Per-and polyfluoroalkyl substances (PFAS) is a collective name for approximately 4700 synthetic chemicals ubiquitous in the aquatic environment worldwide. They are used in a wide array of products and are found in living organisms around the world. Some PFAS have been associated with cancer, developmental toxicity, endocrine disruption, and other health effects. Only a fraction of PFAS are currently monitored and regulated and the presence and effects on aquatic organisms of many PFAS are largely unknown. The aim of this study is to investigate the health effects of environmentally relevant concentrations of PFAS on aquatic organisms at different consumer trophic levels through a systematic review and meta-analysis. The main result shows that PFAS in concentrations up to 13.5 μg/L have adverse effects on body size variables for secondary consumers. However, no significant effects on liver or gonad somatic indices and neither on fecundity were found. In addition, the results show that there are large research gaps for PFAS effects on different organisms in aquatic environments at environmentally relevant concentrations. Most studies have been performed on secondary consumers and there is a substantial lack of studies on other consumers in aquatic ecosystems.

The circular distribution of the willow warbler Phylloscopus trochilus around the Baltic Sea shares many features with the classic examples of ring species; however, the system is much younger. It has previously been shown that a secondary contact zone is located in central Scandinavia, where there are narrow clines for several morphological traits coincident with a migratory divide. Here we analyse multiple traits and genes from > 1700 males captured on breeding territories at 77 sites spread around the Baltic Sea to test the following hypothesis. If the secondary contact zone in Scandinavia is a result of divergence in two allopatric refuge populations during the last glaciation, we expect to find a similar secondary contact zone somewhere else around the circular distribution. Our results show that the trait clines were wider and displaced from each other along the eastern side of the Baltic Sea. Analyses of 12 microsatellite loci confirmed that the genome is very similar between the terminal forms (F(ST) = 0). Two AFLP-derived markers filtered out from a genomic scan instead appear to be maintained by selection. These markers exhibited steep clines at the secondary contact zone in Scandinavia, but as for the phenotypic traits, had vastly different cline centres east of the Baltic Sea. The trait clines along the ring distribution outside the Scandinavian secondary contact zone thus seem to have been shaped by independent action of selection or drift during the process of postglacial colonization.

BACKGROUND: We still have limited knowledge about the underlying genetic mechanisms that enable migrating species of birds to navigate the globe. Here we make an attempt to get insight into the genetic architecture controlling this complex innate behaviour. We contrast the gene expression profiles of two closely related songbird subspecies with divergent migratory phenotypes. In addition to comparing differences in migratory strategy we include a temporal component and contrast patterns between breeding adults and autumn migrating juvenile birds of both subspecies. The two willow warbler subspecies, Phylloscopus trochilus trochilus and P. t. acredula, are remarkably similar both in phenotype and genotype and have a narrow contact zone in central Scandinavia. Here we used a microarray gene chip representing 23,136 expressed sequence tags (ESTs) from the zebra finch Taeniopygia guttata to identify mRNA level differences in willow warbler brain tissue in relation to subspecies and season.

RESULTS: Out of the 22,109 EST probe sets that remained after filtering poorly binding probes, we found 11,898 (51.8 %) probe sets that could be reliably and uniquely matched to a total of 6,758 orthologous zebra finch genes. The two subspecies showed very similar levels of gene expression with less than 0.1 % of the probe sets being significantly differentially expressed. In contrast, 3,045 (13.8 %) probe sets were found to be differently regulated between samples collected from breeding adults and autumn migrating juvenile birds. The genes found to be differentially expressed between seasons appeared to be enriched for functional roles in neuronal firing and neuronal synapse formation.

CONCLUSIONS: Our results show that only few genes are differentially expressed between the subspecies. This suggests that the different migration strategies of the subspecies might be governed by few genes, or that the expression patterns of those genes are time-structured or tissue-specific in ways, which our approach fails to uncover. Our findings will be useful in the planning of new experiments designed to unravel the genes involved in the migratory program of birds.

