years and some of it has placed an evolving taxon onto a new evolutionary trajectory. For example, one exapted retrovirus with immuno-suppressive qualities has made placental mammals possible without the growing embryo being treated as a parasite and attacked by the mother's immune system.

The researchers have uncovered the complex evolutionary history of retroviruses in birds by analysing their genetic “fossils” — endogenous retroviruses (ERVs) — embedded in bird genomes. They scanned the genomes of 758 bird species and identified more than 470,000 ERV sequences, revealing a vast and previously underestimated diversity of retroviruses. These sequences are the remnants of ancient viral infections that became part of the host DNA, passed down from generation to generation.

What Are Endogenous Retroviruses? Endogenous retroviruses (ERVs) are the remnants of ancient viral infections that have been incorporated into the DNA of their host organisms. Unlike typical viruses, which infect a host temporarily, retroviruses can insert their genetic material into the host’s genome. When this happens in sperm or egg cells, the viral DNA is passed down to offspring and becomes a permanent feature of the species' genome.

Over time, these viral sequences mutate, degrade, or become repurposed by the host. Most ERVs are no longer functional as viruses, but they remain as “molecular fossils” in the genome—preserving a record of past viral encounters that occurred millions of years ago.

ERVs and Evolutionary History

ERVs are powerful tools for studying evolution because:

They accumulate in a lineage-specific way, meaning related species tend to share ERVs in the same genomic locations. This makes them excellent phylogenetic markers — like timestamps that help trace ancestry.
Shared ERVs indicate common ancestry. If two species have the same ERV in the same place, it's strong evidence they inherited it from a common ancestor, not by chance.
ERV divergence reveals timing. By comparing the genetic differences between ERV copies in different species, scientists can estimate when lineages split from one another.
ERV patterns can detect horizontal transmission, showing when viruses have jumped between species and disrupted the expected phylogenetic signals—helping distinguish vertical inheritance from lateral events.

In Summary

ERVs are more than ancient viral relics—they are genomic archives of evolutionary history. By analysing where they appear and how they've changed over time, scientists can reconstruct the branching tree of life and better understand how species, including birds, have evolved over tens of millions of years.

The study found that retrovirus evolution in birds followed two distinct patterns. In many cases, viruses co-evolved with their avian hosts over tens of millions of years, leading to lineage-specific patterns of ERV distribution. In other instances, viruses appear to have jumped between species, leaving behind genetic evidence of cross-species transmission.

One striking finding was that just four major retroviral lineages account for over 90% of the full-length ERVs found in birds, suggesting that some viral families were especially successful at spreading and integrating into bird genomes.

Perhaps most notably, the researchers discovered that ERVs are not merely passive remnants of past infections. They continue to influence the structure and evolution of bird genomes today, contributing to genome rearrangements and even incorporating host genes into viral genomes—showcasing how viruses can become drivers of genetic change and innovation.

This large-scale phylogenomic analysis highlights how ERVs can illuminate deep-time evolutionary processes. It reinforces the role of genetic change, natural selection, and co-evolution as central forces shaping life on Earth—offering a vivid example of evolution not just as history, but as an ongoing process written in the genome.

Publication:

Qinliu He, Qiyan Liu, Zhen Gong, Guan-Zhu Han,
Phylogenomics Unveils the Complex Evolution of Retroviruses in Birds
Molecular Biology and Evolution, 42(7) July 2025, msaf171, https://doi.org/10.1093/molbev/msaf171

Abstract
The rise of birds represents one of the major evolutionary transitions in the history of life. Yet, much remains obscure about the origins and diversification of viruses in birds. Endogenous retroviruses (ERVs), relics of past retroviral infections, provide molecular fossils for interrogating the evolution and ecology of retroviruses. Here, we perform phylogenomic mining of ERVs within the genomes of 758 bird species and identify more than 470,000 ERVs, revealing a highly diverse and complex retrovirus repertoire in birds. These ERVs greatly expand the diversity of retroviruses in birds, indicating that exogenous retroviruses characterized in birds to date are highly underestimated. The evolution of retroviruses in birds is shaped by both coevolution and cross-species transmission. Tens of retrovirus lineages originated during the early evolution of birds, four of which contribute to more than 90% of complete ERVs in birds. We also observe recent ERV activity across the bird phylogeny (particularly in Passeriformes). Moreover, we find that ERVs can mediate genome rearrangements, potentially facilitating the genome evolution of birds. Many bird retroviruses recruited genes of cellular provenience, which might drive the evolution of the genome complexity of retroviruses. Together, these results unveil a diverse and complex retrovirosphere in birds and provide insights into the intricate evolution of retrovirus–bird interaction.

