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At least 19 recordsLinked to original sources

PubMed2026

Adaptive genomic evolution and WD40-regulated temporal dynamics of anthocyanins support leaf photoplasticity in Parrotia subaequalis.

BACKGROUND: Parrotia subaequalis, a Tertiary relict endemic to China, plays a significant role in phylogeny and adaptive evolution as a key species in the early differentiation of angiosperms. It has abundant leaf colors and great potential as an ornamental tree. RESULTS: This study assembled the first chromosome-level genome of P. subaequalis (Contig N50 = 2.15 Mb), revealing transposable element proliferation, key paleopolyploid events and dynamic gene family evolution, including the expansion of secondary metabolite transport and synthesis genes (such as WD40, 2OG-FeII_Oxy) and the contraction of gene families related to flower morphogenesis (such as F-box-like, K-box). Through integrative transcriptomics and targeted metabolomics approaches, we further revealed that the color transition of young leaves from red to green was driven by temporal accumulation differences of malvidin-3,5-O-diglucoside, whose biosynthesis is progressively down-regulated during leaf development. WGCNA revealed that a subset of WD40 genes (light-signaling, TTG1/HOS15-like, etc.) coexpresses with anthocyanin biosynthetic genes, like 4CLL9, GT1, in anthocyanin-related modules enriched for auxin signaling and hydrolase activity, suggesting a potential link between WD40 expansion and photoprotective plasticity. Relevant regulatory networks were found to complement the species-specific gene pool related to leaf color regulation. CONCLUSION: This genomic resource of P. subaequalis advanced our understanding of early angiosperm adaptation through neofunctionalized regulatory networks and established a foundation for molecular breeding aimed at enhancing environmental resilience while preserving ornamental traits.

Anthocyanins↗

PubMed2025

Genomic adaptation in group B Streptococcus following intrapartum antibiotic prophylaxis and childbirth.

Through vaginal colonization, GBS causes severe outcomes including neonatal sepsis and meningitis. Although intrapartum antibiotic prophylaxis (IAP) has reduced neonatal disease rates, persistent GBS colonization has been observed in patients following prophylaxis. To determine whether IAP selects for genomic signatures that enhance GBS survival and persistence, a pangenome analysis was performed on 97 isolates from 58 participants before (prenatal) and after (postpartum) IAP/childbirth. Thirty-one of the 34 paired strains from participants with persistent colonization clustered together in the core gene phylogeny, suggesting that the strains recovered at the postpartum sampling were highly similar to those recovered at the prenatal visit. A core-gene mutation analysis identified mutations in 74% (n=23) of the 31 postpartum genomes when compared to the prenatal strains of the same multilocus sequence type recovered from the same individuals. Several strains had acquired mutations in the same colonization-associated genes, though two postpartum strains accounted for most of the mutations. These two outliers were classified as mutators based on high mutation rates and mutations within DNA repair system genes. Increased biofilm production was observed in half of the postpartum strains relative to the prenatal strains, which is supported by the presence of point mutations in genes associated with adherence. Together, these findings suggest that antibiotics may impose a selective pressure on GBS that selects for mutations and phenotypes that promote adaptation and survival in vivo. Enhanced survival in the genitourinary tract can lead to persistent colonization, increasing the likelihood of invasive disease in subsequent pregnancies and in newborns following IAP.

Journal Article↗

PubMed2026

Comparisons Between Large-Scale Genomic Variants and SNPs in Driving Population Divergence and Local Adaptation.

