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Understanding why certain host species harbor more parasites is an important question in parasite and fish ecology. Parasite infection among sympatric species may integrate various processes affecting parasite assembly, including the species-specific ecology and the success of invaders. We focused on spatial, environmental, and host-related determinants of parasite assembly in three riverine fish species: the native three-spined stickleback and stone loach, and the invasive topmouth gudgeon. Parasite community structure differed significantly between the three host species. Three-spined stickleback harbored the most ectoparasites. Host density and nutrients were the strongest predictors of its parasite communities. Topmouth gudgeon harbored the lowest number of parasites, both in terms of abundance and species richness. None of the parasites identified originated from its expanded range, suggesting that enemy release occurred during invasion. Temperature and host density predicted parasite assemblages of topmouth gudgeon. Stone loach hosted the most endoparasites, likely resulting from its varied diet, benthic lifestyle, and larger size. Additionally, host size and condition were positively correlated with parasite infection, which was similar among the three host species. The results suggest that host-related factors have a similar effect among host species, while the importance of environmental and spatial factors differs according to host ecology.

Lake Tanganyika, East Africa, is the oldest and deepest African Great Lake and harbours one of the most diverse fish assemblages on earth. Two clupeid fishes, Limnothrissa miodon and Stolothrissa tanganicae, constitute a major part of the total fish catch, making them indispensable for local food security. Parasites have been proposed as indicators of stock structure in highly mobile pelagic hosts. We examined the monogeneans Kapentagyrus limnotrissae and Kapentagyrus tanganicanus (Dactylogyridae) infecting these clupeids to explore the parasites' lake-wide population structure and patterns of demographic history. Samples were collected at seven sites distributed across three sub-basins of the lake. Intraspecific morphological variation of the monogeneans (n = 380) was analysed using morphometrics and geomorphometrics of sclerotised structures. Genetic population structure of both parasite species (n = 246) was assessed based on a 415 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Overall, we observed a lack of clear geographical morphological differentiation in both parasites along a north-south axis. This lack of geographical population structure was also reflected by a large proportion of shared haplotypes, and a pattern of seemingly unrestricted gene flow between populations. Significant morphological and genetic differentiation between some populations might reflect temporal differentiation rather than geographical isolation. Overall, the shallow population structure of both species of Kapentagyrus reflects the near-panmictic population structure of both host species as previously reported. Morphological differences related to host species identity of K. tanganicanus were consistent with incipient speciation at the genetic level. Both parasite species experienced a recent demographic expansion, which might be linked to paleohydrological events. Finally, interspecific hybridisation was found in Kapentagyrus, representing the first case in dactylogyrid monogeneans. (C) 2020 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved. The authors would like to thank L. Raisingerová, C. Rahmouni, H. Zimmermann, A. P. H. Bose and W. Salzburger for help with collecting host samples. M. Jorissen is gratefully acknowledged for fruitful discussions about monogenean morphological variability and help in the laboratory. Special thanks to the staff of the parasitological group at Masaryk University, Brno (Czech Republic), the Research Group Zoology at Hasselt University (Belgium), Research Centre of Hydrobiology in Uvira (DR Congo) and Fisheries Research Unit in Mpulungu (Zambia) for their hospitality. Research was supported by the Czech Science Foundation (P505/12/G112 (ECIP) and GA19-13573S), EMBRC Belgium – FWO project GOH3817N as well as by a joint program between the Austrian Agency for International Cooperation in Education and Research (OEAD; project number CZ 08/2018; to SK) and the Ministry of Education, Youth and Sports (project number 8J18AT007). MPMV was co-financed by institutional funding of the Finnish Museum of Natural History and the Belgian Directorate-General for Development Cooperation and Humanitarian Aid (CEBioS program). ELRDK was supported by the Belgian Development Cooperation through VLIR-UOS (VLADOC scholarship NDOC2016PR006 to ELRDK and South Initiative project CD2018SIN218A101). Fieldwork was carried out with the approval of the competent local authorities under mission statement 031/MINRST/CRH-U/2016 and the permission of the Fisheries Department of Zambia and under a study permit issued by the government of Zambia (SP 008732).

Background Current influenza vaccines are strain specific and demonstrate low vaccine efficacy against H3N2 influenza disease, especially when vaccine is mismatched to circulating virus. The novel influenza vaccine candidate, M2-deficient single replication (M2SR), induces a broad, multi-effector immune response. Methods A phase 2 challenge study was conducted to assess the efficacy of an M2SR vaccine expressing hemagglutinin and neuraminidase from A/Brisbane/10/2007 (Bris2007 M2SR H3N2; clade 1). Four weeks after vaccination, recipients were challenged with antigenically distinct H3N2 virus (A/Belgium/4217/2015, clade 3C.3b) and assessed for infection and clinical symptoms. Results Adverse events after vaccination were mild and similar in frequency for placebo and M2SR recipients. A single dose of Bris2007 M2SR induced neutralizing antibody to the vaccine (48% of recipients) and challenge strain (27% of recipients). Overall, 54% of M2SR recipients were infected after challenge, compared with 71% of placebo recipients. The subset of M2SR recipients with a vaccine-induced microneutralization response against the challenge virus had reduced rates of infection after challenge (38% vs 71% of placebo recipients; P = .050) and reduced illness. Conclusions Study participants with vaccine-induced neutralizing antibodies were protected against infection and illness after challenge with an antigenically distinct virus. This is the first demonstration of vaccine-induced protection against a highly drifted H3N2 challenge virus.

The current and projected environmental change of the Arctic Ocean contrasts sharply with the limited knowledge of its genetic biodiversity. Polar cod Boreogadus saida (Lepechin, 1774) is an abundant circumpolar marine fish and ecological key species. The central role of polar cod in the Arctic marine food web warrants a better understanding of its population structure and connectivity. In this study, the genetic population structure of 171 juveniles, collected from several fjords off West-Svalbard (Billefjorden, Hornsund and Kongsfjorden), the northern Sophia Basin and the Eurasian Basin of the Arctic Ocean, was analysed using nine DNA microsatellite loci. Genetic analyses indicated moderate to high genetic diversity, but absence of spatial population structure and isolation-by-distance, suggesting ongoing gene flow between the studied sampling regions. High levels of connectivity may be key for polar cod to maintain populations across wide spatial scales. The adaptive capacity of the species will be increasingly important to face challenges such as habitat fragmentation, ocean warming and changes in prey composition. In view of a limited understanding of the population dynamics and evolution of polar cod, a valuable next step to predict future developments should be an integrated biological evaluation, including population genomics, a life-history approach, and habitat and biophysical dispersal modelling. ispartof: JOURNAL OF FISH BIOLOGY vol:99 issue:1 pages:49-60 ispartof: location:England status: published

Freshwater snails act as intermediate hosts (IH) for schistosomiasis, a tropical disease affecting over 200 million people worldwide. Despite their medical importance, an extensive understanding of IH snail ecology remains absent. Especially data on the tolerance limits to different abiotic factors are fragmented and incomplete. Consequently, the construction of accurate species distribution models to identify snail habitats and guide targeted snail control efforts remains difficult. Here, we compiled a summary on the tolerance limits to abiotic factors of African IH snails of human schistosomiasis. A systematic search on Web of Science, PubMed, and Embase identified 45 relevant studies. Synthesis of these studies indicates that research efforts differ greatly between IH snail species, life stages, and abiotic factors. The importance of each abiotic factor in determining snail presence and abundance is discussed. Furthermore, attention was drawn to knowledge gaps and the lack of standardised experimental designs, which impedes comparisons between studies. This in turn prevents us from making firm conclusions and calls for best practices adopted by all malacologists. In doing so, IH snail ecological data could serve as a basis to assess schistosomiasis risk and guide snail control efforts in order to support schistosomiasis control. ispartof: Hydrobiologia vol:848 issue:8 pages:1773-1793 status: Published online

Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population-specific information. We conclude that the management of fish stocks has to consider species-specific genetic structures and may benefit from the documentation of the genetic seascape and life-history traits. ispartof: EVOLUTIONARY APPLICATIONS vol:14 issue:2 pages:536-552 ispartof: location:England status: published

Aim The formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units.Location Continental Africa.Taxon Clarias gariepinus sl.Methods We investigated mitochondrial cytb sequences of 443 individuals from 97 localities, using a haplotype network and a genetic landscape analysis. We inferred a dated phylogeny using maximum likelihood and Bayesian inference approaches and reconstructed ancestral areas with S-DEC and S-DIVA models. Microsatellite genotyping complemented the mitochondrial approach in the Congo basin, where the latter revealed complex patterns.Results Limited differentiation is found in northern and south-western Africa, and sharp genetic differentiation in the continent's east and centre. Populations with affinities to neighbouring basins occur at the edges of the Congo province. High diversity exists in the south of the Congo basin. The Zambezi province is partitioned into eastern, central and western sectors. In the east, specimens were related to those from the Congo. In the west, they were similar to Southern representatives. Phylogenetic inference placed the origin of C. gariepinus in the East Coast, with intraspecific diversification starting around the Great Lakes. These events occurred ca. 4.8-1.65 and 2.3-0.8 MYA respectively.Main conclusions Clades of C. gariepinus sl. show a clear geographical signature. The origin of C. gariepinus in the East Coast and diversification around the Great Lakes coincided with the periods of increased aridity. Low genetic differentiation in northern and southern Africa may result from connectivity during recent periods of higher rainfall. In contrast to other widespread African freshwater fish, colonization rather than extinction seemed to mediate distribution patterns. This can be explained by a high ecological tolerance. We highlight the species' suitability to study landscape and climate evolution at various scales. A.A. received a postdoctoral research fellowship from the KU Leuven and the Research Foundation - Flanders (FWO). M.V.S. and M.P.M.V. received PhD fellowships from FWO. MVS received travel grants of the FWO and the Leopold III funds for Nature Exploration and Conservation. A.C.M. received support from the Belgian Development Agency and the BTCCTB project PRODEPAAK. We sincerely thank the following colleagues for sample collection: J.-F. Agnèse, B. Benade, R. Bills, L. and G. Chapman, P. de Villiers, the late L. De Vos, J. Engelbrecht, P. Fouche, P. Galbusera, K. Goudswaard, D. Impson, R. Karssing, J. Munyandorero, A. Piers, C. Maguswi, J. Southey, the late G. Teugels, K. Van Lerberghe and the Department of Fisheries and Agriculture of Zambia. We benefited from insights from J.-F. Agnèse, T. Huyse, J. Maley, P. Skelton, J. Snoeks, K. Van Doninck and C. Sturmbauer. This study was performed on historical collections and on samples collected by researchers from certified institutes of the countries where collections were made. All material was collected prior to the implementation of the Nagoya protocol for access and benefit sharing.

Larval dispersal and juvenile survival are crucial in determining variation in recruitment, stock size and adult distribution of commercially important fish. This study investigates the dispersal of early-life stages of common sole (Solea solea L.) in the southern North Sea, both empirically and through modeling. Age at different life-history events of juvenile flatfish sampled along the coasts of Belgium, the Netherlands and the United Kingdom in 2013, 2014 and 2016, was determined through the counting of daily growth rings in the otoliths. Juveniles captured between August and October were estimated to be on average 140 days old with an average pelagic larval duration of 34 days. The hatching period was estimated between early April and mid-May followed by arrival and settlement in the nurseries between May and mid-June. Growth rates were higher off the Belgian coast than in the other nursery areas, especially in 2013, possibly due to a post-settlement differentiation. Empirical pelagic larval duration and settlement distributions were compared with the Larvae&Co larval dispersal model, which combines local hydrodynamics in the North Sea with sole larval behavior. Yearly predicted and observed settlement matched partially, but the model estimated a longer pelagic phase. The observations fitted even better with the modelled average (1995-2015) distribution curves. Aberrant results for the small juvenile sole sampled along the UK coast in March 2016, led to the hypothesis of a winter disruption in the deposition of daily growth rings, potentially related to starvation and lower food availability. The similarities between measured and modelled distribution curves cross-validated both types of estimations and accredited daily ageing of juveniles as a useful method to calibrate biophysical models and to understand early-life history of fish, both important tools in support of efficient fisheries management strategies. ispartof: PLOS ONE vol:16 issue:9 ispartof: location:United States status: published

Schistosomiasis is widely distributed along the Senegal River Basin (SRB), affecting both the human population and their livestock. Damming of the Senegal River for irrigation purposes in the 1980s induced ecological changes that resulted in a large outbreak of Schistosoma mansoni, followed a few years later by an increase and spread of Schistosoma haematobium infections. The presence of hybrid crosses between the human and cattle schistosomes, S. haematobium and Schistosoma bovis, respectively, is adding complexity to the disease epidemiology in this area, and questions the strength of the species boundary between these two species. This study aimed to investigate the epidemiology of S. haematobium, S. bovis and their hybrids along the Senegal River basin using both microsatellite genetic markers and analysis of mitochondrial and nuclear DNA markers. Human schistosome populations with a S. haematobium cox1 mtDNA profile and those with a S. bovis cox1 mtDNA profile (the so-called hybrids) appear to belong to a single randomly mating population, strongly differentiated from the pure S. bovis found in cattle. These results suggest that, in northern Senegal, a strong species boundary persists between human and cattle schistosome species and there is no prolific admixing of the populations. In addition, we found that in the SRB S. haematobium was spatially more differentiated in comparison to S. mansoni. This may be related either to the presence and susceptibility of the intermediate snail hosts, or to the colonisation history of the parasite. (C) 2019 Published by Elsevier Ltd on behalf of Australian Society for Parasitology.

Basal rot is a common disease in Belgian lettuce, which is mainly controlled by fungicides and chemical soil disinfestation. A seasonal appearance of the basal rot pathogens: Rhizoctonia solani, Sclerotinia spp., Botrytis cinerea and Pythium spp. has been reported, but lettuce growers use standard spraying schemes, irrespective of the occurrence of the pathogen. Due to stricter regulations and environmental concerns the superfluous use of fungicides should be omitted. We investigated if the use of fungicides could be reduced by only controlling the active pathogens. Therefore, lettuce was continuously grown in three glasshouses without any fungal disease control and the active pathogens causing basal rot were identified. The occurrence of basal rot pathogens appeared to be glasshouse specific and the different basal rot pathogens were active throughout the year. However, a seasonal appearance of R. solani anastomosis groups and Pythium spp. was observed with AG4-HGI and Pythium ultimum active at higher temperatures and AG2–1, AG-BI, AG1-IB and Pythium sylvaticum at lower temperatures. We report for the first time the isolation of AG-BI from infected plants. Each R. solani anastomosis group had its own optimal growth rate in vitro. Differences in pathogenicity between R. solani anastomosis groups were observed on detached leaves. AG1-IB and AG4-HGI were most pathogenic, followed by AG2–1 and AG-BI. These results show that the fungicide spraying scheme should be adapted to the occurring pathogens in the glasshouse. This information is of high importance in developing a sustainable control strategy for basal rot pathogens.

