Elucidating how habitat degradation facilitates extinction is critical for effective conservation efforts. Here, we propose integrating physiologically-structured population models into stochastic population viability analyses to assess how differing consequences of habitat degradation interact to drive extinction dynamics in a focal population. Using the isolated spectacled caiman Caiman crocodilus population/ecomorph from the Apaporis River as a case study, we find that threatening the resource base, which individuals increasingly rely upon, to outgrow vulnerable size ranges and mature accelerates extinction. We also found that when habitat degradation impacts both the primary adult and juvenile resource bases, this can have marked synergistic effects on threatening population viability. By contrast, destroying nesting sites has only a small effect on accelerating the impact of deteriorating prey availability. Through integrating community-level feedback between habitat degradation/change and population dynamics/structure, our approach provides a comparative framework for assessing the relative importance of distinct mechanisms through which habitat degradation ultimately drives extinction risk.
Science Journals
Strong population contractions can leave a persistent genomic legacy that can influence populations long after their demographic recovery. While bottlenecks facilitate the removal of strongly deleterious mutations, the effectiveness of purging may be limited in historically small populations. The Kirtlands warbler (Setophaga kirtlandii) is a rare North American songbird with an ancestrally small population. After narrowly evading extinction, they are one of few species that have been delisted from federal protections in the USA. Despite their recovery, a previous study showed evidence for recent inbreeding and a high burden of deleterious mutations that may have not been purged despite strong bottlenecks. Historical DNA offers a unique opportunity to understand the consequences of recent demographic declines on genetic diversity. Here, we use DNA from over 100-year-old museum specimens to estimate changes in genetic load in the Kirtlands warblers pre- and post-bottleneck. We validate our results with forward-in-time genetic simulations and explore how sample size and missing data can affect estimates. Both empirical data and simulations suggest a reduced ability to purge deleterious mutations in this historically small population. Our simulations also highlight that limited sampling design and data quality can constrain the ability to detect changes.
The evolution of reproductive isolation is central to speciation, yet the earliest stages of this process remain poorly understood. In particular, it is unclear how rapidly barriers to mating arise during adaptation, whether they accumulate predictably, and how they depend on ecological context. Here, we investigate the evolution of mating efficiency during prolonged asexual adaptation in diploid Saccharomyces cerevisiae. Twelve replicate populations were evolved for 1200 generations in two distinct carbon environments, glucose and galactose, under strictly asexual conditions. At regular intervals, we induced sporulation and quantified mating efficiency using three complementary assays: within-population crosses, crosses between populations evolved in different environments, and crosses between evolved populations and the ancestral strain. We find that mating efficiency evolves during asexual adaptation, with outcomes that depend strongly on the environment. While glucose-evolved populations remain largely stable, galactose-evolved populations exhibit a reversible decline. Overall, changes in mating efficiency are dynamic, heterogeneous, and often transient, with evidence for both intrinsic reductions in mating competence and context-dependent incompatibilities between populations. Together, these results show that asexual adaptation can generate rapid but non-monotonic changes in mating compatibility. Early reductions in mating efficiency are heterogeneous, environment-dependent, and often reversible, and do not accumulate into stable reproductive isolation over the timescale examined. Our findings suggest that the initial stages of divergence are characterized by dynamic and contingent perturbations of reproductive traits, rather than a steady progression toward speciation.
Terpenes constitute the largest and most structurally diverse class of plant secondary metabolites, with critical roles in plant-environment interactions and broad industrial applications. Although nuclear genome engineering of terpene pathways has been extensively explored, chloroplast genome engineering remains largely undeveloped, with all reported studies restricted to the model plant Nicotiana. Here we report successful chloroplast genome engineering for diterpene production in the crop plant potato (Solanum tuberosum). First, we identified the trnT/trnL plastomic locus as optimal for minimizing integration-associated growth penalties. Insertion of a bifunctional diterpene synthase gene into this plastomic site yielded transplastomic plants with successful diterpene production, but with reduced growth. The co-expression of a geranylgeranyl diphosphate synthase gene to enhance precursor supply restored normal growth while elevating diterpene accumulation. Transplastomic plants were otherwise agronomically comparable to wild-type. This work expands chloroplast engineering as a viable strategy for terpene pathway engineering in crop improvement and high-value terpene production.