Genomic variations, such as indels (2-49 bp) and structural variants (SVs, ≥50 bp), are larger-scale mutations than single nucleotide polymorphisms (SNPs) and can substantially impact evolutionary processes, including speciation, adaptation, and phenotypes. Despite their functional importance, integrative population genetic analyses that jointly consider genome-wide SNPs, indels, and SVs remain under-explored. The ground tit (Pseudopodoces humilis), an endemic species to the Qinghai-Tibet Plateau (QTP), exhibits divergence across distinct glacial refugia, accompanied by habitat and morphological divergence, making it an excellent example for investigating how different types of genomic variants contribute to population divergence and local adaptation. Here, by retrieving 81 whole-genome sequence data, over 13 million SNPs, 2 million indels, and 22,101 SVs were identified. Variants were unevenly distributed across the genome, characterized by distinct hotspot regions. Indels and SVs revealed four genetic clusters consistent with previous SNP-based results, thereby validating the reliability of our variant datasets. FST and genotype-environment association (GEA) analyses independently revealed numerous candidate indels and SVs; each showed minimal overlap with previously identified SNPs, and were enriched in similar functional pathways such as signal transduction, skeletal muscle development, water transport, DNA repair, reproduction, nervous system development, and immunity. Collectively, our results demonstrated that indels and SVs could capture additional signatures besides SNPs. Furthermore, similar but distinct gene functions among different types of genomic variants collectively and complementarily drive genomic divergence across environmental gradients in such a high-elevation endemic species, underscoring its evolutionary relevance in local adaptation.

indels↗

PubMed2025

Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.

Natural selection leaves detectable patterns of altered spatial diversity within genomes, and identifying affected regions is crucial for understanding species evolution. Recently, machine learning approaches applied to raw population genomic data have been developed to uncover these adaptive signatures. Convolutional neural networks (CNNs) are particularly effective for this task, as they handle large data arrays while maintaining element correlations. However, shallow CNNs may miss complex patterns due to their limited capacity, while deep CNNs can capture these patterns but require extensive data and computational power. Transfer learning addresses these challenges by utilizing a deep CNN pretrained on a large dataset as a feature extraction tool for downstream classification and evolutionary parameter prediction. This approach reduces extensive training data generation requirements and computational needs while maintaining high performance. In this study, we developed TrIdent, a tool that uses transfer learning to enhance detection of adaptive genomic regions from image representations of multilocus variation. We evaluated TrIdent across various genetic, demographic, and adaptive settings, in addition to unphased data and other confounding factors. TrIdent demonstrated improved detection of adaptive regions compared to recent methods using similar data representations. We further explored model interpretability through class activation maps and adapted TrIdent to infer selection parameters for identified adaptive candidates. Using whole-genome haplotype data from European and African populations, TrIdent effectively recapitulated known sweep candidates and identified novel cancer, and other disease-associated genes as potential sweeps.

Selection, Genetic↗

PubMed2025

Efficient detection and characterization of targets of natural selection using transfer learning.

Natural selection leaves detectable patterns of altered spatial diversity within genomes, and identifying affected regions is crucial for understanding species evolution. Recently, machine learning approaches applied to raw population genomic data have been developed to uncover these adaptive signatures. Convolutional neural networks (CNNs) are particularly effective for this task, as they handle large data arrays while maintaining element correlations. However, shallow CNNs may miss complex patterns due to their limited capacity, while deep CNNs can capture these patterns but require extensive data and computational power. Transfer learning addresses these challenges by utilizing a deep CNN pre-trained on a large dataset as a feature extraction tool for downstream classification and evolutionary parameter prediction. This approach reduces extensive training data generation requirements and computational needs while maintaining high performance. In this study, we developed TrIdent, a tool that uses transfer learning to enhance detection of adaptive genomic regions from image representations of multilocus variation. We evaluated TrIdent across various genetic, demographic, and adaptive settings, in addition to unphased data and other confounding factors. TrIdent demonstrated improved detection of adaptive regions compared to recent methods using similar data representations. We further explored model interpretability through class activation maps and adapted TrIdent to infer selection parameters for identified adaptive candidates. Using whole-genome haplotype data from European and African populations, TrIdent effectively recapitulated known sweep candidates and identified novel cancer, and other disease-associated genes as potential sweeps.

Journal Article↗

PubMed2026

Genomic signatures of adaptation across a landscape of crickets following the introduction of a parasitoid fly.

Novel species interactions provide an opportunity to assess the earliest stages of genetic adaptation. We combined population genomics and field selection surveys to explore the genomic and geographic landscape of adaptation in small, fragmented Hawaiian cricket populations, which are parasitized by larvae of an introduced fly that targets singing males. Multiple protective male-silencing cricket morphs have recently spread under this novel selection pressure, despite song's important roles in mate attraction. We find evidence of sharp declines in cricket effective population sizes following the fly's introduction and identify regions under spatially varying selection mediated by infestation risk, which are linked to an adaptive morph and other genes implicating in resisting infestation. Despite repeated bottlenecks, genetic variation is dominated by structural variant polymorphisms seemingly maintained under balancing selection. Our study illustrates pervasive consequences of abrupt changes in selection on small populations. Fly-mediated selection remains strong despite the spread of adaptive male-silencing phenotypes, which also reduce male fitness in the context of mate attraction.

