ABSTRACTCrustaceans, such as shrimp and crabs, are pivotal to global aquaculture, yet their productivity is severely impacted by low‐temperature stress. This study employs comparative transcriptomic and genomic analyses to elucidate the molecular mechanisms underlying crustacean responses to cold stress across five economically significant species: Litopenaeus vannamei, Penaeus indicus, Eriocheir sinensis, Cherax quadricarinatus, and Macrobrachium rosenbergii. We identified 4711 conserved orthogroups and analyzed differential gene expression under low‐temperature conditions. Results revealed species‐specific responses, with 25 orthogroups shared across all five species and 113 orthogroups common to at least four species. Functional enrichment highlighted pathways such as oxidation–reduction, hormone metabolism, immune regulation, and spliceosomes. Key genes, including EcKL, CYP2W1, HSPA5, and SLCs, were implicated in signaling, metabolic, immunological, and developmental adaptations. Phylogenetic analysis was used to trace the evolutionary origins of stress‐responsive genes, enabling the identification of both ancient conserved genes and lineage‐specific genes. The results indicated that “younger” genes tend to exhibit greater transcriptional plasticity than ancient conserved genes. These findings provide critical insights into shared and species‐specific low‐temperature adaptation mechanisms, offering a foundation for breeding cold‐tolerant crustacea strains to enhance aquaculture resilience.

The Tianshan Mountains, which host two native subspecies of western honeybees, represent the easternmost natural distribution limit of Apis mellifera. The managed Xinjiang black honeybee (XJ), introduced a century ago and designated as a Chinese National Animal Genetic Resource, has expanded rapidly under anthropogenic management. However, this expansion simultaneously threatens populations of native subspecies Apis mellifera sinisxinyuan and Apis mellifera pomonella. Herein, we performed the first whole-genome resequencing of the XJ population and analyzed whole-genome data from 19 XJ workers and 172 global A. mellifera samples to clarify the evolutionary history of XJ and evaluate its interactions with native bees. Population structure and phylogenomic analyses showed that XJ clustered within C lineage but formed a divergent clade distinct from other C lineage subspecies, with the closest affinity to Apis mellifera carnica (FST = 0.053). Despite higher inbreeding than other C lineage subspecies, XJ displayed comparatively higher genetic diversity (Θπ = 2.15 × 10-3) and heterozygosity (0.0028) than other C lineage populations (0.0015), although XJ's value falls within the global range of A. mellifera. This genetic pattern can be attributed to substantial introgression (~10%-15%) from the M lineage, specifically from the native A. m. sinisxinyuan. TreeMix and F-branch analysis identified significant gene flow from A. m. sinisxinyuan into the ancestral population of the XJ. Functional enrichment analysis suggested that genes within introgressed regions are involved in cold adaptation and foraging efficiency, and independent transcriptome validation confirmed differential expression of key candidate genes (e.g., LOC552291/MCM4) within these introgressed regions. Overall, our findings indicate that XJ represents an introduced population that has undergone regional adaptation, facilitated by the introgression of potentially adaptive alleles from native taxa. This case underscores the need for conservation strategies balancing management of economically valuable populations with protection of native lineages from genetic swamping and ecological competition.

Human activities are changing the natural world at an accelerating pace, and as a consequence exerting novel and often strong selection pressures on living organisms. For species with traits conferring huge inherent evolutionary potential, like parasites, the outcome may be rapid adaptive responses spanning multiple phenotypic traits. The rise of drug resistance in parasites of domesticated animals is well documented; however, rapid changes in other key parasite traits may go unnoticed. In this contribution to the Scientists' Warning series, we argue that parasites are capable of evolving quickly to meet the new pressures of the Anthropocene. After summarizing evidence demonstrating their ability to evolve quickly and the magnitude of the anthropogenic selection pressures they now face, we discuss the basic types of adaptive responses we might expect. Next, we propose methods to track rapid parasite evolution in real time, as well as possible approaches to either slow it down or mitigate its impact on animal production systems. Our aim is to raise awareness of this concerning but underappreciated phenomenon and appeal for greater research into rapid parasite evolution in the Anthropocene and its consequences.

