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From Jurassic Germs to Gymnosperms: A Speculative Strategy for Reconstructing Dinosaur Genomes

Submitted:

10 July 2026

Posted:

13 July 2026

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Abstract
The longstanding dream of resurrecting dinosaurs faces formidable obstacles. DNA decays rapidly, making direct recovery impossible. Even if successful in their aims, and modern “synthetic” methods achieve a complete and functioning non-avian genome, they cannot recreate specific dinosaur species because at least some of the crucial genetic information is completely absent from living relatives. Alternatively, it is suggested here that microbial vectors once mediated horizontal gene transfer (HGT) between dinosaurs and the ancestors of extant species. While HGT appears rare, the ecological continuity between dinosaurs, microbes, and coexisting plants offers a faint but plausible route for fragments of dinosaur DNA to survived in extant species. Building on advances in paleogenomics, synthetic biology, and comparative genomics, we outline a multi-step strategy to search for, validate, and functionally test dinosaurian “genetic shrapnel” preserved in the “dark genome” of candidate organisms – particularly that of gymnosperms. If such material could be recovered, it might provide missing pieces needed to reconstruct extinct dinosaur species. Even if the goal of dinosaur de-extinction remains forever beyond reach, pursuing this line of research could yield transformative insights in evolutionary biology, synthetic biology, and conservation science — and offer a compelling narrative to engage the public.
Keywords: 
horizontal gene transfer
;  
gymnosperm
;  
genomics
;  
synthetic biology
;  
transposable elements
Subject: 
Biology and Life Sciences  -   Ecology, Evolution, Behavior and Systematics
University of New South Wales, Address: Level 4, Matthews Building, UNSW Sydney; douglas.roy@student.unsw.edu.au; Phone: 0425210178

Introduction

The prospect of dinosaur de-extinction has long fascinated scientists and the public alike—a fascination famously amplified by Michael Crichton’s Jurassic Park. Central to that story is the so-called “Mosquito Model”: the idea that dinosaur DNA might be recovered from the blood of ancient mosquitoes preserved in fossilized amber. Although conceptually compelling at the time, this approach is now widely regarded as scientifically implausible (Penney et al., 2013; Peris et al., 2020). DNA degrades far too rapidly due to chemical processes such as oxidation and has a half-life of just over 500 years (Allentoft et al., 2012). Moreover, fossilized amber is not airtight, which means there is, in practice, much opportunity for environmental factors to accelerate this degradation (Penney et al., 2013). Despite early enthusiasm in the 1990s and occasional reports of ancient DNA recovery from amber, later attempts failed to replicate those results (Peris et al., 2020; Penney et al., 2013). As such, the Mosquito Model has not brought us any closer to resurrecting dinosaurs in the decades since Jurassic Park first popularized the idea. Today, it survives more as a kind of scientific “fossil”—preserved not in amber, but in the collective imagination.
Two alternative approaches to the dream of dinosaur de-extinction have emerged with more scientifically credible foundations. One is the so-called “Dino-Chicken” project, which builds on the evolutionary continuity between non-avian theropod dinosaurs and modern birds. Birds are not merely descended from dinosaurs—they are dinosaurs. In fact, the genome of a modern chicken is likely closer to that of Tyrannosaurus rex than T. rex’s genome was to that of many other well-known but phylogenetically more distantly related dinosaurs, such as Allosaurus, Brontosaurus, or Stegosaurus. The Dino-Chicken approach rests on the idea that modifying gene expression in modern birds could reawaken dormant developmental pathways, producing phenotypes that resemble their non-avian ancestors (Horner & Gorman, 2009). Evolution often proceeds not by erasing old genetic instructions, but by overwriting or layering new adaptations over older ones—more like a palimpsest than a clean slate (Dawkins, 2024). This helps explain the appearance of atavisms: ancestral traits that occasionally re-emerge, such as chickens developing teeth or horses growing extra toes (Carroll, 2005; Gould, 1983). These phenomena suggest that the genetic instructions for long-lost traits may still be present, albeit silenced. On this view, the chicken genome is akin to a modern software program—for example, Microsoft Word Version 7—that retains legacy code from earlier versions, like Microsoft Word Version 3 (Dennett, 2017). By reactivating these latent instructions, researchers might engineer a bird with a long tail, toothed snout, and clawed forelimbs—features more typical of non-avian theropods than modern birds (Horner, 2009). While not identical to any specific dinosaur that has existed before, such a creature could be morphologically and functionally reminiscent of one. Evidence from experimental developmental biology supports this view, suggesting that bird genome retains many features inherited from its non-avian ancestors (Bhullar et al., 2015).
The second major approach to reconstructing dinosaur genomes draws on comparative genomics, which seeks to infer hypothetical ancestral genomes by analyzing the DNA of living relatives. This strategy—hereinafter referred to as the “synthetic approach”—focuses on sequencing the genomes of modern archosaurs, namely birds and crocodilians, and applying phylogenetic algorithms to reconstruct ancestral sequences (Griffin, Hassan, & Trifonov, 2019; O’Connor et al., 2018). These computational tools analyze genetic similarities and differences across species to estimate the genomic composition of their common ancestors. Such algorithms can identify conserved regions, estimate mutation rates, and model how genes diverged over time. The resulting phylogenetic trees not only map evolutionary relationships but also serve as scaffolds for assembling synthetic reconstructions of ancestral genomes (O’Connor et al., 2018). By comparing the genomes of birds and crocodilians, researchers can retroactively approximate segments of extinct dinosaur genomes (Griffin, Hassan, & Trifonov, 2019; Royal Veterinary College, 2024).
Additionally, the synthetic approach may be supplemented by insights from developmental biology and palaeontology. Fossil evidence can offer detailed anatomical and physiological information—such as tail length, limb proportions, or skull shape—that provide constraints on what genes must have been doing, even if their exact sequences are lost. In principle, if researchers develop a deep enough understanding of how genes regulate specific traits, it may be possible to functionally substitute missing genomic segments with sequences that encode the same developmental outcome, even if the original genetic "syntax" remains unknown. For instance, if fossil data suggest that Tyrannosaurus had a tail of a particular length, and if the genetic control of tail development is well understood, then new instructions could potentially be inserted into a synthetic genome to recapitulate this trait.
The three approaches discussed summarized in Figure 1 below. Despite their scientific merit, both the Dino-Chicken and synthetic approaches face inherent limitations that transcend current technological constraints. Even in the best-case scenario, the Dino-Chicken project could only reconstruct dinosaurs that are direct ancestors of modern birds. Crucial genetic components may be irretrievable from bird genomes due to mutations, deletions, or replacement by genes specific to avian adaptations. Similarly, while the synthetic approach may allow researchers to approximate a generalized non-avian dinosaur genome, it cannot recreate any specific species. Genes unique to Triceratops, Ankylosaurus, Deinonychus, and other extinct taxa would remain inaccessible—unless they were independently recovered from another source.
These limitations do not diminish the scientific value of either approach in advancing our understanding of developmental biology and evolutionary transitions. However, they mean these avenues offer little comfort to those hoping for true dinosaur de-extinction — or even a more plausible premise for dinosaur-themed films. The aim of this article is to explore a third, speculative possibility that may offer a new frontier. Namely, it is conceivable that fragments of dinosaur DNA endure within the cells of modern-day plants and fungi. If so, these overlooked reservoirs might provide a path toward recovering ancient genetic material.