Animals↗

PubMed2025

Genomic analysis of xerophyte Salweenia species provides insights into the alpine dry-warm valleys divergence and survival history.

Salweenia species are evergreen shrubs capable of preventing desertification and maintaining the health of alpine dry-warm ecosystems in the Hengduan Mountains. However, both the narrowly distributed S. bouffordiana and its more widespread close relative S. wardii are endemic and endangered. Furthermore, their small population sizes render each of these species at risk of extinction. To infer how past climate changes have shaped the evolutionary history of these species, we developed a chromosome-level S. bouffordiana genome (788 Mb) and compared the two species' evolutionary histories, genetic loads and the genomic adaptions to local environmental conditions using whole-genome resequencing data. Our findings reveal a sharp population decline from the Pliocene to the Quaternary. However, populations of S. bouffordiana then started to recover before declining further, while S. wardii populations continued to decline until recently. Abundant homozygous-derived variants accumulated in the two species, particularly in S. bouffordiana, while the species with the most heterozygous variants was S. wardii. Accumulated extensive inbreeding effects but possessed few LOF mutations and few highly deleterious variants in the S. bouffordiana that have experienced the most severe demographic bottlenecks, most likely because of purging effects. This accelerating decline cascade will likely be detrimental to the consequences for the species' future viability and adaptive potential. Overall, this study improves our understanding of the evolutionary history of Salweenia shrubs tolerant to extreme environments and offers a genetic resource for future breeding and conservation efforts.

Genome, Plant↗

PubMed2025

Comparative genomic analysis of Acer tsinglingense and A. davidii provides insights into nervonic acid biosynthesis, population evolution and genome vulnerability of endangered A. tsinglingense.

Global biodiversity is facing threats from climate change, habitat fragmentation, and anthropogenic activities-pressures that particularly endanger endemic and narrowly distributed species. In this study, the high-quality chromosome-level genomes of two ecologically divergent maples were assembled: the endangered and range-restricted Acer tsinglingense (791.40 Mb) and its widespread congener Acer davidii (1291.99 Mb). Phylogenomic analysis indicates that the two species diverged ~16.3 million years ago, with A. tsinglingense showing notable gene family expansions in secondary metabolite pathways. Notably, the 3-ketoacyl-CoA synthase gene family, which is involved in nervonic acid biosynthesis, underwent significant expansion and tandem duplication in A. tsinglingense, exhibiting high expression in buds. Population genomic analysis revealed that, compared with the widely distributed A. davidii, A. tsinglingense possesses lower genetic diversity, higher harmful mutation load, and signatures of a severe population bottleneck during the Late Pleistocene. Genome-environment association analysis further identified climate-adaptive genomic variations linked to five key environmental factors and projected potential genomic offsets under future climate scenarios. The southern lineage of A. tsinglingense exhibited greater climate sensitivity and genomic vulnerability under strong selective pressures, underscoring its importance as a conservation priority. Our research reveals that metabolic specializations in A. tsinglingense (such as the synthesis of nervonic acid) may confer competitive advantages in specific habitats. However, factors including its restricted distribution, historical population bottlenecks, and accumulated genetic load severely constrain its evolutionary potential to cope with rapid climate change. These findings emphasize the importance of elucidating the genomic basis and mechanisms of endangerment in metabolically specialized and threatened plant species to inform effective conservation strategies.

Genome, Plant↗

PubMed2026

Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.

