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PubMed2026

De-extinction technology and its application to conservation.

De-extinction, once the realm of science fiction, has evolved into a tangible scientific endeavor thanks to breakthroughs in genome sequencing, engineering, advanced assisted reproductive technologies, and stem cell biology. Alongside this work are innovations in reintroduction science and artificial intelligence, which are refining strategies for species translocations, rewilding, and long-term ecosystem monitoring of de-extinct species and populations. While the primary motivation for de-extinction is restoring lost ecological functions to eroded ecosystems, each of these technologies can also be applied to conservation biology for de-endangerment, offering new solutions for biodiversity preservation. This review synthesizes the technological advancements emerging from de-extinction science and explores their broad applications in conservation, demonstrating how de-extinction is both about resurrecting lost species and about expanding the conservation toolkit to sustain and rebuild biodiversity in the face of accelerating environmental change.

Conservation of Natural Resources↗
PubMed2025

PUS7-dependent Ψ reshapes specific synaptic gene exons to facilitate fear extinction memory formation.

RNA modifications serve as dynamic regulators of neural plasticity through their ability to fine-tune transcript stability and splicing. Pseudouridine (Ψ), an evolutionarily conserved RNA modification catalyzed by pseudouridine synthases, plays established roles in neurodevelopment, yet its functional significance in activity-dependent behavioral adaptation remains poorly defined. Here, we investigate Ψ-mediated epitranscriptomic regulation within the infralimbic prefrontal cortex (ILPFC), a brain region requiring precise synaptic remodeling for the clinically relevant form of fear extinction memory. Combining transcriptome-wide pseudouridylation profiling with behavioral analysis in mice, we identified selective Ψ enrichment at exons of synaptic regulatory genes within ILPFC during fear extinction learning. Fear extinction in the ILPFC drives concomitant exonic Ψ deposition and upregulation of synaptogenic transcripts, processes that involve pseudouridine synthase PUS7. Crucially, PUS7 knockdown in the ILPFC selectively impaired fear extinction memory formation without altering baseline fear expression, establishing a causal link between Ψ-dependent RNA processing and activity-dependent synaptic structural remodeling in this microcircuit. Our findings demonstrate that PUS7-mediated Ψ modification spatiotemporally regulates activity-dependent RNA dynamics in the ILPFC, providing the evidence that epitranscriptomic mechanisms precisely coordinate synaptic gene expression within behaviorally defined brain sub-region. This work bridges molecular RNA biology with systems neuroscience, revealing a novel mechanism for activity-dependent regulation of fear extinction in ILPFC.

Animals↗
PubMed2025

Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss.

Gene loss shapes lineage-specific traits but is often overlooked in species survival. In this study, we investigate the role of ancestral gene loss using the extinction icon-thylacine (Thylacinus cynocephalus). While studies of neutral genetic variation indicate a population decline before extinction, the impact of thylacine-specific ancestral gene losses remains unexplored. The availability of a chromosomal-level genome of the extinct thylacine offers a unique opportunity for such comparative studies. Here, we leverage palaeogenomic data to compare gene presence/absence patterns between the Tasmanian devil and thylacine. We discovered ancestral (between 13-1 Ma) loss of SAMD9L, HSD17B13, CUZD1 and VWA7 due to multiple gene-inactivating mutations, corroborated by short-read sequencing. The timing of gene loss mirrors the thylacine's shift towards hypercarnivory and increased body size. Notably, the loss of SAMD9 correlates with a carnivorous diet. Our genome-wide analysis reveals olfactory receptor loss and relaxed selection, aligning with reduced olfactory lobes in the thylacine, indicating olfaction is not its primary hunting sense. By integrating palaeogenomic data with comparative genomics, our study reveals ancestral gene losses and their impact on species survival and resilience to environmental changes. Our approach can be extended to other extinct and endangered species, helping to identify genetic factors for conservation efforts.

Animals↗
PubMed2026

The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids.