Chromosome-scale assemblies are increasingly available for non-model organisms, but functional annotation remains limited when deep evolutionary divergence erodes primary amino-acid sequence identity even though protein structural similarity can remain conserved. We present a hybrid annotation framework that decouples gene-model discovery from cross-species similarity assignment by combining Evo2-based ab initio prediction of exon-intron structures with ESM-2 protein-embedding-based structural similarity mapping. Applied to the sea lamprey, the framework derives high- or medium-confidence cross-species similarity assignments for 73,485 Evo2-derived translated protein models, including 35,395 high-confidence calls, and expands the deduplicated structural catalog to 31,286 loci, including 20,871 additions absent from the Ensembl baseline. A joint alignment-structure classification identifies 21,391 structurally supported catalog loci that a fixed human DIAMOND protein search does not confidently assign on its own, including 21,184 loci with no detectable human protein-sequence match and 207 loci with only low-confidence matches in the classical 20-30% amino-acid-identity twilight zone. These rescue-space totals describe catalog loci rather than validated one-to-one human-absent genes. In a single-cell RNA sequencing application, a stricter UTR-aware Ensembl+Evo2 reference improves gene recovery and expands the interpretable feature space of the lamprey immune compartment relative to the Ensembl baseline. This enables more resolved annotation of four transcriptionally defined immune cell states, including VLRA+-associated T-like and VLRB+-associated B-like programs together with oxidative iron-handling and iron-associated VLR-linked states. Together, these results show that structural protein signal often persists beyond the limits of pairwise sequence alignment and that an embedding-based annotation layer can extend that signal to improve downstream comparative and…
Reef restoration practitioners aim to preserve coral genetic diversity by protecting reefs and cultivating diverse genotypes in coral nurseries. However, cryptic genetic lineages in most corals complicate restoration strategies, as the role of between-lineage genetic divergence remains unclear regarding adaptation. In Montastraea cavernosa, researchers have identified cryptic lineages, some strongly segregated by depth. We conducted a ten-week reciprocal transplantation experiment using two cryptic lineages restricted to shallow water (<10m depth), with one lineage more common on nearshore reefs and the other on offshore reefs. We aimed to quantify lineage-specific responses to the environment that explain the genetic and ecological divergence between the two lineages. Surprisingly, the strongest response was not lineage-specific. Instead, both lineages exhibited strong and similar changes in growth and metabolomic profiles, depending on the transplantation habitat. These results suggest that cryptic lineages employ similar mechanisms of adaptation and acclimatization to environmental challenges, despite their genetic distinction.
Gene duplication is a major driver of evolution, yet how it generates fundamentally new molecular functions remains poorly understood. Here, we show how such novelty arose in KLMT-1, a selfish toxin that causes genetic incompatibilities in Caenorhabditis tropicalis. KLMT-1 evolved via duplication of an essential tRNA synthetase but, strikingly, lost its ancestral role in tRNA biology and translation. Instead, KLMT-1 localizes to centrosomes, where it targets Aurora kinase A (AIR-1). This innovation is mediated by a three-amino acid insertion that extends a beta-hairpin loop, enabling electrostatic interaction with a regulatory interface on the kinase. Our results demonstrate how changes in selective pressure, combined with minimal modifications in neutrally evolving regions, allow duplicated proteins to access new functional space and evolve entirely new molecular activities.