The Genetic Shrapnel Approach

Consider an analogy from forensic ballistics — the science of reconstructing crime scenes from projectile fragments and impact patterns. Forensic experts infer a projectile’s type, trajectory, weapon of origin, firing distance, and number of shooters by analysing even the smallest surviving traces. In a similar way, dinosaurs — the dominant terrestrial vertebrates for nearly 180 million years—have left behind an abundance of indirect evidence. Although fossilization requires exceptional conditions, the sheer timespan and ecological dominance of dinosaurs have produced a diverse trace record: bones, footprints, coprolites, gastroliths, burrows, nests, eggshells, and feeding marks on other organisms. Palaeontologists, like forensic investigators, use these clues to reconstruct the morphology and behaviour of extinct species. If we set aside the fading hope of intact dinosaur DNA preserved in amber—and exclude birds as their direct descendants—we are left with a provocative question: could remnants of dinosaur DNA persist elsewhere in the biosphere? Like shrapnel embedded in unsuspected places, might genetic fragments survive today in unexpected forms?
One possibility is that fragments of dinosaur DNA were copied into the genomes of other organisms during the Mesozoic through horizontal gene transfer (HGT). HGT refers to the movement of genetic material between organisms by means other than parent-to-offspring inheritance. It often occurs via transposable elements (TEs), or “jumping genes”—mobile DNA sequences that can replicate and insert themselves throughout a genome and occasionally leap across species boundaries (Dunning Hotopp, 2011; Feschotte & Pritham, 2007; Richardson et al., 2015). In humans, for example, TEs make up roughly 50% of the genome, most of which are non-coding, but some are thought to have originated from ancient cross-species transfers embedded in what is sometimes called the “dark genome” (Dunning Hotopp, 2011; Richardson et al., 2015). We propose that similar mechanisms may have ferried dinosaur DNA into the genomes of other organisms – where it could persist in their descendants today, buried like genetic shrapnel in non-coding regions of extant taxa. This bypasses the problem of dinosaur DNA degrading, because the organisms that contain this genetic shrapnel have been actively duplicating it along with the rest of the genetic information that it has been embedded among.
It must be acknowledged that HGT from animals into other organisms is considered rare, and it appears that only a small fraction of well-characterized modern genomes to contain genes known to have arrived via this route (Crisp et al., 2015). However, a more optimistic perspective emerges when one considers the ecological context, evolutionary timescales, and the role of microbial intermediaries, to suggest that HGT from dinosaurs might have occurred with sufficient frequency to preserve meaningful genetic fragments—potentially enough to contribute to a reconstructed dinosaurian genome. The same line of reasoning also points to which types of organisms are most promising for detecting such ancient transfers.
HGT involving large animals is best documented in association with microorganisms, particularly bacteria and viruses. This is due to several biological features of microbes: they replicate rapidly, possess frequent genetic exchange mechanisms, and can integrate foreign DNA into their genomes. For instance, viruses can incorporate host genetic material during infection and later transfer it to other organisms, while bacteria can acquire DNA through transformation, transduction, or conjugation (Dunning Hotopp, 2011). Indeed, microbial genomes have been found to contain fragments of animal DNA, often embedded within TEs or associated with viral integration events (Boto, 2014). These findings raise the intriguing possibility that modern-day bacteria might harbor remnants of dinosaur DNA—molecular shrapnel preserved from ancient interactions. However, while microbes may have played a key role in facilitating gene transfer, they are unlikely themselves to serve as reliable long-term reservoirs of paleogenetic material. Bacterial genomes are small and highly dynamic, evolving quickly and subject to strong selection against non-functional DNA. As a result, any dinosaur-derived sequences that were once present are likely to have been degraded, lost, or mutated beyond recognition over the intervening 65 million years. Thus, while microbial vectors may have mediated ancient genetic transfers, they are unlikely to yield recoverable sequences suitable for genome reconstruction.
In contrast to bacteria and viruses, fungi may offer a more promising vehicle for preserving dinosaur DNA beyond the Cretaceous–Tertiary (K–T) extinction. Like bacteria, fungi engage in horizontal gene transfer (Richards et al., 2011) but possess far larger genomes that evolve more slowly (Narango-Ortiz & Gabaldón, 2019), increasing the likelihood of long-term DNA retention. There is some evidence of genetic material in fungi of animal origin (Alexander et al., 2016). Several fungal lineages that exist today were widespread during the age of dinosaurs, making ancient host–parasite interactions plausible (Redecker, Kodner, & Graham, 2000). Additionally, it seems reasonable to suppose that fungi’s capacity to infiltrate diverse host tissues could have facilitated acquisition of a broader array of host genes than would be likely of other parasites. Fungal genomes remain comparatively underexplored relative to those of bacteria, animals, and plants, and perhaps targeted genomic mining of fungi could reveal preserved dinosaur DNA fragments, although these sequences are likely to be fragmented and heavily modified by random mutational drift. We therefore advocate for targeted efforts to identify fungal lineages that likely interacted with dinosaurs and to survey their genomes for preserved genetic fragments. All that said, most fungi remain constrained by relatively modest genome sizes, meaning any retained dinosaur DNA is likely to be highly fragmented or heavily modified due to accumulated mutations. While fungi present a more favourable source than bacteria or viruses for discovering dinosaur genetic shrapnel, expectations for recovering complete or near-complete dinosaur genomes from fungal sources must remain tempered. Nonetheless, the potential insights gained from even partial sequences may warrant focused exploration.