Urbanisation is a pervasive global phenomenon that exerts strong influence on biodiversity and ecosystems. Many species can thrive in urban landscapes by capitalising on generalist traits and environmental resilience; however, this does not safeguard against potential biases exerted by urban environments on population processes. The Egyptian fruit bat (Rousettus aegyptiacus) is a species with both urban and rural distribution across its range, and some populations show behavioural and physiological differences. Using reduced representation genome sequencing (ddRAD-seq), we tested for genetic underpinnings of these differences between urban and rural bat populations sampled across Israel. Despite a genetically homogenous landscape presenting no population structure, we show clear isolation by distance and landscape effects on genetic connectivity, where open areas, but not urbanisation, constitute a barrier to movement. Using genotype-environment association analysis, we identify 59 candidate SNPs spanning 56 genes potentially associated with urbanisation. This suite of genes entails wide-ranging functions including neurotransmission, metabolism, gene expression regulation, reproductive biology, and retinoic acid and sensory function. Gene Ontology enrichment analysis revealed non-random functional clustering with exceptional enrichment in GABAergic synapse components (98.6-fold), monoatomic ion transport (122.2-fold), and ATP-dependent chromatin remodelling (68.6-fold), evidencing coordinated selection across interconnected neural, metabolic, and regulatory systems. A predominance of intronic variants within this candidate SNP suite (51/59) is suggestive that adaptation in response to urbanisation proceeds primarily through changes in gene regulation, rather than protein-coding modifications. This study shows how a highly mobile species may undergo microevolutionary shifts in response to urban pressures despite ongoing gene flow, elucidating the complex interplay between genetics and the urban environment in a non-model organism.

ABSTRACT By modifying biotic and abiotic environments, urbanisation can influence the evolutionary adaptation of organisms, especially when their distribution is fragmented. However, the effects of urbanisation on evolutionary adaptation remain poorly understood within a metapopulation framework, where high gene flow and recurrent extinctions/colonisations may counteract local adaptation. To bridge this gap, we integrated phenotypic and genomic data and explored how urbanisation shaped the evolutionary processes in the wild radish Raphanus raphanistrum , a widely distributed ruderal species. We conducted field surveys and a common garden experiment to compare phenotypic differences between urban and natural populations in a Mediterranean area. Additionally, population genetic analysis and a genome‐wide association study (GWAS) were performed to uncover the genetic basis of urban adaptation and population structure. Our findings indicate that urban populations of the wild radish exhibit significantly smaller flowers and earlier flowering times compared to natural populations. Their correlations with fitness suggest that earlier flowering and longer petal length have higher adaptive values. However, a trade‐off between these traits indicates that earlier flowering is advantageous in urban environments, whereas larger flowers are favoured in natural habitats. Genomic analyses reveal low genetic differentiation and frequent gene flow among urban and natural populations. The GWAS identified 46 single‐nucleotide polymorphisms (SNPs) significantly associated with urbanisation, 32 of which are located within gene regions. Notably, one of these genes, AT3g27390, is associated with the shift to the reproductive phase. Overall, our results demonstrate how natural selection in an urban context promotes rapid phenotypic divergence in R. raphanistrum despite ongoing gene flow.

Alzheimer's disease (AD) is an important, non-curable disease today. Several possible risk factors have been discussed, among others sleep. Evolutionary hypotheses were proposed to explain sleep variation and AD risk, such as a potential advantage of short or interrupted sleep in ancient insecure environments, the evolution of increased plasticity of the human brain, or antagonistic pleiotropy with increased AD risk. The aim of this systematic review was to investigate in which way sleep is associated with AD risk, in the light of evolutionary hypotheses. Following PRISMA guidelines, the databases PubMed and Embase were searched for longitudinal observational studies on the association between sleep and incident AD in cognitively healthy people at baseline. Potential confounders were assessed (e.g., age, sex, country, etc.). Search results were deduplicated and assessed for inclusion or exclusion by two independent reviewers. We summarized the results in tables and performed meta-analyses in risk factor subgroups where appropriate. Out of 5800 studies, 39 were suitable for this review and 35 were meta-analyzed. Long sleep duration showed a positive association with AD (HR = 1.35, 95% CI = 1.12-1.63) that was not significant after accounting for heterogeneity using prediction intervals (95% CI = 0.74-2.49). Short sleep duration showed a weak, non-significant association with AD risk (HR = 1.07, 95% CI = 0.98-1.18). Several measures of sleep quality (hypnotics use, daytime sleepiness, bad overall sleep quality, and early bedtime) showed an increased risk for AD, while others (e.g., late bedtime) showed a protective effect. This systematic review showed possible associations between sleep characteristics and the risk for AD. However, several results showed heterogeneity that we could not explain with the information given in the publications. More work is therefore needed to assess the risk factors for AD connected to sleep.

