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ABSTRACT Crohn’s disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities. In the current study, we used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their nondiseased first-degree relatives (NCDR) in 9 familial clusters living in northern France-Belgium and in healthy individuals from 4 families living in the same area (non-CD unrelated [NCDU]). Principal component, diversity, and abundance analyses were conducted, and CD-associated inter- and intrakingdom microbial correlations were determined. Significant microbial interactions were identified and validated using single- and mixed-species biofilms. CD and NCDR groups clustered together in the mycobiome but not in the bacteriome. Microbiotas of familial (CD and NCDR) samples were distinct from those of nonfamilial (NCDU) samples. The abundance of Serratia marcescens and Escherichia coli was elevated in CD patients, while that of beneficial bacteria was decreased. The abundance of the fungus Candida tropicalis was significantly higher in CD than in NCDR (P = 0.003) samples and positively correlated with levels of anti-Saccharomyces cerevisiae antibodies (ASCA). The abundance of C. tropicalis was positively correlated with S. marcescens and E. coli, suggesting that these organisms interact in the gut. The mass and thickness of triple-species (C. tropicalis plus S. marcescens plus E. coli) biofilm were significantly greater than those of single- and double-species biofilms. C. tropicalis biofilms comprised blastospores, while double- and triple-species biofilms were enriched in hyphae. S. marcescens used fimbriae to coaggregate or attach with C. tropicalis/E. coli, while E. coli was closely apposed with C. tropicalis. Specific interkingdom microbial interactions may be key determinants in CD. IMPORTANCE Here, we characterized the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in multiplex families with CD and healthy relatives and defined the microbial interactions leading to dysbiosis in CD. We identified fungal (Candida tropicalis) and bacterial (Serratia marcescens and Escherichia coli) species that are associated with CD dysbiosis. Additionally, we found that the level of anti-Saccharomyces cerevisiae antibodies (ASCA; a known CD biomarker) was associated with the abundance of C. tropicalis. We also identified positive interkingdom correlations between C. tropicalis, E. coli, and S. marcescens in CD patients and validated these correlations using in vitro biofilms. These results provide insight into the roles of bacteria and fungi in CD and may lead to the development of novel treatment approaches and diagnostic assays.

Hybrid zones provide an ideal natural experiment to study the selective forces driving evolution of reproductive barriers and speciation. If hybrid offspring are less fit than the parental species, pre-zygotic isolating barriers can evolve and strengthen in response to selection against the hybrids (reinforcement). Four contact zones between the intertidal macroalgae Fucus serratus (Fs) and Fucus distichus (Fd), characterized by varying times of sympatry and order of species introduction provide an opportunity to investigate reinforcement. We examined patterns of hybridization and reproductive isolation between Fs and Fd in: (i) northern Norway (consisting of two natural sites, 10 000 years old), (ii) the Kattegat near Denmark (Fd introduced, nineteenth century) and (iii) Iceland (Fs introduced, nineteenth century). Using 10 microsatellites and chloroplast DNA, we showed that hybridization and introgression decreased with increasing duration of sympatry. The two younger contact zones revealed 13 and 24% hybrids and several F1 individuals, in contrast to the older contact zone with 2–3% hybrids and an absence of F1s. Cross-fertilization experiments revealed that the reduction in hybridization in the oldest zone is consistent with increased gametic incompatibility.

The spread of antimicrobial resistance (AMR) is a major global concern, and the islands of the Southwest Indian Ocean (SWIO) are not exempt from this phenomenon. As strategic crossroads between Southern Africa and the Indian subcontinent, these islands are constantly threatened by the importation of multidrug-resistant bacteria from these regions. In this systematic review, our aim was to assess the epidemiological situation of AMR in humans in the SWIO islands, focusing on bacterial species listed as priority by the World Health Organization. Specifically, we examined Enterobacterales, Acinetobacter spp., Pseudomonas spp. resistant to carbapenems, and Enterococcus spp. resistant to vancomycin. Our main objectives were to map the distribution of these resistant bacteria in the SWIO islands and identify the genes involved in their resistance mechanisms. We conducted literature review focusing on Comoros, Madagascar, Maldives, Mauritius, Mayotte, Reunion Island, Seychelles, Sri Lanka, and Zanzibar. Our findings revealed a growing interest in the investigation of these pathogens and provided evidence of their active circulation in many of the territories investigated. However, we also identified disparities in terms of data availability between the targeted bacteria and among the different territories, emphasizing the need to strengthen collaborative efforts to establish an efficient regional surveillance network.