Another candidate group are ticks because of their prolonged and intimate contact with host animals. Relative to microbial parasites, ticks contain a lot of genetic information, with most of this being a “dark genome”. The “dark genome” refers to the large portion of an organism’s genome that is not functionally active and tends to be where TEs reside (Feschotte & Pritham, 2007). There is reason to suspect that these regions, in ticks, contain genetic material that originated from host species, such as mammals and birds (Guilia-Nuss et al., 2016). At least six major extant genera of ticks share a common ancestor dating back to well before the extinction of dinosaurs (Klompen et al., 1996), meaning that potentially hundreds of species could trace their roots to lineages that independently engaged in HGT with dinosaurs. There is some direct evidence that ticks parasitized dinosaurs while not necessarily specializing on dinosaurs and so did not go extinct with them (Peñalver et al., 2017). A particularly interesting example of a tick that probably fed on dinosaur blood is Nuttallielliella namaqua. This is referred to as a “living fossil” because both molecular studies and morphological analysis of its fossilized ancestors suggest it has persisted virtually unchanged for hundreds of millions of years (Mans et al., 2011). These slow rates of evolutionary change mean that genes acquired through HGT from dinosaurs may still be present and hidden in their dark genome. In short, given ticks are notable because they have relatively large genomes for parasitic organisms – much of which is “dark” — and may be receptive to HGT from their host organisms, they could be especially worth searching to determine if they have been repositories for dinosaur genetic shrapnel.
Among the organisms with which dinosaurs likely maintained sustained ecological interactions, plants gymnosperms (particularly gymnosperms such as conifers, cycads, and ginkgo) possess some of the largest and most structurally stable dark genomes known. Unlike microorganisms, these plants possess vast, inherently slowly evolving genomes, and, in contrast to flowering plants or angiosperms, which undergo recurrent cycles of expansion and subsequent sequence purging, gymnosperm genomes are extremely large and stable. Genome sizes typically range from 12 to over 20 Gbp, with the Norway spruce (Picea abies) and loblolly pine (Pinus taeda) spanning approximately 19.6 Gbp and 22 Gbp, respectively (Nystedt et al., 2013).A crucial reason their genomes are so large is because they have especially enormous dark genomes rich in TEs (particularly long terminal repeat (LTR) retrotransposons), comprising up to 60–80% of the total sequence (De La Torre et al., 2017) and many times larger than the largest of known terrestrial animal genomes (Leitch & Leitch, 2012).
In most plant lineages, the expansion of transposable elements is counteracted by efficient removal mechanisms, chiefly unequal homologous recombination between flanking LTRs, which converts full-length elements into truncated solo-LTRs (Cossu et al., 2017). However, this process is markedly attenuated in gymnosperms. For example, Picea abies exhibits a solo-LTR to intact element ratio of approximately 1:9, in contrast to ratios approaching or exceeding 1:1 in many angiosperms such as Arabidopsis thaliana and Oryza sativa, and up to 16:1 in highly dynamic genomes such as Hordeum vulgare (Nystedt et al., 2013). This severe deficit of solo-LTRs indicates that once inserted, repetitive elements are rarely excised.
This observation brings up a related point. Gymnosperm genomes exhibit active gene conversion, which homogenizes sequences without reducing genome size, thereby preserving structural integrity while limiting large-scale deletion (Cossu et al., 2017). These contrasts are summarized in Table 1, which compares the structural properties of several major genomic environments with respect to their theoretical capacity for long-term sequence retention. Together, suppressed recombinational deletion, massive intronic expansion, and relatively slow molecular evolution create unusually favourable conditions for the long-term retention of inserted sequences. In this sense, gymnosperms represent unusually stable genomic environments in which foreign DNA fragments may persist as molecular fossils over hundreds of millions of years. These properties make gymnosperms particularly strong candidates for the long-term preservation of horizontally acquired genetic fragments under the genetic shrapnel model, given that direct trophic interactions between plants and animals provide a plausible interface for cross-kingdom genetic transfer.
