Modern wheat breeding has significantly improved yield and agronomic uniformity, but its collateral impact on adaptive plasticity is not fully understood. Iranian wheat landraces, as a primary center of diversity, provide a unique reservoir for studying ancestral variation. This study investigates the genomic architecture of diversity loss and identifies selective footprints associated with the erosion of stress resilience during the transition to modern cultivars. Analysis of 298 Iranian genotypes using 45,218 high-quality SNPs revealed a severe genetic bottleneck, with modern cultivars occupying a significantly restricted genotypic space compared to landraces (P < 2.2 × 10⁻¹⁶). Temporal tracking of derived allele frequencies (DAF) showed that genetic erosion intensified post-1990, with DAF increasing from 0.07 to 0.43, identifying recent breeding-rather than domestication-as the primary driver of resilience loss. Genomic scans detected hard selective sweeps on chromosomes 3B, 4A, 4D, and 6B. While selection on chromosome 3B successfully fixed Rht dwarfing alleles (d = -0.96), it was linked to a significant resilience penalty. Haplotype reconstruction indicated that the loss of ancestral ABC transporters (Chr 4D) and NBS-LRR receptors (Chr 6B) is associated with reduced stress tolerance index (STI) and disrupted ion homeostasis (P < 0.05). A Breeding Feasibility Score (BFS) of 79.7 identifies these regions as viable targets for recombination-based recovery. Selection for yield-specialist haplotypes has driven the fixation of alleles deficient in environmental defense through "Negative Genetic Hitchhiking." We propose Haplotype-Based Surgical Introgression as a strategy to re-introduce these ancestral-adaptive blocks into modern wheat without compromising yield gains.

Genetic parameters, genomic scans, and gene-set analysis of semen traits in Italian Brown Swiss dairy cattle.

Color polymorphism is an important trait due to its role in defense strategies, feeding habits, environmental responses such as temperature regulation, and overall fitness. While the genetic basis of color polymorphism is well understood in mammals, it remains relatively understudied in nonavian reptiles. Vipera berus, the European adder, is the most widely distributed and northernmost terrestrial snake in the world. Similar to other European vipers, V. berus exhibits a range of dorsal color patterns spanning from zig-zag to complete melanism. However, a unique longitudinal dorsal stripe pattern was recently discovered in the isolated Gossa Island (∼45 km2) population of Norway, where ∼5% of snakes exhibit this distinct pattern instead of the common dorsal zig-zag pattern. In this study, we investigated the genetic basis of the unique phenotype observed on Gossa by combining low-depth whole-genome shotgun sequencing and pairwise FST genome scanning. We discovered a moderately sized, significantly differentiated genomic region containing five associated genes, including the premelanosome gene (PMEL) that encodes a well-known transmembrane glycoprotein that is a key component of melanosome organelles. We implicate a functionally relevant variant in the encoded premelanosome protein. Our results provide insight into the evolution and genetic basis of pigmentation of squamate reptiles using the unbiased approach of genome scanning, a method that has rarely been used in this context.

Click chemistry reveals sialylated glycoprotein biosynthesis in Ixodes ricinus ticks and tick-derived cells.

ABSTRACTIntraspecific genetic diversity is a crucial aspect of biodiversity conservation as it preserves evolutionary potential and enhances resilience to environmental change. Genomic‐informed delineation of Conservation Units (CUs) offers ways of subdividing species into groups based on demographic independence and adaptive differentiation, to develop biologically relevant conservation and management policies. CUs have been defined in many species of harvested anadromous salmonids, but broad‐scale data remain lacking in the Canadian Arctic, where anadromous Arctic Char (Salvelinus alpinus) dominates catches in Indigenous‐led subsistence and commercial fisheries. In this study, we use low‐coverage whole‐genome data from 30 Canadian Arctic Char populations to define CUs based on population structure, connectivity, and adaptive genetic variation. We highlight two main genetic groups, each of which comprises three subgroups, or candidate CUs: the North (above the 67th parallel), including the North Baffin Island, Kitikmeot, and Inuvialuit Settlement Region CUs; and the South (below the 67th parallel), including the South Baffin Island, Ungava Bay, and Hudson Bay CUs. This delimitation is supported by areas of low effective migration between candidate CUs, as well as isolation‐by‐environment, which suggests adaptive differentiation. Finally, we discuss opportunities and caveats related to genetic linkage when identifying adaptive variation from whole‐genome sequencing data using genome scans and gene–environment associations.