UNLABELLED: Predator-mediated selection is an important ecological force shaping bacterial evolution, but its effects on genomic adaptation and virulence in opportunistic pathogens are not fully understood. Here, we used experimental evolution to study how exposure to the ciliate predator Tetrahymena thermophila affects Pseudomonas aeruginosa. Replicate populations were evolved for 60 days with or without the predator, followed by whole-genome shotgun metagenomic sequencing and phenotypic analyses. Both treatments showed strong selection and evidence of parallel evolution at gene and nucleotide levels, indicating constrained adaptation. However, predator exposure altered evolutionary dynamics. Predator-evolved populations showed a wider distribution of mutation frequencies, with many mutations persisting at intermediate frequencies, consistent with increased clonal interference and ongoing competition among lineages. In contrast, populations evolved without predators showed more high-frequency mutations, consistent with selective sweeps, although some low-frequency variants remained. Despite substantial genomic change, phenotypic outcomes were variable. Virulence in an invertebrate host model did not consistently increase. Instead, evolved isolates showed context-dependent changes, including modest decreases or occasional increases. Competition assays also showed no consistent fitness advantage for predator-evolved isolates, suggesting trade-offs between predator resistance and growth in other environments. Overall, predator-mediated selection reshaped evolutionary dynamics by maintaining diversity and altering the balance of lineages rather than producing uniform increases in virulence. These results highlight how ecological complexity influences adaptive evolution and the context-dependent nature of pathogen traits. IMPORTANCE: Opportunistic pathogens such as Pseudomonas aeruginosa often evolve in environmental settings before infecting hosts, raising questions about how ecological interactions influence virulence. Predator-mediated selection has been suggested to increase virulence via coincidental evolution, but evidence is inconsistent. Here, we show that exposure to a eukaryotic predator does not consistently elevate virulence but does reshape evolutionary dynamics by altering how mutations spread in populations. Predator-exposed populations retained more intermediate-frequency mutations, consistent with increased clonal interference and ongoing competition among lineages, whereas non-predator populations were dominated by selective sweeps. These differences were also reflected in functional targets of adaptation, with predator exposure favoring mutations in genes involved in environmental sensing and interaction. Together, these findings suggest that ecological complexity shapes the dynamics of adaptation rather than driving a single evolutionary outcome, highlighting that virulence is an emergent property influenced by underlying evolutionary processes.

Pseudomonas aeruginosa↗

PubMed2026

The Spatial and Temporal Repeatability of Genomic Responses to Natural Selection as Demonstrated in Stickleback Populations Experiencing Highly Dynamic Environments.

The evolution of genotypic parallelism under shared environmental conditions provides strong evidence for the role of natural selection. However, analyses typically examine genomic signatures of selection long after the putative selection event and only assess the repeatability of responses across spatial population replicates. This impedes our ability to attribute a particular response to a given selection pressure and to distinguish non-parallel responses caused by stochastic processes from those caused by local selection. As such, the consistency of natural selection over space and time is unknown, and the role of persistent local selection pressures is unclear. Here, we leveraged the natural bar-built estuary system of Santa Cruz, California, to examine the repeatability of seasonal genomic change in threespine stickleback (Gasterosteus aculeatus) over space and time. By comparing allele-frequency shifts that are shared across locations (spatial repeatability) with those that are shared across years within locations (temporal repeatability), we identified both spatially shared and local components of putative selection. We found that repeated seasonal outlier responses occurred more often than expected under a neutral null model. Although repeatability declined as the number of estuaries sharing an outlier increased, enrichment above neutral expectations increased with broader spatial sharing, particularly for outliers repeated across both years. While the precise outlier SNPs varied across years, estuary-specific patterns of responses were broadly consistent, suggesting an important role for local conditions. Together, our findings show that temporal sampling can reveal components of putative selection that would be missed from spatial comparisons alone. More broadly, they highlight the importance of examining repeatability over both space and time to understand the parallel and non-parallel components of adaptive genomic change.

Animals↗

PubMed2025

Intraspecific divergence within Microcystis aeruginosa mediates the dynamics of freshwater harmful algal blooms under climate warming scenarios.