Some empirical evidence may be mentioned in support of this theoretical possibility. For instance, the sweet potato whitefly (Bemisia tabaci) has acquired a plant-derived detoxification gene via horizontal transfer (Xia et al., 2021). This suggests that sustained herbivore–plant interactions can facilitate stable gene integration across kingdom boundaries, plausibly mediated by shared microbial or viral vectors. Importantly, there is direct empirical evidence that gymnosperm genomes can acquire and retain animal-derived transposable elements over deep evolutionary timescales. Lin et al. (2016) identified a lineage of Penelope-like retroelements (“Dryads”) embedded within the nuclear genomes of conifers that are phylogenetically nested within arthropod elements and entirely absent from other plant groups. This pattern is most parsimoniously explained by an ancient cross-kingdom horizontal transfer from an arthropod donor into conifers approximately 340 million years ago. Crucially, these elements have been retained and diversified within gymnosperm genomes over vast timescales, provides empirical support for the possibility that such genomes can act as long-term, stable repositories for foreign, animal-derived genetic material. Further consistent with the HGT mechanism, the cross-kingdom transfer of TEs between animals and plants has been documented: non-LTR retrotransposons of the RTE clade — typically associated with animals — have been identified in multiple plant lineages and shown to be more closely related to arthropod sequences than to plant homologs, indicating horizontal transfer from an animal donor (Gao et al., 2018). These findings demonstrate that “copy-and-paste” retrotransposition mechanisms are indeed capable of traversing large phylogenetic distances and successfully integrating into plant genomes.
Gymnosperms dominated the ecosystems dinosaurs inhabited. Their ecological prominence alongside dinosaurs, combined with the presence of myriad ancient microbial symbionts they also surely interacted with, creates fertile ground for horizontal gene transfer bridging dinosaurs and plants via microbial intermediaries such as soil bacteria, gut microbes, and parasitic fungi. Crucially, this trophic interface was probably mediated by wood-boring insects and their associated fungal symbionts. Giant sauropods and large ornithischians processing hundreds of kilograms of gymnosperm biomass daily did not delicately browse; they fractured bark, sheared branches, and shattered woody crowns. This destructive feeding left massive structural wounds coated in liters of dinosaur saliva, oral epithelial cells, and blood from abrasions, creating a direct conduit into the open vascular systems of the host plants. These high-volume biological wound sites acted as ecological beacons for wood-boring insects and their associated fungal symbionts, such as ancient lineages of Ophiostomatales. Because these wood-associated fungi and boring beetles are heavily documented to exhibit highly elevated rates of cross-kingdom horizontal transfer, they served as the primary physical intermediaries. Scaled across entire populations over 140 million years, this continuous, high-density biological loop creating repeated opportunities for rare horizontal transfer events across evolutionary timescales, continually concentrating fragmented dinosaur sequences into the hyper-stable, "obese genomes" of gymnosperm sinks. Moreover, hundreds of extant lineages of gymnosperms were already separated from common ancestors well before the extinction of dinosaurs (Biswas & Johri, 2013). This means that each of these lineages could be searched to collectively provide hundreds of samples potentially carrying dinosaur genomic fragments from ancient times to the present.
The point here is not that the retention of recognizable dinosaurian fragments is common, but that even extremely low-probability events become relevant over immense ecological and temporal scales. Thus, given this ecological and genomic continuity, we propose a novel and potentially viable strategy for reconstructing dinosaur genomes, one that involves searching for genetic fragments — what we term “genetic shrapnel”— that may have been horizontally transferred into the germlines of organisms surviving the K-T extinction (the basic idea is illustrated in Figure 2). These fragments could have been transposed via microbial intermediaries such as viruses, bacteria, or fungi into the genomes of ancestral gymnosperms or other long-lived lineages. If present in sufficient quantity and quality, these genetic remnants could help fill gaps in dinosaur genomes, thereby complementing reconstructions based on comparative genomics of birds and crocodilians (i.e., what we summarized as the “synthetic approach” above).
We propose the following stepwise strategy to pursue this line of inquiry:
  • Perform comprehensive genome sequencing of extant gymnosperm genera—particularly conifers—as well as relatively primitive (plesiomorphic) fungal and tick lineages.
  • Screen the “dark genome” of these organisms—regions enriched with transposable elements and non-coding DNA—for sequences that appear to originate from non-plant sources.
  • Cross-reference candidate sequences against known animal genomes and databases of horizontally transferred genes, focusing on segments plausibly derived from vertebrates.
  • Apply molecular dating methods to estimate the timing of HGT events and evaluate whether these events plausibly occurred during the Mesozoic era.
  • Use phylogenetic and comparative analyses to determine if these sequences correspond with known archosaur genomic features and to assess their likelihood of being dinosaurian in origin.
While speculative, this approach offers a novel and potentially transformative avenue for paleogenomic research. By leveraging the vast, slowly evolving genomes of gymnosperms and the ecological as well as microbial continuity spanning from the Mesozoic to the present, it explores the possibility that fragments of extinct dinosaur genomes may still be hiding in plain sight.

