publications

2025

1. Cell

   Ancient host-associated microbes obtained from mammoth remains

   Benjamin Guinet, Nikolay Oskolkov, Kelsey Moreland, and 3 more authors

   Cell, Sep 2025

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   Ancient DNA research has primarily focused on host genomes, but the recovery of microbial genomes associated with extinct species remains a major challenge. This study reports the recovery and analysis of ancient host-associated microbial DNA obtained from mammoth remains. By combining state-of-the-art sequencing, authentication frameworks, and comparative genomics, the study identifies microbial lineages preserved in permafrost-preserved mammoth specimens. The findings highlight both the preservation potential of host-associated microbes and their evolutionary significance in understanding host–microbiome interactions over deep time.

2. ProcRoyalB

   Dating the origin of a viral domestication event in parasitoid wasps attacking Diptera

   Benjamin Guinet, Jonathan Vogel, Nabila Kacem Haddj El Mrabet, and 4 more authors

   Proceedings of the Royal Society B: Biological Sciences, Jan 2025

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   Over the course of evolution, hymenopteran parasitoids have developed a close relationship with heritable viruses, sometimes integrating viral genes into their chromosomes. For example, in Drosophila parasitoids belonging to the Leptopilina genus, 13 viral genes from the Filamentoviridae family have been domesticated to deliver immunosuppressive factors to host immune cells, thereby protecting parasitoid offspring from the host immune response. The present study aims to comprehensively characterize this domestication event in terms of the viral genes involved, the wasp diversity affected by this event and its chronology. Our genomic analysis of 41 Cynipoidea wasps from six subfamilies revealed 18 viral genes that were endogenized during the early radiation of the Eucoilini/Trichoplastini clade around 75 million years ago. Wasps from this highly diverse clade develop not only from Drosophila but also from a variety of Schizophora. This event coincides with the radiation of Schizophora, a highly speciose Diptera clade, suggesting that viral domestication facilitated wasp diversification in response to host diversification. Additionally, in one of the species, at least one viral gene was replaced by another gene derived from a related filamentovirus. This study highlights the impact of viral domestication on the diversification of parasitoid wasps.

3. GigaScience

   Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes

   Nikolay Oskolkov, Chenyu Jin, Samantha López Clinton, and 7 more authors

   GigaScience, 2025

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   Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant assemblies. We show that masking these microbial-like regions significantly improves the reliability of taxonomic assignments in ancient environmental metagenomic datasets.

4. JGenVirol

   Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Animal DNA Viruses and Retroviruses Subcommittee, 2025

   Arvind Varsani, Adly M. M. Abd-Alla, Niklas Arnberg, and 71 more authors

   Journal of General Virology, Jul 2025

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   The International Committee on Taxonomy of Viruses (ICTV) holds a ratification vote annually after review of newly proposed taxa by ICTV Study Groups and members of the virology community. In March 2025, the vote outcome of the 11 proposals within the mandate of the Animal DNA Viruses and Retroviruses Subcommittee was made public. Here, we provide a summary of the newly accepted proposals. These include reorganization of taxa in the realm Varidnaviria, classification of the polinton-like viruses into a new family (Phypoliviridae) within a new order Archintovirales; establishment of a new phylum (Commensaviricota) in the kingdom Shotokuvirae; the establishment of a new family called Filamentoviridae with two new genera and three new species; the addition of four new genera in the family Anelloviridae with 70 new species; and the addition of 85 new species in the families Adenoviridae (n=16), Baculoviridae (n=5), Circoviridae (n=5), Parvoviridae (n=55) and Polyomaviridae (n=4).

5. MolEcol

   Reticulate and hybrid speciation is promoted by environmental instability in an Indo-Pacific species complex of whistlers (Aves: \emphPachycephala)

   Martin Irestedt, Ingo A. Müller, Filip Thörn, and 5 more authors

   Molecular Ecology, Nov 2025

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   Genomic studies have revealed introgressive hybridisation as a common phenomenon across the tree of life, particularly among young radiations. In this study, we use whole-genome data to investigate spatio-temporal introgression patterns in a songbird radiation that has colonised a highly dynamic island region in the Indo-Pacific. Some taxa within this radiation have colonised remote oceanic islands, whereas others occur on landmasses and islands in the Sahul region that were periodically connected during Pleistocene periods of lower sea levels. Our results show that introgressive hybridisation has been pervasive within this young radiation despite prominent plumage differences between taxa. Geographical proximity has been an important factor for hybridisation, and species occupying islands in the environmentally unstable Sahul region exhibit particularly strong signatures of introgression, while at least one species appears to have been shielded from hybridisation, potentially due to ecological specialisation.

6. Biorxiv

   The impact of reference genome divergence on ancient DNA damage detection in metagenomic contexts

   Benjamin Guinet, Bilal Muhammad Sharif, and Tom Valk

   Jul 2025

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   The reliability of ancient DNA (aDNA) authentication depends on detecting characteristic damage patterns, particularly cytosine deamination at fragment ends. However, in ancient metagenomic studies, sequence divergence between aDNA reads and available reference genomes may obscure such damage signals. We systematically evaluated how reference genome divergence, read count, read length and damage levels affect aDNA damage profiles using both empirical datasets and controlled simulations. Using ancient \emphYersinia pestis and hepatitis B virus data, we show that mapping to divergent reference genomes significantly reduces the detectability and intensity of characteristic damage patterns, particularly at low read counts. Simulations further revealed that reference genome identity is the strongest predictor of damage intensity, while read count primarily influences damage stochasticity. We introduce a correction matrix that adjusts C-to-T damage profiles for reference divergence, improving damage signal recovery. Our findings highlight methodological considerations for authenticating aDNA in metagenomic contexts, particularly when closely related reference genomes are unavailable.

2024

1. VirusEvolution

   A novel and diverse family of filamentous DNA viruses associated with parasitic wasps

   Benjamin Guinet, Matthieu Leobold, Elisabeth A Herniou, and 11 more authors

   Virus Evolution, Apr 2024

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   Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.

2. ScienceAdvances

   Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis

   Ricardo Rodríguez-Varela, Reyhan Yaka, Zoé Pochon, and 12 more authors

   Science Advances, Aug 2024

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   Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated. , Medieval genomes unveil genetic continuity, infections, and family relationships within an isolated population in Northern Iberia.

2023

1. eLife

   Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

   Benjamin Guinet, David Lepetit, Sylvain Charlat, and 8 more authors

   eLife, Jun 2023

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   The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.

2020

1. MBE

   A behavior-manipulating virus relative as a source of adaptive genes for Drosophila parasitoids

   D Di Giovanni, D Lepetit, B Guinet, and 6 more authors

   Molecular Biology and Evolution, Feb 2020

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   Some species of parasitic wasps have domesticated viral machineries to deliver immunosuppressive factors to their hosts. Up to now, all described cases fall into the Ichneumonoidea superfamily, which only represents around 10% of hymenoptera diversity, raising the question of whether such domestication occurred outside this clade. Furthermore, the biology of the ancestral donor viruses is completely unknown. Since the 1980’s, we know that Drosophila parasitoids belonging to the Leptopilina genus, which diverged from the Ichneumonoidea superfamily 225My ago, do produce immuno-suppressive viruslike structure in their reproductive apparatus. However, the viral origin of these structures has been the subject of debate. In this paper, we provide genomic and experimental evidence that those structures do derive from an ancestral virus endogenization event. Interestingly, its close relatives induce a behaviour manipulation in present-day wasps. Thus, we conclude that virus domestication is more prevalent than previously thought and that behaviour manipulation may have been instrumental in the birth of such associations.