Abstract Although island endemic bats are a source of considerable conservation concerns, their biology remains poorly known. Here, we studied the phenology and roosting behavior of a tropical island endemic species: the Reunion free‐tailed bat (Mormopterus francoismoutoui). This widespread and abundant species occupies various natural and anthropogenic environments such as caves and buildings. We set up fine‐scale monitoring of 19 roosts over 27 months in Reunion Island and analyzed roost size and composition, sexual and age‐associated segregation of individuals, as well as the reproductive phenology and body condition of individuals. Based on extensive data collected from 6721 individuals, we revealed a highly dynamic roosting behavior, with marked seasonal sex‐ratio variation, linked to distinct patterns of sexual aggregation among roosts. Despite the widespread presence of pregnant females all over the island, parturition was localized in a few roosts, and flying juveniles dispersed rapidly toward all studied roosts. Our data also suggested a 7‐month delay between mating and pregnancy, highlighting a likely long interruption of the reproductive cycle in this tropical bat. Altogether, our results suggest a complex social organization in the Reunion free‐tailed bat, with important sex‐specific seasonal and spatial movements, including the possibility of altitudinal migration. Bat tracking and genetic studies would provide additional insights into the behavioral strategies that shape the biology of this enigmatic bat species. The fine‐scale spatiotemporal data revealed by our study will serve to the delineation of effective conservation plans, especially in the context of growing urbanization and agriculture expansion in Reunion Island.

Abstract Co-infections have a key role in virus transmission in wild reservoir hosts. We investigated the simultaneous presence of astroviruses, coronaviruses, and paramyxoviruses in bats from Madagascar, Mayotte, Mozambique, and Reunion Island. A total of 871 samples from 28 bat species representing 8 families were tested by polymerase chain reactions (PCRs) targeting the RNA-dependent RNA-polymerase genes. Overall, 2.4% of bats tested positive for the presence of at least two viruses, only on Madagascar and in Mozambique. Significant variation in the proportion of co-infections was detected among bat species, and some combinations of co-infection were more common than others. Our findings support that co-infections of the three targeted viruses occur in bats in the western Indian Ocean region, although further studies are needed to assess their epidemiological consequences.

Astroviruses (AstVs) are RNA viruses infecting a large diversity of avian and mammalian species, including bats, livestock, and humans. We investigated AstV infection in a free-tailed bat species, Mormopterus francoismoutoui, endemic to Reunion Island. A total of 380 guano samples were collected in a maternity colony during 38 different sampling sessions, from 21 June 2016 to 4 September 2018. Each sample was tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene using a pan-AstV semi-nested polymerase chain reaction assay. In total, 27 guano samples (7.1%) tested positive, with high genetic diversity of the partial RdRp gene sequences among positive samples. Phylogenetic analysis further revealed that the detected viruses were genetically related to AstVs reported in rats, reptiles, dogs, and pigs, but did not cluster with AstVs commonly found in bats. Although more investigations need to be conducted to assess the prevalence of infected bats in the studied population, our findings show that Reunion free-tailed bats are exposed to AstVs, and suggest that cross-species transmission may occur with other hosts sharing the same habitat.