Finding a Dinosaur in a Haystack

Stephen Jay Gould’s essay “Dinosaur in a Haystack” exemplifies how scientific paradigms can shift through improved data sampling and theoretical reframing (Gould, 1995). Early palaeontologists interpreted the fossil record as showing a gradual dinosaur decline prior to the K–T extinction. However, the asteroid impact hypothesis prompted more systematic examination of fossil layers, revealing that dinosaurs remained diverse and abundant until the abrupt extinction event. This shift—from selective sampling to comprehensive scrutiny—offers a valuable methodological lesson for investigating rare biological phenomena. By analogy, HGT between animals and plants has long been considered vanishingly rare, based on limited data, theoretical barriers to cross-kingdom transfer, and perhaps underappreciation of the potential for HGT mediated by microbial intermediaries such as parasites (Bock, 2010; Crisp et al., 2015; Gilbert et al., 2010; Kambayashi et al., 2022). There is some clear evidence of HGT in the genomes of gymnosperms (Bergthorsson et al., 2004) although none, to our knowledge, thought to have originated in animals. However, a more systematic and targeted search may uncover unexpected genetic remnants of dinosaurs.
Another reason to suspect that HGT from dinosaurs to other organisms may have been more extensive than previously thought is that HGT events were likely more frequent during the Mesozoic than in subsequent eras. This period was generally characterized by warm, and humid environments with high levels of CO2, resulting in highly productive terrestrial ecosystems. Warmth and moisture increased microbial and parasite diversity and density, thereby enhancing opportunities for genetic exchange via HGT (González Villa & Vinas, 2019; Wani et al., 2022). Such high ecosystem productivity, combined with vast gymnosperm vegetation, supported dense and diverse microbial communities in soil and sediments — conditions known to foster horizontal gene transfer through physical proximity, biofilms, and abundant extracellular DNA. These relatively stable conditions were frequently punctuated by dramatic disturbances such as volcanic activity and continental drift, which would have disrupted habitats. Such evolutionary challenges are also known to elevate rates of HGT (González Villa & Vinas, 2019), and so rates may have been at levels during the Mesozoic that are beyond what prevail in more recent history.
While it is tempting to suppose that this pipeline could be piloted on more recently extinct Cenozoic megafauna — such as the Woolly Mammoth (Mammuthus primigenius) — as a proof of concept, such an approach risks overlooking paleoecological differences in time-depth and host genome dynamics. For example, Pleistocene mammoth-steppe was an ecologically transient system dominated by fast-evolving, highly dynamic angiosperm grasses that possess aggressive sequence-purging mechanisms. In contrast, Mesozoic ecosystems offered a continuous, 140-million-year coevolutionary window heavily dominated by gymnosperms, which we have reasons to suppose are more effective as genomic sinks due to their slow molecular clocks and suppressed transposable element removal. This does not imply that Pleistocene megafauna are poorer candidates for conventional paleogenomic recovery. Rather, under the specific logic of the genetic shrapnel model, long-term sequence retention may depend less on recency alone than on the structural stability of the host genomes into which foreign DNA became embedded.
Several considerations further justify optimism about this strategy’s prospects. First, detailed knowledge of modern taxa can help guide extensive searches through the vast “haystack” of plant and fungal genomes to identify likely dinosaur DNA. For example, regions adjacent to sequences that overlap with or are compatible with bird and synthetic archosaur genomes—but are conspicuously missing from these references—may represent uniquely dinosaurian genes. By “daisy-chaining” these overlapping fragments to progressively reconstruct a more complete core dinosaur genome, researchers could continually improve the sensitivity and accuracy of subsequent searches in a virtuous cycle.
Secondly, to further shrink the gap that remains to be filled by our genetic shrapnel approach, it should be noted that, although birds have evolved rapidly since their split with the ancestors of crocodilians, crocodilians have undergone relatively little genetic change (Green et al., 2014), helping to provide a potentially robust genomic template for archosaurs. Moreover, molecular evidence confirms Tyrannosaurus Rex and birds are more related to each other than birds are to any non-Avian animal today (Asara et al., 2007), and it is reasonable to suppose they would have shared approximately 80 per cent of the same genetic information needed to produce a viable organism. So, if some of this difference can be made up for by the synthetic approach (i.e., using a generic archosaurian template, infer functionally equivalent genetic information for helping to control some phenotypic differences such as in growth rates or integumentary structures), the truly irreplaceable portion of the genome may be reduced further still.
Thirdly, if genetic information was transferred from dinosaurs to plants, this transfer may not represent random sampling. Genes located in genomic “hotspots” — regions that evolve rapidly and frequently underlie species-specific adaptations (Edsinger et al., 2024) —may be especially prone to be involved in HGT from host to microorganisms. This is because these genetic regions are more likely to be copied by microorganisms if those regions are especially highly expressed (Feschotte & Pritham, 2007) and structurally dynamic (Crisp et al. 2015). So, if these hotspots disproportionately contained traits that distinguished different dinosaur genera from one another and from their modern relatives, then the genetic shrapnel preserved and transferred according to our model may disproportionately represent fragments relevant to distinctive dinosaurian traits.
While genes encoding such traits may be more prone to horizontal acquisition, the "complexity hypothesis" provides a plausible mechanism for their long-term persistence within gymnosperm architectures. Traditionally, this hypothesis predicts that informational genes involved in highly interconnected macromolecular networks (such as transcription, translation, and developmental regulation) exhibit exceptionally low rates of successful functional domestication following HGT, as their products cannot easily integrate into foreign cellular backgrounds (Jain et al., 1999; Burch et al., 2023). However, functional integration is not a prerequisite under the genetic shrapnel model. Indeed, dinosaur-derived sequences with low physiological compatibility may have been preferentially transcriptionally silenced and relegated to heterochromatic genomic regions. Within the exceptionally massive and slowly purged genomes of gymnosperms, these silenced inserts could persist as dormant molecular fossils: effectively shielded from selective pressures precisely because of their likely lack of functional integration into the host’s biology.
Another consideration worth emphasizing is the vast biological throughput of dinosaurs. Well-known species like Tyrannosaurus rex existed for millions of years and were abundant across wide geographic ranges. It is estimated that approximately 2.5 billion adult T. rex individuals have ever lived (Marshall, Ward, & Smith, 2021) and would have widely roamed environments dominated by conifers, cycads, and fungi. Thus, even if the per-event probability of HGT into gymnosperm or fungal genomes was minuscule, this immense biological volume could have yielded meaningful quantities of genetic fragments. Moreover, this estimate likely underrepresents the potential for genetic recovery. Dinosaurs form a clade, meaning genomic information recovered from one lineage can inform missing segments in related lineages through comparative genomics (O’Connor et al., 2018). For example, while T. rex existed for roughly 2 million years, the broader Tyrannosauridae family persisted for around 7 million years (Brusatte & Carr, 2016). Genetic data missing from T. rex may be partially recoverable from other tyrannosaurids and theropods, with overlap proportional to their relatedness. Similarly, Brontosaurus lived for perhaps 2 million years, but their broader clade of sauropods thrived for roughly 70 million years and represent a sister clade to the theropod clade that gave rise to other groups like Tyrannosauridae and birds. Thus, although, say, Brontosaurus material would be less relevant to T. rex, it would still probably contribute information that would otherwise be missing and go some way in contributing to the reconstruction of sauropod genomes, and so forth. In other words, overlapping sequences among more abundant and longer-lasting relatives reduce the burden of recovering unique DNA for any particular dinosaur species that was around for less long, and so had less opportunity to leave behind much genetic shrapnel.
In short, genetic material from widespread and long-lived dinosaur clades likely contains overlapping sequences useful for reconstructing rarer varieties, thereby improving the prospects for comprehensive genome recovery. Far from replacing the Dino-Chicken and synthetic approaches, the genetic shrapnel strategy is predicated on their continued advancement. These existing approaches help minimize the genetic information that must be recovered as shrapnel and guide searches to be more targeted and effective. A maximally developed, “core archosaurian genome,” derived from extant birds and crocodilians, is fundamental.