Rapid connectivity alterations of thalamic nuclei during initial learning of goal-directed behaviour
The thalamus is essential for learning, dynamically engaging with other subcortical and cerebral cortex regions throughout the learning process. Here, the thalamus serves as a critical connector hub and synchroniser within the thalamocortical system of the brain. However, whilst higher order thalamic nuclei are known to be particularly important for this process, the exact contributions of individual higher order and first order thalamic nuclei, alongside their individual involvement with cortical networks and subcortical regions, remains unexplored within the initial phase of learning. In light of this, we analysed fMRI data obtained within a paradigm which is designed to examine initial learning processes within feedback-driven stimulus-response learning, in order to explore thalamic contributions. We investigated dynamic learning-related functional connectivity alterations between various thalamic nuclei with other subcortical regions and cortical networks. Our results show that the initial phase of learning was associated with: (1) decreasing functional connectivity between thalamic nuclei and frontoparietal and cingulo-opercular networks, (2) increasing functional connectivity between thalamic nuclei with default mode and salience networks, (3) decreasing functional connectivity between thalamic nuclei and the putamen, and (4) decreasing functional connectivity amongst higher order thalamic nuclei. Furthermore (5) these dynamic alterations were associated primarily by mediodorsal thalamus. Altogether, these results indicate that higher order thalamic nuclei play a crucial role within initial learning and in the generation of novel goal-directed behaviour. This was demonstrated through enhanced functional connectivity with selected cortical networks which drive goal-directed behaviour, alongside decreased functional connectivity with striatal regions which drive motor selectivity.
The hippocampus is organized along dorsal-ventral and left-right axes, but whether and how these axes interact within defined neuronal populations across behavioral states remains unresolved. Here, we combined within-animal slice electrophysiology with dual-site fiber photometry to compare dorsal and ventral CA1 activity across contralateral hemispheric configurations in mice expressing CaMKII-jGCaMP8s and SynI-jRCaMP1b at distinct longitudinal sites. Ventral CA1 pyramidal neurons exhibited greater intrinsic excitability and stronger AMPAR-mediated synaptic responses than dorsal CA1 neurons. In vivo, CaMKII-defined pyramidal recordings during home cage rest revealed a left-biased event-rate asymmetry within dorsal but not ventral CA1, with no comparable asymmetry in pan-neuronal SynI recordings. Apparent dorsal-ventral differences in spontaneous event rate were therefore configuration-dependent and resolved into a hemispheric, cell-type-specific effect restricted to the CaMKII-defined population. Lead-lag analysis showed that dorsal-ventral temporal coordination was likewise reorganized across configurations and was restricted to pyramidal-cell-biased recordings. During open-field center entries, dorsal CA1 was preferentially recruited before entry across both configurations, whereas non-coordinated entries revealed a relative post-entry suppression of contralateral ventral CA1. Together, these findings suggest that dorsal-ventral CA1 organization cannot be inferred from hemisphere-pooled designs and identify a pyramidal-cell-specific left dorsal CA1 asymmetry as a structural feature that shapes both spontaneous activity and behaviorally driven recruitment along the longitudinal hippocampal axis.
LINE-1 retrotransposons are the only autonomous mobile elements still active in human genomes and remain a potent source of mutation, genome remodeling, and disease risk. However, young, full-length, potentially active copies (the elements most likely to shape present-day genomes) have been largely inaccessible to population-scale analysis because they are long, repetitive, and poorly resolved by short-read sequencing. Here, we use 47 phased long-read assemblies from the Human Pangenome Reference Consortium, representing 94 haplotypes, to build an allele-resolved view of recent human LINE-1 evolution. We identify 13,617 LINE-1 alleles with intact ORF1 and ORF2 across 683 unique insertion sites, revealing that every genome carries a distinct repertoire of potentially active source elements. These intact LINE-1 profiles recapitulate broad human population structure while exposing a large, rare, and population-enriched reservoir of mobile-element diversity missed by single-reference approaches. We also resolve a structurally variable chromosome 11 LINE-1 array, demonstrating that local duplication and rearrangement can amplify LINE-1 sequence independently of canonical retrotransposition. By comparing full-length LINE-1 sequences, we define activity signatures that separate ancient remnants from recently expanding lineages and uncover young LINE-1 groups whose activity is not fully explained by canonical subfamily labels. Sequence-network analyses further reveal a dynamic history of lineage turnover, in which successful source elements rise, seed new insertions, and are replaced by descendants marked by specific nucleotide changes. Together, these data transform human LINE-1s from a repetitive background into a resolved evolutionary system, linking insertion polymorphism, coding potential, population history, and recent retrotransposon adaptation. Our findings establish the human pangenome as a framework for discovering active source elements and for testing how mob…
