Peer Community Journal

The recent large-scale circulation of High Pathogenicity Avian Influenza (HP AI) viruses H5Nx of clade 2.3.4.4b has been responsible for massive die-offs in wild species, notably in long-lived seabirds, with unknown implications for the immunity of surviving individuals. In the North Atlantic, northern gannet colonies were heavily affected in 2022, with more than 40% mortality observed among breeding adults and some surviving individuals developing dark irises. Using samples collected in 2023 and 2024 on Rouzic colony (France), we report persistent individual anti-AI antibody levels and seroneutralisation titres, with most of the immune individuals showing dark irises. A modelling approach further stressed the importance of long-lasting immunity in such species by showing that the proportion of individuals which kept their immunity between years strongly limited decreases in population size in case of repeated outbreaks. Overall, our results highlight the existence and importance of long-lasting immunity in long-lived species for population persistence.

Hunt s ancestor-descendant parameterization for fitting of evolutionary models to empirical paleontological sequences assumes independent log-likelihoods for the transitions between populations (Hunt, 2006). This is not quite correct, as he also pointed out in his paper. The reason is that adjacent trait differences share a trait mean value and its sampling error, and ignorance of this fact may give large errors in the estimated step size. Here, the problem is solved by use of the N-1 dimensional normal density for a random vector, where N is the number of samples. This results in a tridiagonal covariance matrix instead of Hunt s diagonal matrix, and the estimated step sizes, and thus prediction slopes, in cases where the estimated step variance is zero will then be identical to those found by weighted least squares estimation.

The fieldwork was carried out between December 2023 and June 2025, with the aim, among others, of confirming the possible presence of the North African Gerbil (Gerbillus campestris) in Melilla. To this end, 56 camera trap stations were installed, each equipped with a camera trap. Of the total number of camera trap stations installed, the presence of Gerbillus campestris was detected in six of them, representing a capture success rate of 10.71%. Following the detection of the species, a specimen was captured using cage traps. For identification purposes, samples of epithelial tissue from the ear and faeces were collected. These samples were sent to the Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic, for analysis. There, DNA was extracted from the samples using the Innu PREP DNA Mini Kit 2.0 (IST Innuscreen GmbH, Germany) according to the manufacturer's protocol. The results obtained confirm, for the first time through records of the species, the presence of Gerbillus campestris in Melilla and, therefore, in Spain and Europe.

Reliable population estimates are essential for wildlife management, yet monitoring schemes often do not match the administrative scale at which decisions are made. We illustrate this challenge using the Eurasian lynx in the canton of Valais, Switzerland, where official state monitoring is fragmented across three reference areas surveyed in different years. We analyzed three winters (2023-2026) of independent, canton-wide camera trap data, recording 899 independent lynx captures (27, 31 and 34 adults per winter). Lynx distribution and reproduction concentrated in the Northwest and connected to the thriving Pre-alpine populations. Density modelling for 2025/2026 estimated 37 independent lynx (95% CI: 26-52) on the whole cantonal territory, corresponding to a density of 1.09 (0.77-1.56) individuals per 100 km2. These estimates are substantially below the figures improperly extrapolated from a cross-cantonal reference area and conveyed by political authorities. Future lynx management decisions should be rooted in scientifically sound, scale-relevant information.

Parasites decrease host fitness, more so during physiologically challenging life stages such as migration. However, parasites are unevenly distributed among individuals, and hosts with different physiological condition may face different costs of migration with infections. We tested whether the relationship between infection by haemosporidian parasites and oxidative balance during autumn migration in blackcaps depends on individual age and sex, two major sources of variation in prevalence and physiological condition. We captured blackcaps at stopover in central Spain and measured infection status and physiological parameters. Blackcaps physiologically more prepared to depart from stopover had lower antioxidant capacity of plasma, probably because of physiological adjustments prior to the upcoming flight stage. Plasmodium parasites occurred only in coinfections, which were more frequent among young blackcaps. Regardless of individual sex and age, coinfected birds had lower antioxidant capacity of plasma, and blackcaps coinfected with Plasmodium had more oxidative damage to lipids in their red blood cells. Our results support the idea that haemosporidian infections impair the oxidative balance of blackcaps during autumn migration, which could impair individual performance and ultimately fitness, with increased population impacts during the first year of life when a larger proportion of individuals migrate coinfected with harmful Plasmodium parasites.

