Spatial and seasonal variation in reproductive indices of the clupeids Limnothrissa miodon and Stolothrissa tanganicae in the Congolese waters of northern Lake Tanganyika

Knowledge on the reproductive biology of the endemic clupeids Limnothrissa miodon and Stolothrissa tanganicae, two main target species of the pelagic fisheries of Lake Tanganyika, is constrained by fragmented monitoring activities. Here, we investigate the nursing areas of L. miodon, the timing of reproductive activities of littoral and pelagic L. miodon, and the timing of reproductive activities of pelagic S. tanganicae in the Congolese waters of the northern end of Lake Tanganyika (Bujumbura sub-basin). Nursing areas were determined year-round (2009-2010) based on the presence of clupeid larvae at two sandy and two stony beaches. The gonadosomatic index (GSI) and the proportion of fish having ripe gonads were used to study variation in reproductive indices in space (littoral vs. pelagic zones) during one year (2013-2014), as well as in time (dry vs. rainy season) during three years (2013-2016). Larvae of L. miodon were more frequently encountered on sandy than on stony beaches. Mature L. miodon females were more abundant in the littoral than in the pelagic zone, while the proportion of mature males in both habitats was similar. Irregular, low amplitude peaks could be distinguished in the GSI and proportion of mature males and females, but averages only differed between the dry and the rainy season in males. In contrast, GSI and proportions of mature males and females in S. tanganicae were higher in the dry season than in the rainy season. The reproductive effort of males and females of S. tanganicae and littoral L. miodon, but not pelagic L. miodon, was strongly synchronized. Interestingly, reproductive investment was also synchronised between pelagic male L. miodon, and pelagic S. tanganicae. Our time series strongly supports the view that L. miodon reproduces year-round in the littoral zone, while reproduction in S. tanganicae is seasonal. For fisheries management, we recommend year-round protection of sandy beaches, which are the main breeding grounds for L. miodon

К вопросу о табулировании функций распределения отказов

Проведена перепараметризация основных строго вероятностных функций распределения отказов: экспоненциального распределения, логарифмически нормального распределения и распределения Вейбулла. Разработаны таблицы функций распределения отказов и примеры их использования для решения некоторых задач по надежности.Проведено перепараметризацію основних строго ймовірнісних функцій розподілів відмов: експоненційного розподілу, логарифмічно нормального розподілу, розподілу Вейбулла. Розроблено таблиці функцій розподілів відмов та приклади їх використання для рішення деяких задач з надійності.The reparametrization of the basic strictly probabilistic functions of refusals distribution: exponential distributions, logarithmically normal distribution and distribution Weibull are carried out. Tables of refusals distribution functions and examples of their use for the decision of some tasks on reliability are developed

Computational identification of miRNAs, their targets and functions in three-spined stickleback (Gasterosteus aculeatus)

An intriguing question in biology is how the evolution of gene regulation is shaped by natural selection in natural populations. Among the many known regulatory mechanisms, regulation of gene expression by microRNAs (miRNAs) is of critical importance. However, our understanding of their evolution in natural populations is limited. Studying the role of miRNAs in three-spined stickleback, an important natural model for speciation research, may provide new insights into adaptive polymorphisms. However, lack of annotation of miRNA genes in its genome is a bottleneck. To fill this research gap, we used the genome of three-spined stickleback to predict miRNAs and their targets. We predicted 1486 mature miRNAs using the homology-based miRNA prediction approach. We then performed functional annotation and enrichment analysis of these targets, which identified over-represented motifs. Further, a database resource (GAmiRdb) has been developed for dynamically searching miRNAs and their targets exclusively in three-spined stickleback. Finally, the database was used in two case studies focusing on freshwater adaptation in natural populations. In the first study, we found 44 genomic regions overlapping with predicted miRNA targets. In the second study, we identified two SNPs altering the MRE seed site of sperm-specific glyceraldehyde-3-phosphate gene. These findings highlight the importance of the GAmiRdb knowledge base in understanding adaptive evolution

Genetically based differences in nest characteristics between lake, inlet, and hybrid threespine stickleback from the Misty system, British Columbia, Canada

Hypotheses: Adaptation to different environments can drive the evolution of mating isolation and thereby contribute to ecological speciation. Adaptive divergence in nest characteristics, which could be one avenue to mating isolation, has received little attention. For it to be important, populations adapted to different environments should show genetic differences in nest characteristics.status: publishe

Differential modes of MHC class IIB gene evolution in cichlid fishes

Cichlid fishes are emblematic models for the study of adaptive radiation, driven by natural and sexual selection. Parasite mediated selection is an important component in these processes, and the evolution of their immune system therefore merits special attention. In this study, light is shed on the phylogeny of the b family of cichlid major histocompatibility complex (MHC) class IIB genes. Full-length coding sequences were used to reconstruct phylogenies using criteria of maximum parsimony, maximum likelihood and Bayesian inference. All analyses suggest monophyly of the b family of cichlid MHC class IIB genes, although sequences of the cichlid sister taxa are currently not available. Two evolutionary lineages of these genes, respectively encompassing the recently defined genomic regions DBB-DEB-DFB and DCB-DDB, show highly contrasting levels of differentiation. To explore putative causes for these differences, exon 2 sequences were screened for variation in recombination rate and strength of selection. The more diversified lineage of cichlid MHC class IIB b genes was found to have higher levels of both recombination and selection. This is consistent with the observation in other taxa that recombination facilitates the horizontal spread of positively selected sites across MHC loci and hence contributes to fast sequence evolution. In contrast, the lineage that showed low diversification might either be under stabilizing selection or is evolutionary constrained by its low recombination rate. We speculate whether this lineage might include MHC genes with non-classical functions

