Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.

The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species.

The promise of community-driven preprints in ecology and evolution.

Publishing preprints is quickly becoming commonplace in ecology and evolutionary biology. Preprints can facilitate the rapid sharing of scientific knowledge establishing precedence and enabling feedback from the research community before peer review. Yet, significant barriers to preprint use exist, including language barriers, a lack of understanding about the benefits of preprints and a lack of diversity in the types of research outputs accepted (e.

Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.

Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.

Anatomic variations in origin and coursing of the transverse cervical artery: morphogenesis and relation to the high arch-shaped subclavian artery.

This case report presents an atypical transverse cervical artery with its detailed anatomy, morphogenesis, and association with the high arch-shaped subclavian artery. The atypical arteries, related arteries, and adjacent cervical and brachial plexuses were macroscopically examined in a 98-year-old Japanese female cadaver donated to The Nippon Dental University for medical education and research. The atypical deep branch of the transverse cervical artery originated from the internal thoracic artery and passed through between the C5 and C6 roots, in close contact with the C5 and C6 junction, to reach the dorsal side of the brachial plexus.

Maximising informativeness for target capture-based phylogenomics in (Ericaceae).

Plant phylogenetics has been revolutionised in the genomic era, with target capture acting as the primary workhorse of most recent research in the new field of phylogenomics. Target capture (aka Hyb-Seq) allows researchers to sequence hundreds of genomic regions (loci) of their choosing, at relatively low cost per sample, from which to derive phylogenetically informative data. Although this highly flexible and widely applicable method has rightly earned its place as the field's standard, it does not come without its challenges.

A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species.

We examined the evolutionary history of Phytophthora infestans and its close relatives in the 1c clade. We used whole genome sequence data from 69 isolates of Phytophthora species in the 1c clade and conducted a range of genomic analyses including nucleotide diversity evaluation, maximum likelihood trees, network assessment, time to most recent common ancestor and migration analysis. We consistently identified distinct and later divergence of the two Mexican Phytophthora species, P.

Microscopic evidence for nanoparticle-mediated growth of native gold in sulfide deposits at the Higashi-Aogashima Knoll Caldera hydrothermal field.

Gold (or electrum) in hydrothermal fluid precipitates directly from gold sulfide complex and/or partly via suspended nanoparticles. The hydrothermal fluid contains "invisible gold" that is atomically dispersed in sulfide minerals or as nanoparticles with a size of less than 10 nm. However, the contribution of these gold nanoparticles to the formation of native gold and its alloy with silver (electrum) remains unclear.

Multiple, Single Trait GWAS and Supervised Machine Learning Reveal the Genetic Architecture of Fraxinus excelsior Tolerance to Ash Dieback in Europe.

Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among genotypes in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F.

Cursorial ecomorphology and temporal patterns in theropod dinosaur evolution during the mid-Cretaceous.

Coelurosauria, including modern birds, represents a successful group of theropod dinosaurs that established a high taxonomic diversity and significant morphological modifications. In the evolutionary history of this group, a specialized foot morphology, the arctometatarsus, evolved independently in several lineages and has been considered an adaptation for cursoriality. While its functional significance has been extensively studied, the temporal pattern of this parallel evolution, as well as its origin and influencing factors, remains largely unresolved.

Rapid Parallel Adaptation in Distinct Invasions of Ambrosia Artemisiifolia Is Driven by Large-Effect Structural Variants.

When introduced to multiple distinct ranges, invasive species provide a compelling natural experiment for understanding the repeatability of adaptation. Ambrosia artemisiifolia is an invasive, noxious weed, and chief cause of hay fever. Leveraging over 400 whole-genome sequences spanning the native-range in North America and 2 invasions in Europe and Australia, we inferred demographically distinct invasion histories on each continent.

Potential plant extinctions with the loss of the Pleistocene mammoth steppe.

During the Pleistocene-Holocene transition, the dominant mammoth steppe ecosystem across northern Eurasia vanished, in parallel with megafauna extinctions. However, plant extinction patterns are rarely detected due to lack of identifiable fossil records. Here, we introduce a method for detection of plant taxa loss at regional (extirpation) to potentially global scale (extinction) and their causes, as determined from ancient plant DNA metabarcoding in sediment cores (sedaDNA) from lakes in Siberia and Alaska over the past 28,000 years.

Dorsoventral comparison of intraspecific variation in the butterfly wing pattern using a convolutional neural network.

Butterfly wing patterns exhibit notable differences between the dorsal and ventral surfaces, and morphological analyses of them have provided insights into the ecological and behavioural characteristics of wing patterns. Conventional methods for dorsoventral comparisons are constrained by the need for homologous patches or shared features between two surfaces, limiting their applicability across species. We used a convolutional neural network (CNN)-based analysis, which can compare images of the two surfaces without focusing on homologous patches or features, to detect dorsoventral bias in two types of intraspecific variation: sexual dimorphism and mimetic polymorphism.

HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.

The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues.

The trophic distribution of biomass in ecosystems with co-occurring wildlife and livestock.

Trophic interactions regulate populations, but anthropogenic processes influence primary productivity and consumption by both herbivore and carnivore species. Trophic ecology studies often focus on natural systems such as protected areas, even though livestock globally comprise the majority of terrestrial vertebrate biomass. Here we explore spatial and temporal patterns in the distribution of biomass between plants, and large herbivores and carnivores (> 10 kg) in Norwegian rangelands, including both wildlife and livestock.

