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Data from: Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

Ecologists increasingly rely on molecular delimitation methods (MMs) to identify species boundaries, thereby potentially increasing the number of putative species because of the presence of morphologically cryptic species. It has been argued that cryptic species could challenge our understanding of what determine large-scale biodiversity patterns which have traditionally been documented from morphology alone. Here, we used morphology and three MMs to derive four different sets of putative species among the European groundwater crustaceans. Then, we used regression models to compare the relative importance of spatial heterogeneity, productivity and historical climates, in shaping species richness and range size patterns across sets of putative species. We tested three predictions. First, MMs would yield many more putative species than morphology because groundwater is a constraining environment allowing little morphological changes. Second, for species richness, MMs would increase the importance of spatial heterogeneity because cryptic species are more likely along physical barriers separating ecologically similar regions than along resource gradients promoting ecologically-based divergent selection. Third, for range size, MMs would increase the importance of historical climates because of reduced and asymmetrical fragmentation of large morphological species ranges at northern latitudes. MMs yielded twice more putative species than morphology and decreased by 10-fold the average species range size. Yet, MMs strengthened the mid-latitude ridge of high species richness and the Rapoport effect of increasing range size at higher latitudes. Species richness predictors did not vary between morphology and MMs but the latter increased the proportion of variance in range size explained by historical climates. These findings demonstrate that our knowledge of groundwater biodiversity determinants is robust to overlooked cryptic species because the latter are homogeneously distributed along environmental gradients. Yet, our findings call for incorporating multiple species delimitation methods into the analysis of large-scale biodiversity patterns across a range of taxa and ecosystems.

opencc-zeroFeb 2020View details →

The role of environmental vs. biotic filtering in the structure of European ant communities: a matter of trait type and spatial scale

<p>Functional trait-based approaches are increasingly used for studying the processes underlying community assembly. The relative influence of different assembly rules might depend on the spatial scale of analysis, the environmental context and the type of functional traits considered. By using a functional trait-based approach, we aim to disentangle the relative role of environmental filtering and interspecific competition on the structure of European ant communities according to the spatial scale and the type of trait considered. We used a large database on ant species composition that encompasses 361 ant communities distributed across the five biogeographic regions of Europe; these communities were composed of 155 ant species, which were characterized by 6 functional traits. We then analysed the relationship between functional divergence and co-occurrence between species pairs across different spatial scales (European, biogeographic region and local) and considering different types of traits (ecological tolerance and niche traits). Three different patterns emerged: negative, positive and non-significant regression coefficients suggest that environmental filtering, competition and neutrality are at work, respectively. We found that environmental filtering is important for structuring European ant communities at large spatial scales, particularly at the scale of Europe and most biogeographic regions. Competition could play a certain role at intermediate spatial scales where temperatures are more favourable for ant productivity (i.e. the Mediterranean region), while neutrality might be especially relevant in spatially discontinuous regions (i.e. the Alpine region). We found that no ecological mechanism (environmental filtering or competition) prevails at the local scale. The type of trait is especially important when looking for different assembly rules, and multi-trait grouping works well for traits associated with environmental responses (tolerance traits), but not for traits related to resource exploitation (niche traits). The spatial scale of analysis, the environmental context and the chosen traits merit special attention in trait-based analyses of community assembly mechanisms.</p>

Data from: Low rates of hybridization between European wildcats and domestic cats in a human-dominated landscape

Hybridization between wild species and their domestic congeners is considered a major concern for species conservation. Genetic integrity of the European wildcat, for instance, is of interest as the species is outnumbered by domestic cats by several orders of magnitude throughout its range. We genotyped 1071 individual wildcat samples obtained from hair traps and roadkills collected across the highly fragmented forests of western central Europe, in Germany and Luxembourg, to assess domestic cat introgression in wildcats in human-dominated landscapes. Analyses using a panel of 75 autosomal SNPs suggested a low hybridization rate, with 3.5 % of wildcat individuals being categorized as F1, F2 or backcrosses to either parental taxon. We report that SNP data appeared to be more consistent than our set of 14 microsatellite markers and that SNPs showed higher accuracy to detect hybrids and their class in simulation analyses and were less affected by underlying population structure. Our results strongly suggest that very high hybridization rates previously reported for central Europe may be partly due to inadequate choice of markers and/or sampling design. Our example documents that a carefully selected SNP panel for hybrid detection may be used as an alternative to commonly applied microsatellite markers, including studies relying on non-invasively collected samples. In addition, our finding of overall low hybridization rates in central European wildcats provides an example of successful wildlife coexistence in human-dominated, fragmented landscapes.

opencc-zeroDec 2013View details →

Data from: Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer

Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective-neutral loci and to transfer of fitness-related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex-linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex-specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after LGM. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8–10.0 ka BP). Initially introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human-mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression.

Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic

Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site associated DNA sequencing (RAD-seq), microsatellite loci, and COI mtDNA sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2), and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.

opencc-zeroNov 2019View details →

Population history explains the performance of an annual herb - within and beyond its European species range

1. The centre-periphery hypothesis (CPH) predicts a decrease in population performance from the centre of the species range towards the edge, hindering further species expansion. To overcome ecological limitation, local adaptation of peripheral populations is assumed necessary to extend niche space and thus to potentially facilitate species' range expansion. However, adaptive changes do not necessarily correspond to current ecological marginality. Instead, population history may provide a fuller context for understanding patterns of local adaptation within the species range. Here, we test whether local adaptation to current conditions or population history explains current species distribution in an annual heterocarpic species, Atriplex tatarica, in Europe. 2. The ecological marginality and population history were estimated using species distribution modelling (SDM) and 13 microsatellite markers. To test for local adaptation, we evaluated the population performance of both currently central and currently peripheral populations by examining germination and growth traits under three temperature regimes which correspond to climates within, and also beyond, the species' current range. In addition, we compared Bayesian estimates of population differentiation in neutral genetic markers and quantitative traits to test whether phenotypic differentiation evolved by local adaptation and/or by genetic drift. 3. We found population performances were not higher under temperature regimes corresponding to their own habitats, suggesting that patterns of local adaptation in A. tatarica do not correspond to current centre-periphery gradient. In contrast, population genetic structure indicated a strong influence of population history on variation in the germination phenotype. Species distribution modelling suggested a more cold-tolerant genetic lineage was located at the species' range periphery during the last glacial period. Meanwhile, a less cold-tolerant lineage occurred in more suitable areas of the Balkan Peninsula and southeastern Europe. Thus, the strong adaptive divergence of evolutionary lineages may reflect a past spatial arrangement of populations, suggesting evolutionary processes were ongoing before the species expansion in the Holocene. 4. Synthesis. There is continuing debate concerning the speed of trait evolution during range expansion with climate change. Our results indicate that even though organisms expand rapidly, the accompanying evolutionary changes in phenotype may be much slower.

opencc-zeroAug 2019View details →

Data from: Seasonal shifts and complementary use of pollen sources by two bee, a lacewing and a ladybeetle species in European agricultural landscapes

1. Continuous availability of food resources, such as pollen, is vital for many insects that provide pollination and pest control services to agriculture. However, there is a lack of knowledge about the shared or complementary use of floral resources by such species, which hampers more effective landscape management to simultaneously promote them in agroecosystems. 2. Here, we simultaneously quantified pollen use by a bumblebee (Bombus terrestris) and a mason bee (Osmia bicornis), two bee species recognized as important crop pollinators, as well as a lacewing (Chrysoperla carnea) and a ladybeetle species (Harmonia axyridis), both common predators of crop aphids, throughout the season in 23 agricultural landscapes in Germany and Switzerland. 3. Pollen diets were more diverse and similar among C. carnea and H. axyridis compared to the two bee species, but all four species shared key pollen types early in the season such as Acer, Quercus, Salix and Prunus. All species exhibited a pronounced shift in pollen sources from primarily woody plants (mainly trees) in spring to primarily herbaceous plants in summer. The majority of pollen (overall ≥64%) came from non-agricultural plants even in crop-dominated landscapes. 4. Synthesis and applications. Our results highlight the importance of trees as pollen sources for many insect species, particularly early in the season. Our findings support incentives that promote heterogeneous agricultural landscapes including both woody and herbaceous semi-natural habitats, ensuring phenological complementarity of floral resources for insect species that can provide pollination and pest control services to agriculture. The identified key plant species can help to design and optimize agri-environment schemes to promote these functionally important insects.