Sifting for Shrapnel

To move from theoretical plausibility to any chance of real-life progress, a systematic and multi-pronged methodological approach is required. Figure 3 recapitulates the recommendations made above on how researchers might begin to identify, validate, and interpret potential dinosaur genetic fragments embedded in extant genomes while extending the synthetic approach toward resurrecting dinosaurian biology. A potential concern is that identifying rare, deeply diverged genetic fragments within large eukaryotic genomes may be intractable if approached as an unconstrained search across all taxa. However, the genetic shrapnel model lends itself to a far more targeted comparative framework. Rather than attempting to scan broadly across Eukaryota, the search can be restricted to biologically motivated pairwise comparisons between candidate "genomic sink" lineages—such as gymnosperms and long-lived fungi—and reconstructed ancestral archosaur genomes. Ancestral archosaurian reference sequences could be inferred using standard ancestral-state reconstruction methods applied to extant avian and crocodilian genomes within fossil-calibrated phylogenetic frameworks.
In such a pipeline, candidate genomes would first be partitioned to focus on regions enriched in non-coding DNA and transposable elements, where horizontally transferred fragments are most likely to persist. These regions could then be queried against inferred archosaurian ancestral sequences using sensitive homology-detection methods, including profile hidden Markov models capable of detecting deeply diverged sequence similarity (Eddy, 2011). Putative matches would subsequently be grouped into orthologous clusters and subjected to gene-tree reconstruction using established orthology-inference approaches (Emms & Kelly, 2019), allowing identification of sequences whose phylogenetic placement is incongruent with established species relationships, a widely recognised hallmark of horizontal gene transfer (Boto, 2014; Zhu et al., 2014). Additional filtering could be applied using Alien Index-type metrics (Rancurel, Legrand, & Danchin, 2017), which quantify whether a sequence exhibits stronger similarity to distant taxa than to its expected phylogenetic neighbours.
This approach dramatically reduces the effective search space by focusing only on comparisons motivated by ecological and evolutionary priors while leveraging well-established heuristics for detecting horizontal transfer, including phylogenetic incongruence, atypical sequence similarity, and anomalous taxonomic distribution (Boto, 2014; Zhu et al., 2014). Similar methodological frameworks have successfully identified ancient and cross-kingdom transfers of both transposable elements and protein-coding genes among plants, fungi, and animals (Moran & Jarvik, 2010; Lin et al., 2016; Gao et al., 2018), demonstrating that highly localized evolutionary signals can be recovered despite deep phylogenetic divergence. At least initially, the objective would not be exhaustive genome reconstruction but rather the identification of a limited set of high-confidence candidate sequences exhibiting signatures consistent with ancient horizontal transfer.
The feasibility of detecting such signals, even across deep evolutionary divergence, is supported by recent findings of cross-kingdom horizontal transfers, including predator–prey transmission of transposable elements among vertebrates, metazoan-derived genes embedded within fungal genomes, and widespread gene exchange across plant, fungal, and animal lineages. Within this framework, the objective at initial stages would not be exhaustive genome reconstruction, but the identification of a limited set of high-confidence candidate sequences exhibiting signatures consistent with ancient horizontal transfer.
The next stage would involve large-scale sequencing of candidate organisms likely to harbour dinosaurian genetic fragments. Revolutions in Next-Generation Sequencing (NGS) technology allow the entire genomes of species to be sequenced at rates that were unimaginable when the mosquito model was first contemplated, making it viable to sequence the complete genomes of gymnosperms, arachnid parasites such as ticks, and phylogenetically ancient fungal networks. Computational pipelines can then systematically scan these genomes for regions exhibiting hallmarks of ancient HGT events. These candidate sequences can be filtered based on molecular markers indicating likely animal origin. If substantial amounts of such genetic material are found, they can be organized according to their resemblance to regions likely encoding proteins or serving regulatory roles, with comparisons made to the known or inferred “core archosaurian” genome. Molecular clock methods could then be employed to date these HGT events, helping to determine whether candidate sequences originated from the same or related Mesozoic genera. This temporal information would guide hypotheses about functional relationships between regions and their genomic organization. Finally, these hypotheses could undergo iterative generate-and-test cycles using gene-editing technologies combined with synthetic biology approaches, aiming to establish how these fragments might be workably incorporated into a more complete archosaurian genome with the long-term aim of integrating such fragments into increasingly complete synthetic archosaurian genomes.
Recent advances in large-scale comparative genomics make such approaches increasingly tractable. Tools like GATOR-GC (Genomic Assessment Tool for Orthologous Regions and Gene Clusters), for example, exemplify this progress. GATOR-GC enables researchers to efficiently examine millions of gene clusters across hundreds of genomes. This approach promises to combine information about evolutionary conservation and the surrounding genomic context at scales not imagined by approaches based on earlier methods (Cediel-Becerra et al., 2025).
Complementary approaches such as transcriptomics and metabolomics may further aid functional interpretation of candidate sequences by identifying associated regulatory activity and biochemical pathways (Go et al., 2024; Prabahar, 2022). In parallel, increasingly sophisticated computational methods—including network-based approaches and machine learning techniques—may improve detection of weak or deeply diverged signatures of ancient horizontal transfer within large genomic datasets (Abby et al., 2014; Perkel, 2025).
It must be noted that long mutational histories, recombination, gene conversion, and shifting selective pressures could substantially obscure the signals required to identify ancient HGT events. These processes may also violate assumptions underlying traditional molecular clock approaches. A variety of techniques have evolved to help address these challenges. An example is the use of “relaxed clock models” that allow for the possibility of mutation rates varying across lineages (Bromham et al., 2020; Drummond & Rambaut, 2007; Ho & Duchêne, 2014). Statistical techniques are being developed to detect and account for rate variation and recombination (Rasmussen & Kellis, 2012). Reliable molecular dating of ancient HGT events could combine several approaches to reconcile speculative gene and species phylogenetic trees with information from the fossil record (Szöllősi et al., 2015), relaxed clock models applied to suspected transferred genes (Drummond & Rambaut, 2007; Ho & Duchêne, 2014), and integration of genomic and ecological data to constrain timing despite mutational complexities (Rasmussen & Kellis, 2012). By using some combination of methods like these, we may be able to approximate the ages of specific HGT events with improving accuracy as data and models improve.