Introduction
Birds (the class Aves), with more than 10,000 extant species, evolved from theropod dinosaurs probably during the Middle–Late Jurassic period (Jarvis et al. 2014; Xu et al. 2014.1; Brusatte et al. 2015). Modern birds are classified into two major groups, namely Palaeognathae (the volant tinamous and flightless ratites) and Neognathae (Jarvis et al. 2014; Brusatte et al. 2015; Prum et al. 2015.1; Feng et al. 2020). Neognathae can be further divided into two subgroups, namely Galloanserae (the fowls, including ducks, chicken, and pheasants) and Neoaves (a diverse clade encompassing all the other living birds) (Jarvis et al. 2014; Brusatte et al. 2015; Prum et al. 2015.1; Feng et al. 2020). The rise of birds represents one of the major evolutionary transitions in the history of life on Earth. Over hundreds of millions of years of evolution, birds have achieved exceptional diversity in morphology, behaviors, ecological niches, and microbe associations (Xu et al. 2014.1; Brusatte et al. 2015). Whereas diverse viruses have been reported and isolated in birds, it remains largely obscure how these viruses originated and diversified during the rise and evolution of birds.

Retroviruses have long been known to infect birds, as exemplified by the landmark discovery of Rous sarcoma virus (RSV) more than 100 years ago (Rous 1911; Weiss and Vogt 2011). Yet, only tens of exogenous retroviruses (XRVs) have been characterized in birds, manly in the fowls. Among them, about 12 retroviruses have been formally classified by the International Committee on Taxonomy of Viruses (ICTV) (Coffin et al. 2021). Therefore, our current knowledge on the diversity of retroviruses remains highly fragmental and biased in birds.

The replication of retroviruses requires reverse transcription and integration into host genomes. When retroviruses infect germ line cells, the integrated retroviruses can be transmitted vertically, passing on to offspring and becoming endogenous retroviruses (ERVs) (Stoye 2012; Johnson 2019; Zheng et al. 2022). ERVs thus partially record retroviral infections that occurred in past and provide molecular fossils for studying the diversity and evolution of retroviruses as well as the evolution of interaction between retroviruses and their hosts (Stoye 2012; Johnson 2019; Zheng et al. 2022). ERVs have been found to be ubiquitously distributed in the genomes of vertebrates (Hayward et al. 2013; Hayward et al. 2015.2; Xu et al. 2018; Zheng et al. 2021.1; Chu et al. 2023; Wang and Han 2023.1), but ERVs were analyzed only in the genomes of a very limited number of birds or certain groups (such as Darwin's finches) of birds (Bolisetty et al. 2012.1; Cui et al. 2014.2; Hayward et al. 2015.2; Hill et al. 2022.1; Chen et al. 2024). The recent dense sequencing of bird genomes (Jarvis et al. 2014; Feng et al. 2020; Stiller et al. 2024.1) provides opportunities to interrogate the origin, diversification, and evolution of retroviruses during the rise and evolution of birds.

In this study, we leveraged phylogenomic approaches to mine ERVs in the genomes of 758 bird species, covering 97.5% of the orders of modern birds, and identified more than 470,000 ERVs. These ERVs greatly expand the diversity of retroviruses infecting or having infected birds. Our analyses reveal that the evolution of retroviruses in birds is shaped by both coevolution and host switching. We reconstructed the possible evolutionary scenarios for many retroviral lineages. Moreover, we found that ERVs can mediate host genome rearrangements, potentially shaping the genome evolution in birds. ERVs also captured diverse cellular genes, which might drive the evolution of the genome complexity of retroviruses. Together, these results provide a snapshot of the highly diverse and complex retrovirosphere in birds and have implications in understanding the evolution of bird–retrovirus interaction.

Qinliu He, Qiyan Liu, Zhen Gong, Guan-Zhu Han,
Phylogenomics Unveils the Complex Evolution of Retroviruses in Birds
Molecular Biology and Evolution, 42(7) July 2025, msaf171, https://doi.org/10.1093/molbev/msaf171

Copyright: © 2025 The authors/Society for Molecular Biology and Evolution.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The findings of this study strike another blow to creationist claims that species were created independently and recently. The shared presence of identical endogenous retroviruses (ERVs) at the same genetic locations across diverse bird lineages is precisely what we would expect if those species descended from a common ancestor. Such patterns are not only predicted by evolutionary theory—they are exceedingly difficult to explain under any creationist model. Why, for instance, would a designer insert the same broken viral DNA into multiple species in the same place, mimicking descent with modification?

Moreover, the sheer scale and temporal depth of ERV insertions—spanning tens of millions of years—completely contradict the idea of a young Earth or a fixed “created kind.” These are ancient, mutating viral fossils embedded in genomes, showing clear evidence of gradual divergence, lineage-specific accumulation, and occasional cross-species transmission. This is not a static, designed genome — it is a dynamic, evolving one.

Evolutionary theory predicts these patterns because it is grounded in testable, naturalistic principles. ERVs offer powerful, independent confirmation of the tree of life by tracing genetic history in ways that align with fossil, anatomical, and molecular data. Far from being random “junk” or design artefacts, ERVs are informative markers that reveal the deep and interconnected history of life. Once again, the theory of evolution not only explains what we observe in nature—it predicts it, tests it, and refines it. Creationism, in contrast, offers no mechanism, no predictive framework, and no explanation beyond “it was made that way”—an answer that collapses under the weight of evidence.

This study reaffirms evolution not as a hypothesis, but as the central organising principle of modern biology. The genome, once a mystery, has become a vast and intricate record of life’s unfolding history — written not by design, but by descent.

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