Assessing population genetic structure is a crucial step to support fisheries and conservation management. DNA microsatellite molecular markers are a widely used tool in population genotyping. In the present study, we characterised and developed 14 novel polymorphic microsatellite markers for a decapod crustacean, the Atlantic seabob shrimp Xiphopenaeus kroyeri (Heller, 1862), through rapid and cost-effective Illumina shotgun sequencing and a Galaxy-based bioinformatic pipeline. We genotyped 60 individuals from 2 populations with the newly developed microsatellites, resulting in the detection of 3 to 29 alleles per locus. Four loci deviated from Hardy-Weinberg equilibrium. Cross-amplification in a cryptic congeneric species was successful for eight loci (57%). The microsatellite loci developed in this study will be highly relevant for genetic and evolutionary studies of X. kroyeri, and for the stock management of this commercially exploited species.

The recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.

This study presents the first case of the joint DNA metabarcoding of prey items and microbiome community analysis in wild juvenile fish. Juvenile European plaice (Pleuronectes platessa) were caught at 11 locations in the southern North Sea and eastern English Channel. Stomach fullness varied ontogenetically in time and space. Food uptake seemed to be slightly limited for the smallest plaice individuals up to a size of 20 to 30 mm. Furthermore, strong homogeneity for microbiome and prey item composition prevailed. Little seasonal, annual and regional (on-offshore/depth) variation was observed in prey item composition. Brown shrimp Crangon crangon made up >70% of the reads in all stomachs, length classes, regions, seasons and years. Offshore samples differentiated with a distinct lack of β-Proteobacteria in the gut microbiome. Based on a visual similarity network analysis, there was no observable correlation between prey item and microbiome composition, indicating that the microbiome composition wasn't driven by diet, but might be determined by the benthic bacterial community. DNA metabarcoding yields clear insights in the prey and microbiome composition of plaice, even for seemingly empty stomachs, and should therefore be considered for future dietary and microbiome studies.

© 2019 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography. Connectivity and dispersal are important factors for ecosystem dynamics, conservation, and resource management. Dispersal and recruitment success are determined in early life for many marine species. For those larvae that are pelagic, transport from spawning to nursery grounds is driven by hydrodynamic processes. Other environmental factors such as temperature and biological factors such as ecophysiology, behavior, and reproductive strategy (spawning period and spawning grounds) influence the final dispersal pattern and larval survival. We utilized a Lagrangian particle tracking model coupled with a three-dimensional hydrodynamic model (Larvae&Co) to assess the connectivity patterns between spawning and nursery grounds of six commercially exploited flatfish species in the North Sea over a 10-yr period (1997–2006). Standardized analyses have highlighted how spawning and nursery grounds are connected under the combined pressure of environment and life-history traits. Results showed that the six flatfishes can be divided in two groups, each with their specific connectivity patterns. Turbot, common sole, and brill live in two subpopulations in the North Sea; common dab, European flounder, and European plaice represent a single mixed population. In general, the modeled and genetic patterns match, hence showing the strong impact of larval connectivity. The large overlap in connectivity for species that spawn during the same period and the seasonal change in hydrodynamics highlight the strong impact of a summer front in larval dispersal. Our results prove that individual-based modeling is a powerful tool to guide resource management, even in cases of limited biological information. ispartof: LIMNOLOGY AND OCEANOGRAPHY vol:64 issue:3 pages:1150-1171 status: published

Background: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology., SCOPUS: ar.j, info:eu-repo/semantics/published

Fishery products are often subject to substitution fraud, which is hard to trace due to a lack of morphologic traits when processed, gutted, or decapitated. Traditional molecular methods (DNA barcoding) fail to identify products containing multiple species and cannot estimate original weight percentages. As a proof of concept, an Atlantic salmon (Salmo salar) specific ddPCR assay was designed to authenticate mixed food products. The method proved to be specific and able to accurately quantify S. salar when using DNA extracts, even in the presence of DNA from closely related salmon species. The ddPCR estimates correlated well with the percentage of S. salar in artificially assembled tissue mixtures. The effect of common salmon processing techniques (freezing, smoking, poaching with a "Bellevue" recipe and marinating with a 'Gravad lax' recipe) on the ddPCR output was investigated and freezing and marinating appeared to lower the copies detected by the ddPCR. Finally, the assay was applied to 46 retail products containing Atlantic or Pacific salmon, and no indications of substitution fraud were detected. The method allows for a semi-quantitative evaluation of the S. salar content in processed food products and can rapidly screen Atlantic salmon products and flag potentially tampered samples for further investigation. ispartof: FOOD AND CHEMICAL TOXICOLOGY vol:154 ispartof: location:England status: published

Anthropogenic stressors, such as pollutants, act as selective factors that can leave measurable changes in allele frequencies in the genome. Metals are of particular concern among pollutants, because of interference with vital biological pathways. We use the three-spined stickleback as a model for adaptation to mercury pollution in natural populations. We collected sticklebacks from 21 locations in Flanders (Belgium), measured the accumulated levels of mercury in the skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The spread of muscle mercury content across locations was considerable, ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome-wide association study (GWAS) between 28,450 single nucleotide polymorphisms (SNPs) and the accumulated levels of mercury, using different approaches. Based on a linear mixed model analysis, the GWAS yielded multiple hits with a single top hit on Chromosome 4, with eight more SNPs suggestive of association. A second approach, a latent factor mixed model analysis, highlighted one single SNP on Chromosome 11. Finally, an outlier test identified one additional SNP on Chromosome 4 that appeared under selection. Out of all ten SNPs we identified as associated with mercury in muscle, three SNPs all located on Chromosome 4 and positioned within a 2.5 kb distance of an annotated gene. Based on these results and the genome coverage of our SNPs, we conclude that the selective effect of mercury pollution in Flanders causes a significant association with at least one locus on Chromosome 4 in three-spined stickleback. ispartof: EVOLUTIONARY APPLICATIONS vol:14 issue:10 pages:2553-2567 ispartof: location:England status: published