Intraspecific biodiversity can have ecosystem-level consequences and may affect the accuracy of ecological forecasting. For example, rare genetic variants may have traits that prove beneficial under future environmental conditions. The cyanobacterium responsible for most freshwater harmful algal blooms worldwide, Microcystis aeruginosa, occurs in at least three types. While the dominant type occurs in eutrophic environments and is adapted to thrive in nutrient-rich conditions, two additional types have recently been discovered that inhabit oligotrophic and eutrophic environments and have genomic adaptations for survival under nutrient limitation. Here, we show that these oligotrophic types are widespread throughout the Eastern USA. By pairing an experimental warming study with gene expression analyses, we found that the eutrophic type may be most susceptible to climate warming. In comparison, oligotrophic types maintained their growth better and persisted longer under warming. As a mechanistic explanation for these patterns, we found that oligotrophic types responded to warming by widespread elevated expression of heat shock protein genes. Reduction of nutrient loading has been a historically effective mitigation strategy for controlling harmful algal blooms. Our results suggest that climate warming may benefit oligotrophic types of M. aeruginosa, potentially reducing the effectiveness of such mitigation efforts. In-depth study of intraspecific variation may therefore improve forecasting for understanding future whole ecosystem dynamics.

Microcystis↗

PubMed2026

Whole-Genome Analysis of HEV Under Sequential Ribavirin Pressure Reveals Early Minor Variants Predicting Resistance.

Ribavirin (RBV) failures in chronic hepatitis E virus (HEV) infection may arise from genomic adaptation, yet the contribution of minor variants remains insufficiently explored. Using a shotgun metagenomics based on next-generation sequencing to obtain the full HEV genome, we analyzed longitudinal HEV populations from sequential clinical samples collected from a patient infected by Paslahepevirus balayani genotype 3c, who underwent three different courses of RBV treatment. Viral diversity increased over time, with most amino-acid substitutions detected at sub-consensus frequencies. Several mutations linked to RBV resistance emerged under treatment pressure. Specifically, D1384N and Y1587F became fixed in the final sampling, while additional substitutions at position 1384 (including D1384T) revealed mutational hotspot. Importantly, D1384N and G1634R were already detectable at low allele frequencies after the first treatment cessation and subsequent rebound, showing that the study of minor variant populations can be early predictors for the development of RBV resistance. These findings underscore the genomic plasticity of HEV under antiviral pressure and highlight the value of deep variant profiling for anticipating RBV treatment failure.

Ribavirin↗

PubMed2026

Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.

Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.

Metagenome↗

PubMed2026

The History of Transposable Element Invasions in Drosophila melanogaster.

As a fundamental biological principle, genomic information is typically transmitted vertically from parent to offspring. Occasionally, however, genetic material is transferred horizontally between species. Transposable elements (TEs) are frequently involved in such horizontal transfer (HT), possibly due to their ability to move in genomes. HT has been particularly well-studied in Drosophila melanogaster, a key model organism for evolutionary and ecological research. Recent studies have revealed that HT triggered the invasion of 12 different TEs in the D. melanogaster genome over the past 200 years. This finding challenges our traditional view of genome evolution, suggesting that TE invasions may not only be isolated events that can be ignored as rare exceptions but could represent recurrent events that continuously reshape genomes. In this review, we trace the history of how these 12 invasions were discovered and outline the lines of evidence supporting them. We also discuss the potential evolutionary consequences of these TE invasions, including their roles in adaptation, genome evolution, speciation, and extinction risk. Finally, we highlight open questions and directions for future research. In particular, it will be essential to test whether other organisms also exhibit similarly high rates of recent TE invasions and to assess whether human activity triggered the high rate of invasions.

Journal Article↗

PubMed2026

Comparative dynamics of Japanese encephalitis virus adaptation in porcine macrophages and insect cells.

BACKGROUND: Japanese encephalitis virus (JEV) is a zoonotic mosquito-borne Orthoflavivirus that circulates primarily in birds and pigs. Previous observations of vector-free transmission between pigs indicates the possibility of single-host cycling in swine. Therefore, the aim of this work was to investigate the evolutionary pressure of single host cycling using a relevant primary cell culture model. METHODS: To investigate whether such single-host cycles affect viral infectivity, fitness and genomic adaptations, two strains and a reverse genetic cDNA-derived clone of JEV were serially passaged 12 times in primary porcine monocyte-derived macrophages (MDMs), in Aedes albopictus-derived C6/36 cells, and alternately between both cell types. Next-generation sequencing analysis was used to identify selected single nucleotide variants (SNVs) and haplotypes. Phenotype-to-genotype connections were confirmed using reverse genetics. RESULTS: For all viruses, serial passaging in MDMs - but not in C6/36 cells - led to a rapid increase in relative infectivity toward MDMs, accompanied by reduced plaque sizes in porcine endothelial cells. In contrast to C6/36 cells, MDM imposed a strong selective pressure, rapidly favoring selection of many SNVs and viral haplotypes. In addition, we identified a dominant selection of mutants with glutamic acid to lysine substitutions at positions 49 or 138 in the E protein, which explained the small plaque phenotype and caused viral sensitivity to heparin-mediated inhibition of attachment, indicating enhanced virus binding to glycosaminoglycans (GAG). The E138K mutant also explained the increased relative infectivity for MDM. CONCLUSION: This work demonstrates a high evolutionary pressure on JEV in MDM causing rapid selections of minor haplotypes. Furthermore, the efficient selection of E49K and E138K SNV, which were responsible for the phenotype, are likely caused by a selective pressure for GAG binding, observed in vitro with other mammalian cells.