Introduction Primate brain evolution is characterized by neocortical expansion, yet secondary reductions in brain size have occurred in several lineages. This study reconstructs the evolutionary dynamics of relative neocortex size in anthropoid primates and explores genomic correlates of identified neocortical reductions in New World monkeys to investigate whether such changes reflect direct selection on neural traits or arise from other mechanisms. Methods Neocortex and medulla volumes were compiled for anthropoid species. Phylogenetic modeling of relative neocortex size was performed using Fabric-regression with medulla volume as covariate. Genomic analyses involved codon-based tests for positive selection (aBSREL) and shifts in selection intensity (RELAX) across 18,177 orthologous protein-coding genes, followed by functional enrichment and characterization of candidate genes. Results Phylogenetic analyses revealed heterogeneous changes in relative neocortex size across anthropoids, with a statistically significant reduction along the ancestral Callitrichinae + Aotus branch. Genomic scans identified 12 genes under positive selection, two under intensified and none under relaxed selection on this branch, with no enrichment for neurodevelopmental or brain-related pathways. Only a single candidate with potential neurodevelopmental relevance was identified (ZNF512B). Conclusion The absence of a clear neurodevelopmental genomic signal contrasts with previously reported signatures of positive selection on brain-related genes in encephalized cebids, suggesting that brain expansions and reductions in anthropoids may not share a common genomic basis. This also opens up the possibility that the neocortical reduction detected here emerged as a by-product of selection on other traits (e.g. body size or life-history), rather than as a direct target of selection on neural phenotypes.

Cercospora leaf spot, caused by Cercospora beticola, is the most destructive foliar disease of sugar beet. Management has relied heavily on fungicides, but widespread fungicide resistance emphasized the need for resistant varieties. To assess how varietal resistance shapes C. beticola populations, we conducted a 3-year field experiment at four locations in Germany using sugar beet varieties ranging from susceptible to highly resistant. Infected leaves were collected separately per variety and location to serve as inoculum for the following year, maintaining variety- and location-specific pathogen populations under controlled selective conditions. A total of 900 isolates were subjected to whole-genome sequencing and population genetic analyses. Isolates collected in 2022 showed extensive admixture among locations. Equal mating-type ratios were observed in some populations but skewed in others, suggesting that sexual reproduction may occur locally. Location-specific re-inoculation preserved population continuity but did not produce detectable local adaptation. By contrast, the population was affected to some extent by variety-specific re-inoculation. Populations from one highly resistant variety formed two divergent lineages with reduced diversity and altered allele frequency spectra, consistent with host-driven selection. Genome scans identified 26 candidate genes, including two putative effectors, associated with adaptation to the highly resistant variety. These findings demonstrate rapid C. beticola adaptation to resistant varieties, highlighting the role of host-driven selection in resistance management.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-026-52994-7.

Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes) are among the world's rarest penguins and considered taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the New Zealand mainland have been affected by a deadly neonatal disease, respiratory distress syndrome, contributing to a decline to fewer than 115 breeding pairs. To investigate the putative genetic basis of this disease, we generated high-quality whole-genome data from 249 individuals spanning the species range, including New Zealand mainland (Northern range) and sub-Antarctic Enderby (Auckland Islands) and Campbell Islands (Southern range). Population genomic analyses unexpectedly revealed three deeply divergent lineages with negligible gene flow, which is consistent with recognition of three distinct subspecies. Phylogenetic divergence dating suggests that these splits predate human arrival by several millennia, with the Northern lineage diverging from the Southern populations 5-16 thousand years. Genome scans for local adaptation revealed regions of strong differentiation, while genome-wide association analyses identified candidate immune and respiratory genes linked to respiratory distress syndrome. In partnership with Ngāi Tahu, who hold Indigenous guardianship over yellow-eyed penguins, we recommend recognition of three subspecies, urgent conservation action for the critically small and rapidly declining Northern subspecies and the need for immediate population size and trend assessments for the Auckland and Campbell Island populations.