This study represents the first exploration of the parasite fauna of cichlid fishes in the Mweru-Luapula subregion (Central Africa). Twelve species of cichlids and 14 species of Monogenea from three genera (Cichlidogyrus, Gyrodactylus and Scutogyrus) were collected. We present a first record of the gill parasite fauna of eight host species, Oreochromis mweruensis, Orthochromis sp. ‘Mambilima’, Sargochromis mellandi, Serranochromis angusticeps, S. stappersii, S. thumbergi and Tylochromis mylodon. The host range of 10 parasite species was expanded. The study further includes the description of Cichlidogyrus consobrini sp.n. from S. mellandi and Orthochromis sp. ‘Mambilima’. A new morphotype of C. halli is characterized and three species, C. papernastrema, C. quaestio and C. zambezensis are redescribed. Furthermore, the biodiversity and host-specificity of these parasites are compared with cichlid parasites from Lake Kariba and Cameroon. Two species, including C. consobrini sp.n. and a new morphotype of C. halli, are putative endemics. Additionally, the parasite fauna is highly similar in species composition to Lake Kariba, but in Bangweulu-Mweru the same parasite species are more host-specific, probably because of hydrogeographical differences between the two regions. This research was supported by the Belgian Federal Science Policy Office (BRAIN-be Pioneer Project BR/132/PI/TILAPIA), the University Development Cooperation of the Flemish Interuniversity Council (VLIR-UOS, South Initiative Renforcement des capacites locales pour une meilleure evaluation biologique des impacts miniers au Katanga (RDC) sur les poissons et leurs milieux aquatiques, ZRDC2014MP084) and the Mbisa Congo project, a framework agreement project of the RMCA with the Belgian Development Cooperation. M.P.M.V. was supported by a travel grant from the Research Foundation - Flanders (FWO-Vlaanderen) and Czech Science Foundation project no. P505/12/G112 (ECIP). Moise Katumbi Chapwe is cordially thanked for his kind hospitality and support. Also E. Abwe, B. Katemo Manda and C. Mukwene Mulele are cordially thanked for their help with the fish sampling, and W. Fannes, M. Kasongo Ilunga Kayaba and C. Kalombo Kabalika for their effort in parasite preparation. M. Barson, T. Dube and the technical team at the University of Zimbabwe Lake Kariba Research Station are thanked for delivering fresh gills of S. macrocephalus from Lake Kariba, Zimbabwe; J.-L. Justine (MNHN) and A.J. Phillips (Smithsonian) for the loan of type material; I. Přikrylová for sharing her expertise on Gyrodactylus; M. Van Steenberge for his valuable input regarding this ecoregion and its ichthyofauna; A. Henrard for his help with stacking images; G. Cael for his help with constructing fig. 1; and two anonymous referees for their valuable comments.

Background: Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world’s poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. This is an important step towards knowing if the species should be managed separately or as a single stock. Population structure is important for fisheries management, yet understudied for many African freshwater species. We hypothesize that distinct stocks of S. tanganicae could be present due to the large size of the lake (isolation by distance), limnological variation (adaptive evolution), or past separation of the lake (historical subdivision). On the other hand, high mobility of the species and lack of obvious migration barriers might have resulted in a homogenous population. Results: We performed a population genetic study on wild-caught S. tanganicae through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (83 individuals). Samples were collected at five locations along a northsouth axis of Lake Tanganyika. The mtDNA data had low global FST and, visualised in a haplotype network, did not show phylogeographic structure. RAD sequencing yielded a panel of 3504 SNPs, with low genetic differentiation (FST = 0.0054; 95% CI: 0.0046–0.0066). PCoA, fineRADstructure and global FST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (FST = 0.1338 95% CI: 0.1239,0.1445), which do not correspond to sampling locations. Autocorrelation analysis showed a slight increase in genetic difference with increasing distance. No outlier loci were detected in the RADseq data. Conclusion: Our results show at most very weak geographical structuring of the stock and do not provide evidence for genetic adaptation to historical or environmental differences over a north-south axis. Based on these results, we advise to manage the stock as one population, integrating one management strategy over the four riparian countries. These results are a first comprehensive study on the population structure of these important fisheries target species, and can guide fisheries management. Research has been supported by the JEMU pilot project PopGenSprat (BELSPO funding) and the Belgian Development Cooperation through VLIR-UOS (VLADOC scholarship NDOC2016PR006 to ELRDK). MPMV was supported by the Belgian Directorate-General for Development Cooperation and Humanitarian Aid (CEBioS program). MPMV and NK are supported by the Czech Science Foundation (P505/12/G112 (ECIP)). These funding sources had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution and can complement each other to inform on population structure. We assessed and compared the discriminatory power of genetic markers and otolith shape to reveal the population structure on evolutionary and ecological time scales of the common sole (Solea solea), living in the Eastern English Channel (EEC) stock off France and the UK. First, we genotyped fish with Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subunits using otolith shape as an integrative tracer of life history. Finally, a supervised machine learning framework was applied to genotypes and otolith phenotypes to probabilistically assign adults to subunits and assess the discriminatory power of each approach. Low but significant genetic differentiation was found among subunits. Moreover, otolith shape appeared to vary spatially, suggesting spatial population structure at fine spatial scale. However, results of the supervised discriminant analyses failed to discriminate among subunits, especially for otolith shape. We suggest that the degree of population segregation may not be strong enough to allow for robust fish assignments. Finally, this study revealed a weak yet existing metapopulation structure of common sole at the fine spatial scale of the EEC based on genotypes and otolith shape, with one subunit being more isolated. Our study argues for the use of complementary tracers to investigate marine population structure. ispartof: PLOS ONE vol:15 issue:11 ispartof: location:United States status: published

Seafood is an important component of the human diet. With depleting fish stocks and increasing prices, seafood is prone to fraudulent substitution. DNA barcoding has illustrated fraudulent substitution of fishes in retail and restaurants. Whether substitution also occurs in other steps of the supply chain remains largely unknown. DNA barcoding relies on public reference databases for species identification, but these can contain incorrect identifications. The creation of a high quality genetic reference database for 42 European commercially important fishes was initiated containing 145 Cytochrome c oxidase subunit I (COI) and 152 Cytochrome b (cytB) sequences. This database was used to identify substitution rates of Atlantic cod (Gadus morhua) and common sole (Solea solea) along the fish supply chain in Belgium using DNA barcoding. Three out of 132 cod samples were substituted, in catering (6%), import (5%) and fishmongers (3%). Seven out of the 41 processed sole samples were substituted, in wholesale (100%), food services (50%), retailers (20%) and catering (8%). Results show that substitution of G. morhua and S. solea is not restricted to restaurants, but occurs in other parts of the supply chain, warranting for more stringent controls along the supply chain to increase transparency and trust among consumers. ispartof: FOOD AND CHEMICAL TOXICOLOGY vol:141 ispartof: location:England status: published

Understanding the influence of man-made infrastructures on fish population dynamics is an important issue for fisheries management. This is particularly the case because of the steady proliferation of offshore wind farms (OWFs). Several flatfish species are likely to be affected because areas with OWFs in place or planned for show a spatial overlap with their spawning grounds. This study focuses on six commercially important flatfish species in the North Sea: common sole (Solea solea), European plaice (Pleuronectes platessa), turbot (Scophthalmus maximus), brill (Scophtalmus rhombus), European flounder (Platichthys flesus), and common dab (Limanda limanda). We used a particle-tracking model (Larvae&Co) coupled to a 3D hydrodynamic model to assess the effects of spatial overlap of OWFs with the species’ spawning grounds on the larval fluxes to known nursery grounds. An important overlap between planned areas of OWFs and flatfish spawning grounds was detected, with a resulting proportion of settlers originating from those areas varying from 2% to 16%. Our study suggests that European plaice, common dab, and brill could be the most affected flatfish species, yet with some important local disparities across the North Sea. Consequently, the study represents a first step to quantify the potential impact of OWFs on flatfish settlement, and hence on their population dynamics.

