The aurochs, the wild ancestor of domestic cattle, was a keystone herbivore in Late Pleistocene Eurasian ecosystems and a major prey species for Palaeolithic hunter-gatherers. Despite its significance, the genetic structure of aurochs populations that survived the Last Glacial Maximum (LGM) remains poorly understood, especially in southeastern Europe. Here, we present the first directly dated ancient genomes of aurochs from the eastern Adriatic region, recovered from the Upper Palaeolithic site of Šandalja (Istria, Croatia). Two female individuals, dated to approximately 14,800-14,200 and 11,800-11,400 calibrated years before present, were sequenced for low-coverage whole genomes and near-complete mitochondrial genomes. Bayesian phylogenetic analyses and median-joining network reconstruction place both specimens within mitochondrial haplogroup P, the dominant European aurochs lineage. However, they do not cluster within the main P sub-haplogroup observed in most ancient aurochs samples and in modern cattle carrying P-type mitochondrial lineages. Instead, one specimen is placed within an 'alternative' P sub-haplogroup, whereas the position of the other appears more isolated and should be interpreted cautiously, as it may be influenced by limited sequence coverage and the resulting uncertainty in phylogenetic placement. At the nuclear genomic level, the two Šandalja aurochs show affinity to Late Pleistocene and Early Holocene aurochs from Italy. Although based on a limited number of specimens, this pattern is consistent with possible genetic connectivity across the Adriatic region, potentially associated with the now-submerged Great Adriatic Plain (GAP). Overall, our results suggest regional structure among Late Pleistocene aurochs, potentially associated with the exposed Adriatic Plain as a refugium and dispersal corridor between the Apennine and Balkan Peninsulas. By filling a major geographic and temporal gap in the aurochs genomic record, this study highlights the Adriatic Basin as a potentially overlooked centre of Pleistocene megafaunal diversity and refines models of postglacial recolonization and cattle evolutionary history.

ABSTRACTEarly‐life telomere length can be an integrated and accessible biomarker of lifetime fitness. Telomere length can result from complex interactions between heritable genetic variation, inherited gametic variation and accumulated environmental effects acting on individuals and parents. Consequently, to understand early‐life telomere length and its fitness consequences, both offspring traits and intergenerational effects resulting from parental traits need to be studied simultaneously. This is, particularly, true for inbreeding as poor performance or impaired telomere maintenance in offspring as well as poor parental reproductive effort or changes in gametic telomeres can reduce telomere length of offspring. Here, we explore the effects of individual inbreeding, parental inbreeding and parental age in a large dataset (n = 679) of nestling telomere length in a long‐term studied wild population of purple‐crowned fairy‐wrens (Malurus coronatus coronatus) with multigenerational ecological and environmental data. We find no effect of nestling inbreeding on telomere length, even in adverse (hot and dry) climatic conditions. Offspring telomere length was not associated with paternal inbreeding or age (neither within‐ nor between‐fathers). However, nestling telomere length declined with maternal inbreeding and with increasing maternal age. Combined, these results do not support inherited gametic effects but rather suggest that effects of inbreeding and ageing on the mother's phenotypic state may affect pre‐ and/or post‐natal reproductive investment. Offspring from older and more inbred mothers, with shorter telomeres, will suffer reduced lifetime fitness. Moreover, inheritance of shorter telomeres could lead to population‐level changes in performance.

The Hawaiian Drosophila radiation exemplifies rapid adaptation and species diversification. Many factors have been attributed to these phenomena, including allopatry, sexual selection, and ecological specialization. In recent years, the microbiome has come to the forefront as an important driver of adaptation that is capable of facilitating host survivorship, enhancing resilience to local environmental challenges, and enabling the use of different dietary resources. To determine the factors that contribute to microbiome community variation in natural populations, we conducted a survey of bacterial and fungal communities from over 500 wild flies collected from across six islands of the Hawaiian archipelago. These samples represent a breadth of host plant specializations, habitats, lifestyles and endemicity. Our findings reveal that microbiome variation is largely driven by abiotic factors including elevation, temperature, rainfall, and evapotranspiration, but is not strongly constrained by phylogenetic relatedness. Identical species inhabiting three separate locations exhibited different microbiomes. By contrast, distantly related species inhabiting the same site had more similar microbiomes. The microbiomes of endemic species also differ from recently introduced invasive Drosophila in terms of diversity, composition, and predicted function. Given the myriad roles of the microbiome in nutrition, reproduction, and mate choice, these results provide a foundation for determining the roles of the microbiome in the ecological divergence of Hawaiian Drosophila.