Since mid-June 2026, an acute, non-fatal syndrome with high herd morbidity, reduced milk yield, diarrhea, fever and lethargy affected dairy cattle in southern Germany and Switzerland. Major viral pathogens were excluded. Pan-Simbuvirus PCR first detected an orthobunyavirus, subsequently confirmed by metagenomic sequencing, which enabled recovery of a complete "Shamonda-like" genome. One sentence summary lineMore than a decade after the emergence of Schmallenberg virus in 2011, a novel "Shamonda-like" orthobunyavirus of the Simbu serogroup has now emerged in Central Europe.

Using long read sequencing, we report here a NUMT (nuclear fragment of mitochondrial origin) in a sawfly species Euura vittata that contains the entire coding region with all the genes in the same order as in the mitochondrion. The NUMT is 3.2% different from the mitochondrial sequence (4.1% divergence for COI barcode region), yet appears entirely functional when assuming mitochondrial genetic code. Examination of the NUMT containing contig of the whole genome assembly revealed no assembly issues and showed depth of coverage as expected for single copy nuclear genes, strongly suggesting nuclear integration rather than heteroplasmy. Based on mitochondrial COI data, the NUMT is most similar to a cluster of sequences containing mostly Euura tillbergi and related species (but also a few E. vittata specimens). The NUMT, therefore, may result from recent mitochondrial introgression explaining its divergence and functional appearance. The implications are that reports of divergent heteroplasmy need to be validated with long read or RNA sequencing, or by other appropriate experiments.

The shell colour polymorphism in the land snail Cepaea nemoralis is maintained by environmentally variable light intensity and predation. Previous work showed that divergence in colour polymorphism between habitat pairs of open and closed areas increased with age of the habitat. However, that study was limited to a time span of 80 years (27 snail generations). Here, we investigate shell colour divergence over habitat pair ages of 95 to 325 years. We did find an increase in evolutionary divergence of colour polymorphism with increasing age, however equilibrium could not be determined. This is possibly due to the evolutionary effect of camouflage working in opposite direction to light intensity in certain locations, consequently clouding the results. Therefore, camouflage might also be an important factor to take into account in the search for the evolutionary equilibrium of colour polymorphism in Cepaea nemoralis.

Lateral gene transfer (LGT) from organellar to eukaryotic genomes is ubiquitous, resulting in the presence of widespread nuclear mitochondrial DNA segments (NUMTs) and/or plastid gene transfers. While LGT from bacterial associates of eukaryotes is generally less common, many arthropod genomes are littered with LGT originating from Wolbachia (order Rickettsiales) - a vertically transmitted, obligate intracellular symbiont of invertebrates. This contrasts with Rickettsia, a related genus including many important human pathogens, which has not been shown to promulgate LGT within its arthropod vectors. Here, we present the 8.6 Gb genome of a cell line derived from A. variegatum (the tropical bont tick), which is the primary vector of Rickettsia africae (agent of African tick-bite fever). In addition to numerous NUMTs and diverse families of transposable elements, an almost-complete chromosome of R. africae origin was identified in the cell line genome, localised to the putative sex chromosome. Sequencing of field-collected A. variegatum confirmed the presence of this large LGT in wild ticks, although the absence of transferred genes from the R. africae plasmid provided a means to differentiate LGT from genuine rickettsial infections. These findings highlight the imperative to consider the possibility of LGT when screening vectors for pathogens by PCR.