Admixed genomes, particularly those with an evolutionary history of genetic exchange with an endangered or extinct species, are valued for innovative and unconventional conservation actions. Here, we show the substantial conservation value that the admixed canids of the Gulf Coast have as they retain high amounts of contemporary Red Wolf ancestry and unique genetic variation of past Red Wolf lineages (e.g. ghost ancestry). We analyzed 54,439 loci genotyped across the genome of 413 North American canids and investigated the role that assortative mating with respect to ancestry proportions played in the retention of endangered genetic variation. We report high correlations of inter-chromosomal ancestry proportions that varied with geographic location along Texas and Louisiana Gulf Coast populations, with the stronger signatures reported in the latter. We found that models of assortative mating promoted greater ancestry variance compared with random mating leading to increased efficiency of selection for Red Wolf and ghost alleles. Despite the Red Wolf being extinct in the wild, original, and ghost genomic variation persists in Gulf Coast admixed canids. We suggest two conservation strategies that value and preserve this unique and endangered genomic variation through designed breeding programs. Ultimately the incorporation of this ghost genetic variation would be valuable to boost the genetic viability of the ex situ Red Wolf breeding program, create in situ redundancy, and avoid extinction for this endemic American wolf species.

Animals↗
PubMed2025

Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.

Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.

Animals↗
PubMed2026

Skull morphology of the extinct Tasmanian tiger suggests unique biting style.

The recently extinct thylacine (Tasmanian tiger) was the largest modern marsupial predator. It is considered a classic example of evolutionary convergence due to striking similarities with placental canids (e.g., foxes and wolves), particularly in the skull, despite ~160 million years of evolutionary separation. However, we here present geometric and linear morphometric evidence that the thylacine's cranial form arises from a mosaic of traits not represented among canids or other living mammalian carnivores. Thylacines had disproportionately large heads, tall and gracile snouts with a flared canine region, and conspicuously large infraorbital foramina. Many of these traits suggest adaptations to fast, high-impact snapping behaviour in prey capture, as proposed for several living and extinct predatorial vertebrates with similar trait combinations. The thylacine's cranial function may therefore not be inferable from observation of living mammals. However, genomic progress presents new opportunities for future insights into the evolution and development of thylacine cranial adaptation.

Animals↗
PubMed2026

Sexual selection purges mutation load, but not overall genetic diversity, decreasing vulnerability to extinction.

Theory suggests sexual selection will enhance population viability by purging deleterious alleles. However, direct genomic evidence for this fundamental idea is scarce and contradictory. We combined long-term experimental evolution with whole-genome resequencing to directly test how sexual selection affects mutation load, genomic divergence, and extinction risk in small populations (maximum Ne = 40) of Tribolium castaneum. After 156 generations, populations evolving under strong sexual selection carried substantially fewer deleterious alleles than populations under weak sexual selection, based on both individual-level estimates of missense and nonsense variants and population-level Rxy analyses, indicating more efficient purging of deleterious alleles. In contrast, nucleotide diversity and runs of homozygosity were similar across treatments, indicating that purging acted most strongly on deleterious variation, and that reduced mutation load in these small populations under strong sexual selection was not explained by demographic effects. Importantly, population-level mutation load estimates best explained extinction risk under inbreeding, directly linking sexual selection to purging and population viability. Genome scans of high and low sexual selection populations revealed peaks of divergence, which included genes involved in courtship, sex discrimination, and seminal fluid proteins. Our results provide direct genomic evidence that sexual selection can reduce mutation load without eroding standing genetic diversity and thus adaptive potential, while driving adaptive divergence in reproductive traits. This beneficial purging may help explain the widespread prevalence of sexual reproduction in nature despite inherent costs and have important ramifications as to how we manage populations of conservation concern.

Animals↗
PubMed2026

Genomic erosion in the assessment of species' extinction risk and recovery potential.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

Extinction, Biological↗
PubMed2026

Evolutionary history of Aotearoa New Zealand's extinct mātuhituhi | bush wren.

The reconstruction of ecosystem responses to past climate change has historically focused on large vertebrates. In contrast, small vertebrates with potentially stricter habitat preferences have been neglected in ancient DNA studies despite their potential utility as proxies for inferring geographic and temporal changes in habitat. Aotearoa New Zealand's acanthisittid wrens are a speciose group of tiny perching birds, including the mātuhituhi | bush wren (Xenicus longipes ssp.). Despite its relatively recent extinction in the 1970s, very little is known about this enigmatic bird. Here we sequence mitochondrial genomes and nuclear ultra conserved genomic elements from 32 historical bush wren specimens to reconstruct their evolutionary history. We also genetically sex specimens and reanalyse their plumage to reconstruct aspects of bush wren plumage variation. Our analyses suggest North and South Island bush wren populations diverged 2.6 million years ago when narrowing and closure of Plio-Pleistocene seaways allowed colonisation of new habitats, followed by rapid glaciation-driven diversification of South Island populations 470,000-94,000 years ago. Genetic sexing allowed an accurate reconstruction of ontogenetic, sexual, and geographic variation in plumage. Our multidisciplinary data supports recognition of North and South Island populations as separate species, and the description of a new subspecies X. longipes perditus subsp. nov. This research shows how ecosystems can buffer against the impacts of climate change up to an ecological tipping point, which has important lessons for conservation management in a fast-changing world.