Accurate and reproducible assessment of foliar disease severity is essential for evaluating the performance of heterogeneous plant communities and understanding host-pathogen interactions. However, traditional visual scoring methods remain subjective, with limited precision, and difficult to scale in large phenotyping experiments. Here, we present a semi-automated image analysis workflow designed to quantify multiple foliar disease symptoms simultaneously on wheat flag leaves sampled from varietal mixtures. The workflow combines three methodological components: (i) a standardized protocol for leaf sampling and imaging, (ii) supervised machine learning segmentation using Random Forest implemented in Ilastik to classify multiple symptoms (powdery mildew and yellow rust), and (iii) a graphical user interface facilitating pipeline deployment by non-specialist operators. To evaluate the influence of image representation on classification performance, four color spaces (RGB, HSV, HLS, LAB) were systematically compared. The approach was validated using images of durum wheat flag leaves collected from a field experiment assessing eight-way varietal mixtures under natural fungal pressure. Cross-validation against manually annotated images demonstrated high segmentation accuracy across all symptom. Comparison among color spaces revealed only minor differences in performance. Overall, this workflow offers a cost-effective, annotation-efficient and reproducible alternative to deep learning approaches, leveraging open-source and actively maintained tools while requiring limited training data and enabling objective, reproducible and scalable disease phenotyping.
Phyllanthus niruri (Phyllanthaceae) is a medicinally important herb known for producing phyllanthin, a bioactive dibenzylbutane lignan with reported hepatoprotective and antioxidant properties. However, the biosynthetic basis of phyllanthin production remains unresolved, largely due to the absence of a reference genome for the species. We report a chromosome-scale assembly of P. niruri generated by integrating PacBio HiFi long reads and Illumina short reads, followed by reference-guided scaffolding against Phyllanthus cochinchinensis. The assembly has an L50 of 7 and 97.6% BUSCO completeness. Annotation predicted 19,254 protein-coding genes, of which 91.1% were functionally annotated, with phenylpropanoid biosynthesis emerging as the most enriched specialized-metabolism pathway in the genome. Using pathway-guided genome mining, structural similarity analysis, and comparative metabolic reconstruction, we propose a putative biosynthetic pathway for phyllanthin originating from the phenylpropanoid-lignan branch through secoisolariciresinol-like intermediates followed by terminal O-methylation reactions. A total of 305 unique candidate genes associated with the proposed pathway were identified, including expanded families of dirigent proteins, peroxidases, secoisolariciresinol dehydrogenases, and O-methyltransferases. Comparative transcriptomic analyses across related Phyllanthus species further supported the proposed pathway through coordinated expression of lignan-associated genes and tissue-specific enrichment of O-methyltransferases. This work provides the first reference genome for P. niruri and a prioritized candidate gene set for functional characterization of phyllanthin biosynthesis.
Wildlife vaccination could become a powerful strategy to mitigate disease-induced biodiversity losses, yet many vaccines for wildlife diseases provide only limited protection. Notably, tools to control the fungal pathogen Batrachochytrium dendrobatidis (Bd) are urgently needed for amphibian conservation. Laboratory experiments have demonstrated that prophylactic exposure to Bd metabolites increases host resistance, significantly reducing infection intensity in amphibians subsequently challenged with live Bd. Because Bd metabolites are non-infectious and applied topically, this treatment has potential to be administered to waterbodies to vaccinate and protect amphibians. We developed an agent-based model that indicated imperfect vaccination could reduce or amplify Bd infections at the population level, depending on degree of enhanced resistance or tolerance. Utilizing a Before-After-Control-Impact design with ten years of data, we conducted an ecosystem-level trial where we applied low levels of Bd metabolites or a sham control treatment to ponds in California and subsequently quantified Bd prevalence and infection intensity in metamorphosing Pacific chorus frogs (Pseudacris regilla). Unexpectedly, infection intensity was significantly greater in treated ponds relative to control ponds following metabolite addition. Additional model simulations indicated that this could occur via two mechanisms: (1) if treatment greatly increased tolerance alone or in combination with smaller increases in resistance, or (2) if a deleterious environmental interaction caused the treatment to increase susceptibility, rather than promote resistance. Future research is needed to determine whether tolerance or environmental factors drove heightened Bd infection intensities in this field trial to identify contexts in which this treatment can be used as a conservation tool.
