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Partial migration is a phenomenon where migratory and resident individuals of the same species co-exist within a population, and has been linked to both intrinsic (e.g., genetic) as well as environmental factors. Here we investigated the genomic architecture of partial migration in the common blackbird, a songbird that comprises resident populations in the southern distribution range, partial migratory populations in central Europe, and exclusively migratory populations in northern and eastern Europe. We generated whole-genome sequencing data for 60 individuals, each of which was phenotyped for migratory behavior using radio-telemetry tracking. These individuals were sampled across the species' distribution range, including resident populations (Spain and France), obligate migrants (Russia), and a partial migratory population with equal numbers of migratory and resident individuals in Germany. We estimated genetic differentiation (F ST ) of single-nucleotide variants (SNVs) in 2.5 kb windows between all possible population and migratory phenotype combinations, and focused our characterization on birds from the partial migratory population in Germany. Despite overall low differentiation within the partial migratory German population, we identified several outlier regions with elevated differentiation on four distinct chromosomes. The region with the highest relative and absolute differentiation was located on chromosome 9, overlapping PER2 , which has previously been shown to be involved in the control of the circadian rhythm across vertebrates. While this region showed high levels of differentiation, no fixed variant could be identified, supporting the notion that a complex phenotype such as migratory behavior is likely controlled by a large number of genetic loci., Competing Interests: The authors declare no conflicts of interest., (© 2025 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Modelling population connectivity is central to biodiversity conservation and often relies on resistance surfaces reflecting multi-generational gene flow. ResistanceGA (RGA) is a common optimization framework for parameterizing these surfaces by maximizing the fit between genetic distances and cost distances using maximum likelihood population effect models. As the reliability of this framework has rarely been studied, we investigated the conditions maximizing its accuracy for both prediction and interpretation of landscape features' permeability. We ran demo-genetic simulations in contrasted landscapes for species with distinct dispersal capacities and specialization levels, using corresponding reference cost scenarios. We then optimized resistance surfaces from the simulated genetic distances using RGA. First, we evaluated whether RGA identified the drivers of the genetic patterns, that is, distinguished Isolation-by-Resistance (IBR) patterns from either Isolation-by-Distance or patterns unrelated to ecological distances. We then assessed RGA predictive performance using a cross-validation method, and its ability to recover the reference cost scenarios shaping genetic structure in simulations. IBR patterns were well detected and genetic distances were predicted with great accuracy. This performance depended on the strength of the genetic structuring, sampling design and landscape structure. Matching the scale of the genetic pattern by focusing on population pairs connected through gene flow and limiting overfitting through cross-validation further enhanced inference reliability. Yet, the optimized cost values often departed from the reference values, making their interpretation and extrapolation potentially dubious. While demonstrating the value of RGA for predictive modelling, we call for caution and provide additional guidance for its optimal use., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Light-dependent reduction of carbon dioxide (CO 2 ) into value-added products can be catalyzed by a variety of molecular complexes. Here we report a rare example of a structurally characterized artificial enzyme, resulting from the combination of a heme binding protein, heme oxygenase, with cobalt-protoporphyrin IX, with good activity for the photoreduction of CO 2 to carbon monoxide (CO). Using a copper-based photosensitizer, thus making the photosystem free of noble metals, a large turnover frequency value of ∼616 h -1 , a turnover value of ∼589, after 3 h reaction, and a CO vs H 2 selectivity of 72% were obtained, establishing a record among previously reported artificial CO 2 reductases. Thorough photophysical studies allowed tracking of reaction intermediates and provided insights into the reaction mechanism. Thanks to a high-resolution crystal structure of the artificial enzyme, both in the absence and in the presence of the protein-bound CO 2 substrate, a rational site-directed mutagenesis approach was used to study the effect of some modifications of the active site on the activity.

