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Marie Chevereau-Choquet,1 Benjamin Thoreau,2,3 Camille Taillé,4,5 Sylvain Marchand-Adam,1,6 Hugues Morel,7 Laurent Plantier,1,6,* Laurent Portel8,* 1Service de Pneumologie et Explorations Fonctionnelles Respiratoires, CHRU de Tours, Tours, France; 2Service de Médecine Interne, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP, Hôpital Cochin, Paris, France; 3Inserm U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France; 4Service de Pneumologie A, AP-HP Nord, Hôpital Bichat Claude Bernard, Paris, France; 5Inserm U1152, Université Paris Cité, Paris, France; 6CEPR, Inserm UMR1100, Université de Tours, Tours, France; 7Service de Pneumologie, CHR d’Orléans, Orléans, France; 8Service de Pneumologie, Centre Hospitalier Robert Boulin, Libourne, France*These authors contributed equally to this workCorrespondence: Laurent Plantier, Service de Pneumologie et Explorations Fonctionnelles Respiratoires, CHRU de Tours, 2 Bd Tonnellé, Tours, 37044, France, Email laurent.plantier@univ-tours.frPurpose: Severe asthma affects 5 to 10% of asthmatics and accounts for a large part of asthma-related morbidity and costs. The determinants of asthma severity are poorly understood. We tested the hypothesis that asthma severity was associated with 1) atopy and allergy and 2) markers associated with environmental exposure.Patients and Methods: Data from the FASE-CPHG study, a cross-sectional, observational, multicenter investigation, were analyzed to identify markers associated with asthma severity. Asthma severity was gauged using the ASSESS score, encompassing symptom control, exacerbations, FEV1 and therapeutic load. Bivariate and multivariate analyses were used to identify patient characteristics associated with the ASSESS score.Results: The analysis involved 948 patients, with 592 women, of which 447 patients (47%) had severe asthma. Among these, 491 patients (52%) had at least one positive aeroallergen skin prick test and 525 (55%) had at least one allergic disease among atopic dermatitis, chronic rhinitis and food allergy. The mean±SD ASSESS score was 11.2± 3.4. Characteristics associated with a higher ASSESS score were female sex, secondary or lower education, unemployed occupational status, smoking, work-aggravated asthma and urban housing. There was no association between the ASSESS score and allergic diseases, aeroallergen-specific skin prick tests and IgEs, or blood eosinophil counts.Conclusion: While atopy and allergy were frequent among asthmatics, neither was associated with asthma severity. Modifiable environmental factors such as smoking, urban housing and work-aggravated asthma were independently associated with asthma severity.Keywords: allergy, ASSESS, asthma, environment, severity

Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target-capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP-based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re-assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Two Calanus species, C. glacialis and C. finmarchicus, due to different life strategies and environmental preferences act as an ecological indicators of Arctic Atlantification. Their high lipid content makes them important food source for higher trophic levels of Arctic ecosystems including the most abundant Northern Hemisphere's seabird, the little auk (Alle alle). Recent studies indicate a critical need for the use of molecular methods to reliably identify these two sympatric Calanus species. We performed genetic and morphology-based identification of 2600 Calanus individuals collected in little auks foraging grounds and diet in summer seasons 2019-2021 in regions of Svalbard with varying levels of Atlantification. Genetic identification proved that 40% of Calanus individuals were wrongly classified as C. finmarchicus according to morphology-based identification in both types of samples. The diet of little auks consisted almost entirely of C. glacialis even in more Atlantified regions. Due to the substantial bias in morphology-based identification, we expect that the scale of the northern expansion of boreal C. finmarchicus may have been largely overestimated and that higher costs for birds exposed to Atlantification could be mostly driven by a decrease in the size of C. glacialis rather than by shift from C. glacialis to C. finmarchicus., (© 2023. Springer Nature Limited.)

We used ancient DNA (aDNA) extraction methods to sequence museum voucher samples of Oligobrachia webbi, a frenulate siboglinid polychaete described from a northern Norwegian fjord over fifty years ago. Our sequencing results indicate a genetic match with the cryptic seep species, Oligobrachia haakonmosbiensis (99% pairwise identity for 574 bp mtCOI fragments) . Due to its similarity with O. webbi , the identity of O. haakonmosbiensis has been a matter of debate since its description, which we have now resolved. Furthermore, our results demonstrate that chemosynthesis-based siboglinids, that constitute the bulk of the biomass at Arctic seeps are not seep specialists. Our data on sediment geochemistry and carbon and nitrogen content reveal reduced conditions in fjords/sounds, similar to those at seep systems. Accumulation and decomposition of both terrestrial and marine organic matter results in the buildup of methane and sulfide that apparently can sustain chemosymbiotic fauna. The occurrence of fjords and by extension, highly reducing habitats, could have led to Arctic chemosymbiotic species being relatively generalist with their habitat, as opposed to being seep or vent specialists. Our stable isotope analyses indicate the incorporation of photosynthetically derived carbon in some individuals, which aligns with experiments conducted on frenulates before the discovery of chemosynthesis that demonstrated their ability to take up organic molecules from the surrounding sediment. Since reduced gases in non-seep environments are ultimately sourced from photosynthetic processes, we suggest that the extreme seasonality of the Arctic has resulted in Arctic chemosymbiotic animals seasonally changing their degree of reliance on chemosynthetic partners. Overall, the role of chemosynthesis in Arctic benthos and marine ecosystems and links to photosynthesis may be complex, and more extensive than currently known., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors.)

Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbps). As an alternative to whole-genome sequencing in Calanus spp., we sequenced and de novo assembled transcriptomes of five Calanus species: Calanus glacialis , C. hyperboreus , C. marshallae , C. pacificus , and C .  helgolandicus . Functional assignment of protein families based on clusters of orthologous genes (COG) and gene ontology (GO) annotations showed analogous patterns of protein functions across species. Phylogenetic analyses using maximum likelihood (ML) of 191 protein-coding genes mined from RNA-seq data fully resolved evolutionary relationships among seven Calanus species investigated (five species sequenced for this study and two species with published datasets), with gene and site concordance factors showing that 109 out of 191 protein-coding genes support a separation between three groups: the C .  finmarchicus group (including C .  finmarchicus , C. glacialis , and C. marshallae ), the C .  helgolandicus group (including C .  helgolandicus , C. sinicus , and C .  pacificus ) and the monophyletic C. hyperboreus group. The tree topology obtained in ML analyses was similar to a previously proposed phylogeny based on morphological criteria and cleared certain ambiguities from past studies on evolutionary relationships among Calanus species., Competing Interests: The authors declare they have no conflict of interest., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)