WOS: 000442210300011, 30151043, Science Citation Index Expanded, Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming., 7th Framework Programme for research (FP7) under "Knowledge-Based Bio-Economy - KBBE", Theme 2: "Food, Agriculture and fisheries, and Biotechnologies" [FP7-KBBE-2012-6-singlestage, 311920]; Spanish Regional Government Xunta de Galicia [GRC2014/010], 7th Framework Programme for research (FP7) under "Knowledge-Based Bio-Economy - KBBE", Theme 2: "Food, Agriculture and fisheries, and Biotechnologies" Project identifier: FP7-KBBE-2012-6-singlestage, Grant/Award Number: 311920; Spanish Regional Government Xunta de Galicia, Grant/Award Number: GRC2014/010

A high demand for seafood in combination with overfishing threatens living marine resources worldwide. Sound regulation and enforcement is needed for sustainable management, yet the seafood business is characterized by high levels of uncertainty regarding product identity. Here, 280 fish dishes sold in commercial restaurants, canteens of the European Union and sushi bars throughout Brussels, Belgium were assessed for mislabeling using DNA barcoding. Overall 31.1% mislabeled samples were detected, with mislabeling present in all types of vendors. Cod and sole were the most frequently sampled and were also mislabeled regularly (13.1% and 11.1%). Bluefin tuna was substituted almost always (95% mislabeling), mostly by other tuna species. Results show that seafood labeling rules and controls are not sufficient, particularly in the food service industry, where for example commercial denominations can be ambiguous and scientific species denomination is not compulsory. Irrespective if negligent or fraudulent, mislabeling practices are detrimental for economical and sustainability goals and also consumers' trust.

Local adaptation is often found to be in a delicate balance with gene flow in marine species with high dispersal potential. Genotyping with mapped transcriptome-derived markers and advanced seascape statistical analyses are proven tools to uncover the genomic basis of biologically relevant traits under environmental selection. Using a panel of 426 gene-linked single nucleotide polymorphisms (SNPs), we scanned 17 samples (n¼539) of sole (Solea solea L.) from the Northeast Atlantic Ocean and applied a node-based seascape analysis. Neutral loci confirmed a clear distinction between the North Sea–Baltic Sea transition zone and the other Eastern Atlantic samples. At a more subtle level, the latter unit split in an English Channel and North Sea group, and a Bay of Biscay and Atlantic Iberian coast group. A fourth group, the Irish and Celtic Sea, was identified with 19 outlier loci. A pattern of isolation by distance (IBD) characterized the latitudinal distribution. Seascape analyses identified winter seawater temperature, food availability and coastal currents to explain a significant component of geographically distributed genetic variation, suggesting that these factors act as drivers of local adaptation. The evidence for local adaptation is in line with the current understanding on the impact of two key ecological factors, the life-history trait winter mortality and the behaviour of inshore/offshore spawning. We conclude that the subtle differentiation between two metapopulations (North Sea and Bay of Biscay) mirrors local adaptation. At least three genomic regions with strong population differentiation point to locally divergent selection. Further functional characterization of these genomic regions should help with formulating adaptive management policies.

Climate change not only alters ocean physics and chemistry but also affects the biota. Larval dispersal patterns from spawning to nursery grounds and larval survival are driven by hydrodynamic processes and shaped by (a)biotic environmental factors. Therefore, it is important to understand the impacts of increased temperature rise and changes in wind speed and direction on larval drift and survival. We apply a particle-tracking model coupled to a 3D-hydrodynamic model of the English Channel and the North Sea to study the dispersal dynamics of the exploited flatfish (common) sole (Solea solea). We first assess model robustness and interannual variability of larval transport over the period 1995-2011. Then, using a subset of representative years (2003-2011), we investigate the impact of climate change on larval dispersal, connectivity patterns and recruitment at the nursery grounds. The impacts of five scenarios inspired by the 2040 projections of the Intergovernmental Panel on Climate Change are discussed and compared with interannual variability. The results suggest that 33% of the year-to-year recruitment variability is explained at a regional scale and that a 9-year period is sufficient to capture interannual variability in dispersal dynamics. In the scenario involving a temperature increase, early spawning and a wind change, the model predicts that (i) dispersal distance (+70%) and pelagic larval duration (+22%) will increase in response to the reduced temperature (–9%) experienced by early hatched larvae, (ii) larval recruitment at the nursery grounds will increase in some areas (36%) and decrease in others (-58%), and (iii) connectivity will show contrasting changes between areas. At the regional scale, our model predicts considerable changes in larval recruitment (+9%) and connectivity (retention -4% and seeding +37%) due to global change. All of these factors affect the distribution and productivity of sole and therefore the functioning of the demersal ecosystem and fisheries management. This article is protected by copyright. All rights reserved.

Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes—three-spined and nine-spined stickleback—differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes., The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.

Connectivity between spawning and nursery grounds influences the colonization, replenishment and resilience of populations of marine organisms. Connectivity rate, measured as the exchange of individuals between spawning and nursery grounds, is therefore a crucial determinant of stock size. However, connectivity of early-life stages is hard to explore due to sampling limitations and insufficient knowledge on potential larval sources. Here we present new insights into pre- and post-settlement dispersal of the common sole (Solea solea L.) at a spatial scale of 5–500 km in the Southern North Sea. Patterns at a scale of

© 2018, Springer Nature Switzerland AG. While otolith shape analysis can provide a valuable tool for discriminating between fish populations, factors which may influence otolith shape, such as the effect of size, directional asymmetry in growth, and local environmental conditions, are often unknown. Here, we analyzed differences in otolith shape across three size classes of age-0 common sole Solea solea L. from nursery grounds off the Belgian coast and in the Wadden Sea. Across size classes, form-factor decreased and roundness remained consistently high in both nursery grounds, while ellipticity increased in the Belgian nursery. Directional asymmetry between left and right otoliths measured by Fourier coefficients accounted for 0.96 and 7.2% of the variance when comparing otoliths overall, and for each size class, respectively. Within the Belgian nursery, results were consistent across sampling years and locations. In addition, otolith shape was marginally different between nursery grounds, but highly variable within nursery grounds. A small divergent group, which seems partly related to fish size, was noted at both spatial and temporal scales. Based on these results and before embarking on a study of population structure using otolith shape in age-0 common sole, we recommend testing for directional asymmetry and fish size effects across the entire region of interest. ispartof: HYDROBIOLOGIA vol:845 issue:1 pages:95-108 status: published

Metabolic impairments associated with obstructive sleep apnea syndrome (OSA) are linked to tissue hypoxia, however, the explanatory molecular and endocrine mechanisms remain unknown. Using gas-permeable cultureware, we studied the chronic effects of mild and severe hypoxia on free fatty acid (FFA) uptake, storage, and oxidation in L6 myotubes under 20, 4, or 1% O2. Additionally, the impact of metformin and the peroxisome proliferator-activated receptor (PPAR) β/δ agonist, called GW501516, were investigated. Exposure to mild and severe hypoxia reduced FFA uptake by 37 and 32%, respectively, while metformin treatment increased FFA uptake by 39% under mild hypoxia. GW501516 reduced FFA uptake under all conditions. Protein expressions of CD36 (cluster of differentiation 36) and SCL27A4 (solute carrier family 27 fatty acid transporter, member 4) were reduced by 17 and 23% under severe hypoxia. Gene expression of UCP2 (uncoupling protein 2) was reduced by severe hypoxia by 81%. Metformin increased CD36 protein levels by 28% under control conditions and SCL27A4 levels by 56% under mild hypoxia. Intracellular lipids were reduced by mild hypoxia by 18%, while in controls only, metformin administration further reduced intracellular lipids (20% O2) by 36%. Finally, palmitate oxidation was reduced by severe hypoxia, while metformin treatment reduced non-mitochondrial O2 consumption, palmitate oxidation, and proton leak at all O2 levels. Hypoxia directly reduced FFA uptake and intracellular lipids uptake in myotubes, at least partially, due to the reduction in CD36 transporters. Metformin, but not GW501516, can increase FFA uptake and SCL27A4 expression under mild hypoxia. Described effects might contribute to elevated plasma FFA levels and metabolic derangements in OSA.