Dihydrouridine (D) is a common modified base found predominantly in transfer RNA (tRNA). Despite its prevalence, the mechanisms underlying dihydrouridine biosynthesis, particularly in prokaryotes, have remained elusive. Here, we conducted a comprehensive investigation into D biosynthesis in Bacillus subtilis through a combination of genetic, biochemical, and epitranscriptomic approaches. Our findings reveal that B. subtilis relies on two FMN-dependent Dus-like flavoprotein homologs, namely DusB1 and DusB2, to introduce all D residues into its tRNAs. Notably, DusB1 exhibits multisite enzyme activity, enabling D formation at positions 17, 20, 20a and 47, while DusB2 specifically catalyzes D biosynthesis at positions 20 and 20a, showcasing a functional redundancy among modification enzymes. Extensive tRNA-wide D-mapping demonstrates that this functional redundancy impacts the majority of tRNAs, with DusB2 displaying a higher dihydrouridylation efficiency compared to DusB1. Interestingly, we found that BsDusB2 can function like a BsDusB1 when overexpressed in vivo and under increasing enzyme concentration in vitro. Furthermore, we establish the importance of the D modification for B. subtilis growth at suboptimal temperatures. Our study expands the understanding of D modifications in prokaryotes, highlighting the significance of functional redundancy in this process and its impact on bacterial growth and adaptation., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

French Guiana is a French territory in South America. The exposome of persons living there is quite different from that in mainland France and the ethnic make-up of the population is also quite different. Poverty is also widespread with difficulties in accessing care magnified by the low medical-professional density. In this singular context, we aimed to measure the incidence of pediatric cancers and to compare it with other continents. We used French Guiana's certified cancer registry to study this between 2003 and 2017. Incidences were standardized using the world population with three strata: 0-4 years, 5-9 years, and 10-14 years. There were 164 solid tumors or hematologic malignancies diagnosed in children under the age of 15 (92 in boys and 72 in girls). Over the study period, the standardized incidence rate was 14.1 per 100,000 among children aged under 15 years. There was no significant trend during the study period. The three most common causes of cancer were leukemias-mostly lymphoblastic-CNS tumors, and sarcoma. The standardized incidence of pediatric cancers in French Guiana was similar to those in Western Europe and North America. As others have discovered, we found that males tended to be more likely to develop cancer, notably leukemia, CNS tumors, sarcoma, and retinoblastoma. As elsewhere, the predominant cancer types changed with age. Our initial assumption was that given the singular context of French Guiana, there may have been differences in pediatric cancer incidences. Here we showed that overall, contrary to our assumption and to trends in tropical countries, the incidence of pediatric cancers was in a range between Western Europe and North America with some apparent but non-significant differences in the main types of cancers observed in global statistics. Quality cancer registry data in this tropical region confirm the suspicion that lower incidences in tropical low- and middle-income countries are likely to result from incomplete diagnosis and data collection.