The deployment of clothianidin-based insecticide formulations in malaria vector control has highlighted the capacity of Anopheles funestus to displace more susceptible mosquito species in treated areas and to rapidly evolve resistance under selection pressure. Metabolic detoxification, together with structural and genetic changes in nicotinic acetylcholine receptors (nAChRs), the primary molecular targets of neonicotinoids, can reduce insecticide efficacy. Here, we characterized amino acid substitutions across all 11 nAChR subunits in An. funestus to assess standing variation that may facilitate adaptive responses to chemical exposure. Using whole-genome sequencing data from 656 mosquitoes sampled in 13 African countries, we found marked contrasts in the distribution of nonsynonymous variants among nAChR subunits. Most subunits are strongly constrained and carry no missense variants, whereas two loci (3 and 7) display three geographically widespread amino acid substitutions across the continent. In contrast, 9 and {beta}2 accumulate dozens of nonsynonymous mutations occurring at intermediate to high frequencies, including within domains involved in orthosteric ligand binding and channel gating. Genetic differentiation at nAChR loci among populations from different countries is low to moderate, although several nonsynonymous mutations display high FST values consistent with geographic structuring. These results highlight relaxed constraint on two subunits that may provide opportunities for evolutionary diversification within a conserved family of multimeric receptor assemblies. Such diversification has not been observed in vector species displaced by An. funestus in indoor residual spraying areas, and the potential implications for reduced sensitivity to neonicotinoids are discussed.
Birds and mammals are shrinking and shapeshifting as global temperatures rise. Ecogeographic rules predict that such changes should ease heat stress by increasing surface-area-to-volume ratios, and thus, the capacity for heat exchange. This has led to the hypothesis that body size reductions are driven by thermoregulatory selection or adaptive plasticity, although recent syntheses point to more complex, multifactorial causes. Crucially, recent theoretical models predict that thermoregulatory benefits of smaller body size only emerge at extreme deviations from average phenotypes. Here, we exploit agricultural selection in Japanese quail to directly test this hypothesis, using three breeds spanning extreme differences in body mass, surface area, and relative appendage lengths. Evaporative cooling capacity and the scope for evaporative water loss broadly followed allometric predictions when contrasting small and larger breeds. As expected, this allowed the smallest breed to tolerate higher air temperatures. However, differences in heat tolerance limits between breeds were consistently much smaller than predicted. Additionally, the breadth of thermoneutral zones overlapped in full, and upper critical temperatures were remarkably similar, between breeds. Together, these results show that heat tolerance is only weakly linked to surface-area-to-volume relationships and cannot be explained by size alone. Thus, although smaller bodies may modestly enhance heat dissipation when size variation in a population is substantial, our findings suggest that recent body size reductions and morphological shifts are unlikely to be driven primarily by thermoregulatory benefits.
Cancer progression is increasingly understood as an evolutionary process shaped not only by competition but also by cooperative interactions including those mediated through diffusible ``public goods'' (PGs). Classical evolutionary game theory predicts that PG-producing (altruistic) subclones cannot invade well-mixed populations of non-producers, creating a paradox given their observed emergence in tumors. Here, we resolve this contradiction by combining stochastic spatial simulations with an analytically tractable Moran model to study the invasion dynamics of PG-producing cells in structured populations. Starting from a single producer cell, we explicitly model stochastic PG secretion, diffusion, binding/unbinding, and cell proliferation across biologically relevant parameter ranges. We demonstrate that spatial structure fundamentally alters invasion dynamics, enabling PG producers to invade and establish even when production incurs a fitness cost. Both numerical and analytical approaches converge on a key unifying parameter, a characteristic length scale {delta}, that captures the combined effects of diffusivity, binding kinetics, and degradation. This length scale determines the spatial extent of PG availability and thus the selective advantage of producers. We identify distinct regimes: when PGs are localized (small {delta}), producers preferentially benefit and invasion is likely; when PGs are widely dispersed (large {delta}), benefits are shared and invasion approaches neutrality or is suppressed by costs. Our results highlight that invasion of cooperative traits is governed by spatially mediated resource localization rather than intrinsic fitness alone. This framework provides a mechanistic basis for understanding the emergence of cooperative subclones in tumors and suggests that modulating biophysical transport properties of signaling molecules could influence tumor evolution, metastasis, and therapeutic resistance.