Integrative genomic and transcriptomic analysis to identify potential candidate genes influencing plumage color variation in mule ducks.

Integrative morphological and genomic analyses reveal diversity, reticulate evolution, and adaptation in diploid and tetraploid Rosa species from Xinjiang.

Seasonal migration patterns and geological barriers can impact population structure. In particular, migratory behaviour (resident vs. migratory) differences are thought to promote genetic structure within species. Using a ddRADseq approach, we genotyped 43 purple finches (Haemorhous purpureus) from eight populations across their range comprising both subspecies and examined the effect of migratory behaviour on population structure in this species. We also used genome scans to identify loci under selection and tested whether these differences are associated with migratory behaviour differences. The two subspecies were genetically distinct and within H. p. californicus, we found that populations formed three genetic clusters. Population structure was not strongly associated with resident or migratory behaviour, although we did identify five regions under selection that were distinct between migratory and resident populations. Two of the genes identified in these scans were related to ghrelin hormone and liver fat deposit; Ghrelin is a key component of migratory restlessness, while liver fat deposits are used to fuel migration in birds. Combined our results suggest that population genetic differences between subspecies reflect historical isolation during the Last Glacial Maximum, and indicate that some genetic differences occur between resident and migratory populations. These genetic differences appear to be associated essential for pre-migratory and migratory behaviour in birds.

Understanding lineage divergence is crucial for uncovering cryptic biodiversity. Adaptive divergence, geographic isolation and life-history traits drive speciation in heterogeneous environments. The gentoo penguin complex (Pygoscelis spp.), historically treated as a single species, provides an ideal system to examine divergence across its full distribution. Here, we show the existence of four divergent evolutionary lineages (northern, southern, southeastern, and eastern), supported by phylogenomic and lineage-specific selective pressures, despite ancestral gene flow. South Georgia and Macquarie individuals whose status has been debated, were included. Genomic scans reveal lineage-specific signals of positive selection in genes related to thermoregulation, oxygen transport, metabolism, and skeletal development, consistent with ecological and morphological differentiation across the Antarctic Polar Front. Future niche projections indicate severe habitat losses for three lineages, whereas the southern gentoo may expand its range. We propose a taxonomic revision recognizing four distinct gentoo penguinspecies, including Pygoscelis kerguelensis sp. nov., with important conservation implications.

Background/Objectives: Bud sports (somatic mutations) offer a quick way to develop new bougainvillea varieties by altering specific traits while keeping the desirable genetic background of the original cultivar. However, we still lack a comprehensive understanding of their genomic architecture and the molecular mechanisms behind their formation. This study aimed to characterize the population genomic characteristics of bud sports derived from the commercial variety Bougainvillea × buttiana 'Miss Manila'. Methods: We employed genotyping by sequencing (GBS) on 39 accessions, including 27 bud sports and 12 conventional varieties. Population genomic analyses, such as principal component analysis (PCA), phylogenetic reconstruction, ADMIXTURE, and diversity statistics (π, He, Tajima's D), were performed on 64,810 high-quality SNPs. Genome-wide scans for differentiation (FST) and selective sweeps (XP-CLR) were also conducted. Results: Bud sports showed significantly lower genetic diversity (π and He) than conventional varieties, which matches their clonal origin. PCA, phylogenetic, and ADMIXTURE analyses (optimal K = 4) revealed clear genetic differentiation and distinct population structures between the two groups. The bud sport population possessed fewer private alleles and a less negative Tajima's D value. Genomic scans identified regions under selection in bud sports, with functional annotation pointed to genes involved in ubiquitin-mediated proteolysis and RNA transport. Notably, Bou_119143 (UDP-rhamnose rhamnosyltransferase 1) showed a high mutation frequency specifically in bud sports. Conclusions: We provide the first population-genomic evidence that bud sports of 'Miss Manila' are genetically distinct clonal lineages, shaped by somatic mutation and selection. These findings support bud sports as efficient sources for germplasm innovation. The identified genomic regions and candidate genes lay a foundation for future marker-assisted selection and molecular breeding in bougainvillea.