Understanding the spatial scale and structure of marine connectivity is essential for uncovering how ocean currents shape gene flow, population structure and larval transport in reef organisms. We examined range-wide patterns of gene flow and population structure in the tomtate (Haemulon aurolineatum), an abundant reef fish with a broad distribution from southern Brazil to Bermuda in the western Atlantic. We used genome-wide SNPs, mitochondrial DNA sequences and a re-evaluation of morphological variation to assess connectivity, demographic history and lineage boundaries across 22 locations spanning all major biogeographic provinces within the species' range. Population structure and phylogenetic analyses identified three main genetic groups: (1) the Caribbean and Southwestern Atlantic (CSA), (2) the Gulf of Mexico (GOM) and (3) Bermuda (BDA), with further substructure within CSA. Demographic modelling and migration analyses supported early divergence followed by sustained but asymmetric gene flow, particularly into BDA, which acts as a long-term demographic sink, likely maintained by episodic larval input from CSA and GOM. This pattern aligns with previous findings from biophysical models and larval transport studies. Recognized marine barriers such as the Eastern and Western Caribbean breaks contributed to population differentiation, while coastal corridors along Brazil and the Guianas facilitated northward gene flow. Coalescent-based species delimitation supported three species-level lineages, but we interpret these as subspecies: morphologically and genomically distinct, yet not fully reproductively isolated. Taken together, these results demonstrate how asymmetric dispersal and oceanographic isolation can structure genetic diversity in marine organisms by creating peripheral demographic sinks like Bermuda, where limited and unidirectional connectivity promotes long-term differentiation-a pattern we describe as the 'Bermuda Triangle effect.'

The productivity and sustainability of legume crops are highly dependent on their tripartite symbiotic system with rhizobia and arbuscular mycorrhizal fungi (AMF), a system currently facing significant pressure from long-term excessive nitrogen (N) fertilization. However, how long-term N input and host niche selection jointly regulate the structure and function of this tripartite symbiotic system remains poorly understood. Using a soybean pot experiment with soils collected in 2022 from a 24-year field experiment (winter wheat-summer maize rotation, receiving annual urea at 0, 200, 400, 600 kg N ha-1 year-1 since 1998), we systematically elucidated these mechanisms. The results demonstrate that host niche selection is the dominant driver structuring the core symbiotic network. This manifests as a progressive, stringent homogeneous selection for rhizobia from soil to nodules, and as dispersal limitation for AMF, imposed by strong physical filtration at the root epidermis. Long-term N input nonlinearly disrupted this host-dominated framework. Specifically, excessive N fertilization shifted rhizobial community assembly from deterministic to stochastic dominance, weakened their cross-kingdom synergy with AMF, and triggered a transition in the systemic N-cycling pathway. This transition moved from an efficient, low-loss internal symbiotic N-fixation mode to a high-loss-risk external N metabolism mode. This functional trade-off ultimately compromised the system's nutrient accumulation and retention capacity, offering a mechanistic explanation for how excessive N fertilization drives agroecosystems from symbiosis-dependence to fertilizer-dependence. These findings demonstrate that optimizing N management sustains nutrient retention and productivity by preserving the host-shaped symbiotic network, offering a reference for reducing fertilizer dependence and improving the sustainability of legume production.

Epigenetic modifications to DNA are proposed to underpin plastic responses to environmental change, and the manner in which DNA methylation contributes to plasticity likely differs among tissues. However, few studies have investigated tissue-specific DNA methylation responses to ecologically relevant environmental stressors in natural settings. Here, we used reduced representation bisulfite sequencing to examine the influence of insitu microhabitats on DNA methylation in gill and foot of juvenile California mussels (Mytilus californianus), a foundation species with widespread dispersal and little evidence of genetic population structure. We examined mussels from a one-month reciprocal transplant experiment between a cool, wave-exposed and a warm, wave-protected microhabitat. These manipulations-which were previously shown to alter juvenile mussels' heat tolerance-led to significant and tissue-specific changes in CpG methylation, including within a number of genes with roles in stress response pathways. Differentially methylated genes were involved in processes including heat shock response, proteolysis, and temperature sensing. In gills, differentially methylated CpGs were more likely to occur in introns relative to other inter- and intragenic features. This study expands on previous research that examined environmentally driven shifts in DNA methylation by documenting plastic and tissue-specific changes in DNA methylation between microhabitats in a natural setting.