The genomic organisation of the major histocompatibility complex (MHC) seems to vary considerably between different bird species. In order to understand this variation it is important to gather information from different species. We have, for the first time, investigated MHC class 11 polymorphism in a wader species, the great snipe (Gallinago media). Eleven alleles were found in five sequenced individuals; these come from at least three different loci, but RFLP data suggest that a larger number of genes may be present. For MHC genes, amino acid substitutions followed the, for MHC genes, general pattern of high non-synonymous substitution rates in peptide-binding regions, suggesting that the sequenced alleles may be expressed. The number of genes, lengths of introns and exon sequences of the great snipe MHC seem to be intermediate between those of chicken and passerine birds.

Genes of the major histocompatibility complex (MHC) play a major part in the activation of the vertebrate immune system. In addition, they also appear to function as cues for mate choice. In mammals especially, several kinds of MHC-dependent mate choice have been hypothesized and observed. These include choice of mates that share no or few alleles with the choosing individual, choice of mates with alleles that differ as much as possible from the choosing individual, choice of heterozygous mates, choice of certain genotypes and choice of rare alleles. We investigated these different aspects of mate choice in relation to MHC in a lekking bird species, the great snipe (Gallinago media). We found no evidence for MHC disassortative mating, no preference for males with many MHC alleles and no preference for rare alleles. However, we did find that some allelic lineages were more often found in males with mating success than in males without mating success. Females do not seem to use themselves as references for the MHC-dependent mate choice, rather they seem to prefer males with certain allele types. We speculate that these alleles may be linked to resistance to common parasites.

The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism.

We examined the reproductive success of 48 adult brown trout (Salmo trutta L.) which were allowed to reproduce in a stream that was controlled for the absence of other trout. Parentage analyses based on 11 microsatellites permitted us to infer reproductive success and mate choice preferences in situ. We found that pairs with intermediate major histocompatibility complex (MHC) dissimilarity mated more often than expected by chance. It appears that female choice was the driving force behind this observation because, compared with other individuals, males with intermediate MHC dissimilarity produced a larger proportion of offspring, whereas female reproductive output did not show this pattern. Hence, rather than seeking mates with maximal MHC dissimilarity, as found in several species, brown trout seemed to prefer mates of intermediate MHC difference, thus supporting an optimality-based model for MHC-dependent mate choice.

In the environment, pollution generally acts over long time scales and exerts exposure of multiple toxicants on the organisms living there. Recent findings show that pollution can alter the genetics of populations. However, few of these studies have focused on long-term exposure of mixtures of substances. The relatively short generation time (ca. 4-5 weeks in sediments) of the harpacticoid copepod Attheyella crassa makes it suitable for multi generational exposure studies. Here, A. crassa copepods were exposed for 60 and 120 days to naturally contaminated sediments (i.e., Svindersviken and Trosa; each in a concentration series including 50% contaminated sediment mixed with 50% control sediment and 100% contaminated sediment), and for 120 days to control sediment spiked with copper. We assayed changes in FST (fixation index), which indicates if there is any population subdivision (i.e., structure) between the samples, expected heterozygosity, percent polymorphic loci, as well as abundance. There was a significant decrease in total abundance after 60 days in both of the 100% naturally contaminated sediments. This abundance bottleneck recovered in the Trosa treatment after 120 days but not in the Svindersviken treatment. After 120 days, there were fewer males in the 100% naturally contaminated sediments compared to the control, possibly caused by smaller size of males resulting in higher surface: body volume ratio in contact with toxic chemicals. In the copper treatment there was a significant decrease in genetic diversity after 120 days, although abundance remained unchanged. Neither of the naturally contaminated sediments (50 and 100%) affected genetic diversity after 120 days but they all had high within treatment FST values, with highest FST in both 100% treatments. This indicates differentiation between the replicates and seems to be a consequence of multi-toxicant exposure, which likely caused selective mortality against highly sensitive genotypes. We further assayed two growth-related measures, i.e., RNA content and cephalothorax length, but none of these endpoints differed between any of the treatments and the control. In conclusion, the results of the present study support the hypothesis that toxicant exposure can reduce genetic diversity and cause population differentiation. Loss of genetic diversity is of great concern since it implies reduced adaptive potential of populations in the face of future environmental change.

