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PubMed2026

Larval Genomics as a Viable, Fisheries-Independent Tool for Investigating Population Structure in Tropical Pacific Tunas.

Understanding how dispersal, life history, and environmental variability shape genetic connectivity in the open ocean remains a central challenge in evolutionary biology. Highly migratory marine predators like tunas have traditionally been considered genetically homogeneous across ocean basins, yet emerging genomic evidence suggests that cryptic population structure can persist even in species with high gene flow and large effective population sizes. We used 2bRAD sequencing of 348 larval and subadult skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), and bigeye tuna (T. obesus) collected from the central Pacific across 7 years of sampling to examine species boundaries, population genetic information, genetic structure, and connectivity. Larval sampling revealed consistent spawning by all three species and enabled unbiased detection of genetic patterns prior to recruitment bottlenecks. We found strong divergence amongst species, no evidence of structuring within skipjack or bigeye, and a divergent yellowfin population detected in 2 consecutive sampling years north of American Samoa. Comparisons between larvae and subadults suggest that sampling early life history stages can be a valuable tool for assessing population genetic information before recruitment bottlenecks, selective harvest by fisheries, adult dispersal, and selective pressures acting on adult populations, thereby contributing novel insights to the research and effective management of these species. These results highlight how larval genomics can complement traditional population genomic studies of adult tunas and reveal fine-scale structure in highly vagile species, providing new perspectives on connectivity in the open ocean.

Animals↗
PubMed2026

Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.

An important question in evolutionary biology is how polyploidization generates raw material for phenotypic diversification. Transposable elements (TEs) represent an underestimated source of genetic variation in eukaryotic genomes. By integrating 516 whole-genome resequencing datasets and 236 transcriptomes from common carp (Cyprinus carpio), a representative allotetraploid fish, we constructed the first population-scale landscape of TE insertions in teleosts. TE insertions are widespread in the carp genome and preferentially associated with stress-responsive genes, with DNA transposons as major contributors. Relaxed purifying selection and TE burst events coexist, generating abundant variation for subsequent subspecies differentiation. Compared with a closely related diploid species, carp exhibits more exonic TE insertions and shorter TE-gene distances, and multiple TE superfamilies expanded during tetraploidization. Genome-wide association analyses uncovered intragenic TE variants underlying domesticated traits missed by SNPs, including DNA transposon deletions associated with scale reduction and altered body shape. Notably, lighter-colored individuals harbor homozygous deletions of LTR and DNA transposons within mdfic2, whose knockout in zebrafish reduces pigmentation. Most trait-associated variants reflect lineage-specific loss of ancient TE insertions rather than recent transposition. Overall, these findings highlight the distinct role of TEs in polyploid genome evolution and phenotypic diversification, providing new insights into TE dynamics in vertebrates.

allotetraploidization↗
PubMed2026

Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation.

Uncovering the key genetic basis of complex phenotypic convergence in distantly related species has been a long-standing focus in evolutionary biology and genetics, and the convergent evolution of gliding in mammals offers a valuable opportunity to address this question. Here, we investigated the genomic basis of convergent evolution of gliding in mammals by analyzing both protein-coding genes and conserved non-coding elements (CNEs). We first de novo assembled and annotated two chromosome-level genomes of gliding mammals, the red and white giant flying squirrel (Petaurista alborufus) and sugar gliders (Petaurus breviceps), and conducted comprehensive comparative genomic analysis combined with another gliding mammal, the Sunda flying lemur (Galeopterus variegatus) and 14 background species. We found that the convergent evolution of protein-coding genes provided relatively limited but functionally relevant evidence linked to gliding phenotypes. By contrast, we found that gliding-accelerated CNEs (GACNEs) cluster near functionally equivalent genes and frequently aggregate into highly diverged yet functionally convergent hotspot regions. Across the three gliding lineages, both GACNEs and hotspot GACNEs show strong convergence in their functional enrichment profiles, suggesting a broad genetic basis underlying the convergent gliding phenotype. Furthermore, we identified 72 core transcription factors underpinning the genetic basis of gliding convergence, including EMX2 and ZFHX3, potentially involved in multiple aspects of gliding adaptation. Our study highlights the role of functional convergence in regulatory regions as a key mechanism in mammalian gliding convergence, offering valuable insights and strategies for uncovering the genetic basis of complex convergent traits, thereby advancing understanding of the molecular basis of convergent traits.

