The Baltic Sea is a young, semi-enclosed brackish ecosystem shaped by postglacial history; restricted exchange with the North Sea; and strong gradients in salinity, temperature, and oxygen. These conditions have produced a species-poor but highly productive and ecologically important system. This review synthesizes evidence that Baltic populations persist not only through phenotypic plasticity but also through rapid evolutionary change, local adaptation, hybridization, and demographic history. Population genomic studies reveal sharp genetic differentiation between Baltic and Atlantic populations in many taxa, often across the Danish Straits, and fine-scale structuring within the Baltic itself. Case studies of eelgrass, bladderwrack, blue mussels, Baltic clam, cod, flounder, and herring illustrate how clonality, hybrid swarm formation, reproductive isolation, and habitat-specific selection shape resilience and vulnerability. Rapid warming, hypoxia, eutrophication, overfishing, and low functional redundancy increase ecosystem sensitivity. Long-term resilience will depend on protecting locally adapted populations and integrating genomic knowledge into ecosystem-based management and conservation.
The surge in chromosome-scale genome sequences from across the tree of life, as well as new comparative methods, has made it possible to study the impact of genomic changes on macroevolution. In this review, we discuss the state of animal comparative genomics. We outline developments in genomic taxonomic sampling and technological advancements in sequencing as well as emerging 3D genomics and provide a perspective on outstanding problems in biodiversity-driven comparative genomics. We discuss the importance of studying genomes holistically and propose the recently introduced evolutionary genome topology framework for topological, multi-scale comparisons across distantly related clades. We highlight how this approach is crucial to understanding the interlinked evolution of subchromosomal and chromosomal changes and their functional implications (e.g., via regulatory entanglement). Lastly, we provide a vision for future areas of research in these approaches and make predictions about the future potential of animal genome evolution.
Spontaneous cancers in client-owned dogs often closely recapitulate their human counterparts with respect to clinical presentation, histological features, molecular profiles, response and resistance to therapy, and the evolution of drug-resistant metastases. In several instances, the incorporation of dogs with cancer into the preclinical development path of cancer therapeutics has influenced outcomes by helping to establish pharmacokinetic/pharmacodynamics relationships, dose/regimen, expected clinical toxicities, and ultimately the potential for biologic activity. As our understanding regarding the molecular drivers and immune landscape of canine cancers has improved, unique opportunities have emerged to leverage this spontaneous model as a mechanism to better guide cancer drug development so that therapies likely to fail are eliminated earlier, whereas those with true potential are optimized prior to human trials. Both pets and people benefit from this approach, because it provides dogs with access to cutting-edge cancer treatments and helps to insure that people are given treatments with a greater probability of success.
Ruminant species are vital for agriculture, ecosystems, and conservation and remain vulnerable to infectious and zoonotic diseases. Advances in genome sequencing and genomics now enable high-resolution analysis of immunoglobulin (IG) loci and antibody repertoires uncovering extensive germline diversity, structural variation, and lineage-specific adaptations, such as ultralong cysteine-rich Abs in cattle. This review summarizes current knowledge of ruminant IG locus organization and repertoire generation and discusses the evolutionary origins of ultralong Abs. It also examines the challenges highly repetitive IG loci pose for assembly, annotation, and nomenclature and highlights emerging solutions. Finally, it describes genomic approaches for linking immune genotypes to phenotypes that create promise for improving ruminant health.
The transmissible spongiform encephalopathies are a group of fatal, progressive neurodegenerative disorders caused by the misfolding of prion proteins, leading to severe neuropathology and death. Since the description of scrapie in sheep several centuries ago, significant advancements have been made in understanding the spectrum of prion diseases, including bovine spongiform encephalopathy and Creutzfeldt–Jakob disease. Despite decades of research, critical gaps remain in our understanding of prion replication mechanisms, interspecies transmission, and the environmental persistence of prions. Advances in molecular imaging, including cryo-electron microscopy, have been instrumental in visualizing prion-associated aggregates in affected brain tissues, providing critical insights into their conformation and strain-specific structures. We explore the development of transmissible spongiform encephalopathy research in animals, major scientific breakthroughs, and the pressing need for innovative diagnostic and therapeutic approaches. Addressing these challenges is essential for controlling the spread of prion diseases, and reducing their impact on public health and agriculture.