One of the goals of environmental risk assessment (ERA) is to understand effects of toxicant exposure on individual organisms and populations. We hypothesized that toxicant exposure can reduce genetic diversity and alter genotype composition, which may ultimately lead to a reduction in the average fitness of the exposed population. To test this hypothesis, we exposed a copepod, Nitocra psammophila, to a toxic reference compound and assayed resulting alterations in genetic structure, i.e. expected heterozygosity and percent polymorphic loci, as well as other population- and fitness-related measures, i.e. population abundance, demographic structure and juvenile growth. The copepods were exposed to 0.11-1.1 mu g of the pentabromo-substituted diphenyl ether (BDE-47) mg(-1) freeze-dried algae for 24 days (i.e. > 1 generation). There was no significant decline in total population abundance. However, there were significant alterations in population structure, manifested as diminished proportion of nauplii and increased proportion of copepodites. In addition, individual RNA content in copepodites decreased significantly in exposed individuals, indicating declined growth. Finally, in the exposed populations, heterozygosity was lower and genotype composition was altered compared to the controls. These results therefore confirm the hypothesized reduction in overall genetic variability resulting from toxicant exposure. Multilevel approaches, such as the one used in the present study, may help unravel subtle effects on the population level, thus increasing the predictive capacity of future ERA.

Concentrated chemical spills have been shown to impact adversely on fish populations and even cause localized population extinctions. Evaluating population-level impacts of sublethal exposure concentrations is, however, complex and confounded by other environmental pressures. Applying effect measures derived from laboratory-based chemical exposures to impacts in wild fish populations is constrained by uncertainty on how biochemical response measures (biomarkers) translate into health outcomes, lack of available data for chronic exposures and the many uncertainties in available fish population models. Furthermore, wild fish show phenotypic plasticity and local adaptations can occur that adds geographic and temporal variance on responses. Such population-level factors are rarely considered in the chemical risk assessment process and can probably be derived only from studies on wild fish. Molecular technologies, including microsatellite and SNP genotyping, and RNASeq for gene expression studies, are advancing our understanding of mechanisms of eco-toxicological response, tolerance, adaptation and selection in wild populations. We examine critically the application of such approaches with examples including using microsatellites that has identified roach (Rutilus rutilus) populations living in rivers contaminated with sewage effluents that are self-sustaining, and studies of stickleback (Gasterosteus aculeatus) and killifish (Fundulus heteroclitus) that have identified genomic regions under selection putatively related to pollution tolerance. Integrating data on biological effects between laboratory-based studies and wild populations, and building understanding on adaptive responses to sublethal exposure are some of the priority research areas for more effective evaluation of population risks and resilience to contaminant exposure.

Studies on genetic connectivity are important for the management of fisheries. In this study we used AFLP to investigate population structure of the endemic Spinefoot shoemaker, Siganus sutor, from 6 countries, Kenya, Tanzania, Comoros, Seychelles and Mauritius in the Western Indian Ocean. We collected 506 samples from 20 fish landing sites, 171 variable loci were used in the statistical analysis. Global F_ST was significant and showed a pattern of isolation by distance, mostly influenced by remote oceanic islands. In a previous study we have described the temporal variation of Siganus sutor to be about 1/5 of the global variation, and by applying a 1/5 of the global variation cut of value for the pair-wise comparisons we were able to account some of the pair- wise genetic variation as temporal fluctuations. A STRUCTURE analysis was also preformed that corroborates the pair-wise F_ST comparisons. Overall these results show that S. sutor is genetically diverse and subdivided throughout the region, but also that the current management regime might not be optimal. 

Artisanal fisheries in Kenya have been in decline since the 1980’s and are currently managed by gear restriction and no take zones. The fishery is a mixed species fishery but the Shoemaker spinefoot (Siganus sutor) comprise a large portion of the total catches. The sustainable use of these resources is dependent on informed assessment and management of the harvested species. In Kenya there is a lack of critical information about landings, fish stock productivity and genetic stock structure, and there is no knowledge of populations size or genetic variation of S. sutor. In this study we used the molecular marker, AFLP to investigate the genetic variation within and between sites of S. sutor landed along the 200 km coast of Kenya. We compared the spatial genetic variation among sites with the within site temporal genetic variation from a single site, adjacent to a number of spawning aggregations. Our results show that the there is genetic variation among the sites (spatial variation) and that the temporal genetic variation with in a six week period was about 1/5 of the spatial genetic variation. We believe these findings to be an important aspect to considered for both future scientific research as well as management.