Whole-genome resequencing identifies adaptive variation associated with complex terrain in southwestern Chinese ducks

Biomarkers can potentially improve the diagnosis, monitoring, and treatment of posttraumatic stress disorder (PTSD). However, PTSD biomarkers that are scalable and easily integrated into real-world clinical settings have not been identified. The analysis was conducted between June to November 2024 using genomic samples and laboratory test results recorded in the Mass General Brigham (MGB) Health System. The analysis included 23,743 European ancestry participants from the nested MGB Biobank study. The first exposure was polygenic risk score (PRS) for PTSD, calculated using the largest available European ancestry genome-wide association study (GWAS), employing a Bayesian polygenic scoring method. The second exposure was a clinical diagnosis of PTSD, determined by the presence of two or more instances of PTSD-related diagnostic codes in the longitudinal electronic health records (EHR). The primary outcomes were the inverse normal quantile transformed, median lab values of 241 laboratory traits with non-zero h2SNP estimates. Sixteen unique laboratory traits across the cardiometabolic, hematologic, hepatic, and immune systems were implicated in both genomic and phenotypic lab-wide association scans (LabWAS). Two-sample Mendelian randomization analyses provided evidence of potential unidirectional causal effects of PTSD liability on hepatic (decreased albumin and total bilirubin), cardiometabolic (decreased HDL cholesterol and increased VLDL cholesterol), and hematologic (decreased mean platelet volume) markers. These findings demonstrate the potential of a triangulation approach to uncover scalable and clinically relevant biomarkers for PTSD.

Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions-genomic valleys-remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species-Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.

Understanding the genetic basis of adaptation is essential for reconstructing evolutionary processes, and this can be accomplished particularly by studying closely related species occupying diverse ecological niches. In this study, we performed genome-wide scans for recent selective sweeps in the four extant species of the Lynx genus-Lynx canadensis (Canada lynx), Lynx rufus (bobcat), Lynx lynx (Eurasian lynx), and Lynx pardinus (Iberian lynx)-using a composite likelihood ratio test based on genotype frequency spectrum. Analyzing whole-genome sequences from 80 individuals, we identified species-specific selective sweeps and conducted functional enrichment analyses to explore biological processes under selection. Results revealed distinct adaptive mechanisms shaped by ecological specialization and demographic histories of different species. In Canada lynx, enriched functions include olfactory signaling and pigmentation-related processes; the Eurasian lynx showed signals related to cardiac and neural development; the Iberian lynx exhibited enrichment in immune-related pathways, potentially reflecting pathogen-mediated selection under strong genetic drift; and the bobcat displayed functional signals in reproductive and metabolic regulation. Our study revealed the species-specific nature of recent signatures of ecological differentiation in the genomes of closely related species of the genus Lynx, with minimal overlap, illustrating their diverse evolutionary trajectories and shedding light into the mechanism of adaptation among highly specialized carnivores.

Guizhou Province has historically been a region severely affected by malaria in China. For decades, vector control has served as a cornerstone of national efforts to control and eliminate malaria. However, the efficacy of this strategy is largely challenged by the development of insecticide resistance. In the present study, the resistance status to organophosphates (OPs) and carbamates (CBs) ofAnopheles sinensisfield populations across Guizhou Province was investigated with a primary focus on elucidating the underlying mechanisms. From 2017 to 2024, mosquitoes were collected intermittently using mosquito-killing lamps across Guizhou Province.An. sinensisspecimens were identified using morphological and molecular methods. Subsequently, we genotyped theace-1gene via PCR and measured acetylcholinesterase1 (AChE1) residual activity using biochemical assays. Whole-genome sequencing of individual mosquitoes was performed using Illumina sequencing, and the copy number of theace-1gene was quantified by standard genomic DNA quantitative PCR. Two independent-sample t-test and a chi-squared test had been used in this study. FemaleAn. sinensiswere collected from 12 field populations across Guizhou Province. Following species identification, point mutations in theace-1gene were detected in 551 mosquito samples. Only one point mutation, G119S, was identified across all populations, with the frequency ofthe ace-1mutant genotypes (119GS and 119SS) exceeding 66% in 11 out of the 12 populations. Heterozygotes were the predominant genotype. The AChE1 activity was not inhibited by propoxur in 10 populations. A significant departure from Hardy-Weinberg equilibrium was observed in 6 of the 12 populations, indicating an excess of heterozygotes in these populations. Notably, heterogeneous duplication of theace-1gene inAn. sinensiswas detected for the first time through genomic scanning andace-1copy number quantification. Resistance to OPs and CBs is widespread inAn. sinensispopulations across Guizhou Province. Both heterogeneous duplication and point mutation of theace-1gene inAn. sinensislikely contribute to resistance to OPs and CBs. These findings highlight the necessity of monitoring duplicated resistance alleles in natural populations to formulate region-specific resistance management strategies.