RNA-seq experiments routinely identify thousands of differentially expressed genes, but translating these into biological insights and therapeutic hypotheses often requires integrating multiple tools. Existing web platforms such as iDEP, NetworkAnalyst, and GEPIA2 address individual steps, differential expression, network visualization, or TCGA queries, but lack a unified environment spanning raw data processing to clinical and pharmacological interpretation. TransXplorer (https://www.transxplorer.org) is a freely available web platform that addresses this limitation by integrating the complete RNA-seq analytical workflow. It supports processing from raw FASTQ files using HISAT2 or Salmon, as well as direct GEO dataset import with automated metadata handling. Differential expression analysis is implemented via DESeq2, edgeR, and limma-voom, followed by functional enrichment across more than 1,800 species using Bioconductor resources. Batch effects are automatically detected and corrected using a composite of PVCA, kBET, and Silhouette metrics without requiring predefined batch annotations. Downstream analyses include co-expression network construction (WGCNA), protein-protein interaction mapping (STRING), cell-type deconvolution, and transcription factor inference using integrated DoRothEA and TFLink resources. The platform further links gene signatures to drug candidates through DGIdb and OpenTargets and enables survival and tumour-normal comparisons across TCGA cohorts. Application to cardiac endothelial differentiation (GSE151427) and kidney renal papillary cell carcinoma (TCGA-KIRP) datasets demonstrates accurate batch correction, biologically consistent pathway enrichment, recovery of expected cell-type proportions, and identification of clinically relevant genes and drug candidates. TransXplorer is freely available without a login.
Cliffs are environmentally extreme yet biodiversity-rich ecosystems that harbour specialist plants, many endemic and threatened. Plant persistence in these nutrient-poor substrates may depend on tightly linked soil- and root-associated microbial communities, which remain poorly understood. These interactions may become increasingly important with the global expansion of recreational climbing. While physical climbing impacts on vegetation are documented, potential chemical effects, from the use of climbing chalk (magnesium carbonate), on soil properties and plant-associated microbiota remain unknown. We sampled soils and roots beneath cliff-specialist and generalist plants, and unvegetated soils, across climbed and unclimbed routes in northern, central, and southern Spain. Soil physicochemical properties were quantified, fungal communities were characterized using ITS-metabarcoding, and structural equation modelling was used to disentangle direct and indirect effects. Climbing increased soil pH and altered soil chemical properties, driving shifts in fungal diversity and functional composition in soil and roots. The relative read abundance of root-associated symbiotrophic fungi declined, whereas arbuscular mycorrhizal fungi and pathogens increased in climbed cliffs. Overall effects were consistent, with cliff-specialist plants mediating nutrient and fungal shifts. Our findings show that climbing can reshape cliff soil chemistry and fungal communities, with potential cascading consequences for plant functional performance, nutrient dynamics, and ecosystem resilience.
Holcosus orcesi, the Orces Blue Whiptail, is a Critically Endangered lizard endemic to the upper Jubones River basin in southern Ecuador. Restricted to a narrow elevational range within semi-arid Andean shrublands, it represents one of the few montane members of a predominantly lowland lineage. Here we present the first high-quality reference genome for H. orcesi, generated using Oxford Nanopore Technologies long-read sequencing. The assembly spans 1.68 Gb across only 91 contigs, with an N50 of 76.2 Mb and a BUSCO completeness of 96.8%, making it among the most contiguous and complete squamate genomes to date. Structural annotation predicted 25,682 genes, of which 85% showed homology to known proteins and 45% were assigned Gene Ontology terms. Repetitive elements accounted for 46.3% of the genome, with LINEs representing the predominant class. This genome provides a foundational resource for future evolutionary, comparative and conservation-genomic research of H. orcesi and other mountain reptiles, enabling studies of population genomics, local adaptation, and genomic erosion in isolated populations. By expanding the genomic representation of tropical montane reptiles, this work helps address longstanding phylogenetic and geographic gaps in global biodiversity genomics and provides a foundation for evidence-based conservation of H. orcesi and related taxa.
