ArticleProceedings of the National Academy of Sciences of the United States of America2013
Broad-scale phylogenomics provides insights into retrovirus-host evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Integrated molecular and metatranscriptomic evidence of Tacaribe virus and the brain virome profile ofMicrobiology spectrum · 2026Article
- Epigenetic motifs distinguishing endogenous from exogenous retroviral integrants.Journal of virology · 2025Article
- Endogenous Retroviruses in Host-Virus Coevolution: From Genomic Domestication to Functional Innovation.Genes · 2025Review
- Phylogenomics Unveils the Complex Evolution of Retroviruses in Birds.Molecular biology and evolution · 2025Article
- Intact, recombinant, and spliced forms of endogenous mouse mammary tumor viruses in inbred and wild mice.Journal of virology · 2025Article
- Signature of viral fossils: a comparative genomics approach to understand the diversity of endogenous retroviruses in bats.Virus research · 2024Article
- Endogenous retroviral ERVH48-1 promotes human urine cell reprogramming.Cell regeneration (London, England) · 2024Article
- Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes.Molecular biology and evolution · 2024Article
- A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.Genome biology · 2024Article
- A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Endogenous viral elements: insights into data availability and accessibility.Virus evolution · 2024Article
- GALV-KoRV-related retroviruses in diverse Australian and African rodent species.Virus evolution · 2024Article
- Envelope Recombination: A Major Driver in Shaping Retroviral Diversification and Evolution within the Host Genome.Viruses · 2023Review
- Unique Structure and Distinctive Properties of the Ancient and Ubiquitous Gamma-Type Envelope Glycoprotein.Viruses · 2023Review
- Long-term host-pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of recent retroviral introgression.Virus evolution · 2023Article
- Comparative analysis reveals the long-term coevolutionary history of parvoviruses and vertebrates.PLoS biology · 2022Article
- Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.Nature communications · 2022Article
- Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders.PLoS genetics · 2022Article
- Expansion of a retrovirus lineage in the koala genome.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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2 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Genomic data provide an excellent resource to improve understanding of retrovirus evolution and the complex relationships among viruses and their hosts. In conjunction with broad-scale in silico screening of vertebrate genomes, this resource offers an opportunity to complement data on the evolution and frequency of past retroviral spread and so evaluate future risks and limitations for horizontal transmission between different host species. Here, we develop a methodology for extracting phylogenetic signal from large endogenous retrovirus (ERV) datasets by collapsing information to facilitate broad-scale phylogenomics across a wide sample of hosts. Starting with nearly 90,000 ERVs from 60 vertebrate host genomes, we construct phylogenetic hypotheses and draw inferences regarding the designation, host distribution, origin, and transmission of the Gammaretrovirus genus and associated class I ERVs. Our results uncover remarkable depths in retroviral sequence diversity, supported within a phylogenetic context. This finding suggests that current infectious exogenous retrovirus diversity may be underestimated, adding credence to the possibility that many additional exogenous retroviruses may remain to be discovered in vertebrate taxa. We demonstrate a history of frequent horizontal interorder transmissions from a rodent reservoir and suggest that rats may have acted as important overlooked facilitators of gammaretrovirus spread across diverse mammalian hosts. Together, these results demonstrate the promise of the methodology used here to analyze large ERV datasets and improve understanding of retroviral evolution and diversity for utilization in wider applications.
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