Petaurista alborufus↗
PubMed2026

The Adaptive Roles of Active Transposable Elements in Insect Hosts.

Active transposable elements (TEs) are capable of generating new insertions in genomes and have historically been viewed as genomic parasites due to their largely detrimental or neutral effects. However, emerging evidence suggests that these elements also play a crucial role in driving adaptive evolution in insects. This mini-review synthesizes recent findings on how active TEs contribute to insect adaptation through various mechanisms, including regulation of gene expression, structural variation, and epigenetic effects. Notable examples of adaptation driven by active TEs include their roles in insecticide resistance, morphological adaptations, tolerance to harsh climates, and antiviral immune responses. We argue that while host silencing mechanisms, such as the piRNA pathway, tightly regulate TE activity to minimize harmful effects, the context-dependent activation of active TEs can generate beneficial genetic variation that enhances insect adaptations to anthropogenic and climatic pressures. Future research that integrates long-read sequencing, single-cell omics, and gene editing techniques will provide a robust mechanistic foundation for understanding the adaptive significance of active TEs in insects, with important implications for pest management, pollinator protection, and evolutionary biology.

Journal Article↗
PubMed2026

Ancient DNA as a temporal lens: reconstructing evolution, migration, and disease dynamics.

Ancient DNA (aDNA) has transformed evolutionary biology and anthropology by providing direct, chronologically validated genetic evidence over millennia. This review synthesizes significant findings from the paleogenomic era (2010-2025), demonstrating how ancient DNA has resolved persistent debates across four interconnected themes: (i) human migration and admixture, revealing complex population transitions from archaic hominins to Holocene expansions; (ii) adaptation, tracking allele frequency changes during domestication and selection; (iii) pathogen history, clarifying the origins of pandemics and the evolution of microbiomes; and (iv) ecosystem dynamics, identifying extinction causes through sedimentary DNA and conservation genomics. We contend that scientific rigor and ethical stewardship are crucial for accurate conclusions, given ancient DNA study requires the destructive collection of culturally significant remains. This review argues that continued advancement will depend on the integration of genomic data with archaeological, isotopic, and proteomic evidence, and highlights the necessity for equitable involvement with descendant communities. By conceptualizing the past as a continuum of dynamic processes rather than static events, ancient DNA provides a revised historical narrative and insights relevant to contemporary concerns in conservation, health, and social justice.

Evolution↗
PubMed2026

Chromosome level genome assembly and full-length transcriptome of blacktip trevally (Caranx heberi).

Caranx heberi (Bennett, 1830) commonly known as the blacktip trevally belongs to the family Carangidae and is a potential brackishwater aquaculture species. However, the limited genomic resources are hindering the efforts to study its genetic traits and their molecular basis. To bridge this gap, we generated a high-quality reference genome employing multiple sequencing strategies including PacBio Hifi reads (135x), Illumina short reads (150x), and Hi-C chromosome conformation capturing (180x). The high-quality genome assembly consisted of 159 scaffolds summing to 618.71 Mb and an N50 value of 26.72 Mb. Among these, 24 chromosome level scaffolds covered 97.5% of the total assembly. The genome contained 20.94% of repeat elements and 30,354 protein encoding genes. In addition, full-length transcriptomes were generated using the PacBio IsoSeq approach from seven tissues (gill, kidney, liver, muscle, heart, spleen, and intestine). The comprehensive genomic and transcriptomic resources developed in this study will facilitate the domestication and aquaculture development of C. heberi, as well as support research on its nutritional potential, ecological adaptations, and evolutionary biology.