Tick-borne flaviviruses and Borrelia spp. are globally spread pathogens of zoonotic potential that are maintained by a transmission cycle at the interface between ticks and vertebrate hosts, mainly wild animals. Aside data on pathogen burden in ticks, information on the status of various hosts relative to infection is important to acquire. We reviewed how those infections have been studied in wildlife host species in the field to discuss how collected data provided relevant epidemiological information and to identify needs for further studies. The literature was screened for observational studies on pathogen or antibody detection for tick-borne Borrelia spp. and flaviviruses in wildlife host animals. Overall, Borrelia spp. were more studied (73% of case studies, representing 297 host species) than flaviviruses (27% of case studies, representing 114 host species). Studies on both Borrelia spp. and flaviviruses focused mainly on the same species, namely bank vole and yellow-necked mouse. Most studies were order-specific and cross-sectional, reporting prevalence at various locations, but with little insight into the underlying epidemiological dynamics. Host species with potential to act as reservoir hosts of these pathogens were neglected, notably birds. We highlight the necessity of collecting both demographics and infection data in wildlife studies, and to consider communities of species, to better estimate zoonotic risk potential in the One Health context., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Urbanization is increasing worldwide, producing severe environmental impacts. Biodiversity is affected by the expansion of cities, with many species being unable to cope with the different human-induced stressors present in these landscapes. However, this knowledge is mainly based on research from taxa such as plants or vertebrates, while other organisms like protozoa have been less studied in this context. The impact of urbanization on the transmission of vector-borne pathogens in wildlife is still unclear despite its relevance for animal and human health. Here, we investigated whether cities are associated with changes in the prevalence and richness of lineages of three vector-borne protozoans (Plasmodium, Haemoproteus and Leucocytozoon) in Eurasian blackbirds (Turdus merula) from multiple urban and forest areas in Europe. Our results show important species-specific differences between these two habitat types. We found a significant lower prevalence of Leucocytozoon in urban birds compared to forest birds, but no differences for Plasmodium and Haemoproteus. Furthermore, the richness of parasite lineages in European cities was higher for Plasmodium but lower for Leucocytozoon than in forests. We also found one Plasmodium lineage exclusively from cities while another of Leucocytozoon was only found in forests suggesting a certain level of habitat specialization for these protozoan vectors. Overall, our findings show that cities provide contrasting opportunities for the transmission of different vector-borne pathogens and generate new scenarios for the interactions between hosts, vectors and parasites., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

All biological hydroxylation reactions are thought to derive the oxygen atom from one of three inorganic oxygen donors, O 2 , H 2 O 2, or H 2 O. Here, we have identified the organic compound prephenate as the oxygen donor for the three hydroxylation steps of the O 2 -independent biosynthetic pathway of ubiquinone, a widely distributed lipid coenzyme. Prephenate is an intermediate in the aromatic amino acid pathway and genetic experiments showed that it is essential for ubiquinone biosynthesis in Escherichia coli under anaerobic conditions. Metabolic labeling experiments with 18 O-shikimate, a precursor of prephenate, demonstrated the incorporation of 18 O atoms into ubiquinone. The role of specific iron-sulfur enzymes belonging to the widespread U32 protein family is discussed. Prephenate-dependent hydroxylation reactions represent a unique biochemical strategy for adaptation to anaerobic environments., Competing Interests: Competing interests statement:The authors declare no competing interest.

Adrenodoxin reductase (AdxR) plays a pivotal role in electron transfer, shuttling electrons between NADPH and iron/sulfur adrenodoxin proteins in mitochondria. This electron transport system is essential for P450 enzymes involved in various endogenous biomolecules biosynthesis. Here, we present an in-depth examination of the kinetics governing the reduction of human AdxR by NADH or NADPH. Our results highlight the efficiency of human AdxR when utilizing NADPH as a flavin reducing agent. Nevertheless, akin to related flavoenzymes such as cytochrome P450 reductase, we observe that low NADPH concentrations hinder flavin reduction due to intricate equilibrium reactions between the enzyme and its substrate/product. Remarkably, the presence of MgCl 2 suppresses this complex kinetic behavior by decreasing NADPH binding to oxidized AdxR, effectively transforming AdxR into a classical Michaelis-Menten enzyme. We propose that the addition of MgCl 2 may be adapted for studying the reductive half-reactions of other flavoenzymes with NADPH. Furthermore, in vitro experiments provide evidence that the reduction of the yeast flavin monooxygenase Coq6p relies on an electron transfer chain comprising NADPH-AdxR-Yah1p-Coq6p, where Yah1p shuttles electrons between AdxR and Coq6p. This discovery explains the previous in vivo observation that Yah1p and the AdxR homolog, Arh1p, are required for the biosynthesis of coenzyme Q in yeast., (© 2023 The Authors. ChemBioChem published by Wiley-VCH GmbH.)