Parasite spillback, the infection of a non-indigenous organism by a native parasite, is a highly important although understudied component of ecological invasion dynamics. Here, through the first analysis of the parasite fauna of lymnaeid gastropods of Lake Kariba (Zimbabwe). We illustrate how the creation of an artificial lake may lead to a cascade of biological invasions in which an invasive aquatic plant promotes the proliferation of invasive gastropods, which in turn alters the epidemiology of trematodiases of potential medical and veterinary importance. Using a new multiplex Rapid Diagnostic PCR assay, we assessed the prevalence of Fasciola sp. infections in the gastropod populations. Both gastropod hosts and trematode parasites were identified using DNA barcoding. We provide the first record of the invasive North-American gastropod Pseudosuccinea columella in Lake Kariba. This species was found at 14 out of 16 sampled sites and its abundance was strongly positively correlated with the abundance of the invasive South-American water hyacinth (Eichhornia crassipes). About 65% of the P. columella specimens analysed were infected with a hitherto unknown Fasciola species. Phylogenetic analyses indicate close affinity to Fasciola hepatica and F. gigantica, which cause fasciolosis, an important liver disease affecting both ruminants and humans. In addition, another non-native Lymnaeid species was found: a Radix sp. that clustered closely with a Vietnamese Radix species. Radix sp. hosted both amphistome and Fasciola trematodes. By linking an invasion cascade and parasite spillback, this study shows how both processes can act in combination to lead to potentially important epidemiological changes.

Antarctic specimens collected during various research expeditions are preserved in natural history collections around the world potentially offering a cornucopia of morphological and molecular data. Historical samples of marine species are, however, often preserved in formaldehyde which may render them useless for genetic analysis. We sampled stomachs and hindguts from 225 Trematomus specimens from the Natural History Museum London. These samples were initially collected between 20 and 100 years ago and fixed in either formaldehyde or ethanol. A 313 bp fragment of the cytochrome c oxidase subunit I (COI) was amplified and sequenced for prey item identification in the stomach and a 450 bp region of the 16S rRNA gene to investigate microbiome composition in the gut system. Both data sets were characterized by large dropout rates during extensive quality controls. Eventually, no unambiguous results regarding stomach content (COI) were retained, possibly due to degraded DNA, inefficient primers and contamination. In contrast, reliable microbiome composition data (16S rRNA) was obtained from 26 samples. These data showed a correlation in change of microbiome composition with fish size as well as year of the catch, indicating a microbiome shift throughout ontogeny and between samples from different decades. A comparison with contemporary samples indicated that the intestinal microbiome of Trematomus may have drastically changed within the last century. Further extensive studies are needed to confirm these patterns with higher sample numbers. Molecular analyses of museum stored fish can provide novel micro evolutionary insights that may benefit current efforts to prioritize conservation units in the Southern Ocean.

© 2018 Christiansen, Dettai, Heindler, Collins, Duhamel, Hautecoeur, Steinke, Volckaert and Van de Putte. Small mesopelagic fish are ubiquitous in the ocean, representing an important trophic link between zooplankton and tertiary consumers such as larger fish, marine mammals and birds. Lanternfishes (Myctophidae) are common worldwide as well as in the Southern Ocean. However, only 17 of the approximately 250 myctophid species occur exclusively in sub-Antarctic or Antarctic waters. It is unclear whether they colonized these latitudes once and diversified from there, or whether multiple colonization events took place in which multiple ancestral phenotypes entered the Southern Ocean at various times. Phylogeographic patterns have been investigated for individual myctophid species, but so far no study has compared species across the Southern Ocean. Here, we present a dataset with previously unpublished cytochrome c oxidase I (COI; n = 299) and rhodopsin (rh1; n = 87) gene sequences from specimens collected at various locations in the Southern Ocean. Our data extend the DNA barcode library of Antarctic mesopelagic fish substantially. Combined morphological and molecular taxonomy lead to confident species level identification in 271 out of 299 cases, providing a robust reference dataset for specimen identification, independently of incomplete morphological characters. This is highly topical in light of prospective ecological metabarcoding studies. Unambiguous sequences were subsequently combined with publicly available sequences of the global DNA barcode library yielding a dataset of over 1,000 individuals for phylogenetic and phylogeographic inference. Maximum likelihood trees were compared with results of recent studies and with the geographical origin of the samples. As expected for these markers, deep phylogenetic relationships remain partially unclear. However, COI offers unmatched sample and taxon coverage and our results at the subfamily to genus level concur to a large extent with other studies. Southern Ocean myctophids are from at least three distant subfamilies suggesting that colonization has occurred repeatedly. Overall, spatial divergence of myctophids is rare, potentially due to their enormous abundance and the homogenizing force of ocean currents. However, we recommend further investigation of the phylogenetic position of Symbolophorus boops and highlight potential (pseudo-)cryptic or unrecognized species in Gymnoscopelus bolini, Lampanyctus achirus, and the non-myctophid genus Bathylagus. ispartof: FRONTIERS IN ECOLOGY AND EVOLUTION vol:6 issue:SEP status: published

The lung is morphologically structured into a complex tree-like network with branched airways ending distally in a large number of alveoli for efficient oxygen exchange. At the cellular level, the adult lung consists of at least 40–60 different cell types which can be broadly classified into epithelial, endothelial, mesenchymal, and immune cells. Fibroblast growth factor 10 (Fgf10) located in the lung mesenchyme is essential to regulate epithelial proliferation and lineage commitment during embryonic development and post-natal life, and to drive epithelial regeneration after injury. The cells that express Fgf10 in the mesenchyme are progenitors for mesenchymal cell lineages during embryonic development. During adult lung homeostasis, Fgf10 is expressed in mesenchymal stromal niches, between cartilage rings in the upper conducting airways where basal cells normally reside, and in the lipofibroblasts adjacent to alveolar type 2 cells. Fgf10 protects and promotes lung epithelial regeneration after different types of lung injuries. An Fgf10-Hippo epithelial-mesenchymal crosstalk ensures maintenance of stemness and quiescence during homeostasis and basal stem cell (BSC) recruitment to further promote regeneration in response to injury. Fgf10 signaling is dysregulated in different human lung diseases including bronchopulmonary dysplasia (BPD), idiopathic pulmonary fibrosis (IPF), and chronic obstructive pulmonary disease (COPD), suggesting that dysregulation of the FGF10 pathway is critical to the pathogenesis of several human lung diseases.

Hybridization events between Schistosoma species (Digenea, Platyhelminthes) are reported with increasing frequency, largely due to improved access to molecular tools. Nevertheless, little is known about the distribution and frequency of hybrid schistosomes in nature. Screening for hybrids on a large scale is complicated by the need for nuclear and mitochondrial sequence information, precluding a ‘simple’ barcoding approach. Here we aimed to determine and understand the spatiotemporal distribution of Schistosoma haematobium × Schistosoma bovis hybrids in the Senegal River Basin. From ten villages, distributed over the four main water basins, we genotyped a total of 1236 schistosome larvae collected from human urine samples using a partial mitochondrial cox1 fragment; a subset of 268 parasites was also genotyped using ITS rDNA. Hybrid schistosomes were unevenly distributed, with substantially higher numbers in villages bordering Lac de Guiers than in villages from the Lampsar River and the Middle Valley of the Senegal River. The frequency of hybrids per village was not linked with the prevalence of urinary schistosomiasis in that village. However, we did find a significant positive association between the frequency of hybrids per village and the prevalence of Schistosoma mansoni. We discuss the potential consequences of adopting a barcoding approach when studying hybrids in nature.