1. Species monitoring programmes regularly encounter missing data, which complicates tasks such as estimating population size or detecting temporal trends. Selecting an imputation method suited to the properties of the data is therefore an important practical challenge, particularly for species exhibiting overdispersion and zero-inflation. 2. We compare seventeen imputation methods, comprising thirteen Poisson-based statistical models (accounting for overdispersion and zero-inflation, with fixed, random and multivariate structures) and four contrast-based approaches (LORI, MICE, missForest, correspondence analysis). Using four complete monitoring datasets of waterbird species surveyed across France and Italy over 21 years, illustrating a variety of abundance distributions, we introduced missing observations under a realistic Missing At Random mechanism, at rates from 5% to 70%. We evaluated all methods on computational burden, prediction accuracy for positive and null counts, quantification of uncertainty, and accuracy of population-size estimates. 3. No single method dominates across all criteria. Statistical models and contrast-based approaches yield similar point predictions, but only statistical models provide a genuine measure of uncertainty. Models that jointly account for overdispersion and zero-inflation perform best at predicting zero counts and achieving reliable prediction intervals, and the most suitable method ultimately depends on the abundance distribution of the target species. 4. These results provide practical guidance for ecologists selecting an imputation strategy for incomplete count data, highlighting the trade-offs between predictive accuracy, computational cost, and the ability to propagate uncertainty through subsequent ecological analyses such as population-trend estimation.

The ectoparasitic mite Varroa destructor is the principal threat to managed honey bees, and a test case for the genome-scale methods applied to non-model organisms, nearly all of which infer from orthology. We reconstructed the first genome-wide protein-interaction network for V. destructor (7,080 proteins, 335,914 interactions), whose modular structure exceeds a degree-preserving null by 368 standard deviations, but whose every edge is interolog-transferred and every node conserved at least to Eukaryota. None of the 791 genes lacking an orthologous group enters it - arithmetic rather than discovery - yet the excluded compartment is large and coherent. It comprises 3,161 genes (30.9% of the proteome), shorter and less annotated than the rest; an annotation-free genome search detects orphans in a tick genome at 4.0% against 70.4% for networked genes. Within the orthology-bearing compartment visibility is non monotonic: the Acari-level bin (74.1%) falls below the Arthropoda-level bin (89.9%). The same logic applied to host comparison yields a benchmarked error: of genes called absent from Apis on group identity alone, 67.4% recover a sequence homologue - against zero for a shuffled null and 1.3% in the presence direction - rising to 78.3% in the least panel-biased stratum. Both figures are properties of the calling rule: under an identity floor the error directions cross near 34% identity; orthology cannot be said to err in either direction without fixing the criterion first. Host divergence resolves into gene absence and residue level substitution, falling in those two compartments respectively. A bee-sparing target map follows as broader impact.

The goat research community benefits from one of the most comprehensive livestock genome assemblies, ARS1. However, the rich diversity of goat breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate very high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, nine goat breeds were selected to represent French goat genetic diversity: Alpine, Boer, Creole, Fosses, Poitevine, Provencale, Pyreneenne, Rove and Saanen. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. There reads were used to generate de novo assemblies and were aligned onto the public reference to call structural variants. PacBio HiFi and parental Illumina reads were used to assemble phased haplotypes of the Alpine breed. For the other breeds, PacBio raw (CLR) or ONT reads were generated. Our work demonstrates the feasibility of assembling genomes with a reasonable amount of data and appropriate software packages, delivering one high-quality assembly and 8 standard goat assemblies that pave the way for pangenome construction and structural variant functional studies.

Selection-intensity estimates from RELAX are reported as a point value of K with a likelihood-ratio P. We report that, at default settings and on data of ordinary size, the program does not reproduce its own fits. Of 27 enzyme entries refitted under two optimiser configurations, none reproduced its log-likelihood to within 0.01 units; the median change was 103 units, the largest over 3,400, and four verdicts reversed. Eighty null orthologues reproduced none. A byte-identical command returned a distinct likelihood on every repetition, single-threaded, across three releases, and on alignments simulated under the fitted model, where 3.3 per cent of replicates reproduced. The documented random-number seed never reaches the generator when assigned on the command line, yet reads back as the value supplied. PAML localises the cause: its two-ratio model, without site classes, reproduced its log-likelihood for all 288 genes; its site-class models agreed for 27 to 67 per cent. The instability follows the mixture over sites, not the program. The output does not show it: 46 of 410 fits ended with a negative likelihood-ratio statistic, impossible under convergence, and 123 of 410 report a K re-estimated under a domain restriction rather than the unconstrained maximum. Of 234 published studies using RELAX, none reported a seed. Seeding while holding the thread count at one reproduced sixty of sixty runs on twenty genes under two releases; the seed alone reproduced none of five, and no documentation states the second condition. We recommend that fits be repeated and their dispersion published.