Acanthisittidae↗
PubMed2026

Past genomes guide future conservation: insights from extinct populations of the endangered Pacific pocket mouse.

Efforts to recover endangered species often rely on restoring populations to their historical range, yet reestablishing lost genetic variation is challenging when the ancestral genetic landscape is poorly understood. The Pacific pocket mouse (Perognathus longimembris pacificus), a federally endangered heteromyid rodent, has been extirpated from most of its range in coastal southern California. Recovery efforts call for establishing new populations in their historic range through translocation, but the extent to which historical patterns of genetic variation can be recapitulated is unknown. To inform conservation planning, we sequenced whole genomes of historical samples, including individuals from populations that went extinct in the mid-1900s. Phylogenetic analyses revealed that mice from the southernmost extirpated population form a clade with a different subspecies, while populations to the north form a sister clade. These findings support morphological evidence calling for a taxonomic revision, which would modify the definition of the historic range and complicate the interpretation of suitable reintroduction sites. Despite this divergence, D-statistics and demographic models indicate historical gene flow among coastal populations, suggesting that alleles reintroduced to the southern coast may echo ancestral connectivity. Thus, management efforts should consider potential receiver sites that contain suitable habitat within this range as viable for population creation. These results highlight the value of historical genomics in guiding conservation decisions, particularly when taxonomic uncertainty, extirpation, and limited genetic diversity constrain modern management. Although historical baselines often cannot be restored, conservation strategies can leverage genomic insights to enhance future adaptive potential and long-term resilience of threatened species.

Endangered Species↗
PubMed2025

NANOG is repurposed after implantation to repress Sox2 and begin pluripotency extinction.

Loss of pluripotency is an essential step in post-implantation development that facilitates the emergence of somatic cell identities essential for gastrulation. Before implantation, pluripotent cell identity is governed by a gene regulatory network that includes the key transcription factors SOX2 and NANOG. However, it is unclear how the pluripotency gene regulatory network is dissolved to enable lineage restriction. Here, we show that SOX2 is required for post-implantation pluripotent identity in the mouse, and cells that lose SOX2 expression in the posterior epiblast are no longer pluripotent. Using in vitro and in vivo analyses, we demonstrate anticorrelated expression of NANOG and SOX2 preceding gastrulation, culminating in an early disappearance of pluripotent identity from posterior NANOGhigh/SOX2low epiblast. Surprisingly, Sox2 expression is repressed by NANOG and embryos with post-implantation deletion of Nanog maintain posterior SOX2 expression. Our results demonstrate that the distinctive features of post-implantation pluripotency are underpinned by altered functionality of pluripotency transcription factors, ensuring correct spatio-temporal loss of embryonic pluripotency.

Animals↗
PubMed2026

Emerging trends in genome editing of wild animals.

Globally, nearly one million species are currently threatened with extinction, highlighting the need for more efficient solutions to biological conservation. Genome editing, which allows for faster and more precise changes in genomes, is a promising technique for boosting populations through facilitated adaptation, management of invasive or pathogenic populations, and potentially even facilitating the revival of extinct species. These approaches belong to a new field of research termed conservation biotechnology, which places a great responsibility on researchers and decision makers to ensure sustainability. In this paper, we have mapped the emerging trends in genome editing of wild animals. Current projects primarily focus on population control and de-extinction, with fewer initiatives aimed at preserving threatened species. We then explore four critical dimensions of conservation biotechnology: the technology itself, new perspectives on conservation practices, research organization, and governance and policy. Despite its potential, key questions remain-particularly whether genome editing can increase genetic diversity without causing unintended non-target impacts. Genome editing also provokes new perspectives on conservation practices where ecosystem-wide impact assessment, case-by-case evaluations, and post-release monitoring needs to be prioritized. Furthermore, conservation biotechnology is heavily funded through private funding showing varying stakeholder interest, which can lead to untraditional and less transparent research processes. Stakeholders, including local and indigenous people, are only to a certain degree involved, which may weaken inclusion of local knowledge and monitoring efforts. Finally, concerning governance and policy, there is an urgent need to develop more adequate regulation of conservation biotechnology, as environmental release of genome-edited animals challenges definitions and guidelines in current nature protection laws and GMO regulations. Based on our analysis, we outline key points for further investigation toward a more sustainable approach to conservation biotechnology.