Bully for Brontosaurus

To evaluate the true viability of this model, it is helpful to conceptualize the genetic shrapnel hypothesis not as a singular, all-or-nothing gamble on de-extinction, but as a spectrum of progressive milestones. Each level of this spectrum represents a distinct gradation of empirical testability, computational investment, and potential scientific yield, shifting from immediate, low-cost bioinformatic verification to long-term synthetic exploration (Table 2). Even if the ultimate and most ambitious goal of resurrecting a dinosaur remains elusive, pursuing this research trajectory promises transformative benefits across multiple scientific fields and society at large. Efforts to identify ancient genetic fragments embedded in modern genomes could pioneer novel techniques in the emerging field of genomic archaeology. By combining comparative genomics, machine learning, and synthetic biology, these methods could be extended to other extinct lineages, greatly deepening our understanding of evolutionary history and the persistence of genomes over deep time.
This research could also significantly advance our understanding of HGT in multicellular eukaryotes. While HGT is well documented in microbes, its role in plants and animals remains poorly understood. Demonstrating that ancient animal genes are preserved through HGT may challenge and potentially reshape evolutionary theory and open new avenues for studying gene flow across kingdoms. Reconstructing extinct traits from partial genetic information would push the frontiers of synthetic biology, driving the development of novel tools for gene synthesis, regulatory network modelling, and developmental pathway engineering. These technologies could have wide-ranging applications in medicine, agriculture, and bioengineering. Furthermore, attempts to reverse-engineer dinosaur traits from genomic fragments could provide valuable insights into the genetic foundations of form and function. Such work could lead to new models in evolutionary developmental biology (evo-devo), especially concerning how complex traits emerge, diversify, and are shaped by phylogenetic constraints. More broadly, the pursuit of dinosaur gene recovery may provide a compelling framework for public engagement with genetics, palaeontology, and biotechnology. Like earlier landmark scientific projects, ambitious long-term goals can stimulate curiosity, attract interdisciplinary collaboration, and promote scientific literacy.

Summary and Conclusions

Dinosaur genes may have been channelled by fungi or microbial vectors in a way that resulted in fragments of dinosaur DNA becoming embedded into the genomes of plants and fungi, thereby preserving molecular echoes of these long-extinct animals. While this hypothetical scenario may seem improbable, whether sufficient, if any, dinosaur DNA could be recovered in this way remains an open empirical question. By applying systematic search strategies — guided by knowledge of phylogenetic relationships and targeting the “dark genomes” of living species where such shrapnel is most likely to reside (we have suggested gymnosperms) — the recovery of meaningful dinosaur genetic remnants could shift from speculation toward strategic plausibility and practical possibility. Even if full de-extinction remains out of reach, pursuing this research could yield profound scientific rewards, such as galvanizing public support for advances in molecular and developmental biology and deepening our understanding of horizontal gene transfer in complex multicellular organisms. If nothing else, if this article can provide some comfort to those who dream of dinosaurs one day again walking the earth, then it has achieved its purpose.

Data Availability Statement

Data sharing is not applicable to this article as no new data were created or analysed in this study.
Statements and Declarations: I received no funding for the production of this manuscript and have no conflicts of interest to declare.