Beef cattle farming plays a crucial role in the livestock-related economies of both Italy and Argentina. Although both countries have grazing systems of meat production, the heterogeneity of those systems leads to different parasitological scenarios regarding epidemiology and the presence of resistance to commonly used anthelmintic drugs. Considering ivermectin (IVM) is the most widely used anthelmintic for treating gastrointestinal nematode (GIN) infections in cattle, the current studies evaluated the efficacy of ivermectin (IVM) given subcutaneously (SC) to both young calves and adult cows in ten (10) commercial cattle farms from Italy (A to E) and Argentina (F to J). The work was complemented with the assessment of the IVM plasma exposure and disposition kinetics both in young and adult animals. While adult cows and young calves were included in the study performed in Italy (Campania region), only calves aged 8-14 months old were selected to perform the efficacy trials in Argentina (central area of the Buenos Aires province). Fifteen (15) calves/cows naturally infected with GINs were treated with IVM (0.2 mg/kg) in each of the Farms. The therapeutic response (efficacy) was determined at 14 days after treatment by the faecal egg count reduction test. Six (6) adult cows and eight (8) young calves treated with IVM were randomly selected to perform the pharmacokinetic (PK) study with blood samples being taken 2 h and 21 days post-treatment. Drug concentrations were measured by HPLC. Similar IVM PK trends were obtained for both adult and young cattle. The IVM systemic exposure (expressed as AUC) obtained for adult cattle (380{+/-}158 ng.d/mL) was similar to that observed in calves group (313{+/-}85.5 ng.d/mL). No statistical differences between animals from both ages were observed for the most representative PK parameters (P>0.05). Surprisingly, while in Argentina IVM resistance was present in all the farms evaluated (90% CI = 0%-95%), in Italy a fully susceptible nematode population was presented in three farms (90% CI = 96%-100%) and only a very low level of IVM resistance was detected in the rest of the farms (90% CI = 92%-98%). Whereas Cooperia spp. and Haemonchus spp. were identified as the principal genera exhibiting resistance to IVM in Argentina, Cooperia spp., Ostertagia spp., and Oesophagostomum spp. were reported to display low levels of resistance under the Italian field scenario. In conclusion, IVM can be safely and effectively used in both young and adult cattle with similar disposition kinetic patterns. While its therapeutic response is failing under the conditions investigated in the Argentinian farms, its efficacy remains notably high in the Italian region under study. However, the use of IVM, as well any other active antiparasitic principle, should always be preceded by a diagnostic assessment of the nematode populations resistance status.

Recent work on the design of spatial capture-recapture (SCR) studies has largely focused on settings with a single set of movement and detection parameters. In many applied contexts, however, populations are naturally stratified-for example, when different sexes exhibit markedly different movement scales and encounter processes, or when more than one focal species is monitored. Designs that perform well for one group may be inefficient or suboptimal for others, despite the substantial logistical effort typically required to implement an SCR survey. We describe several potential SCR design strategies for surveying multiple groups, and compare these using simulation. Designs considered include regular and optimised grids, clustered and lacework designs, and designs generated using genetic algorithms, including new approaches that optimise information from both groups and a recently published two-stage design. Using proximity detectors such as camera traps, we evaluate design performance in terms of precision, bias, and coverage, and examine how performance changes with the number of available resources. Our results show that multi-group SCR surveys can perform well even when focal groups differ greatly in movement scale and encounter rate, provided that some simple guidelines are followed. Systematic layouts accommodating more than one characteristic spacing e.g. cluster designs, performed consistently well and are a reliable default option. Regular grid designs with a single spacing between detectors are feasible when differences between groups are moderate but performed poorly as differences increased. Establishing when these designs become problematic adds unnecessary risk to the design process. Algorithmic designs did not outperform systematic designs even in highly-skewed scenarios expected to favour them. In practice, when there is more than one focal group we recommend identifying the smallest and largest plausible movement scales and rejecting potentially pathological designs, primarily those that cannot generate recaptures at the smaller scale or cover a substantial area at the larger scale.