Animals↗
PubMed2026

Stability in the face of global decline: a 20-year study of arthropods in an oceanic archipelago.

Insect declines are of global concern, yet no long-term ecological studies (LTER) have confirmed this trend on islands. This study utilises the first available LTER data on island arthropods, targeting epigeal and canopy species from the Azores Archipelago (Portugal), and covering over 20 years in three distinct sampling events from 30 standard sites. We investigate changes in abundance, biomass, and species richness within native forest arthropod communities, focusing on the proportions of endemic and introduced species, and temporal patterns among single-island endemics and forest-dependent endemics. Results reveal significant temporal variability, but overall abundance, biomass, and species richness remain stable across endemic and native non-endemic taxa. Among the species studied, 28% declined, 17% increased, and 55% showed no significant differences. Exotic invasions and related extinctions appear minimal. Forest-dependent endemic species declined below anticipated levels, suggesting that the extinction debt for these species may be less severe than initially expected. Nonetheless, some forest specialists have declined significantly, and seven species, not seen over 20 years, are considered to be extinct. The three-decade-long conservation of Azorean native forests may have contributed to the stability of some populations, thus these findings underscore the need for continued and enhanced conservation efforts of insular forest-associated diversity.

Animals↗
PubMed2026

Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change.

Understanding the genetic basis of rapid adaptation is key to predicting species' evolutionary responses to environmental change. However, it is still debatable whether many small-effect mutations or a few large-effect mutations underlie rapid adaptation, and how this knowledge can predict population survival or extinction. To address this question, we performed a series of ecologically grounded forward-in-time genetic simulations to study rapid adaptation and extinction with increasing magnitudes of environmental change. These simulations were seeded with genomic variation of the plant Arabidopsis thaliana to have a realistic genomic structure, with one (monogenic) to 1,000 (polygenic) variants with varying heritabilities contributing to an environmental adaptive trait. Our results revealed two distinct scenarios of rapid adaptation and population rescue. Under small-to-moderate environmental shifts, high polygenic traits increased evolutionary rescue probability. Under extreme environmental shifts, high polygenic traits lead predictably to extinction, yet monogenic traits sometimes produce one-off winning adaptive genotypes. We interpret our rapid evolutionary rescue findings in terms of the fundamental theorem of natural selection, where trait polygenicity shapes the distribution of genetic variance in fitness across replicates and, in turn, the probability of population survival, with polygenic architectures producing more stable and predictable fitness variance and monogenic architectures generating highly skewed and variable outcomes. These results highlight the insights genomics gives us into the (un)predictability of species' evolutionary responses to global change, with management implications for assisted adaptation and conservation.

Arabidopsis↗
PubMed2026

Cooperation, competition and enforcement in transposon evolution.

Transposons are powerful drivers of genome evolution, but we lack a clear understanding of how these selfish genetic elements evolve and co-evolve with their hosts. Here, we develop a new general model of transposon-host co-evolution that incorporates key details of transposon and host biology. Our model reveals that the way that transposons replicate is critical for their evolutionary prognosis. Publicly-replicating transposons (such as DNA transposons), which cooperatively share their replication machinery, are predicted to be self-limiting. However, privately-replicating transposons (such as long interspersed nuclear elements, or LINEs), which do not replicate cooperatively, are under continual selection to increase their duplication rate even to the point of host extinction, a so-called tragedy of the commons. Neither selection against transposons' deleterious effects nor exploitation by parasitic elements is sufficient to prevent host extinction. Instead, our analysis shows that only active suppression by hosts avoids population collapse. In particular, suppression must act post-transcriptionally in order to prevent continuous escalation of the transposon-host genetic conflict. We argue that only with host enforcement of transposons can complex life exist.

DNA Transposable Elements↗
PubMed2026

A chromosome-level genome of the Nicobar pigeon, Caloenas nicobarica.