Animals↗
PubMed2025

aPhyloGeo: a Python application for correlating genetic and climatic conditions.

MOTIVATION: Environmental variation and its influence on genetic diversity is a central topic in evolutionary biology and phylogeography. Accurate correlations between genetic and climatic datasets to understand the genetic adaptations of different species to specific environments. It requires integrated and reproducible workflows. RESULTS: We developed aPhyloGeo, an open-source and multiplatform application implemented in Python, for investigating correlations between genetic variation and environmental data within a phylogenetic framework. The workflow integrates multiple analytical steps, including sequence alignment, sliding window phylogenetic inference, and statistical approaches such as the Mantel test and the Procrustean randomization test. These analyses enable the identification of mutation hotspots that exhibit strong associations with environmental variables. In addition, aPhyloGeo supports multicore data processing and provides a fully reproducible pipeline for evaluating localized relationships between genomic variation and climatic distributions. AVAILABILITY AND IMPLEMENTATION: aPhyloGeo is freely available on GitHub at: https://github.com/tahiri-lab/aPhyloGeo, as both a PyPI package and as Python scripts for Linux, macOS, and Windows.

Software↗
PubMed2026

Dissecting fluctuating selection: A unified population and quantitative genetics framework.

One of the longstanding debates in evolutionary biology is the effect of fluctuating selection on genetic changes in populations. However, the extent to which these periodic forces influence organisms at both genomic and phenotypic levels remains unclear. Despite the compelling evidence of fluctuating selection from recent studies, there is a disconnect between empirical and theoretical findings concerning the underlying mechanisms due to the limited evidence regarding the scale and processes that generate genome-wide oscillations. This study aims to elucidate how both genetic factors (e.g. heritability, number of causative loci) and ecological factors (e.g. season length, the difference in the phenotypic optima between seasons, population size dynamics) drive fluctuating selection and to identify the parameters that produce consistent oscillatory patterns. We developed a modeling framework integrating quantitative and population genetics to simulate a population under various selection regimes. We applied spectral analysis to detect periodicity, indicating cyclical selective environments. Our simulations highlight the conditions sustaining oscillations in allele frequencies over time. Spectral analysis successfully identifies the periodic patterns from allele frequency trajectories, even under highly complex selection regimes. Not only does our study clarify the conditions that yield oscillatory behaviors, but these parameters can also potentially be estimated in natural populations, providing a possibility of empirically testing these models.

Fluctuating selection↗
PubMed2026

Adaptation to seasonal drought in Arabis alpina is linked to the demographic history and climatic changes since the last glacial maximum.

Understanding how species adapt to new environments is a central goal in evolutionary biology, and a topical question in climate change research. Here, we sequenced the genomes of 426 individuals of the perennial, Arctic-alpine herb Arabis alpina to study demography and adaptation, with a focus on populations in Northern Spain, that experience warm and dry summers. Our inference supports a scenario in which A. alpina colonized Northern Spain in a range expansion event that started near the Alps around 216 thousand years ago (kya). During the last glacial episode (115 to 12 kya), this expansion proceeded westward, and effective population sizes were large across Europe, likely due to a larger suitable habitat for A. alpina. These ancient demographic events gave rise to a highly diverged genetic lineage in Northern Spain. In the present interglacial (between 12 kya and present), populations became increasingly fragmented, and lost genetic diversity across Europe. Furthermore, we detected signatures of selection at genes associated with responses to abiotic stress, including drought stress, and regulation of growth, for instance at SC5D and NAC055, which reflects the climatic changes since the last glacial period. Notably, an ancient polymorphism at the gene FRL1 emerged as a candidate for conferring variation in flowering behavior, and for contributing to adaptation to drought. Our study suggests that the combination of ancestral variation in flowering behavior, and positive selection on new mutations involved in drought responses, underlies the evolution of a new trait syndrome, and adaptation to climate change.