Data from: Fishing pressure impacts the abundance gradient of European lobsters across the borders of a newly established marine protected area

Marine protected areas (MPAs) are considered as viable fisheries management tools due to their potential benefits of adult spillover and recruitment subsidy to nearby fisheries. However, before-after-control-impact (BACI) studies that explore the biological and fishery effects of MPAs to surrounding fisheries are scarce. We present results from a fine-scale spatial gradient study conducted before and after the implementation of a 5km2 lobster MPA in southern Norway. A significant non-linear response in lobster abundance, estimated as catch-per-unit-effort (CPUE) from experimental fishing, was detected within two years of protection. After 4 years, CPUE values inside the MPA had increased by a magnitude of 2.6 compared to before-protection values. CPUE showed a significant non-linear decline from the center of the MPA, with a depression immediately outside the border and a plateau in fished areas. Overall fishing pressure almost doubled over the course of the study. The highest increase in fishing pressure (by a magnitude of 3) was recorded within 1 km of the MPA border, providing a plausible cause for the depression in CPUE. Taken together, these results demonstrate the need to regulate fishing pressure in surrounding areas when MPAs are implemented as fishery management tools.

opencc-zeroDec 2015View details →

Data from: Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.

opencc-zeroDec 2018View details →

Data from: Environment and evolutionary history shape phylogenetic turnover in European tetrapods

Phylogenetic turnover quantifies the evolutionary distance among species assemblages and is central to understanding the main drivers shaping biodiversity. It is affected both by geographic and environmental distance between sites. Therefore, analyzing phylogenetic turnover in environmental space requires removing the effect of geographic distance. Here, we apply a novel approach by deciphering phylogenetic turnover of European tetrapods in environmental space after removing geographic land distance effects. We demonstrate that phylogenetic turnover is strongly structured in environmental space, particularly in ectothermic tetrapods, and is well explained by macroecological characteristics such as niche size, species richness and relative phylogenetic diversity. In ectotherms, rather recent evolutionary processes were important in structuring phylogenetic turnover along environmental gradients. In contrast, early evolutionary processes had already shaped the current structure of phylogenetic turnover in endotherms. Our approach enables the disentangling of the idiosyncrasies of evolutionary processes such as the degree of niche conservatism and diversification rates in structuring biodiversity.

opencc-zeroDec 2018View details →

Data from: Love them all: mothers provide care to foreign eggs in the European earwig Forficula auricularia

The rejection of foreign individuals is considered a central parameter in the evolution of social life. Within family units, parents are typically thought to reject foreign offspring to ensure that their investment into care is directed towards their own descendants. Whereas selection for such kin bias is expected to be high when parental care is extended and involves numerous and energetically costly behaviours, it can be reduced when the acceptance of foreigners provide subsequent benefits to offspring and when alternative parental strategies limit the risk of clutch parasitism. In this study, we investigated the outcome of these conflicting selection pressures in the European earwig. Our results overall demonstrate that mothers do not eliminate foreign eggs, provide the same level of care to both foreign and own eggs (egg grooming, egg defense and maternal return) and pay the same costs of care in terms of weight loss and immunity when tending each type of eggs. We also show that foreign and own eggs exhibit similar development time, hatching success and lead to comparable juvenile quality. Interestingly, our results reveal that tending eggs (of any origin) reduces mothers' weight loss during this long period, possibly due to egg cannibalism. Hence, these findings emphasize the difficulty to predict the occurrence of kin bias, and stress the need to broaden our knowledge on the net benefits of egg rejection for parents to better understand the general importance of kin bias in the evolution of pre-hatching parental care.

Data from: Study on the foraging behaviour of the European nightjar Caprimulgus europaeus reveals the need for a change in conservation strategy in Belgium

Effective nature conservation requires coherent actions based on the best available evidence concerning protected species. Recent studies have suggested that European nightjars Caprimulgus europaeus forage outside their recognized breeding habitats, yet, for Flanders (northern Belgium) information on nightjar foraging behaviour and key foraging habitats is lacking. To assess whether the foraging ecology of nightjars in Flanders is similar to that observed in other parts of Europe, we studied the crepuscular behaviour of this species in Bosland (northeastern Flanders) during a five-year radio telemetry study. Tracking of 48 individuals within a coniferous forest was standardized and home ranges were calculated using a kernel density estimator (fixed kernel). Habitat use was investigated by comparing kernel placement to available habitat. Average maximal foraging distance was 2603 ± 1094 m and home ranges extended up to 691 ha. We identified the key foraging habitats to be extensively-cultivated grasslands and recreational areas, areas that were previously assumed unsuitable for Belgian nightjars. Our results indicate the importance of foraging sites outside the breeding territory, confirming the findings of previous studies performed elsewhere in Europe. Incorporating our findings into future conservation plans could, therefore, lead to improved efficiency of EU conservation measures, designed for the protection of this bird species in Flanders.