There is a growing demand for wild caught juvenile fish to supply the market for aquaculture. However, little is known about the genetic effects of juvenile collection from wild populations. There are a number of imminent threats to both aquaculture systems and wild fish populations. Juvenile collection from a single population can for example reduce population’s evolutionary potential as well as the disease resistance within an aquaculture pond. In this study, we investigated the local genetic structure of juvenile mullets collected from five sites around Bagamoyo (Tanzanian mainland) and Zanzibar Island, East Africa. Fish were caught in low tide using a seine net. The fish were morphologically identified, and then genetically identified using direct sequencing of the CO1 gene with cross referencing with the Barcode of Life Database (BOLD) systems.  Molecular variance analyses were used to infer genetic subdivision based on geographic sampling site as well as inferring population structure through the Bayesian assignment test implemented in STRUCTURE 2.3. Our results showed that samples morphologically identified as Mugil cephalus where in fact Valamugil buchanani and we also found evidence of an introgression genome event, where the gene flow from one species may have affected the general gene pool. The Bayesian analysis revealed a clear genetic population structure among the sampled fish; the main difference was the presence of a unique mainland cluster. Our findings may have important implications for management and conservation of mullet fishes in the region and elsewhere.

Environmental change challenges local and global survival of populations and species. In a species-poor environment like the Baltic Sea this is particularly critical as major ecosystem functions may be upheld by single species. A complex interplay between demographic and genetic characteristics of species and populations determines risks of local extinction, chances of re-establishment of lost populations, and tolerance to environmental changes by evolution of new adaptations. Recent studies show that Baltic populations of dominant marine species are locally adapted, have lost genetic variation and are relatively isolated. In addition, some have evolved unusually high degrees of clonality and others are representatives of endemic (unique) evolutionary lineages. We here suggest that a consequence of local adaptation, isolation and genetic endemism is an increased risk of failure in restoring extinct Baltic populations. Additionally, restricted availability of genetic variation owing to lost variation and isolation may negatively impact the potential for evolutionary rescue following environmental change.

We have tested the importance of genetic variation in the major histocompatibility complex (MHC) class IIB in Atlantic salmon (Salmo salar) for survival after challenge with a highly virulent bacterial pathogen. Forty juvenile full siblings from each of 120 families were infected with the bacterium Aeromonas salmonicida, which causes high mortality in salmon due to furunculosis. Fishes from high-resistance (HR, < 35% mortality) and low-resistance (LR, > 80% mortality) families were screened for their MHC class IIB genotypes using the denaturing gradient gel electrophoresis (DGGE) technique. The exon 2 sequences, encoding the major part of the peptide-binding region, were established far each DGGE fragment. One allele, e, containing a missense single base substitution was significantly more prevalent in HR families than in LR families. An odds-ratio test showed that broods carrying this allele had a 12-fold higher chance of being HR than broods without the e allele. A second allele, i, showed significantly higher frequencies in uninfected and surviving individuals than in infected dead individuals. A third allele, j, tended to be more prevalent both in LR families and in individuals that had died of the infection. There was no correlation between MHC heterozygosity and resistance to A. salmonicida. Our results support the hypothesis that MHC polymorphism is maintained through pathogen-driven selection acting by means of frequency-dependent selection rather than heterozygous advantage.