Animals↗

PubMed2025

NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.

MOTIVATION: Oncoviruses, pathogens known to cause or increase the risk of cancer, include both common viruses such as human papillomaviruses and rarer pathogens such as human T-lymphotropic viruses. Computational methods for detecting viral DNA from data acquired by modern DNA sequencing technologies have enabled studies of the association between oncoviruses and cancers. Those studies are rendered particularly challenging when multiple species of oncovirus are present in a tumor sample. In such scenarios, merely detecting the presence of a sequencing read of viral origin is insufficiently informative-instead, a more precise characterization of the viral content in the sample is required. RESULTS: We address this need with NextVir, to our knowledge the first multi-class viral classification framework that adapts genomic foundation models to detecting and classifying sequencing reads of oncoviral origin. Specifically, NextVir explores several foundation models-DNABERT-S, Nucelotide Transformer, and HyenaDNA-and efficiently fine-tunes them to enable accurate identification of the sequencing reads' origin. The results demonstrate superior performance of the proposed framework over existing deep learning methods and suggest downstream potential for foundational models in genomics.

Humans↗

PubMed2025

Transcriptomic analysis at 48 h postmortem: a proof of concept for the identification of biomarkers to estimate time since death.

BACKGROUND: The postmortem interval (PMI) refers to the time elapsed between an individual's death and the examination of the body. Tissues undergo a sequence of anatomical changes following death, which are routinely used to estimate the PMI. METHODS: To determine if these anatomical changes are associated with identifiable genomic adaptations that could characterize the PMI more accurately, we analyzed the rat skeletal muscle transcriptome at 0 and 48 h postmortem using Clariom™ S arrays. This study investigates whether specific transcriptomic changes correlate with PMI progression, offering a potential molecular tool to complement established anatomical methods. RESULTS: A total of 3,873 differentially expressed mRNAs were identified, of which 2,787 downregulated and 1,086 upregulated transcripts. The most significantly downregulated mRNA was Tnni1 (FC = -30.95, p = 1 × 10-3), while the most upregulated were mt-ATP6, mt-ATP8, and mt-CO3 (FC > 7.78, p < 1.36 × 10-12). Gene ontology (GO) enrichment analyses revealed that mRNAs upregulated at 48 h in the PMI were primarily associated with vascular and endothelial processes, including nitric oxide transport and angiogenesis. Conversely, downregulated mRNAs were linked to mitochondrial activity and cellular metabolism, reflecting both a transient vascular response and metabolic pathway shutdown in the rat skeletal muscle. CONCLUSION: Our results demonstrate significant transcriptomic changes at 48 h postmortem, highlighting specific genes and biological pathways that may serve as candidate biomarkers for PMI estimation.

Animals↗

PubMed2026

Post-colonial human admixture and natural selection: disentangling signals in complex demographic contexts.

Natural selection and admixture are defining population genetic features of modern human populations, yet their interaction has only recently emerged as a major focus in human evolutionary genomics. While the influence of natural selection on population structure and trait diversity is well established, the ways in which selective pressures operate after admixture have historically received far less attention. In this review, we synthesise the latest progress in understanding post-admixture selection and highlight case studies that illustrate how novel environments, pathogen exposure, dietary shifts and socio-historical transformations have driven genomic adaptation. We conclude by identifying key gaps that remain in the field with the aim of motivating future research and facilitating new insights into how admixture and selection jointly shape human diversity.

Journal Article↗