Malaria in Latin America is largely caused by Plasmodium vivax, but the closely related monkey parasite Plasmodium simium has recently been observed in humans, thus raising new public health concerns. By screening 719 monkey samples from five Latin America countries, we identified 23 Plasmodium-positives. However, only four samples yielded sufficient mitochondrial DNA sequencing data to allow reliable species identification, and their inclusion in genome-wide population analyses. Using whole-genome variation data from these samples together with whole genome variations of 19 P. simium and 405 P. vivax isolates, we investigated their evolutionary history and population genetics. P. vivax, typically restricted to humans, was identified in three Colombian and one Brazilian monkeys, suggesting possible host niche expansion. Genetic analyses reveal recent genetic exchanges between both species and indicate that P. simium originated from a host jump approximately one to two centuries ago. Also other alternatives are possible, this host shift may have followed P. vivax migration from Central/North America to Brazil. Genome-wide scans revealed signals of positive selection in P. simium genes implicated in interactions with primate hosts, including PvRBP2a and PvRBP1b, as well as genes involved in interactions with mosquito vectors, such as PvCMRP1, PvPAT, and Pvs47. These findings shed light on P. simium evolutionary history. They also underscore the zoonotic risks, and the need to include monkeys in malaria prevention measures while ensuring human-wildlife coexistence.

The African catfish (Clarias gariepinus) is a commercially important species, for both fisheries and aquaculture, and is now the most commonly farmed fish in sub-Saharan Africa. However, knowledge about the genetic diversity and population structure of natural and farmed populations, which is crucial for effective conservation and sustainable aquaculture management, is scarce. Using mitochondrial DNA (mtDNA) cytochrome c oxidase 1 gene (COI) sequencing and genomic analysis using triple restriction site-associated DNA sequencing (3RAD), we investigated the genetic diversity and population structure of farmed and natural C. gariepinus populations from Nigeria including an albino form found in the natural environment. Eleven COI haplotypes were identified, of which seven were unique to natural samples. From the 3RAD results, natural sampling sites had a slightly broader range and higher maximum values for observed heterozygosity (H o = 0.150-0.178), expected heterozygosity (H e = 0.173-0.213) and nucleotide diversity (pi = 0.181-0.228) compared to the farmed populations (H o = 0.133-0.161, H e = 0.116-0.149, pi = 0.121-0.156). Conversely, genetic differentiation (F st) was higher among farmed sampling sites compared to the natural ones and there was high genetic differentiation between the farmed and natural C. gariepinus sampling sites (F st = 0.29-0.44). Admixture patterns suggested occasional mixing, possibly driven by hydrological connectivity and fish transport practices. Notably, five albino individuals sampled from the wild supported evidence of farm escapees. Outlier analyses and GO enrichment revealed loci potentially under selection related to lipid metabolism, immune signalling and apoptotic processes, indicating metabolic and immune-related adaptations to environmental stress. Our finding of potential farm escapees highlights the potential risks associated with increasing aquaculture activities and the need for greater regulation of fish farms, which could aid monitoring and reduce the risk of escapes.

ABSTRACTUltraconserved elements (UCEs) have emerged as a powerful tool for resolving deep evolutionary relationships due to their low DNA quality requirements and broad taxonomic applicability. While their utility for intraspecific and shallow‐divergence studies is growing, only a few studies have explored their performance in marine taxa, some of them with metapopulations spanning thousands of kilometers. Here, we employed the UCE approach to investigate the population genomics of Gigantidas platifrons—a deep‐sea mussel with a long larval dispersal period that exhibits a panmictic genetic structure across its extensive distribution range in the chemosynthetic ecosystems of the Western Pacific. With its published whole genome and prior restriction site‐associated DNA sequencing using IIB restriction enzymes (2b‐RAD seq) study, this species is an excellent candidate for evaluating the effectiveness of UCEs. We conducted UCE target capture sequencing on 123 individuals collected from two hydrocarbon seeps and four hydrothermal vents, yielding 1960 UCEs. To assess the impact of different reference choices, we identified 11,870 single‐nucleotide polymorphisms (SNPs) by mapping against the published genome and 8936 SNPs by mapping to the representative 1960 UCEs. Both datasets were similar, with over 80% of the SNPs located in intronic and intergenic regions. Analyses based on both datasets consistently implied a clear genetic divergence between the South China Sea (SCS) and Okinawa Trough‐Sagami Bay (OT‐SB) populations, with predominant gene flow from OT to SB, consistent with previously published 2b‐RAD seq findings. Additionally, UCE‐based SNPs identified a dynamic decline in population size for individuals in the three regions and revealed selective adaptation signals to their environments. Overall, our study serves as a proof‐of‐concept demonstrating that UCEs provide a comparable resolution to RAD‐Seq in detecting shallow‐level genetic divergence and delineating conservation units in a high‐dispersal marine species, even when lacking a sequenced genome.