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Purpose: Meibomian gland dysfunction (MGD) may cause chronic ocular surface pain (COSP) with a neuropathic component that can significantly impact quality of life and be poorly responsive to conventional treatments of MGD. Intense pulsed light (IPL) is an emerging treatment already acknowledged as improving refractory MGD, potentially modulating inflammatory mediators on the ocular surface. This study aimed to assess the impact of IPL on COSP associated with unresponsive MGD. Methods: A monocentric prospective study has been conducted from 2021 to 2023 on patients presenting with moderate MGD and COSP non-responsive to conventional treatments of MGD. Neuropathic pain components were suspected when severe discomfort (OSDI score above 33/100) was observed despite moderate objective signs. Three sessions of IPL were performed at a two-week interval. The primary outcome was change in OSDI at day 60. Secondary outcomes included OSDI modification at D120, DEQ-5, and Pentascore results at D60/D120, together with changes in clinical [Schirmer I, Fluorescein Break-up time (BUT), fluorescein staining, and MGD classification] and paraclinical tests [noninvasive BUT, tear meniscus height (TMH), and meibography]. Results: A significant improvement of COSP ( p < 0.05 for changes in OSDI and Pentascore results) was observed 2 and 4 months after the last IPL session, together with an improvement in tear film stability, corneal epitheliopathy, meibomian gland obstruction, and TMH. Conclusion: The results of this study suggest the beneficial effect of IPL on neuropathic component of COSP associated with MGD. The underlying mechanisms involved in that improvement, presumably related to downgrading of inflammatory effectors, remain however to be explored.

The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans, 1 , 2 is classified as Vulnerable globally 3 -with global abundance having dropped to 63% of 1970s estimates, 4 -and as Critically Endangered in Europe. 5 Identification of evolutionary significant units and their management are crucial for conservation, 6 especially as the white shark is facing various but often region-specific anthropogenic threats. 7 , 8 , 9 , 10 , 11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers. 12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites, 13 , 14 , 15 , 16 , 17 , 18 , 19 which can be plagued by various genotyping artefacts and thus require cautious interpretation. 20 Sequencing and computational advances are finally allowing genomes 21 , 22 , 23 to be leveraged into population studies, 24 , 25 , 26 , 27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC) 28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range, 12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Diagnosis of herpes simplex keratitis (HSK) is mostly based on clinical findings, yet biological confirmation supports management of challenging cases. This study evaluated the place of real-time quantitative PCR (RT-qPCR) on tear samplings in the management of HSK. Clinical records of patients who underwent tear sampling tested by RT-qPCR for herpes simplex virus type 1 for an acute episode of corneal inflammation or defect between January 2013 and December 2021 were retrospectively reviewed, and results were compared to clinical diagnosis (i.e., HSK or not) based on biomicroscopic findings and medical history. Of 465 tested tear samples from 364 patients, a clinical diagnosis of active (ongoing) HSK was recorded in 240 cases, among which 76 were RT-qPCR positive (global sensitivity of 31.6%, specificity of 99.5%). Sensitivity of RT-qPCR was higher in epithelial (97.4%) and stromal keratitis with ulceration (48.7%), compared to other types of HSK (23.5% in keratouveitis, 13.6% in endotheliitis, 11.1% in postherpetic neurotrophic keratopathy, and 8.1% in stromal keratitis without ulceration). The highest viral loads were detected from epithelial and stromal keratitis with ulceration, while in HSK with no epithelial involvement, the viral load detected was 196-fold lower, on average. The proportion of clinically characterized HSK patients with negative tear samples was higher in patients receiving antiviral treatment ( P < 0.0001). RT-qPCR, performed on tear samples, can help in confirming diagnosis in case of presumed HSK, including clinical forms with no obvious epithelial involvement. The sensitivity of tear sampling is much higher whenever epithelial keratitis is present., Competing Interests: The authors declare no conflict of interest.

Flaviviruses are a group of positive-sense, single-stranded RNA viruses predominantly transmitted by arthropods (mainly mosquitoes) that cause severe endemic infections and epidemics on a global scale. They represent a major cause of systemic morbidity and death and are expanding worldwide. Among this group, dengue fever, the West Nile virus, yellow fever, Japanese Encephalitis, and, recently, the Zika virus have been linked to a spectrum of ocular manifestations. These manifestations encompass subconjunctival hemorrhages and conjunctivitis, anterior and posterior uveitis (inclusive of vitritis, chorioretinitis, and retinal vasculitis), maculopathy, retinal hemorrhages, and optic neuritis. Clinical diagnosis of these infectious diseases is primarily based on epidemiological data, history, systemic symptoms and signs, and the pattern of ocular involvement. Diagnosis confirmation relies on laboratory testing, including RT-PCR and serological testing. Ocular involvement typically follows a self-limited course but can result in irreversible visual impairment. Effective treatments of flavivirus infections are currently unavailable. Prevention remains the mainstay for arthropod vector and zoonotic disease control. Effective vaccines are available only for the yellow fever virus, dengue virus, and Japanese Encephalitis virus. This review comprehensively summarizes the current knowledge regarding the ophthalmic manifestations of the foremost flavivirus-associated human diseases.