In dairy sheep, mammary morphology-related phenotypes are crucial functional traits due to their connection to machine milking aptitude, udder health, particularly mastitis, and animal welfare. This study aimed to dissect the genetic architecture underlying 5 mammary morphology traits (Udder depth, Udder attachment, Teat placement, Teat size, and Udder shape) in Churra dairy sheep by using data generated with the Illumina OvineSNP50 BeadChip. The analyzed population, part of the Churra Dairy Selection Nucleus (ANCHE), comprised 1,680 ewes distributed across 16 half-sib families. Genome scans using linkage analysis and a GWAS detected 5 genome-wide significant QTL regions. Comparison with previously reported sheep QTL revealed no direct overlap; however, several of the identified regions coincided with QTL reported in cattle for mammary morphology and mastitis resistance traits, suggesting the possibility of conserved genetic mechanisms underlying these traits across ruminant species and further supporting the relevance and validity of the genomic regions detected in this study. Interestingly, the genome-wide significant QTL region detected on OAR13 for Teat placement showed overlapping with chromosome-wide effects on Udder shape, suggesting for this region a potential pleiotropy effect or the presence of closely linked variants affecting multiple udder traits. To further explore the genome-wide significant regions identified in this study, all genes within each region were annotated. Among the 84 annotated genes, 3 of them, NCOA3, ASS1, and TMEFF2, directly overlapped with a previously defined reference gene list for udder traits and were therefore considered direct functional candidate genes. These genes were associated with epithelial branching, extracellular matrix regulation, cytoskeletal dynamics, and signaling pathways. For the remaining annotated genes in the target regions, a prioritization analysis was performed to identify additional potential candidate genes that may be relevant to the traits under study. The results reported here offer a valuable insight into the genetic basis of udder morphology traits in dairy sheep and are a first step into the identification of genetic markers that could improve the efficiency of future genomic selection programs in dairy sheep.

ABSTRACTEarly developmental processes significantly influence growth and maturation patterns, aquaculture traits that are critical for physiological adaptation and productivity. The vestigial‐like family member 3 gene (vgll3) plays a key role in growth and maturation across diverse taxa, including mammals and teleost fishes. A single‐nucleotide polymorphism in vgll3 (SNPvgll3) shows evidence of selection under aquaculture conditions in gilthead seabream (Sparus aurata), as demonstrated by previous genome scan and targeted transcriptomic (qPCR) analyses. This study investigated how different SNPvgll3 genotypes (AA, AG and GG) affect gene expression in juvenile gilthead seabream. Genotype‐dependent regulatory signatures were identified, as the transcriptome profiles (over 240 quantified transcripts) of the farming‐associated GG genotype, which also showed significantly lower vgll3 expression according to qPCR, differed markedly from those of individuals with the AA genotype. Reduced vgll3 expression has been associated with improved body condition and altered maturation timing in other teleost species. Consistent with these findings, our transcriptomic analysis identified differential expression of additional genes involved in growth regulation, developmental processes, and sexual maturation. Specifically, genes such as amh, cacng1b, casq2, tnnc2 and igfn1.1, which are known to play roles in puberty onset and muscle physiology in teleosts, were significantly associated with vgll3 genotype differences in gilthead seabream. Overall, our findings support a conserved role of vgll3 in pathways related to somatic growth and reproductive maturation, though its precise mechanistic function remains to be established. This pronounced genotype‐specific transcriptomic divergence, well‐documented in humans and plants but still underexplored in non‐model species such as fish, raises important questions regarding the underlying evolutionary and developmental mechanisms. Future studies integrating phenotypic variation, tissue‐specific expression, and multiple developmental stages will be essential to further resolve the basis of genotype‐dependent regulatory effects.