The Nicobar pigeon (Caloenas nicobarica), the closest living relative of the extinct Dodo (Raphus cucullatus), is endemic to Southeast Asia with a fragmented distribution across numerous small islands. It suffers from habitat loss, hunting, and predation from invasive species, resulting in its classification as Near Threatened by the International Union for the Conservation of Nature. We have generated a haplotype-resolved and chromosome-level genome assembly of the Nicobar pigeon using a combination of PacBio HiFi long-read sequencing and Arima Hi-C chromatin interaction mapping. This assembly includes two haplotypes, each spanning approximately 1.2 Gb. Haplotype 1 has a contig N50 of 25.2 Mb and a scaffold N50 of 79.7 Mb, whereas haplotype 2 has a contig N50 of 24.7 Mb and a scaffold N50 of 107.9 Mb. As the first high-quality genome assembly of any bird in the Columbidae Indo-Pacific clade, this resource provides valuable insights for phylogenetic studies. Furthermore, the phylogenetic proximity of the Nicobar pigeon to the Dodo (R. cucullatus) and the Rodrigues Solitaire (Pezophaps solitaria) offers a unique opportunity to study these extinct species, making this assembly a critical resource for evolutionary studies. It also offers a unique model for studying genetic diversity, adaptation, and speciation in island environments. This genomic resource will not only enhance our understanding of the evolutionary history of the Nicobar pigeon but also serve as a valuable tool for future conservation efforts aimed at preserving this unique species and its fragile island ecosystem.

Animals↗
PubMed2026

The Evolutionary Significance of Leaf Nodulation: Evidence from Ardisia and Its Relatives (Primulaceae: Myrsinoideae).

Interactions between plants and microorganisms have long been a central topic in biological research. Bacterial symbiosis on leaf surfaces represents a distinctive and mutually beneficial system within the phyllosphere microbiome. Leaf nodules are the visible manifestation of the symbiosis and confer ecological advantages to host plants by enhancing host resistance against pathogens and herbivores. It has been hypothesized that these advantages promote higher diversification rates in host lineages, but this remains uncertain. Ardisia subg. Crispardisia and its close relatives (Amblyanthopsis and Amblyanthus) within Primulaceae are typical plant groups with leaf nodule symbiosis, making them an ideal system for testing this hypothesis. In this study, we conducted extensive sampling of "Ardisioids" (Ardisia and its allies) and reconstructed their phylogenetic relationships and evolutionary history using plastid genomes and nuclear datasets (i.e., nuclear ribosomal DNA (nrDNA) and genome-wide single nucleotide polymorphisms (SNPs)). We clarified the phylogenetic positions of several "Ardisioids" genera (e.g., Sadiria, Tapeinosperma, Amblyanthus, and Amblyanthopsis) and multiple subgenera within Ardisia. We further detected a rapid radiation during the middle Miocene in Ardisia and its allies. Notably, we found that the leaf-nodulated clade appears to have originated during this period, approximately 11-8 Ma. BAMM (Bayesian Analysis of Macroevolutionary Mixtures) analyses revealed elevated diversification rates in leaf-nodulated lineages, while HiSSE (Hidden State Speciation and Extinction) analyses indicated that leaf nodule symbiosis might have increased speciation rates without significantly affecting extinction rates. These results provide strong evidence that leaf nodule symbiosis, together with other abiotic and biotic factors, represents a key evolutionary innovation that has promoted diversification in Ardisia and its close relatives.

diversification rate↗
PubMed2026

Beauty bias in butterfly research and conservation.

Conservation biases have been documented since the first emergence of the concept of biodiversity in the 1980s,1,2,3 showing a systematic disproportion in the allocation of research and conservation efforts among taxa.4,5,6,7,8,9,10,11 One factor underlying this disproportion, gaining prominence in recent literature, is species' perceived beauty, shaped by human visual preferences.12,13,14,15,16,17 Here, we integrate a large-scale survey of the perceived beauty of European butterflies yielding >21,000 survey completions from >100 countries into a time-explicit network linking species' beauty, public attention, research and conservation efforts, and the EU regulatory framework. We found that species beauty is consistently associated with public attention, research, and conservation efforts in a temporally structured pattern compatible with a cumulative beauty bias. Research effort and public attention concentrate on widespread and visually attractive species, whereas species included in the legal conservation framework, particularly the Convention on the Conservation of European Wildlife and Natural Habitats (hereafter, Bern Convention, BC, 1979)18 and the EU Habitats Directive (hereafter, HD, 1992)19 are disproportionately represented by visually appealing and historically protected taxa. Because these frameworks guide funding and management actions, early associations between species beauty and BC/HD inclusion have contributed to long-lasting institutional patterns in butterfly research and conservation. By contrast, European IUCN Red Lists20,21 do not overrepresent beautiful species and identify more inconspicuous taxa as threatened. This mismatch reveals a tension between scientific assessments of extinction risk and historically embedded conservation priorities. Our findings suggest that recognizing beauty bias is vital for aligning conservation with actual ecological urgency. VIDEO ABSTRACT.

Animals↗