We compared three different molecular methods currently used for screening of Mhc variation in population studies of Atlantic salmon. Restriction fragment length polymorphism (RFLP) of the entire class II gene detected 22 haplotypes. Seventeen exon 2 sequences were obtained from individuals carrying the 22 haplotypes, two of which had not been detected by RFLP. The six alleles (27%) detected by RFLP and not by exon 2 sequencing probably resulted from sequence variation outside exon 2. Within exon 2, RFLP differentiated 88% of the sequences. Alternatively, denaturing gradient gel electrophoresis (DGGE) performed under two run conditions detected 94% of the sequence variation. Both RFLP using different probes, and the two PCR-based methods using three different primer pairs, suggest that there is only a single Mhc class II B gene in the Baltic populations of Atlantic salmon.

Abstract—Uncontrolled growth of sea urchin populations may have a negative effect on coral reefs, making them barren. To avoid this, different methods of sea urchin reduction have been developed but, without knowledge of their genetic structure and connectivity, these methods may be ineffective. The aim of this study was to examine the fine-scale genetic structure and connectivity in the sea urchin, Diadema setosum, population around Unguja, Zanzibar, using AFLP. We found evidence of different genetic clusters, high migration between the sites and high genetic diversity within the sites. These findings indicate that a manual reduction of sea urchins with similar genetic connectivity, implemented on the same geographic scale as our study, would be ineffective since sites are probably repopulated from many sources.

Connectivity plays an important role in shaping the genetic structure and in evolution of local adaptation. In the marine environment barriers to gene flow are in most cases caused by gradients in environmental factors, ocean circulation and/or larval behavior. Despite the long pelagic larval stages, with high potential for dispersal many marine organisms have been shown to have a fine scale genetic structuring. In this study, by using a combination of high-resolution genetic markers, species hybridization data and biophysical modeling we can present a comprehensive picture of the evolutionary landscape for a keystone species in the Baltic Sea, the blue mussel. We identified distinct genetic differentiation between the West Coast, Baltic Proper and Bothnian Sea regions, with lower gene diversity in the Bothnian Sea. Oceanographic connectivity together with salinity and to some extent species identity provides explanations for the genetic differentiation between the West Coast and the Baltic Sea (Baltic Proper and Bothnian Sea). The genetic differentiation between the Baltic Proper and Bothnian Sea cannot be directly explained by oceanographic connectivity, species identity or salinity, while the lower connectivity to the Bothnian Sea may explain the lower gene diversity. © 2016.

Human-derived environmental pollutants and nutrients that reach the aquatic environment through sewage effluents, agricultural and industrial processes are constantly contributing to environmental changes that serve as drivers for adaptive responses and evolutionary changes in many taxa. In this study, we examined how two types of point sources of aquatic environmental pollution, harbors and sewage treatment plants, affect gene diversity and genetic differentiation in the blue mussel in the Baltic Sea area and off the Swedish west coast (Skagerrak). Reference sites (REF) were geographically paired with sites from sewage treatments plant (STP) and harbors (HAR) with a nested sampling scheme, and genetic differentiation was evaluated using a high-resolution marker amplified fragment length polymorphism (AFLP). This study showed that genetic composition in the Baltic Sea blue mussel was associated with exposure to sewage treatment plant effluents. In addition, mussel populations from harbors were genetically divergent, in contrast to the sewage treatment plant populations, suggesting that there is an effect of pollution from harbors but that the direction is divergent and site specific, while the pollution effect from sewage treatment plants on the genetic composition of blue mussel populations acts in the same direction in the investigated sites.

Anthropogenic pollution including metals, petroleum, toxins, nutrients and many others is a growing problem in the marine environment. These are important factors altering the environment and by that the fate of many local populations of marine organisms. The aim of this study was to assess the impact of selected point pollution sources on resident populations of the blue mussel (Mytilus edulis trossulus) in the Baltic Sea using multiple biomarker approach. The study used a nested sampling scheme in which sites from reference (REF) habitats are geographically paired with selected sites from sewage treatment plants (STP) and harbors (HAR). The results showed that mussels from harbors had a higher frequency of histological abnormalities in the digestive gland compared to mussels from sewage effluent affected areas and reference sites. However these mussels together with mussels from STPs had higher lipid content, body mass index (BMI) and gonado-somatic index (GSI) compared to mussels from reference sites. A marked spatial variability was found with a stronger toxicity of ambient environment affecting resident mussel populations in the Gulf of Gdańsk area, while an opposite pattern was found in Tvärminne area. Yet the blue mussels sampled in the Gulf of Gdańsk were characterized by the highest GSI and BMI values compared to Askö and Tvärminne populations. No differences in analyzed biomarker response related to species identity, measured by a species-specific genetic marker, were found indicative of strong genetic introgression in the Baltic Proper.

Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P < 0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (F(ST) = 0.021, P < 0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei's Hs = 0.11, reference sites Nei's Hs = 0.11). Still, pairwise F(ST): s between three, out of four, pairs of polluted-reference sites were significant. A F(ST)-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P < 0.05 level and therefore indicated to be under divergent selection. When removing 13 F(ST)-outlier loci, significant at the P < 0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment.

Anthropogenic activities are causing change in natural habitats at an accelerating rate and affecting populations by altered selection pressures. One example is human-induced eutrophication in the Baltic Sea, were behaviour alterations are well documented in three-spined sticklebacks (Gasterosteus aculeatus). Here we have used 204 variable Amplified Fragment Length Polymorphism (AFLP) markers to investigate genetic differences between a set of ten hierarchal sampled populations of sticklebacks, five populations inhabiting eutrophicated habitats and five from control populations, in total 292 individuals. We found significant genetic variation that could be attributed to habitat (4.3% AMOVA). A combination of F_ST outlier analysis and classification analysis revealed seven AFLP-loci likely to be affected by divergent selection by eutrophication. Four of these seven loci have earlier been identified as under selection in stickleback populations living in pulp-mill effluents suggesting some similar selective factors between eutrophication and pulp-mill effluent effected habitats. 

There are three basic types of population structures in marine environments; populations that are distinct, with a continuous change and without any differentiation. In each type the population units are characterized by groups of individuals with panmixia within groups and site fidelity to a limited geographic area. Earlier studies of the population genetic structure on sticklebacks in the Baltic Sea have shown none or only little structure. We have sampled 8 sites (253 individuals) along Sweden’s coast to estimate the genetic structure, using five microsatellites and 173 Amplified Fragment Length Polymorphism (AFLP) markers and detected a fine scale genetic structure (AFLP F_ST= 25%, microsatellites F_ST = 2.7%). With AFLPs the observed variation followed isolation by distance model (but not with microsatellites). Even sites separated by only 2 km of water are significantly separated. Both Bayesian clustering analysis and Capscale separated populations and identified populations from Gulf of Bothnia (4 psu) and from the west coast (20 psu) as genetically distinctly different from Baltic populations (about 7-8 psu).  In conclusion, gene flow is limited between sampled sites, and since no geographic barriers can be distinguished the population structure is likely caused by the sticklebacks’ behavior. Hence, we have probably sampled either stationary populations of marine sticklebacks, or homing sticklebacks. In this study AFLP and microsatellites did not give congruent results; with AFLPs we got high separation, and genetic variation followed isolation by distance model and supported the continuous change type of population structure.

The extreme polymorphism found at some major histocompatibility complex (MHC) loci is believed to be maintained by balancing selection caused by infectious pathogens. Experimental support for this is inconclusive. We have studied the interaction between certain MHC alleles and the bacterium Aeromonas salmonicida, which causes the severe disease furunculosis, in Atlantic salmon (Salmo salar L.). We designed full-sibling broods consisting of combinations of homozygote and heterozygote genotypes with respect to resistance or susceptibility alleles. The juveniles were experimentally infected with A. salmonicida and their individual survival was monitored. By comparing full siblings carrying different MHC genotypes the effects on survival due to other segregating genes were minimized. We show that a pathogen has the potential to cause very intense selection pressure on particular MHC alleles; the relative fitness difference between individuals carrying different MHC alleles was as high as 0.5. A co-dominant pattern of disease resistance/susceptibility was found, indicative of qualitative difference in the immune response between individuals carrying the high- and low-resistance alleles. Rather unexpectedly, survival was not higher among heterozygous individuals as compared with homozygous ones.