Orange protein (Orp) is a small bacterial metalloprotein of unknown function that harbors a unique molybdenum/copper (Mo/Cu) heterometallic cluster, [S 2 MoS 2 CuS 2 MoS 2 ] 3- . In this paper, the performance of Orp as a catalyst for the photocatalytic reduction of protons into H 2 has been investigated under visible light irradiation. We report the complete biochemical and spectroscopic characterization of holo -Orp containing the [S 2 MoS 2 CuS 2 MoS 2 ] 3- cluster, with docking and molecular dynamics simulations suggesting a positively charged Arg, Lys-containing pocket as the binding site. Holo -Orp exhibits excellent photocatalytic activity, in the presence of ascorbate as the sacrificial electron donor and [Ru(bpy) 3 ]Cl 2 as the photosensitizer, for hydrogen evolution with a maximum turnover number of 890 after 4 h irradiation. Density functional theory (DFT) calculations were used to propose a consistent reaction mechanism in which the terminal sulfur atoms are playing a key role in promoting H 2 formation. A series of dinuclear [S 2 MS 2 M'S 2 MS 2 ] (4 n )- clusters, with M = Mo VI , W VI and M' ( n +) = Cu I , Fe I , Ni I , Co I, Zn II , Cd II were assembled in Orp, leading to different M/M'-Orp versions which are shown to display catalytic activity, with the Mo/Fe-Orp catalyst giving a remarkable turnover number (TON) of 1150 after 2.5 h reaction and an initial turnover frequency (TOF°) of 800 h -1 establishing a record among previously reported artificial hydrogenases.

Habitat connectivity is a key objective of current conservation policies and is commonly modeled by landscape graphs (i.e., sets of habitat patches [nodes] connected by potential dispersal paths [links]). These graphs are often built based on expert opinion or species distribution models (SDMs) and therefore lack empirical validation from data more closely reflecting functional connectivity. Accordingly, we tested whether landscape graphs reflect how habitat connectivity influences gene flow, which is one of the main ecoevolutionary processes. To that purpose, we modeled the habitat network of a forest bird (plumbeous warbler [Setophaga plumbea]) on Guadeloupe with graphs based on expert opinion, Jacobs' specialization indices, and an SDM. We used genetic data (712 birds from 27 populations) to compute local genetic indices and pairwise genetic distances. Finally, we assessed the relationships between genetic distances or indices and cost distances or connectivity metrics with maximum-likelihood population-effects distance models and Spearman correlations between metrics. Overall, the landscape graphs reliably reflected the influence of connectivity on population genetic structure; validation R 2 was up to 0.30 and correlation coefficients were up to 0.71. Yet, the relationship among graph ecological relevance, data requirements, and construction and analysis methods was not straightforward because the graph based on the most complex construction method (species distribution modeling) sometimes had less ecological relevance than the others. Cross-validation methods and sensitivity analyzes allowed us to make the advantages and limitations of each construction method spatially explicit. We confirmed the relevance of landscape graphs for conservation modeling but recommend a case-specific consideration of the cost-effectiveness of their construction methods. We hope the replication of independent validation approaches across species and landscapes will strengthen the ecological relevance of connectivity models., (© 2023 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

While ecologists agree that habitat loss has a substantial negative effect on biodiversity it is still very much a matter of debate whether habitat fragmentation has a lesser effect and whether this effect is positive or negative for biodiversity. Here, we assess the relative influence of tropical forest loss and fragmentation on the prevalence of vector-borne blood parasites of the genera Plasmodium and Haemoproteus in six forest bird species. We also determine whether habitat loss and fragmentation are associated with a rise or fall in prevalence. We sample more than 4000 individual birds from 58 forest sites in Guadeloupe and Martinique. Considering 34 host-parasite combinations independently and a fine characterization of the amount and spatial configuration of habitat, we use partial least square regressions to disentangle the relative effects of forest loss, forest fragmentation, landscape heterogeneity, and local weather conditions on spatial variability of parasite prevalence. Then we test for the magnitude and the sign of the effect of each environmental descriptor. Strikingly, we show that forest fragmentation explains twice as much of the variance in prevalence as habitat loss or landscape heterogeneity. In addition, habitat fragmentation leads to an overall rise in prevalence in Guadeloupe, but its effect is variable in Martinique. Both habitat loss and landscape heterogeneity exhibit taxon-specific effects. Our results suggest that habitat loss and fragmentation may have contrasting effects between tropical and temperate regions and that inter-specific interactions may not respond in the same way as more commonly used biodiversity metrics such as abundance and diversity., (© 2022 John Wiley & Sons Ltd.)