Gross chromosomal rearrangements are a hallmark of many diseases and cancers. The study of their biogenesis and the mechanisms underlying their formation is greatly facilitated by the availability of genetic reporter assays in model organisms. We present here a novel GCR assay developed in fission yeast, a highly relevant model for understanding genome instability related to human biology. The reporter employs canavanine counter-selection to detect GCRs within a chromosomal context. Using this assay, we identified natural hotspots for GCRs, including inverted long terminal repeats (IR-LTRs). Structural analysis of GCR events showed that IR-LTR-induced GCRs mainly result in either terminal deletions with adjacent inverted duplications or repair via long-range break-induced replication (BIR). Deleting IR-LTRs reduces the GCR rate and reveals another hotspot driven by BIR between homeologous aldo/keto reductase genes on opposite arms of chromosome I. This is the first evidence that BIR can occur in S. pombe on long tracks reaching up to 600 kb. Besides highlighting genome rearrangement hotspots, the assay also identifies regulators of genome instability in fission yeast. Loss of Nup132, a component of the nuclear pore complex, increases IR-LTRs-induced GCRs, while the budding yeast homolog Nup133 has no effect on the stability of a structurally similar IR. In contrast, disrupting djc9, which encodes a conserved histone H3-H4 binding protein, decreases GCR rates. Overall, this sensitive GCR assay enables the identification of factors that control spontaneous and fragile motif-induced chromosomal instability, including those conserved in humans but lost through evolution in other organisms.
Genetic variation is the raw material for evolution. One source of variation is chromosomal rearrangements, which can bring genes together and form genetic linkage. Rearrangements can also suppress recombination and gene flow, as in the case of sex chromosome evolution. We conducted the first population genomic study of the red harvester ant Pogonomyrmex barbatus to investigate genomic rearrangements that differentiate the lineages J1 and J2 in the "dependent-lineage system" (also known as "social hybridogenesis"). In this unusual reproductive system, males and females from different lineages mate to create hybrids, yet these hybrids develop into sterile offspring (workers), and so the two lineages remain reproductively isolated. We sequenced high-quality reference genomes for the two lineages to search for a potential explanation of the suppression of gene flow between them. Comparison of the two genome assemblies revealed multiple large-scale genomic rearrangements, all of which occurred in the J1 lineage. The rearrangements formed some of the largest J1 chromosomes, including the largest scaffold in the assembly that was formed by at least two translocation events and additional intra-chromosomal rearrangements. The translocations brought together 118 odorant receptor (OR) genes on this rearranged chromosome, 44 of which are 9-exon ORs, which are implicated in chemical communication in ants. We also identified an enrichment of transposable elements in a large synteny gap between the translocated segments. The discovery of multiple translocations that formed large rearranged chromosomes provides a potential explanation for the reproductive isolation between the pair of dependent lineages in this system, and opens the way for the study of the molecular genetic basis of an intriguing evolutionary phenomenon in these and in other ant lineages.