Een belangrijk deel van een ecosysteem bestaat uit micro-organismen zoals bacteriën en schimmels of uit kleine ongewervelden. Deze organismen werken samen met een gastheersoort (symbiose) of er net tegen (parasitisme). Het geheel van micro-organismen in of op een soort, het microbioom, geniet de jongste jaren groeiende aandacht onder biologen. In dit artikel bekijken we hoe verstedelijking de toestand en relaties met parasieten en symbionten beïnvloedt. Het SPEEDY-project leverde tal van nieuwe inzichten over de relaties tussen soorten in verstedelijkte omgevingen.

The impact of escapees from aquaculture is of general concern for the sustainability of natural resources. Turbot Scophthalmus maximus is a marine flatfish of great commercial value whose land-based aquaculture started approx. 40 yr ago; hence, a low impact of escapees is expected on wild populations. However, enhancement of wild stocks using farmed turbot has been carried out along the Northeast Atlantic coasts in the last decades. Recently, a broad panel of single nucleotide polymorphism (SNP) markers (755 SNPs; 1 SNP Mb−1) has been used to evaluate the genetic structure of turbot throughout its distribution range, constituting the baseline to evaluate the impact of farmed fish in the wild. Two distinct origins were identified for farmed turbot (F_ORI1 and F_ORI2; FST = 0.049), which differentiated from wild populations after 5 generations of selection (average FST = 0.059), and consistent evidence of adaptation to domestication was de - tected. A notable proportion of fish of farmed ancestry was detected in the wild (15.5%), mainly in the North Sea, where restocking activities have taken place, determining genetic introgression in wild populations. Conversely, effects of land-based aquaculture appear negligible. A simulation exercise supported panels of 40 and 80 SNPs to identify fishes of F_ORI1 and F_ORI2 ancestry in the wild, respectively. Application to empirical data showed an assignment success (wild/farmed ancestry) of approx. 95% in comparison with the full SNP dataset. The SNP tools will be useful to monitor turbot of farmed ancestry in the wild, which might represent a risk, considering the lower fitness of farmed individuals The project was funded by the 7th Framework Programme for research (FP7) under ‘Knowledge-Based Bio-Economy — KBBE’, Theme 2: ‘Food, Agriculture and fisheries, and Biotechnologies’ Project identifier: FP7-KBBE-2012-6-singlestage Grant agreement no.: 311920 ‘The development of tools for tracing and evaluating the genetic impact of fish from aquaculture: AquaTrace’ and the Spanish Regional Government Xunta de Galicia GRC2014/010. Ciência sem Fronteiras/CAPES − Brazil supported the fellowship for the stay of F.D.P. at USC SI

In 2013 the red swamp crayfish (Procambarus clarkii) was introduced in Lake Yahuarcocha, a tropical, high altitude lake located in the Andes of northern Ecuador. Abundance of this alien invasive species has increased to such extent that it is disturbing the autochthonous aquatic ecosystem. Little is known about its distribution throughout Ecuador. Monitoring is therefore important to assess the current distribution and to control future spread. A molecular method based on environmental DNA (eDNA) was developed and used to assess the distribution of P. clarkii at 21 sites in Lake Yahuarcocha, and three sites each at Lake Caricocha and Lake San Pablo in the Ecuadorian highlands. The molecular detection of crayfish from water samples was compared to capture based distribution patterns obtained from traditional trapping. Results showed an eDNA detection accuracy of 86% in water samples, without false positives. The results indicate that this budget-friendly method is easy to use and can provide important information on the occurrence of alien invasive species in the tropics.

Background Demonstration of protection by a M2SR (M2 deficient Single Replication) monovalent H3N2 vaccine was assessed in a phase 2a clinical trial in which the challenge virus was substantially drifted from the vaccine. M2SR is an investigational, live virus vaccine containing hemagglutinin (HA) and neuraminidase (NA) selected from targeted Type A influenza strains. M2SR undergoes only a single round of infection in the respiratory epithelium but evokes an immune response profile similar to wild-type influenza virus and protects ferrets against both homologous and heterologous influenza variants. Methods A blinded, randomized, placebo-controlled human challenge study (EudraCT #: 2017-004971-30) was conducted with M2SR containing HA and NA from A/Brisbane/10/2007 (H3N2). 18–55-year-old subjects received 1 IN dose of saline or 108 TCID50 of vaccine. 4 weeks later, 99 subjects were challenged IN with 106 TCID50 H3N2 A/Belgium/4217/2015 (Figures 1 and 2). Results Adverse events (AE) were similar between placebo (N = 51) and M2SR recipients (N = 48) during the 28 days after immunization. After challenge with A/Belgium/4217/2015, 35% of M2SR recipients experienced influenza infection and illness, compared with 49% of placebo subjects (Figure 3). An 18% reduction in viral load was noted after challenge for M2SR subjects. Serum microneutralization response to vaccine was detected in 54% of M2SR subjects (vs. 0/51 placebo subjects), and among these subjects a 34% reduction in viral load and 51% reduction in symptom scores was noted after challenge vs placebo. Among the 29% of subjects with post-vaccine response to both vaccine and challenge strains, a 62% reduction in viral load and 56% reduction in symptom scores was noted after challenge with highly drifted H3N2 (Figure 4). Conclusion One dose of M2SR protected healthy adults against influenza infection and illness with a highly drifted challenge strain. This is believed to be the first study to demonstrate protection against challenge with an influenza strain substantially different from the vaccine and indicates potential for improved breadth of protection by M2SR compared with current vaccines. The mild vaccine AE profile supports clinical trials of additional dose levels and regimens to enhance drifted strain protection by M2SR. Disclosures All authors: No reported disclosures.

Partitioning phenotypic variance in genotypic and environmental variance may benefit from the population genomic assignment of genes putatively involved in adaptation. We analyzed a total of 256 markers (120 microsatellites and 136 Single Nucleotide Polymorphisms - SNPs), several of them associated to Quantitative Trait Loci (QTL) for growth and resistance to pathologies, with the aim to identify potential adaptive variation in turbot Scophthalmus maximus L. The study area in the Northeastern Atlantic Ocean, from Iberian Peninsula to the Baltic Sea, involves a gradual change in temperature and an abrupt change in salinity conditions. We detected 27 candidate loci putatively under selection. At least four of the five SNPs identified as outliers are located within genes coding for ribosomal proteins or directly related with the production of cellular proteins. One of the detected outliers, previously identified as part of a QTL for growth, is a microsatellite linked to a gene coding for a growth factor receptor. A similar set of outliers was detected when natural populations were compared with a sample subjected to strong artificial selection for growth along four generations. The observed association between FST outliers and growth-related QTL supports the hypothesis of changes in growth as an adaptation to differences in temperature and salinity conditions. However, further work is needed to confirm this hypothesis.