comparative genomics, evolution, neuroscience, artificial intelligence, computational biology, behavior
Tasmanian devils are globally renowned for their calamitous decline over the past 30 years due to two contagious clonal cancers and the heroic efforts of researchers, conservationists, and the community to bring them back from the brink of extinction. Scientific investigations into the world's largest marsupial carnivore commenced in the early 1900s. This systematic review follows the changing face of scientific research into Tasmanian devils. It reflects on how science moved from biological investigations in the 1950s and 1960s, to ecological studies in the 1980s and 1990s, to the discovery of the first clonal cancer in 1996, followed by a flurry of work to understand the disease and develop a vaccine, establish and manage an insurance program, and then roll out a translocation program that alleviated small population pressures and maintained devils in the wild. Over this period, technology has changed rapidly, from camera traps to satellite collars and microsatellites to whole-genome sequencing. Through this, societal support for the species has never wavered, and the species persists in the wild.
Adult tissue regeneration is a rare phenomenon in mammals. Most mammals heal tissue through scarring, which quickly seals the wound and helps prevent blood loss and infection, but this comes at the cost of poor tissue regeneration. Regeneration is typically studied in worms, amphibians, or fish, which gives insights into the biology of respective species but provides limited translation for human therapies. However, several mammals develop adaptations, typically favored by natural selection pressures, to regenerate a specialized tissue (e.g., antlers in deer or skin in bats) or a systemically reduced scar formation that allows multiple tissues to restore their function (e.g., African spiny mice). In this review, we aim to summarize the examples of mammals that regenerate tissues and discuss potential cellular mechanisms that allow their regeneration. The future studies of these exceptional mammals can allow for a greater understanding of mammalian complexity and provide insights for future therapies.
Sleep is a universal behavior across animals, critical for physiological homeostasis, cognitive function, and development. Throughout evolution, animals have adapted to environmental changes, but current rapid climate change may threaten sleep patterns adapted to specific ecological niches through rising temperatures, shifting precipitation, and extreme weather. Despite the importance of sleep, climate change–driven sleep disruptions are not well-considered. We introduce the importance of sleep and examine how climate change affects sleep in different biogeographical zones (polar, tropical, dry, and marine and coastal regions), highlighting region-specific vulnerabilities. Furthermore, we discuss the cascading effects of sleep disruption on species interactions, population dynamics, and ecosystem functioning. We emphasize the need for long-term ecological studies, advances in sleep-measurement technologies in free-living animals, and the integration of sleep ecology into conservation strategies. Future priorities include assessing variability within and between individuals, the fitness costs of sleep loss, and the potential for evolutionary adaptation.
Dairy cattle industries navigating increasingly frequent climate disruptions and volatile input costs must maintain productivity while simultaneously minimizing environmental impacts. This article examines how resilience (ability to recover from short-term disturbances) and robustness (capacity for long-term adaptation to challenging environments) contribute to longevity and lifetime efficiency in farm animals. Resilience reduces aging costs by enhancing recovery from environmental perturbations, e.g., health challenges, whereas robustness involves resource allocation strategies that facilitate survival in constraining environments. Both traits exhibit moderate heritability, offering opportunities for genetic improvement. However, their expression varies significantly across environments, necessitating context-specific selection approaches. Simulation studies, using models that incorporate robustness and resilience mechanisms, demonstrate that genotype-by-environment interactions strongly influence the economic and environmental benefits of selecting for these traits. In conclusion, incorporating resilience and robustness into breeding objectives can improve lifetime efficiency, particularly in challenging environments, but their economic value must be evaluated carefully in relation to specific production systems and anticipated future conditions.