Droughts↗
PubMed2026

Synonymous mutations in essential genes infrequently produce fitness effects in human cell lines.

The assumption that synonymous mutations are fitness-neutral is central to many foundational results in the fields of genetics, genomics, evolutionary biology, and medicine. However, recent results suggest synonymous mutations have pervasive and strong fitness effects. These vigorously debated studies in non-human model systems have even suggested that the proportion of synonymous mutations and their fitness effect sizes are similar to non-synonymous mutations. To probe the fitness effect of synonymous mutations, we utilized recent advances in base editing to test 8558 potential synonymous mutations in 128 highly essential genes in human cell lines. Importantly, our library design excluded splice-proximal sites, ensuring a direct test of codon-level synonymous effects independent of splicing disruption. We find that synonymous mutations rarely have fitness effects on growth, occurring around 37.9-fold (95% CI: 22.16-81.48-fold) less frequently than missense mutations. In this experimental context, these findings demonstrate that synonymous mutations impact cellular fitness far less frequently than missense mutations. These results deviate from earlier reports of widespread synonymous fitness effects in yeast, yet they align with recent prime editing data observed in other human cell lines.

Humans↗
PubMed2025

The effects of cryptic diversity on diversification dynamics analyses in Crocodylia.

Incomplete taxon sampling due to underestimation of present-day biodiversity biases diversification analysis by favouring slowdowns in speciation rates towards the recent time. For instance, in diversification dynamics studies in Crocodylia, long-term low net-diversification rates and slowdowns in speciation rates have been suggested to characterize crocodylian evolution. However, crocodylian cryptic diversity has never been considered. Here, we explore the effects of incorporating cryptic diversity into a diversification dynamics analysis of extant crocodylians. We inferred a time-calibrated cryptic-species-level phylogeny using cytochrome b sequences of 45 lineages compared with the formally recognized 26 crocodylian species. Diversification rate estimates using the cryptic-species-level phylogeny show increasing speciation and net-diversification rates towards the present time, which contrasts with previous findings. Cryptic diversity should be considered in future macroevolutionary analyses; however, the representation of cryptic extinct taxa represents a major challenge. Additionally, further investigation of crocodylian diversification dynamics under different underlying genomic data is encouraged upon advances in population genetics. Our case study adds to the diversification dynamics knowledge of extant taxa and demonstrates that cryptic species and robust taxonomic assessment are essential to study recent biodiversity dynamics with broad implications for evolutionary biology and ecology.

Animals↗
PubMed2026

Co-option of stomata in the convergent evolution of fern nectaries.

Understanding the origin of new structures is a central goal of evolutionary biology. In many instances, novel phenotypes arise through heterotopy: the expression of a structure in a new location. Using bracken fern (Pteridium aquilinum) as a model, we combine genomics, transcriptomics and metabolomics to begin to explore the origin and developmental routes in the convergent evolution of ant-enticing nectaries. We observe that P. aquilinum does not exclusively express flowering plant 'nectary genes' during nectary development. Rather, this fern builds nectaries through co-option of stomata. Specifically, P. aquilinum heterotopically expresses canonical angiosperm stomatal regulatory genes, leading to stomatal development in novel positions along the petiole. These non-laminar stomata were co-opted for nectar secretion through the expression of putative sugar transport genes, forming secretory nectarostomata. This work provides two advances in our understanding of nectary evolution and the origin of complex structures. First, heterotopic expression of stomata, and later exaptation, represents one realized developmental mechanism for the evolution of nectar glands. Second, while there are many routes to nectary evolution, nectarostomata development is a repeatable path that has evolved in ferns and flowering plants, representing an impressive case of convergent evolution through the same developmental mechanism, despite over 400 million years of divergent history.