Non-indigenous species may have negative impacts on the native fauna in their competition for food and habitat, but they can also introduce non-indigenous parasite species, with sometimes devastating consequences. Co-introduction of parasites should therefore be carefully monitored, but this aspect is mostly overlooked. The round goby Neogobius melanostomus (Pallas, 1814) and the tubenose goby Proterorhinus semilunaris (Heckel, 1937), both known for their invasiveness, have recently been discovered in Belgium. Here, we morphologically and genetically document the co-introduction of the Ponto-Caspian Gyrodactylus proterorhini Ergens, 1967, originally described on tubenose goby in southern Slovakia. Because of their direct life cycle and extraordinary reproductive capacities, gyrodactylid monogenean parasites can readily invade new areas together with the host. Moreover, G. proterorhini has a wide host range and might therefore represent a threat to other gobiid fishes. The Gyrodactylus parasite found on the Belgian round goby population is probably acquired through secondary infection from local fish, as suggested by molecular phylogenetic analysis.

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method.

The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.

The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in “non-model” species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies The research leading to these results has received funding from the European Community's Seventh Framework Programme under agreement no. KBBE-311920 (AquaTrace). Samples used in this study were collected by the AquaTrace partners: Laboratory of Biodiversity and Evolutionary Genomics (LBEG), University of Leuven (European sea bass); Departmento de Genética, Universidad de Santiago de Compostela (turbot); Sabina De Innocentiis, ISPRA (gilthead sea bream). JH benefited from a PhD scholarship from Flanders Innovation & Entrepreneurship (IWT). GK was funded by a PhD scholarship of Onassis Foundation SI

Summary: Idiopathic pulmonary fibrosis is a common form of interstitial lung disease resulting in alveolar remodeling and progressive loss of pulmonary function because of chronic alveolar injury and failure to regenerate the respiratory epithelium. Histologically, fibrotic lesions and honeycomb structures expressing atypical proximal airway epithelial markers replace alveolar structures, the latter normally lined by alveolar type 1 (AT1) and AT2 cells. Bronchial epithelial stem cells (BESCs) can give rise to AT2 and AT1 cells or honeycomb cysts following bleomycin-mediated lung injury. However, little is known about what controls this binary decision or whether this decision can be reversed. Here we report that inactivation of Fgfr2b in BESCs impairs their contribution to both alveolar epithelial regeneration and honeycomb cysts after bleomycin injury. By contrast overexpression of Fgf10 in BESCs enhances fibrosis resolution by favoring the more desirable outcome of alveolar epithelial regeneration over the development of pathologic honeycomb cysts. : FGF10-FGFR2B signaling in bronchial epithelial stem cells is critical to drive both alveolar epithelial regeneration and the development of honeycomb cysts after bleomycin injury. Overexpression of Fgf10 in bronchial epithelial stem cells enhances fibrosis resolution by favoring the more desirable outcome of alveolar epithelial regeneration over the development of pathologic honeycomb cysts. Keywords: lung stem cells, lung regeneration, lung fibrosis, Fgf signaling

SUMMARYHybrid parasites may have an increased transmission potential and higher virulence compared to their parental species. Consequently, hybrid detection is critical for disease control. Previous crossing experiments showed that hybrid schistosome eggs have distinct morphotypes. We therefore compared the performance of egg morphology with molecular markers with regard to detecting hybridization in schistosomes. We studied the morphology of 303 terminal-spined eggs, originating from 19 individuals inhabiting a hybrid zone with natural crosses between the human parasite Schistosoma haematobium and the livestock parasite Schistosoma bovis in Senegal. The egg sizes showed a high variability and ranged between 92·4 and 176·4 µm in length and between 35·7 and 93·0 µm in width. No distinct morphotypes were found and all eggs resembled, to varying extent, the typical S. haematobium egg type. However, molecular analyses on the same eggs clearly showed the presence of two distinct partial mitochondrial cox1 profiles, namely S. bovis and S. haematobium, and only a single nuclear ITS rDNA profile (S. haematobium). Therefore, in these particular crosses, egg morphology appears not a good indicator of hybrid ancestry. We conclude by discussing strengths and limitations of molecular methods to detect hybrids in the context of high-throughput screening of field samples.

Here we assess the role of parasite genetic variation in host disease phenotype in human schistosomiasis by implementing concepts and techniques from environmental association analysis in evolutionary epidemiology. Schistosomiasis is a tropical disease that affects more than 200 million people worldwide and is caused by parasitic flatworms belonging to the genus Schistosoma. While the role of host genetics has been extensively studied and demonstrated, nothing is yet known on the contribution of parasite genetic variation to host disease phenotype in human schistosomiasis. In this study microsatellite genotypes of 1561 Schistosoma mansoni larvae collected from 44 human hosts in Senegal were linked to host characteristics such as age, gender, infection intensity, liver and bladder morbidity by means of multivariate regression methods (on each parasite locus separately). This revealed a highly significant association between allelic variation at the parasite locus L46951 and host infection intensity and bladder morbidity. Locus L46951 is located in the 3' untranslated region of the cGMP-dependent protein kinase gene that is expressed in reproductive organs of adult schistosome worms and appears to be linked to egg production. This putative link between parasite genetic variation and schistosomiasis disease phenotype sets the stage for further functional research.

Adaptive radiation occurs when species diversify rapidly to occupy an array of ecological niches. Since opportunities for parasite infection and transmission may greatly vary among these niches, adaptive radiation is expected to be associated with a turnover of the parasite community. As major agents of natural and sexual selection, parasites may play a central role in host diversification. The study of parasite turnover may thus be of general relevance and could significantly improve our understanding of adaptive radiation. In the present study, we examined the parasite faunas of eleven species belonging to the tribe Tropheini, one of several adaptive radiations of cichlid fishes in Lake Tanganyika. The most parsimonious ancestral foraging strategy among the Tropheini is relatively unselective substrate browsing of aufwuchs. Several lineages evolved more specialized foraging strategies, such as selective combing of microscopic diatoms or picking of macro-invertebrates. We found that representatives of these specialized lineages bear reduced infection with food-web transmitted acanthocephalan helminths, but not with parasites with a direct life cycle. Possibly, the evolution of selective foraging strategies entailed reduced ingestion of intermediate invertebrate hosts of acanthocephalans. We conclude that some species belonging to the Tropheini virtually escape acanthocephalan infection as a by-product effect of trophic specialization. We thank J. Bamps and S. Camey for help with fieldwork and parasitological dissections. Furthermore, we thank L. Makasa, D. Sinyinza, G. Sheltons, C. Sturmbauer, W. Salzburger, W. Mubita and the staff of the Lake Tanganyika Research Station in Mpulungu (Zambia) for help with fieldwork and logistics, S. Koblmuller for sharing AFLP data of the host species, and C. Haag and two anonymous reviewers for valuable comments on the manuscript. Research was supported by the Research Foundation - Flanders (FWO grant project G.0553.10), the Flemish Interuniversity Council (VLIR) and the KU Leuven Research Fund project PF/2010/07. PIH was partially supported by the Janggen-Pohn-Stiftung (St. Gallen, Switzerland). MPMV is partly supported by the Czech Science Foundation, Project no. P505/12/G112 (European Centre of Ichthyoparasitology (ECIP) - Centre of excellence). AFG is a PhD fellow of the Research Foundation - Flanders. JAMR received a EU Marie Sklodowska-Curie Fellowship (IEF 300256).