Selenoproteins incorporate selenocysteine (Sec), a noncanonical amino acid analogous to cysteine with selenium in place of sulfur. Sec is inserted co-translationally via a unique recoding process that redefines the UGA stop codon in selenoprotein transcripts, marked by the Sec insertion sequence (SECIS) element in the 3′ untranslated region. Metazoans display striking diversity in their selenoproteomes. Although many animals, including mammals, depend on selenoproteins for critical roles in redox homeostasis and signaling, thyroid hormone metabolism, and stress responses, other lineages have lost the entire Sec pathway. We summarize the molecular biology of Sec, covering its biosynthesis, metabolism, insertion, and regulatory mechanisms. We then examine the evolutionary dynamics of selenoproteins across metazoa, including gene duplications, losses, and substitutions of Sec to cysteine. Finally, we present an updated survey of known metazoan selenoprotein families, detailing their structure, function, and phylogenetic distribution. Altogether, we offer a comprehensive view of selenoprotein evolution and function in animals.
Adopted in December 2022, the Kunming-Montreal Global Biodiversity Framework (KMGBF) under the Convention on Biological Diversity outlines a visionary road map guiding humanity's relationship with nature. KMGBF commitments require active intervention, sustained monitoring and scientific reporting, capacity building for tools and technologies, and cooperation among 196 signatories. Genetic diversity, which underlies adaptation and fitness, is a core tenet of the KMGBF. This article aims to distill the KMGBF to help researchers, practitioners, and other interested parties achieve its commitments. In five sections, we address (a) the KMGBF's terminology and scope, (b) the intersection of KMGBF targets with genetic diversity, (c) genetic monitoring for tracking its progress, (d) paradigms and decision frameworks to guide genetic conservation actions, and (e) emerging frontiers. A better understanding of the KMGBF will help researchers, practitioners, and other interested parties more effectively engage and fulfill global, national, and local commitments to the conservation of our planet's biodiversity.
Long noncoding RNAs (lncRNAs) have emerged as key regulators of gene expression, yet their annotation and functional characterization remain challenging, especially in nonclassical model organisms. In this review, we explore the landscape of lncRNAs in dogs (Canis lupus familiaris) and other species, highlighting recent advances in genome assemblies, transcriptomic resources, and computational tools for lncRNA discovery. We discuss the advantages of the canine system for studying genotype-phenotype relationships, including its rich breed diversity, well-characterized diseases, and simplified genetic architecture. We describe how both short- and long-read RNA-sequencing technologies, in combination with curated reference annotations from Ensembl and RefSeq, have enabled the detection of thousands of novel canine lncRNAs. However, we also point out discrepancies across assemblies and annotation strategies, which underscore the importance of integrating multi-omic data and refining computational pipelines. Using comparative genomics, we illustrate lncRNA conservation across dog breeds and species and review emerging examples of phenotype-associated or differentially expressed lncRNAs. Finally, we argue for a transition toward pangenome and pan-transcriptome approaches, which can better capture transcript diversity and structural variation across breeds. Such frameworks will be essential for the future functional annotation of lncRNAs and their application to both veterinary and human biomedical research.
In low- and lower-middle-income countries, livestock systems contribute to food and nutritional security, economic growth, and the livelihoods of nearly one billion smallholders. They provide high-quality nutrition through animal-sourced foods, contribute to improved smallholder resilience, and employ more than 873 million people. Yet, persistent feed constraints exacerbated by climate change, land degradation, poor extension, feed markets, and social inequalities continue to undermine livestock productivity. This article explores how feed-focused interventions can deliver a triple win for food and nutrition security, climate resilience, and women and youth empowerment. It reviews the complexity of the regional feed systems and underlying constraints and proposes strategies to improve feed quality, availability, accessibility, and affordability, particularly through greater inclusion of women and youth, who are pivotal to the sector. The article recommends scaling evidence-based strategies to transform feed systems into inclusive and climate-smart systems that optimally enhance livestock productivity, reduce food insecurity, and improve the livelihoods of farmers and pastoralists.
Recent advances in technologies that replicate specific aspects of embryogenesis in vitro by using stem cells have opened new frontiers in our understanding of the earliest steps of mammalian development and creation of promising novel assisted reproductive technologies (ARTs). We begin by summarizing the widely used ARTs in improving animal reproduction. We then explore current progress in deriving embryo-based stem cells from livestock species and highlight the latest breakthroughs in blastoid generation. Furthermore, we examine the potential applications of blastoids in domestic livestock and discuss key challenges and future directions for advancing blastoid models that closely mimic natural embryonic development.