With accelerating biodiversity loss, tracking both inter- and intraspecific diversity is critical, as within-species variation underpins population viability and adaptive potential. We developed a new multi-locus framework, and obtained an Orthoptera-specific marker panel targeting 398 nuclear loci plus the mitogenome and ribosomal DNA to assess species boundaries, population structure and intraspecific diversity. We applied this approach to 645 specimens covering all 105 Swiss Orthoptera species, sampled during the nationwide Red List update. This multi-locus dataset produced a well-supported phylogeny and resolved several taxonomic ambiguities with direct conservation relevance. We demonstrate its ability to identify fine-scale population structure and further illustrate its application to genetic diversity estimation. While species' IUCN threat levels were not correlated with genetic diversity, we found a significant negative association between genetic diversity and dependence on riparian habitats: river-bank specialists showed lower diversity, likely reflecting the severe fragmentation and alteration of these ecosystems. Our results demonstrate that the application of new molecular tools provides valuable, complementary insights not only for taxonomy but also for conservation assessments. The development and application of genetic monitoring frameworks, such as the one presented here, are highly valuable for promoting the inclusion of genetic diversity in future conservation assessments.

ABSTRACTClimate change is threatening crop yield of a broad range of agricultural species, impacting global food security and trade. Crop wild relatives may contain climate adaptations that can be quickly introduced into cultivars, especially in perennial tree crops that use rootstock. Identifying climate resilient genotypes that can potentially be used as alternative rootstock is imperative to mitigate the impacts of climate change. Here, we used whole genome sequence data of 59 wild Juglans hindsii (Northern California black walnut) and 39 wild J. californica (Southern California black walnut) adult trees to: (i) determine predicted adaptedness to future climate based on landscape genomic models, (ii) explore their adaptedness if used as rootstock in existing walnut orchards and (iii) identify potential future planting sites within existing croplands. Wild J. hindsii has the highest predicted adaptedness to the future climate of Northern and Central California walnut orchards, while wild J. californica has the highest predicted adaptedness to Southern and Central California walnut orchards. Juglans californica has high adaptedness to the future climate of more existing cropland than J. hindsii does. If walnut farmers wanted to test new rootstock sources for their existing orchards or convert their farmland into walnut orchards, this study informs the exploration of such ideas. We illustrate how landscape genomic tools can be utilized in agricultural contexts as first steps in identifying climate adapted genotypes.

ABSTRACTConservation translocations have become important assets in saving African wild dogs (Lycaon pictus) from local extinction, which have declined drastically due to anthropogenic pressures. In South Africa, wild dogs were eradicated except for a small, isolated population remaining in Kruger National Park. Due to reintroductions into private reserves, the country now holds a viable metapopulation of over 150 individuals that is used as a donor to repopulate other countries in southern Africa. This Range Expansion Project allows a unique opportunity to quantify the genomic effect of founder events, population isolation and conservation translocations. For this purpose, we harvested 30 whole genomes of wild dogs from Kruger, private reserves and outside protected areas. Demographic reconstructions indicate that populations were historically large (10,000–40,000 individuals) but began declining gradually ~500–100 kya, coinciding with Mid‐Pleistocene climate shifts, followed by a sharp collapse ~2–0.8 kya. The Kruger population showed a substantially higher genetic load and a greater extent of runs of homozygosity (ROHs), indicating that its reduced genetic variation is driven primarily by inbreeding rather than demographic history. In contrast, reintroduced populations in private reserves exhibited the highest genetic diversity and the lowest genetic load. The short ROHs and close genetic affinity to an individual from Kenya support the view that wild dogs historically functioned as a largely panmictic species, and that reconnecting isolated populations can restore evolutionary potential. The absence of drift and relaxed selection implies that genetic resilience can be restored through population admixture, providing valuable guidance for managing threatened species.

Identifying close relatives in wild animal populations is fundamental across many research fields. Genetic estimates of relatedness have expanded rapidly in recent decades, drawing on a range of genetic data types. Here, we review their use and outline opportunities for future studies by combining two complementary approaches. First, we conducted a systematic literature review, assessing 2861 articles in depth to identify how genetic relatedness has been estimated over time. Second, we compare widely used genetic data types for inferring relatedness, conducting computational experiments using data from a rhesus macaque (Macaca mulatta) population in Puerto Rico. We compared other methods against precise identity-by-descent segment-based estimates of relatedness. Our results show that most studies of relatedness (87.8%) continue to rely on short tandem repeat (STR) markers, despite their limited precision. Single-nucleotide polymorphism (SNP)-marker-based relatedness estimates remain underused (8% of studies), even though they yield more reliable estimates when sampled in sufficient numbers. Finally, we find that the simple pairwise-mismatch rate (PMR) method for estimating relatedness in whole-genome sequencing (WGS) data (commonly used in human ancient DNA studies) performs robustly on low-coverage data, for example, DNA retrieved from faecal samples or from cost-effective low-coverage WGS (lcWGS). Together, our findings highlight that lcWGS, combined with PMR-based relatedness estimation, is a promising, cost-effective alternative when DNA quality is limited, genomic resources are scarce, or economic efficiency is essential.