Plant Stomata↗
PubMed2026

Dissecting fluctuating selection: A unified population and quantitative genetics framework.

One of the longstanding debates in evolutionary biology is the effect of fluctuating selection on genetic changes in populations. However, the extent to which these periodic forces influence organisms at both genomic and phenotypic levels remains unclear. Despite the compelling evidence of fluctuating selection from recent studies, there is a disconnect between empirical and theoretical findings concerning the underlying mechanisms due to the limited evidence regarding the scale and processes that generate genome-wide oscillations. This study aims to elucidate how both genetic factors (e.g. heritability, number of causative loci) and ecological factors (e.g. season length, the difference in the phenotypic optima between seasons, population size dynamics) drive fluctuating selection and to identify the parameters that produce consistent oscillatory patterns. We developed a modeling framework integrating quantitative and population genetics to simulate a population under various selection regimes. We applied spectral analysis to detect periodicity, indicating cyclical selective environments. Our simulations highlight the conditions sustaining oscillations in allele frequencies over time. Spectral analysis successfully identifies the periodic patterns from allele frequency trajectories, even under highly complex selection regimes. Not only does our study clarify the conditions that yield oscillatory behaviors, but these parameters can also potentially be estimated in natural populations, providing a possibility of empirically testing these models.

Fluctuating selection↗
PubMed2025

Rapid genome-wide introgression reveals fitness advantage of immigrant genotypes.

Evolutionary biology has long recognized the tendency for populations to be locally adapted to their ancestral habitat, resulting in higher resident fitness. However, immigrants can also introduce beneficial alleles. The resulting adaptive introgression is usually inferred retrospectively, rather than as a contemporary process. Here, we document exceptionally rapid ongoing adaptive introgression in a lake population of threespine stickleback (Gasterosteus aculeatus). In the first generations after a discrete immigration event, all chromosomes exhibited large increases in immigrant ancestry due to linkage disequilibrium. After a decade, the extent of introgression varied across the genome. The fastest-evolving genes included Spi1b, which enables an increased fibrosis defense against a previously common tapeworm, whose prevalence then declined dramatically. This case study highlights the capacity for immigration to supply beneficial alleles that drive rapid genome-wide evolution.

Journal Article↗
PubMed2025

Strong but diffuse genetic divergence underlies differentiation in an incipient species of marine stickleback.

Understanding how lineages proceed along the "speciation continuum" and how species boundaries are maintained over time remain central questions in evolutionary biology. Populations early in the speciation process can give us detailed insight into the reproductive barriers that first initiate speciation. In this study, we explore the nature of genomic divergence between two sympatric marine stickleback ecotypes from Atlantic Canada, "whites" and "commons". Males of each ecotype exhibit distinct nuptial colorations, nesting habits, and parental care strategies. Using population genomic analyses of SNPs and copy number variants (CNVs; deletions and duplications) we show that whites and commons consistently form distinct populations. We uncover genomic differentiation in the white ecotype characteristic of an incipient species, showing extremely low genome-wide differentiation (FST) and very recent divergence (~1 kya). Demographic analysis detected very low levels of ongoing gene flow between populations. Our results and prior genomic studies suggest that reproductive isolation is being maintained between ecotypes despite recent evidence that hybridization in nature does occur. Contrary to other systems, we found many small, but dispersed regions of high differentiation throughout the genome rather than explicitly within chromosomal inversions or the sex chromosomes. On chromosomes VII and XVI, we identified CNVs overlapping genes enriched for olfaction, which may play a role in differences in reproductive strategies between ecotypes. Ultimately, our results demonstrate that genome-wide rather than localized differences can underlie the early stages of divergence, and that this pattern is corroborated by both SNPs and CNVs.

Copy Number Variation↗
PubMed2025

Extensive Introgression Failed to Erode Species Boundaries Among Multiple Sympatric Closely Related Species of Roscoea.