DNA methylation was the earliest epigenetic mark discovered—it is essential for mammalian development and forms a molecular memory that can transcend generations, as in the phenomenon of genomic imprinting. Set against this long-term potential, methylation is dynamic across the life cycle, with genome-wide changes at germ-cell specification, gametogenesis, and preimplantation development accompanying major shifts in cell potency. With a tool kit of precision genetic reagents, the mouse has been a mainstay in developing mechanistic understanding of how methylation is targeted to the genome and in exploring its susceptibility to environmental factors, such as parental diet. The availability of genome sequence from many more species combined with the ability to profile methylation and other epigenetic marks in very small numbers of cells now provides rich epigenomic information from other mammals. This information has begun to reveal both similarities as well as surprising differences in the way in which methylation is patterned across the genome among mammals. Such knowledge will be critical in assessing the outcomes of interventions during assisted reproduction in human clinical practice and livestock production.
Livestock farming faces increasing demands for sustainability and improved animal welfare. Noninvasive approaches for monitoring animal health and physiology are of growing interest. Exhaled breath analysis, or exhalomics, has emerged as a promising tool for detecting volatile organic compounds and gases associated with metabolism, disease states, physiological processes, and microbiome in livestock. This review synthesizes current advancements in breath sampling and analytical technologies and evaluates applications in disease diagnostics, nutritional assessment, and physiological and microbial profiling across livestock species. Although progress is evident, key challenges remain, including sampling variability, incomplete metabolite annotation, and limited scalability for field use. Future efforts should prioritize standardizing protocols; expanding livestock-specific spectral libraries; and developing affordable, real-time sensors for on-farm deployment. Integrating exhalomics with multi-omics and artificial intelligence-driven analytics holds potential to enable earlier disease detection, improve production efficiency, and reduce environmental impacts, ultimately advancing precision livestock farming and animal welfare over the coming decade.
This article charts the history of a scientific career that began in the plant sciences and is ending in research on the placenta-brain axis and on the developmental origins of the mammalian placenta. In the middle was the characterization of uteroferrin and interferon-τ, the role of the latter in maternal recognition of pregnancy, and the development of a commercial pregnancy test for dairy cows. The article also emphasizes the roles personal upheavals and happenchance played in shaping a professional life and dealing with an incident of scientific malfeasance that threatened it. The article concludes with a discussion of the difficulties of practicing science during the twilight years.
Liver function is critical for high-producing dairy cows to achieve high milk production and good fertility, as well as to avoid periparturient health problems. Key processes include gluconeogenesis, fatty acid metabolism, protein synthesis, amino acid metabolism and urea formation, bile acid synthesis, detoxification, endocrine functions, and immune functions. Various tests have been used to assess liver function. Fatty liver develops when fatty acid uptake exceeds the liver's capacity to oxidize fatty acids and export triacylglycerols and may negatively affect hepatic function. Metabolomics, transcriptomics, and proteomics are opening new insights into hepatic adaptations in normal and abnormal situations, such as the roles of acylcarnitines, lysophospholipids, and sphingolipids. Nutritional strategies such as controlled energy dry cow diets and supplemental rumen-protected methionine and choline help maintain liver function during the periparturient period. Nutritional manipulations that impact liver function help to promote health and productivity of high-producing dairy cows.
Transcriptional regulation in response to diverse physiological cues involves complicated biological processes. Recent initiatives that leverage whole genome sequencing and annotation of regulatory elements significantly contribute to our understanding of transcriptional gene regulation. Advances in the data sets available for comparative genomics and epigenomics can identify evolutionarily constrained regulatory variants and shed light on noncoding elements that influence transcription in different tissues and developmental stages across species. Most epigenomic data, however, are generated from healthy subjects at specific developmental stages. To bridge the genotype-phenotype gap, future research should focus on generating multidimensional epigenomic data under diverse physiological conditions. Farm animal species offer advantages in terms of feasibility, cost, and experimental design for such integrative analyses in comparison to humans. Deep learning modeling and cutting-edge technologies in sequencing and functional screening and validation also provide great promise for better understanding transcriptional regulation in this dynamic field.