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.)

In nuclear facilities, the mandatory airborne contamination surveillance is operated by continuous air monitors (CAMs). It samples the ambient air on a filter and measures the deposited activity. It is designed to trig an alarm whenever the measured activity concentration exceeds a defined threshold. However, in some sites, such as dismantling nuclear sites, a high rate of false alarm is experienced, mainly for artificial alpha. It has been shown that false alarms are directly related to a sudden variation of the aerosol mass sizes distribution, i.e. a wrong detection limit (DL) evaluation. Experiments on the ICARE tests bench have been carried out to compare the CAM's DL and an estimated DL as a function of the aerosol characteristics, to the measured one. This new estimation shows significant improvements over the previous one and highlights the need to consider aerosol characteristics for a correct airborne contamination measurement., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Pneumocystis jirovecii is a transmissible fungus responsible for severe pneumonia (Pneumocystis pneumonia [PCP]) in immunocompromised patients. Missense mutations due to atovaquone selective pressure have been identified on cytochrome b (CYB) gene of P. jirovecii. It was recently shown that atovaquone prophylaxis can lead to the selection of specific P. jirovecii CYB mutants potentially resistant to atovaquone among organ transplant recipients. In this context, our objectives were to provide data on P. jirovecii CYB mutants and the putative selective pressure exerted by atovaquone on P. jirovecii organisms in France. A total of 123 patients (124 P. jirovecii specimens) from four metropolitan hospitals and two overseas hospitals were retrospectively enrolled. Fourteen patients had prior exposure to atovaquone, whereas 109 patients did not at the time of P. jirovecii detection. A 638 base-pair fragment of the CYB gene of P. jirovecii was amplified and sequenced. A total of 10 single nucleotide polymorphisms (SNPs) were identified. Both missense mutations C431T (Ala144Val) and C823T (Leu275Phe), located at the Qo active site of the enzyme, were significantly associated with prior atovaquone exposure, these mutations being conversely incidental in the absence of prior atovaquone exposure (P < 0.001). Considering that the aforementioned hospitals may be representative of the national territory, these findings suggest that the overall presence of P. jirovecii CYB mutants remains low in France., (© The Author(s) 2023. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated., Competing Interests: Conflicts of interest statement The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Little is known about when and how planktonic species arise and persist in the open ocean without apparent dispersal barriers. Pteropods are planktonic snails with thin shells susceptible to dissolution that are used as bio-indicators of ocean acidification. However, distinct evolutionary units respond to acidification differently, and defining species boundaries is therefore crucial for predicting the impact of changing ocean conditions. In this global population genomic study of the shelled pteropod Limacina bulimoides, we combined genetic (759,000 single nucleotide polymorphisms) and morphometric data from 161 individuals, revealing three major genetic lineages (F ST  = 0.29-0.41): an "Atlantic lineage" sampled across the Atlantic, an "Indo-Pacific lineage" sampled in the North Pacific and Indian Ocean, and a "Pacific lineage" sampled in the North and South Pacific. A time-calibrated phylogeny suggests that the lineages diverged about 1 million years ago, with estimated effective population size remaining high (~10 million) throughout Pleistocene glacial cycles. We do not observe any signatures of recent hybridization, even in areas of sympatry in the North Pacific. While the lineages are reproductively isolated, they are morphologically cryptic, with overlapping shell shape and shell colour distributions. Despite showing that the circumglobal L. bulimoides consists of multiple species with smaller ranges than initially thought, we found that these pteropods still possess high levels of genetic variability. Our study adds to the growing evidence that speciation is often overlooked in the open ocean, and suggests the presence of distinct biological species within many other currently defined circumglobal planktonic species., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Sex-biased gene expression is considered to be an underlying cause of sexually dimorphic traits. Although the nature and degree of sex-biased expression have been well documented in several animal and plant systems, far less is known about the evolution of sex-biased genes in more distant eukaryotic groups. Here, we investigate sex-biased gene expression in two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. We find that in contrast to evolutionary distant plant and animal lineages, male-biased genes do not experience high turnover rates, but instead reveal remarkable conservation of bias and expression levels between the two species, suggesting their importance in sexual differentiation. Genes with consistent male bias were enriched in functions related to gamete production, along with sperm competition and include three flagellar proteins under positive selection. We present one of the first reports, outside of the animal kingdom, showing that male-biased genes display accelerated rates of coding sequence evolution compared with female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels, resulting in unique properties of differentially expressed transcripts during reproductive development in Fucus algae., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation.)