Tropical forest clearance impacts biodiversity and function, whereas logging changes structure.

The impacts of degradation and deforestation on tropical forests are poorly understood, particularly at landscape scales. We present an extensive ecosystem analysis of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing responses from 82 variables categorized into four ecological levels spanning a broad suite of ecosystem properties: (i) structure and environment, (ii) species traits, (iii) biodiversity, and (iv) ecosystem functions. Responses were highly heterogeneous and often complex and nonlinear.

One-quarter of freshwater fauna threatened with extinction.

Freshwater ecosystems are highly biodiverse and important for livelihoods and economic development, but are under substantial stress. To date, comprehensive global assessments of extinction risk have not included any speciose groups primarily living in freshwaters. Consequently, data from predominantly terrestrial tetrapods are used to guide environmental policy and conservation prioritization, whereas recent proposals for target setting in freshwaters use abiotic factors.

New Silurian aculiferan fossils reveal complex early history of Mollusca.

Mollusca is the second most species-rich animal phylum, but the pathways of early molluscan evolution have long been controversial. Modern faunas retain only a fraction of the past forms in this hyperdiverse and long-lived group. Recent analyses have consistently recovered a fundamental split into two sister clades, Conchifera (including gastropods, bivalves and cephalopods) and Aculifera, comprising Polyplacophora ('chitons') and Aplacophora.

Application of Conservation Genomics to Investigate the Role of Pathogens on the Migration of Sea-Run Brown Trout (Salmo trutta).

Pathogens play a key role in individual function and the dynamics of wild populations, but the link between pathogens and individual performance has rarely been investigated in the wild. Migrating salmonids offer an ideal study system to investigate how infection with pathogens affects performance given that climate change and fish farming portend increasing prevalence of pathogens in wild populations. To test for effects of pathogen burden on the performance of a migrating salmonid, we paired data from individual brown trout tagged with acoustic accelerometer transmitters and gill biopsies to investigate how pathogen infection affected whole animal activity during the spawning migration.

Evaluating seagrass lipid biomarkers as indicator for organic carbon provenance and storage capacity in Zostera marina (L.) sediments.

Seagrass meadows are vital blue carbon habitats, with sedimentary organic carbon (OC) originating from both the seagrass itself and external sources. In this study, lipid biomarkers (n-alkanes), a well-known proxy for tracing OC sources, were used to indicate seagrass presence in sediment records and to correlate with sedimentary OC in cold-temperate seagrass (Zostera marina) sediments. We calculated a Zostera-ratio (seagrass/algae and terrestrial plants-ratio) using identified seagrass biomass n-alkanes (C, C, C, C, C) as a fingerprint for seagrass-derived OC.

Growth and metabolic performance of house fly and black soldier fly larvae differ across densities and waste-based growth substrates.

Large scale production of insect larvae is considered a sustainable way to upcycle various organic waste- and by-products into more valuable food and feed products. The sustainability of insect larvae production depends on the substrates and species being used, but comparative studies that include both growth and efficiency are lacking. Here we compare larval fitness, including survival, development time, weight, substrate conversion efficiency, substrate reduction, and metabolic parameters across different combinations of densities and waste- and by-product-based substrates on the two fly species, the house fly (Musca domestica) and the black soldier fly (Hermetia illucens).

From museum drawer to tree: Historical DNA phylogenomics clarifies the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections.

Although several methods exist for extracting and sequencing historical DNA originating from dry-preserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol (∼€10 per sample), in combination with Ultraconserved Elements (UCEs), is an effective tool for insect phylogenomic studies. We successfully tested our approach by sequencing DNA from scarab dung beetles preserved in both wet and dry collections, including unique primary type and rare historical specimens from internationally important natural history museums in London, Paris and Helsinki.

Past and future effects of climate on the metapopulation dynamics of a Northeast Atlantic seabird across two centuries.

Forecasting population responses to rapidly changing marine ecosystems requires mechanistic models integrating complex demographic processes, fitted to long time series, across large spatial scales. We used a Bayesian metapopulation model fit to colony census data and climatic covariates spanning 1900-2100 for all Northeast Atlantic colonies of an exemplar seabird, the Northern gannet (Morus bassanus) to investigate metapopulation dynamics under two climate scenarios. Fecundity varied non-linearly with near-surface air temperature and recruitment was depressed by sea surface temperature.

The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA.

Small pelagic fish support profitable fisheries and are important for food security around the world. Yet, their sustainable management can be hindered by the indiscriminate impacts of simultaneous exploitation of fish from multiple distinct biological populations over extended periods of time. The quantification of such impacts is greatly facilitated by recently developed molecular tools-including diagnostic single nucleotide polymorphism (SNP) panels for mixed-stock analysis (MSA)-that can accurately detect the population identity of individual fish.

Correlation of forelimb long bone morphology with specific functional adaptations of locomotion.

The significance of forelimb morphology has been discussed with a focus on specific morphological aspects; nonetheless, the correlation of overall morphology, including various linear measurements, with respect to ecological preference and adaptation has not been extensively explored, particularly using multiple taxa. We investigated the morphological characteristics of the long bones in the forelimbs of mammalian species and their relationship with specific functional adaptations using 20 linear measurements and 22 terrestrial species from 7 orders. Principal component analysis and canonical discriminant analysis showed that the lengths of the humerus, radius, and ulna as well as the distance from the smallest width to the proximal and distal ends, and the deltoid tuberosity length distinguished four adaptations: arboreal, terrestrial, fossorial, and semi-aquatic.