Understanding the transmission and persistence of zoonoses in wild reservoirs is crucial for outbreak prevention, demographic assessment, and conservation planning. Host demography, ecology, behaviour and within-host viral kinetics together underpin transmission dynamics but are rarely united within epidemiological models. Here we characterised the transmission dynamics of European bat lyssavirus 2 (EBLV-2) infection dynamics by uniting a long-term study (2010-2018) of the ecology of five greater mouse-eared bat (Myotis myotis) colonies in France (~2700 marked individuals) with diagnostic evidence of virus circulation. Although no lyssavirus was detected in any of the 442 saliva samples tested, seropositivity showed synchronised peaks across colonies (0-100% annually), with the highest seroprevalence in 2015-2017, but remaining low otherwise. Fitting Bayesian compartmental epidemiological models, we found evidence that shifts in EBLV-2 prevalence were primarily driven by the gregarious behaviour of populations during the mating season and age-dependent variation in transmission. The duration of maternal immunity emerged as a key, and still empirically unknown factor, which shaped whether EBLV-2 maintenance was enzootic or required an external force of infection. Lyssavirus outbreaks in M. myotis were associated with few deaths overall and had a negligible impact on population dynamics. These findings underscore the value of integrating ecological and individual-level data with mechanistic modelling to enhance our understanding and management of zoonotic pathogens in wildlife.

Baker's rule predicts that selfing is a beneficial trait for colonizers, whose prediction in the kingdom Fungi is reinforced by recent work showing the invasive ectomycorrhizal basidiomycete Amanita phalloides with self-incompatibility (SI) system has evolved unisexual reproduction in its introduced range. Unlike in plants, the multiallelic SI system of basidiomycetes does not fully prevent selfing among the meiotic offspring of a single dikaryotic (diploid) parent. This distinction allows observation of an intermediate state of selection where selfing is preferred in a species with SI system during colonization before a change in self-incompatibility architecture. Here, we analyzed the genomes of 189 isolates of the ectomycorrhizal basidiomycete Suillus luteus collected from both its native European range and five independently introduced regions to test whether selfing rates increase and whether the SI system had degraded after introduction. Unlike the A. phalloides case, we found no evidence of unisexual reproduction or loss of the SI system in the introduced ranges of S. luteus. Rather, all introduced populations maintained outcrossing rates higher than random mating as in the native populations. However, selfing events were detected in three individuals from a single introduced population, representing the first documented case of selfed sporocarps of Boletales fungi. Our works in S. luteus demonstrates that although selfing is possible in this species, it is not favored during colonization, potentially due to inbreeding depression and higher population density, highlighting the complex interaction among the invasion biology, genetics, and the colonizing context.