Data from: Tree-to-tree competition in mixed European beech-Scots pine forests has different impacts on growth and water-use efficiency depending on site conditions

1. Mixed conifer-hardwood forests can be more productive than pure forests and they are increasingly considered as ecosystems that could provide adaptation strategies in the face of global change. However, the combined effects of tree-to-tree competition, rising atmospheric CO2 concentrations and climate on such mixtures remain poorly characterized and understood. 2. To fill this research gap, we reconstructed 34-year series (1980-2013) of growth (basal area increment, BAI) and intrinsic water-use efficiency (iWUE) of Scots pine (Pinus sylvestris L.) – European beech (Fagus sylvatica L.) mixed stands at two climatically contrasting sites located in the southwestern Pyrenees. We also gathered data on tree-to-tree competition and climate variables in order to test the hypotheses that (i) radial growth will be greater when inter-specific competition exceeds intra-specific competition, i.e. when species complementarity occurs, and (ii) enhanced iWUE could be linked to improved stem radial growth. 3. Growth of both species was reduced when intra-specific competition increased. Species complementarity was linked to improved growth of Scots pine at the continental site, whilst competition overrode any complementarity advantage at the drought-prone Mediterranean site. Beech growth did not show any significant response to pine admixture likely due to shade tolerance and the highly competitive nature of this species. Increasing inter-specific competition drove recent iWUE changes, which increased in Scots pine but decreased in European beech. The iWUE enhancement did not involve any growth improvement in Scots pine. However, the positive BAI-iWUE relationship found for beech suggests an enhanced beech growth in drought-prone sites due to improved water use. 4. Synthesis. Complementarity may enhance growth in mixed forests. However, water scarcity can constrict light-related complementarity for shade intolerant species (Scots pine) in drought-prone sites. BAI-iWUE relationships were negative for Scots pine and positive for European beech. These contrasting behaviours have got implications for coping with the expected increasing drought events in Scots pine-European beech mixtures located near the ecological limit of the two species. Complementarity effects between tree species should be considered to avoid overestimating the degree of future carbon uptake by mixed conifer-broadleaf forests.

Data from: Gene flow in the European coal tit, Periparus ater (Aves: Passeriformes): low among Mediterranean populations but high in a continental contact zone

Extant phylogeographic patterns of Palearctic terrestrial vertebrates are generally believed to have originated from glacial range fragmentation. Post-Pleistocene range expansions have led to the formation of secondary contact zones among genetically distinct taxa. For coal tits (Periparus ater), such a contact zone has been localized in Germany. In this study, we quantified gene flow between Fennoscandian and southern European coal tits using a set of 13 microsatellite loci. STRUCTURE analysis revealed four genetic clusters two of these on Mediterranean islands. German populations were genetically admixed but introgression of southern alleles was evident for Fennoscandian populations. In the South, we found negligible introgression of northern alleles (and haplotypes) but slight admixture of two southern genetic clusters in the Pyrenees and on the Balkan Peninsulae and near complete sorting of these two allelic lineages on the islands of Corsica and Sardinia. Genetic distinctiveness of the Mediterranean island populations reflects general patterns of endemism in the Corso-Sardinian fauna and the Cypriot fauna. Wide-range gene flow in Central Europe suggests a broad zone of intergradation between subspecies of the coal tit rather than a narrow contact zone. This is in accordance with low morphological and bioacoustic differentiation of European coal tit populations.

opencc-zeroDec 2014View details →

Data from: Mapping wood production in European forests

Wood production is an important forest use, impacting a range of other ecosystem services. However, information on the spatial patterns in wood production is limited and often available only for larger administrative units. In this study, we developed high-resolution wood production maps for European forests. We collected wood production statistics for 29 European countries from 2000 to 2010, as well as comprehensive sets of biophysical and socioeconomic location factors. We used regression analyses to produce maps indicating the harvest likelihood on a 1 × 1 km2 grid. These likelihood maps were validated using national forest inventory plot data. We then disaggregated wood production statistics from larger administrative units to the grid level using the harvest likelihood as weights. We verified the resulting wood production maps by correlating predicted and observed wood production at the level of smaller administrative units not used for generating the wood production maps. We conclude that (i) productivity, tree species composition and terrain ruggedness are the most important location factors that determine the spatial patterns of wood production at the pan-European scale and that (ii) incorporating these location factors substantially improves the results of disaggregating wood production statistics compared to a disaggregation based on forest cover only. Our wood production maps give insight into forest ecosystem service provisioning and can be used to improve the assessment of potentials and costs of woody biomass supply.