How species boundaries are maintained among sympatric closely related species experiencing gene flow is a puzzling question in evolutionary biology. Although introgression is commonly documented, the dynamics and gene function of introgression have rarely been explored to probe why frequent introgression does not necessarily destroy species boundaries in sympatry. In this study, we employ whole-genome resequencing data to examine introgression among five closely related species of Roscoea that coexist in a 'sky island' with seventeen distinct morphological traits. Our findings reveal that introgression has led to the phylogenomic discordance between nuclear and chloroplast genomes among these morphologically distinct species. Additionally, introgression is predominantly asymmetrical in both intensity and gene function, particularly concerning recombination. Notably, the majority of gene functions associated with introgressed loci are unrelated to reproductive processes. Our results suggest that closely related species with incomplete allele assortment can coexist despite theoretical predictions, highlighting the semipermeable nature of species boundaries as reproductive isolation develops. This provides a critical conceptual framework for understanding the interplay between introgression and species persistence. Our finding offers insights into how related sympatric species boundaries can be maintained in the face of frequent asymmetrical gene introgression.

Sympatry↗
PubMed2025

Experimental Validation of Genome-Environment Associations in Arabidopsis.

Identifying the genetic basis of local adaptation is a key goal in evolutionary biology. Allele frequency clines along environmental gradients, known as genotype-environment associations (GEA), are often used to detect potential loci causing local adaptation but are rarely followed by experimental validation. Here, we tested loci identified in three moisture-related GEA studies on Arabidopsis. We studied 42 GEA-identified genes using t-DNA knockout lines under drought and tested effects on flowering time, an adaptive trait, and genotype-by-environment (GxE) interactions for performance and fitness. In total, 16/42 genes had significant effects on traits involved in local adaptation or performance responses to the environment. We found that wrky38 mutants had significant GxE effects for fitness; lsd1 plants had a significant GxE effect for flowering time, and 11 genes showed flowering time effects with no drought interaction. However, most GEA candidates did not exhibit GxE. In the follow-up experiments, wrky38 caused decreased stomatal conductance and specific leaf area under drought, indicating potentially adaptive drought avoidance. Additionally, GEA identified natural putative LoF variants of WRKY38 associated with dry environments, as well as alleles associated with variation in LSD1 expression. While only a few GEA-identified genes were validated for GxE interactions for fitness, we likely overlooked some genes because experiments might not well represent natural environments and t-DNA insertions might not well represent natural alleles. Nevertheless, GEAs apparently identified some genes contributing to local adaptation. GEA and follow-up experiments are straightforward to implement in model systems and demonstrate prospects for GEA discovery of new local adaptations.

Arabidopsis↗
PubMed2026

Predictive evolutionary genomics: principles, validation, and practice.

Climate change and habitat loss are driving rapid evolutionary responses in populations world-wide, which creates an urgent need for evolutionary forecasting in conservation and agriculture. Such forecasting can be categorized into three time scales: trait-based models that use multivariate quantitative genetic equations to project correlated phenotypic responses up to c. 20 generations, allele-based analyses that model allele frequency dynamics up to 100 generations, and composite adaptation scores that aggregate many small effects to yield predictions across longer horizons. However, these approaches have remained largely disconnected. Here, we present a Bayesian framework that integrates these three complementary approaches for evolutionary prediction. Our framework combines genomic, phenotypic, and environmental data to yield probabilistic predictions with explicit uncertainty. We show how predictive evolutionary forecasts can be validated with experimental evolution, field experimentation, historical specimens, and reciprocal transplants. These validated forecasts can help advance conservation and agricultural programmes by helping predict which populations are at risk of future extinction, optimizing breeding programmes for future climates, and planning ecosystem management under environmental change. By supporting a shift towards more predictive approaches in evolutionary biology, this framework may help improve our ability to manage biodiversity and food security in a changing world.

Genomics↗