Dihydrouridine (D) is an abundant modified base found in the tRNAs of most living organisms and was recently detected in eukaryotic mRNAs. This base confers significant conformational plasticity to RNA molecules. The dihydrouridine biosynthetic reaction is catalyzed by a large family of flavoenzymes, the dihydrouridine synthases (Dus). So far, only bacterial Dus enzymes and their complexes with tRNAs have been structurally characterized. Understanding the structure-function relationships of eukaryotic Dus proteins has been hampered by the paucity of structural data. Here, we combined extensive phylogenetic analysis with high-precision 3D molecular modeling of more than 30 Dus2 enzymes selected along the tree of life to determine the evolutionary molecular basis of D biosynthesis by these enzymes. Dus2 is the eukaryotic enzyme responsible for the synthesis of D20 in tRNAs and is involved in some human cancers and in the detoxification of β-amyloid peptides in Alzheimer's disease. In addition to the domains forming the canonical structure of all Dus, i.e., the catalytic TIM-barrel domain and the helical domain, both participating in RNA recognition in the bacterial Dus, a majority of Dus2 proteins harbor extensions at both ends. While these are mainly unstructured extensions on the N-terminal side, the C-terminal side extensions can adopt well-defined structures such as helices and beta-sheets or even form additional domains such as zinc finger domains. 3D models of Dus2/tRNA complexes were also generated. This study suggests that eukaryotic Dus2 proteins may have an advantage in tRNA recognition over their bacterial counterparts due to their modularity.

Host age is often evoked as an intrinsic factor aggravating the outcome of host-pathogen interactions. However, the shape of the relationship between age and infection-induced mortality might differ among pathogens, with specific clinical and ecological traits making some pathogens more likely to exert higher mortality in older hosts. Here, we used a large dataset on age-specific case fatality rate (CFR) of 28 human infectious diseases to investigate i) whether age is consistently associated to increased CFR, ii) whether pathogen characteristics might explain higher CFR in older adults. We found that, for most of the infectious diseases considered here, CFR slightly decreased during the first years of life and then steeply increased in older adults. Pathogens inducing diseases with long-lasting symptoms had the steepest increase of age-dependent CFR. Similarly, bacterial diseases and emerging viruses were associated with increasing mortality risk in the oldest age classes. On the contrary, we did not find evidence suggesting that systemic infections have steeper slopes between CFR and age; similarly, the relationship between age and CFR did not differ according to the pathogen transmission mode. Overall, our analysis shows that age is a key trait affecting infection-induced mortality rate in humans, and that the extent of the aggravating effect on older adults depends on some key traits, such as the duration of illness., Competing Interests: The authors have declared that no competing interests exist.

The gut microbiota constitutes a diverse community of organisms with pervasive effects on host homeostasis. The diversity and composition of the gut microbiota depend on both intrinsic (host genetics) and extrinsic (environmental) factors. Here, we investigated the reaction norms of fecal microbiota diversity and composition in three strains of mice infected with increasing doses of the gastrointestinal nematode Heligmosomoides polygyrus . We found that α-diversity (bacterial taxonomic unit richness) declined along the gradient of infective doses, and β-diversity (dissimilarity between the composition of the microbiota of uninfected and infected mice) increased as the infective dose increased. We did not find evidence for genotype by environment (host strain by infective dose) interactions, except when focusing on the relative abundance of the commonest bacterial families. A simulation approach also showed that significant genotype by environment interactions would have been hardly found even with much larger sample size. These results show that increasing parasite burden progressively depauperates microbiota diversity and contributes to rapidly change its composition, independently from the host genetic background., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)