opencc-zeroJul 2019View details →

Data from: Repeated jumps from Northwest Africa to the European continent: the case of peripheral populations of an annual plant

Peripheral populations (i.e., those occurring on the edge of a species' distribution range) can have different origins and genetic characteristics, and they may be critical for conservation of genetic diversity. We investigated European peripheral populations of Scrophularia arguta, a widespread, annual plant distributed from Arabia to Northwest Africa and Macaronesia. Only two small disjunct population groups of this species occur in Europe, specifically in West‐Central and Southeast Iberia. To disclose the origin of these populations and determine their importance for conservation of S. arguta genetic diversity, we analysed DNA sequences from two nuclear and two plastid regions and AFLP markers in populations sampled mainly across the western distribution range of the species, and modelled the species distribution under present and late Quaternary conditions. The analyses revealed the presence of three distinct lineages of S. arguta in Europe, as a result of multiple colonisation waves at different times in the Quaternary. Two of these lineages, occurring in Southeast Iberia, are the result of more or less recent dispersal from Northwest Africa. In contrast, West‐Central Iberian populations are strongly differentiated from the remaining range of S. arguta, and can be considered as peripheral relict populations. Our study is the first to demonstrate the occurrence of at least three colonisations of the European continent from Africa by a native plant species. The diverse histories and genetic makeup of resulting populations confirm the importance of peripheral populations, and particularly of ancient relict populations, for conservation of global genetic diversity in widespread species.

Data from: Altered breeding biology of the European blackbird under artificial light at night

Artificial light at night (LAN) has become a stressor of global extent. Previous work has highlighted the high potential of LAN to interfere with annual and diel rhythms of seasonal organisms as well as to affect interactions at the community level. However, our understanding how LAN induced alterations of activity and breeding cycles affect the reproductive outcome and fitness of the birds is still limited. Here, we focus on the effects of night time illumination on the breeding biology of urban European blackbirds (Turdus merula). Our results indicate that blackbirds prefer illuminated nest sites and advance their date of clutch initiation by 6 days per 1 lux of night time illumination. Furthermore, daily nest survival rates increased with increasing LAN although this effect was most pronounced for the transition from dark to slightly illuminated sites. We suggest that blackbirds breeding under low artificial night light conditions benefit from the LAN-avoidance of their major predators (nocturnal) whereas predominant predators of blackbirds nesting in the city centre are diurnal and are, thus, not affected by LAN. Hence, it seems likely that both direct effects of LAN on the timing of reproduction as well as indirect effects on interspecific interactions might contribute to the observed changes in the breeding biology of European blackbirds.This study emphasizes the diverse ecological effects of the night time illumination which are – in its complexity – still poorly understood.

Data from: Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar)

Understanding the genomic basis of host-parasite adaptation is important for predicting the long-term viability of species and developing successful management practices. However, in wild populations, identifying specific signatures of parasite-driven selection often presents a challenge, as it is difficult to unravel the molecular signatures of selection driven by different, but correlated, environmental factors. Furthermore, separating parasite-mediated selection from similar signatures due to genetic drift and population history can also be difficult. Populations of Atlantic salmon (Salmo salar L.) from northern Europe have pronounced differences in their reactions to the parasitic flatworm Gyrodactylus salaris Malmberg 1957 and are therefore a good model to search for specific genomic regions underlying inter-population differences in pathogen response. We used a dense Atlantic salmon SNP array, along with extensive sampling of 43 salmon populations representing the two G. salaris response extremes (extreme susceptibility vs resistant), to screen the salmon genome for signatures of directional selection while attempting to separate the parasite effect from other factors. After combining the results from two independent genome scan analyses, 57 candidate genes potentially under positive selection were identified, out of which 50 were functionally annotated. This candidate gene set was shown to be functionally enriched for lymph node development, focal adhesion genes and anti-viral response, which suggests that the regulation of both innate and acquired immunity might be an important mechanism for salmon response to G. salaris. Overall, our results offer insights into the apparently complex genetic basis of pathogen susceptibility in salmon and highlight methodological challenges for separating the effects of various environmental factors

opencc-zeroJun 2019View details →

Data from: Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): new genomic tools for breeding programs and management of natural resources

The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non-native species and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980's and showed some degree of innate resistance (long-term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis, and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.