The current monkeypox virus (MPXV) outbreak, raging since May 2022, is the largest ever observed on a world-wide scale. Despite previously being endemic in west and central Africa with a mortality rate of up to 10%, it remained a neglected tropical disease. Along with other recent pandemics gaining much attention, this MPXV outbreak has provided an opportunity to improve our understanding of its physiopathology and better define management strategies, particularly in patients with more serious disease. From the ophthalmologist's perspective, eyelid involvement and conjunctivitis or keratoconjunctivitis are frequently observed and may precede systemic signs or even remain the major site of involvement. While the course of MPXV keratoconjunctivitis is most often favorable, severe cases pose a functional threat, in particular for immunocompromised patients. This review provides an overview of MPXV pathophysiology, diagnosis and treatment, as well as considerations for prevention of transmission. During such an epidemic, the ophthalmologist can be the first to diagnose MPXV, treat the ocular involvement, and set up adequate preventative measures in collaboration with infectious disease specialists., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Abstract: This paper addresses the problem of false positive alarm when using a continuous air monitor (CAM) in decommissioning sites of nuclear facilities. CAMs are used to measure airborne activity and play an important role in the radiation protection of workers likely to be exposed to radioactive aerosols. Monitors usually sample aerosols on a membrane filter. Radioactive particles sampled are detected through the alpha and beta decays that they emit. These latter ionizing particles are measured online by spectrometry thanks to a Passivated Implanted Planar Silicon detector (PIPS). Alpha and beta decays, in this context, come mainly from the natural radon progeny (218Po, 214Pb, and so on) and, in the case of radioactive contamination, also from artificial radionuclides such as 239Pu or 137Cs. The aim of the CAM is to alert the workers when the artificial airborne activity occurs, always considering the presence of a variable background due to the natural particulate airborne activity. The CAM-specific algorithm considers this background dynamically and continuously, often by using a constant parameter. However, non-radioactive aerosols are also sampled on the membrane filter. These latter make the discrimination more difficult as they lead to the deterioration of the alpha-energy spectrum. In this paper, the effect of coarse non-radioactive aerosols on the CAM response is highlighted with four aerosol size-distributions. The evolution of the background is characterized as a function of the aerosol mass sampled, with the example of a simple algorithm. Thus, in this paper, results show a positive correlation of the background with the aerosol mass sampled by the CAM. In addition, results highlight at least two different evolutionary trends according to the aerosol size distribution. An explanation of these evolutions is given by considering the penetration profile of the natural radioactive aerosols in the granular deposit above the CAM filter. The main consequence of these results is that the background could not be considered as proportional to radon progeny as it is currently used., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Health Physics Society.)

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.)

The blue skate ( Dipturus batis ) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain and could be impacted by continued fishing and by-catch pressure, and the projected impacts of climate change. We genotyped 503 samples of  D. batis , obtained opportunistically from the widest available geographic range, across 6 350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity and pH. The paucity of well-annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of  D. batis , further constraining its already-restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs., Competing Interests: The authors declare no conflicts of interest., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)