Signatures of selection in the three-spined stickleback along a small-scale brackish water - freshwater transition zone

Local adaptation is often obvious when gene flow is impeded, such as observed at large spatial scales and across strong ecological contrasts. However, it becomes less certain at small scales such as between adjacent populations or across weak ecological contrasts, when gene flow is strong. While studies on genomic adaptation tend to focus on the former, less is known about the genomic targets of natural selection in the latter situation. In this study, we investigate genomic adaptation in populations of the three-spined stickleback Gasterosteus aculeatus L. across a small-scale ecological transition with salinities ranging from brackish to fresh. Adaptation to salinity has been repeatedly demonstrated in this species. A genome scan based on 87 microsatellite markers revealed only few signatures of selection, likely owing to the constraints that homogenizing gene flow puts on adaptive divergence. However, the detected loci appear repeatedly as targets of selection in similar studies of genomic adaptation in the three-spined stickleback. We conclude that the signature of genomic selection in the face of strong gene flow is weak, yet detectable. We argue that the range of studies of genomic divergence should be extended to include more systems characterized by limited geographical and ecological isolation, which is often a realistic setting in nature.status: publishe

Testing for local adaptation in the Gasterosteus-Gyrodactylus host-parasite system

Background: Parasites are often assumed to be locally adapted to their hosts, while a growing body of literature shows this is not a fixed rule. We used the threespine stickleback (Gasterosteus aculeatus) and its host-specific parasitic flatworm Gyrodactylus gasterostei of the Belgian lowland-upland system to test for local adaptation and assess whether findings are consistent over different life stages. Question: Is the Gasterosteus-Gyrodactylus host-parasite model system an example of local adaptation? Hypothesis: Parasites have higher infection success on sympatric than on allopatric host populations. Methods: F1 laboratory-bred stickleback originating from a lowland and upland population were infected with parasites of lowland and upland origin. We monitored parasite numbers per individual for 6 weeks and for two life stages and calculated the effect size of local adaptation. Results: Infection success of parasites was not higher on sympatric than on allopatric host populations. Instead, total worm load differed among sub-adult host populations, but not among adult host populations. This suggests immune competence differs among host populations at a specific life stage, rather than local adaptation of the parasite

Divergent selection as revealed by P-ST and QTL-based F-ST in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient

Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three-spined stickleback (Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low-plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal-inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P-ST (a phenotypic alternative for Q(ST)) and neutral F-ST. However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F-ST at only one of two QTL was detected as an outlier, although F-ST at both loci correlated significantly with P-ST. No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F(ST)s were detected at dorsal spine QTL, and no significant correlations with P-ST were observed

Quantifying population structure on short timescales

Quantifying the contribution of the various processes that influence population genetic structure is important, but difficult. One of the reasons is that no single measure appropriately quantifies all aspects of genetic structure. An increasing number of studies is analysing population structure using the statistic D, which measures genetic differentiation, next to G(ST) , which quantifies the standardized variance in allele frequencies among populations. Few studies have evaluated which statistic is most appropriate in particular situations. In this study, we evaluated which index is more suitable in quantifying postglacial divergence between three-spined stickleback (Gasterosteus aculeatus) populations from Western Europe. Population structure on this short timescale (10 000 generations) is probably shaped by colonization history, followed by migration and drift. Using microsatellite markers and anticipating that D and G(ST) might have different capacities to reveal these processes, we evaluated population structure at two levels: (i) between lowland and upland populations, aiming to infer historical processes; and (ii) among upland populations, aiming to quantify contemporary processes. In the first case, only D revealed clear clusters of populations, putatively indicative of population ancestry. In the second case, only G(ST) was indicative for the balance between migration and drift. Simulations of colonization and subsequent divergence in a hierarchical stepping stone model confirmed this discrepancy, which becomes particularly strong for markers with moderate to high mutation rates. We conclude that on short timescales, and across strong clines in population size and connectivity, D is useful to infer colonization history, whereas G(ST) is sensitive to more recent demographic events.status: publishe

Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus

An excellent model to elucidate the mechanisms and importance of evolution in the marine environment is the spectral tuning mechanism of the visual pigment in vertebrates. In the sand goby Pomatoschistus minutus (Teleostei; Gobiidae), a distribution-wide study showed that spatial variation at the rhodopsin gene (RH1) matches the characteristics of specific light environments. This match suggests that populations are locally adapted to selective light regimes targeting the RH1 gene. If so, then the direction of selection should depend on the regional spatial and temporal stability of the light conditions. We tested this prediction by comparing goby populations from two regions: the Baltic Sea, characterized by divergent, but temporally stable light conditions, and the North Sea, characterized by locally heterogeneous and temporally variable light conditions. RH1 sequences of 491 Pomatoschistus minutus individuals from 15 locations were analysed. We found that variation at the RH1 gene in the Baltic populations showed signatures of diversifying selection, whereas the RH1 gene in the North Sea showed signatures of stabilizing selection. These different modes of selection are consistent with the regional light conditions and hence support our predictions, but may also be influenced by migration between the open sea and more turbid estuarine environments. An interesting observation is that within one gene, synonymous and non-synonymous SNPs show a totally different pattern between populations. Population differentiation based on non-synonymous SNPs of the RH1 gene correlated with spectral variation of the local environment of the sand goby populations. In contrast, the differentiation based on synonymous SNPs of RH1 reflects more the neutral historical pattern of the species