Domestication of molds for cheese production has repeatedly shaped Penicillium fungi, most notably giving rise to the emblematic P. camemberti lineage, derived from P. biforme. Here, we identified a new P. biforme lineage, named cheesy, likely selected from P. biforme for food fermentation, including cheese and sausage production. This lineage exhibits evidence of a severe bottleneck, with little nucleotide polymorphism and a single mating type. The cheesy lineage has evolved advantageous traits for cheesemaking: compared to other P. biforme strains and its wild relative P. fuscoglaucum, it displays faster growth on cheese, galactose and lactose media, higher sporulation and germination rates on cheese, elevated lipolytic activity, enhanced inhibition capacities, and produced specific volatile organic compounds. Additionally, P. camemberti and P. biforme cheesy differ in their content of Starship mobile elements, acquired through horizontal transfers. These elements carry cargo genes potentially relevant for adaptation to cheese. Notably, the cheesy lineage has acquired a 20 kb Starship element (Rattus), nested within a much larger 160 kb Starship (Bilge), and carrying cargo genes with predicted functions involved in antagonistic interactions among micro-organisms. SignificanceO_LIWe identified a new Penicillium biforme lineage, named cheesy, which was likely selected from P. biforme for food fermentation (cheese and sausage), genetically and phenotypically different from the emblematic P. camemberti lineage. This lineage suffered from a severe bottleneck, displaying very little nucleotide polymorphism and a single mating type. C_LIO_LIThis newly identified lineage has evolved advantageous traits for cheesemaking; compared to other P. biforme strains and its wild relative P. fuscoglaucum, it displayed faster growth on cheese, galactose and lactose media, higher sporulation and germination rates on cheese, higher lipolytic activity, better inhibition capacities and specific volatile organic compounds. C_LIO_LIPenicillium camemberti and P. biforme cheesy also differed by their content in Starship mobile elements, acquired through horizontal transfers, and carrying cargo genes potentially relevant for adaptation to cheese. C_LIO_LINotably, the cheesy lineage has acquired a specific 20 kb Starship nested within a much larger 160 kb Starship, and likely involved in antagonistic interactions. C_LI

The ocean tides influence key Earth system processes at a range of spatial and temporal scales. It is known that the geometry of ocean basins is the leading controller of tidal energetics, so well-constrained palaeogeographic reconstructions and tidal properties for Earths past are imperative when investigating other Earth system processes. Here, we present a novel way to constrain both deep-time tidal model results and reconstructions, by combining palaeoecology with sedimentology. We compare new palaeo-tidal model simulations for the Cambrian period, significant for the early origin and radiation of major animal fauna, to tidal proxies. One of the most abundant soft-bodied organisms preserved during this time are cnidarian medusae (jellyfish). A total of 17 cnidarian medusae localities were obtained through the literature, which had an adequate global distribution and occurred at regular intervals throughout the period of study. In some locations there were also estimates of palaeo-tidal range. Our results show a good agreement between the simulations and proxy data. In the few locations where there is disagreement, it is proposed that the palaeogeographic reconstructions are missing details, e.g., island chains, and our results allow for the palaeogeographic reconstructions to be improved. The proxy method presented is promising and can be applied to other time-periods with different marine fossils, particularly at evolutionary and extinction periods where the marginal marine environment is of importance.

1. Plant roots employ multiple strategies to acquire soil resources, including the outgrowth of root hairs and the association with arbuscular mycorrhizal fungi (AMF). These structures represent alternative pathways to access soil resources. Evidence is derived mostly from studies within single species or multi-species experiments under controlled conditions. It remains unclear whether this trade-off holds under natural conditions and whether it manifests consistently across different scales of biological organization. 2. We analysed 81 grassland species representing grasses, forbs and legumes, sampled under heterogeneous field conditions in three regions across Germany, allowing for analyses (i) across different species (interspecific), (ii) across communities (intercommunity), (iii) within plant species (intraspecific) and (iv) within root systems of individual plants (intra-individual). Fine root traits related to AMF colonization (including scoring of fungal hyphae and arbuscules) and root hair growth (including length and incidence) were quantified. 3. Comparing plant species, we observed a strong negative correlation between mycorrhizal colonization and root hair traits, confirming previous studies working under controlled conditions. The negative relationship between root hair length and mycorrhization was also evident when comparing mean trait values at the plant community scale. Among different individuals of the same species (i.e. intraspecific scale), there was no consistent pattern of trait-trait relationship. When comparing within roots of the same plant (i.e. intra-individual scale), co-occurrence of root hairs and mycorrhiza was less likely than what would be expected by chance, with forbs showing the most consistent negative pattern. 4. Our study demonstrates that the hypothesized trade-off between AMF and root hairs is a robust pattern under field conditions at the community and interspecific scale. At the intraspecific scale, no uniform trade-off pattern can be discerned, and within single root systems the negative trade-off pattern is widespread but weak. This indicates that ecological and evolutionary constraints shape trait-trait relationships at higher scale, whereas physiological limits do not restrict trait co-occurrence at lower scales.