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Figure 1. Three Approaches to Dinosaur Paleogenomics. Venn diagram showing rough overlap of genetic identity between three archosaurians: crocodiles, chickens, and triceratops. The mosquito model hoped to clone dinosaurs from near complete genetic information preserved in fossilized mosquitos. The “dino-chicken” approach seeks to make heterochronic adjustments to the development of chickens to exploit genetic material inherited from their mid-Jurassic ancestors (genetic material shaded in light grey). Some of this genetic information and other material overlapping between crocodilians and both extinct dinosaurs and birds to reconstruct a basic archosaurian genetic template (probably not a functional animal).
Figure 1. Three Approaches to Dinosaur Paleogenomics. Venn diagram showing rough overlap of genetic identity between three archosaurians: crocodiles, chickens, and triceratops. The mosquito model hoped to clone dinosaurs from near complete genetic information preserved in fossilized mosquitos. The “dino-chicken” approach seeks to make heterochronic adjustments to the development of chickens to exploit genetic material inherited from their mid-Jurassic ancestors (genetic material shaded in light grey). Some of this genetic information and other material overlapping between crocodilians and both extinct dinosaurs and birds to reconstruct a basic archosaurian genetic template (probably not a functional animal).
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Figure 2. The Genetic Shrapnel Model. Upward movement depicts genetic information transferred vertically (from parent to offspring) from prehistoric times to the modern day. Meanwhile, horizontal (red dashed lines) represents genes transferred hypothetically through HGT events via microorganisms.
Figure 2. The Genetic Shrapnel Model. Upward movement depicts genetic information transferred vertically (from parent to offspring) from prehistoric times to the modern day. Meanwhile, horizontal (red dashed lines) represents genes transferred hypothetically through HGT events via microorganisms.
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Figure 3. Suggested filtering system for identifying functional genetic information originating in dinosaurs. Starting with mass sequencing of gymnosperm (and possible candidate organisms such as fungi and tics), various filters are applied until genetic material can be organized to be tested in biological tissues. If successful, components needed to recreate uniquely dinosaurian genomes may be accumulated, piece by piece, and combined with an archosaur template provided from modern birds and crocodilians.
Figure 3. Suggested filtering system for identifying functional genetic information originating in dinosaurs. Starting with mass sequencing of gymnosperm (and possible candidate organisms such as fungi and tics), various filters are applied until genetic material can be organized to be tested in biological tissues. If successful, components needed to recreate uniquely dinosaurian genomes may be accumulated, piece by piece, and combined with an archosaur template provided from modern birds and crocodilians.
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Table 1. Caption.
Table 1. Caption.
Lineage Genome Size (Gb) Repetitive Fraction (%) TE Removal Efficiency Long-Term Retention Potential
Gymnosperms
(e.g., Picea abies) 		12.0 – 22.0+ 60% – 80% Highly Attenuated
(Solo-LTR ratio ~1:9)		 Exceptional
(Suppressed deletion; acts as stable genomic sink)
Angiosperms (Dynamic)
(e.g., Hordeum vulgare) 		5.0+ 80%+ Extremely High
(Solo-LTR ratio up to 16:1)		 Very Low
(Rapid sequence purging and turnover)
Angiosperms (Model)
(e.g., Arabidopsis thaliana) 		~0.13 ~10% – 14% High
(Solo-LTR ratio ~1:1)		 Low
(Streamlined, highly compact genome architecture)
Filamentous Fungi
(Ancient lineages) 		0.03 – 0.10 10% – 50% Variable
(Highly dependent on active RIP mechanisms)		 Moderate to High
(Maintained via persistent endophytic intimacy)
Note. Data compiled from Devos et al. (2002), Nystedt et al. (2013), and Vitte et al. (2005). Solo-LTR ratios specifically reflect the efficacy of unequal intra-element homologous recombination, where low ratios indicate a suppressed capacity to purge retrotransposon inserts over evolutionary timescales.
Table 2. caption.
Table 2. caption.
Milestone Hypothesis Testable Via Current Tech Potential Scientific Yield
Level 1
(Basic) 		Uniquely dinosaurian non-coding or coding sequence fragments exist as stable inserts within gymnosperm/fungal genomes. Targeted pairwise bioinformatic pipelines (profile HMMs, alien index screening). Direct empirical proof of Mesozoic cross-kingdom HGT; identification of macroevolutionary "dark matter."
Level 2
(Moderate) 		Discovered fragments are numerous and conserved enough to significantly refine and refine ancestral archosaurian genomic reconstructions. Digital sequence alignment, orthologous clustering, and ancestral node reconstruction. Deepening our understanding of the avian stem lineage, filling critical gaps in the archosaurian evolutionary tree.
Level 3
(Advanced)
 Retained fragments are diverse enough to cluster into distinct taxonomic groupings (e.g., sauropod vs. ornithischian) or functional developmental circuits. Comparative phylogenomics, gene-tree incongruence mapping, and molecular clock dating of HGT insertion events Mapping the divergence of major Mesozoic lineages and identifying the genetic architecture behind unique dinosaurian traits.
Level 4
(Speculative) 		A high-density "patchwork" of overlapping fragments allows the partial or near-complete digital assembly of specific dinosaurian genera. Computational "daisy-chaining" of fragments against inferred core archosaur frameworks using predictive AI. The generation of the first high-confidence, genus-specific digital paleogenomes.
Level 5
(Deeply Speculative) 		Assembled paleogenomic sequences can be functionally integrated into living archosaurian cellular/ developmental systems. Advanced synthetic biology, iterative CRISPR-mediated genome editing, and artificial embryology. The in vitro expression of dinosaurian proteins, localized tissue differentiation, or remote developmental phenotypes.
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