BACKGROUND: Animal migration requires adaptations in morphological, physiological and behavioural traits. Several of these traits have been shown to possess a strong heritable component in birds, but little is known about their genetic architecture. Here we used 454 sequencing of brain-derived transcriptomes from two differentially migrating subspecies of the willow warbler Phylloscopus trochilus to detect genes potentially underlying traits associated with migration.

RESULTS: The transcriptome sequencing resulted in 1.8 million reads following filtering steps. Most of the reads (84%) were successfully mapped to the genome of the zebra finch Taeniopygia gutatta. The mapped reads were situated within at least 12,101 predicted zebra finch genes, with the greatest sequencing depth in exons. Reads that were mapped to intergenic regions were generally located close to predicted genes and possibly located in uncharacterized untranslated regions (UTRs). Out of 85,000 single nucleotide polymorphisms (SNPs) with a minimum sequencing depth of eight reads from each of two subspecies-specific pools, only 55 showed high differentiation, confirming previous studies showing that most of the genetic variation is shared between the subspecies. Validation of a subset of the most highly differentiated SNPs using Sanger sequencing demonstrated that several of them also were differentiated between an independent set of individuals of each subspecies. These SNPs were clustered in two chromosome regions that are likely to be influenced by divergent selection between the subspecies and that could potentially be associated with adaptations to their different migratory strategies.

CONCLUSIONS: Our study represents the first large-scale sequencing analysis aiming at detecting genes underlying migratory phenotypes in birds and provides new candidates for genes potentially involved in migration.

It is well established that differences in migratory behavior between populations of songbirds have a genetic basis but the actual genes underlying these traits remains largely unknown. In an attempt to identify such candidate genes we de novo assembled the genome of the willow warbler Phylloscopus trochilus, and used whole-genome resequencing and a SNP array to associate genomic variation with migratory phenotypes across two migratory divides around the Baltic Sea that separate SW migrating P. t. trochilus wintering in western Africa and SSE migrating P. t. acredula wintering in eastern and southern Africa. We found that the genomes of the two migratory phenotypes lack clear differences except for three highly differentiated regions located on chromosomes 1, 3, and 5 (containing 146, 135, and 53 genes, respectively). Within each migratory phenotype we found virtually no differences in allele frequencies for thousands of SNPs, even when comparing geographically distant populations breeding in Scandinavia and Far East Russia (&gt;6000 km). In each of the three differentiated regions, multidimensional scaling-based clustering of SNP genotypes from more than 1100 individuals demonstrates the presence of distinct haplotype clusters that are associated with each migratory phenotype. In turn, this suggests that recombination is absent or rare between haplotypes, which could be explained by inversion polymorphisms. Whereas SNP alleles on chromosome 3 correlate with breeding altitude and latitude, the allele distribution within the regions on chromosomes 1 and 5 perfectly matches the geographical distribution of the migratory phenotypes. The most differentiated 10 kb windows and missense mutations within these differentiated regions are associated with genes involved in fatty acid synthesis, possibly representing physiological adaptations to the different migratory strategies. The ∼200 genes in these regions, of which several lack described function, will direct future experimental and comparative studies in the search for genes that underlie important migratory traits.

High intraspecific variability and lack of adequate field descriptions or distinguishing skeletal features has made identification of the scleractinian coral Platygyra daedalea challenging. This species displays a number of distinct morphological types that co-occur on lagoonal reefs in Kenya and which often cannot be separated by field observations. To better understand how morphological and genetic variations are related, morphometric and molecular techniques were used to examine phenotypic variation in P. daedalea. A canonical discriminant analysis of measurements of 10 skeletal characters confirmed the existence of 2 morphotypes. No single diagnostic trait could be used to distinguish the 2 morphotypes, though a combination of 4 characters separated them. A mathematical equation is presented to separate colonies into the 2 morphotypes, where field identification is not possible. Genetic differentiation was studied using 5 microsatellite loci and sequence analysis of the internal transcriber spacer (ITS1 and ITS2) and 5.8S region of the nuclear ribosomal RNA gene. AMOVA of the microsatellite and ITS sequence data showed significant genetic differences between the 2 morphotypes. However, phylogenetic analysis of the ITS sequences showed no evidence of sequence divergence between morphotypes, which suggests that they share a gene pool, or that the genetic divergence is recent. We conclude that the occurrence of distinct morphotypes is a characteristic of P. daedalea and that there does appear to be a genetic basis for separating morphotypes. However, genetic differences in P. daedalea could only be detected when combined with morphometric data.