In modular organisms, where growth and fragmentation blur the boundaries between individuals, the interplay between asexual and sexual reproduction creates complex fitness trade - offs. Life - history theory predicts that resources allocated to one fitness component necessarily reduce investment in others, yet detecting these trade - offs in wild populations of clonal organisms remains challenging. Phenotypic plasticity can enhance survival, yet its influence on reproductive capacity and life - history trade - offs remains poorly understood. Using a fully crossed reciprocal transplant design, we tracked 263 colonies of the branching coral Acropora cervicornis across nine reef sites over 42 months, investigating relationships between fragmentation, morphological plasticity, and the capacity for sexual reproduction. Breakage patterns reflected both environmental and genetic factors. Primary branch breaks created a "double negative" effect - simultaneously more than doubling mortality risk and delaying attainment of a validated reproductive size class by ~40%. Conversely, higher morphological plasticity in surface area - to - volume ratio accelerated sexual maturation up to 6 - fold, counteracting the negative effects of fragmentation. In parallel, a simple demographic model parameterized with published fecundity data estimated that primary breakage reduces expected cumulative reproductive output by ~58%, a result robust across a wide range of parameter assumptions. These results demonstrate a fundamental reproductive trade-off in which asexual reproduction through fragmentation undermines sexual reproductive potential by reducing colony size. Moreover, our findings reveal that fragmentation susceptibility is broadly heritable and subject to selection, and identify a compensatory mechanism through which plasticity enhances fitness beyond immediate survival.
As one of the earliest-diverging multicellular eukaryotic lineages, the bladed Bangiales (Rhodophyta) possess a deep evolutionary history with a central role in the multi-billion-dollar global seaweed aquaculture industry. Although North Atlantic representatives are emerging candidates for regional mariculture, the scarcity of high-quality genomic resources for these taxa hinders both fundamental research and commercial optimization. To address this, we present the first chromosome-level genome assemblies for two native European species: Porphyra dioica (150.44 Mbp) and Porphyra linearis (95.22 Mbp). By integrating Oxford Nanopore Technologies (ONT) long-read sequencing with Hi-C proximity ligation, we generated highly contiguous nuclear genomes resolved into five chromosomes. Structural gene models were predicted through the BRAKER3 pipeline, identifying 12,548 and 10,382 protein-coding genes for P. dioica and P. linearis, respectively. Subsequent homology-based functional annotation characterized 57.4% and 59.8% of these predicted proteins. Supplemented by circularized organellar genomes, these reference genomes provide a critical framework for future research, enabling comparative studies of Atlantic-Pacific divergence and facilitating the development of selective breeding programs for sustainable European aquaculture.
Biological sequences are known to be not random. Thus, the comparison of in silico restriction fragment distributions of random and biological sequences may be an indicator of this non-randomness. Our analyses show that for most of the tested combinations of restriction enzyme and genome sequence the fragments per Megabase of the biological sequence deviate at least more then 10% from the corresponding random sequence. This deviation goes into both directions, i.e. clearly increased values are as common as clearly decreased values. Although there is no species- or restriction-enzyme-specific effect, a clear impact of the GC content both of the restriction site and of the genome sequence can be seen. In contrast to the random sequences, the genome sequences show distinct peaks in their fragment length distributions, hinting to repetitive elements such as transposons.
Environmental heterogeneity across freshwater systems often promotes phenotypic variation, yet disentangling environmentally induced variation from heritable differentiation remains a central goal in evolutionary ecology. We investigated the geographic distribution and morphological differentiation, and heritability of shell traits among populations of the freshwater lymnaeid snail Pectinidens diaphanus in Patagonia. Extensive field surveys across 196 freshwater sites revealed that the species occupies a broad range of lentic and lotic habitats and constitutes the only lymnaeid inhabiting southern Patagonia. While reproductive anatomical structures were conserved across populations, shell shape differed markedly among populations from contrasting habitat types, with population identity explaining nearly 50% of total shape variation. Populations from hydrologically unstable habitats (ponds and streams) exhibited more elongated shells and relatively smaller apertures, a pattern consistent with functional responses to hydroperiod variability and desiccation risk. To assess the heritability of this differentiation, we conducted a common-garden experiment across two generations. Shell shape differences between permanent- (lagoon) and temporary- (pond) habitat-derived populations persisted into the G2 generation reared under standardized laboratory conditions, indicating that the observed variation is not solely a response to local environmental conditions but includes a heritable component. Together, our findings demonstrate that P. diaphanus constitutes the sole lymnaeid across southern Patagonia, occupying a broader range than previously documented, and that populations show heritable shell differentiation potentially associated with contrasting freshwater habitats. By integrating large-scale biogeographic surveys with morphometric and experimental approaches, this study provides new insight into how habitat variation may contribute to ecological and evolutionary di…