Vi, 1 620 forskare samt lärare vid universitet och högskolor, är eniga med de unga bakom Auroramålet: De drabbas och riskerar att drabbas allvarligt av klimatkrisen under sin livstid. De klimatåtgärder vi vidtar i närtid avgör deras framtid. Sverige måste ta ansvar och göra sin rättvisa andel av det globala klimatarbetet. 

I strid med Parisavtalet ökar utsläppen av växthusgaser i en takt som gör att 1,5-gradersmålet kan överskridas om några år. De globala effekterna blir allt mer synliga med ständiga temperaturrekord, smältande isar, havshöjning och extremväder som torka, förödande bränder och skyfall med enorma översvämningar, som i Pakistan nyligen. Försörjningen av befolkningen utsätts för allvarliga hot i många länder.

Minskningen av den biologiska mångfalden är extrem. Klimatkrisen är enligt WHO det största hotet mot människors hälsa i hela världen och barn utgör en särskilt sårbar grupp. Med Sveriges nordliga läge sker uppvärmningen här dubbelt så fort som det globala genomsnittet. Det förskjuter utbredningsområden för växtlighet och sjukdomsbärande insekter och ökar förekomsten av extremväder såsom värmeböljor, skogsbränder och översvämningar samt av många olika sorters infektioner och allergier. När extremväder ökar, ökar även stressen och risken för mental ohälsa. Värmeböljor ökar risken för sjukdom och död hos sårbara grupper som äldre, små barn och personer med kroniska sjukdomar. De negativa effekterna på hälsan kommer att öka i takt med klimatkrisen och barn riskerar att drabbas av ackumulerade negativa hälsoeffekter under hela sina liv. Redan i dag är mer än hälften av unga mellan 12 och 18 år i Sverige ganska eller mycket oroliga för klimat och miljö. Detta är förståeligt när våra beslutsfattare inte gör vad som krävs.

Den juridiska och moraliska grunden för arbetet mot klimatförändringarna är att varje land måste göra sin rättvisa andel av det globala klimatarbetet. Centralt i det internationella klimatramverket är att rika länder med höga historiska utsläpp, däribland Sverige, måste gå före resten av världen. Dessa länder måste också bidra till att finansiera klimatomställningen i länderna i det Globala Syd, som är minst ansvariga för klimatkrisen men drabbas hårdast. Denna rättviseprincip är tydlig i Parisavtalet och var en het diskussionsfråga under COP27 i Sharm el-Sheikh, men lyser med sin frånvaro i det svenska klimatarbetet. 

Sverige har satt mål för att minska sina utsläpp. Men de är helt otillräckliga: minskningstakten är för låg och målen tillåter samtidigt att åtgärder skjuts på framtiden. Dessutom exkluderas merparten av Sveriges utsläpp från de svenska nationella utsläppsmålen; bland annat utelämnas utsläpp som svensk konsumtion orsakar utanför Sveriges gränser, utsläpp från utrikes transporter och utsläpp från markanvändning och skogsbruk, exempelvis utsläpp från förbränning av biobränslen eller utsläpp från dikade våtmarker (Prop. 2016/17:146 s.25-28).

Sverige saknar dessutom ett eget mål för att öka upptaget av växthusgaser genom utökat skydd och restaurering av ekosystem, något som krävs för att begränsa de värsta konsekvenserna av klimatkrisen (IPCC s.32). Trots dessa låga ambitioner misslyckas Sverige med att nå sina utsläppsmål, konstaterar både Klimatpolitiska rådet och Naturvårdsverket. En klimatpolitik i linje med Parisavtalet kräver både att alla typer av växthusgasutsläpp minskar samtidigt som – inte i stället för – upptaget av växthusgaser maximeras: i dag misslyckas Sverige på bägge fronter.

Slutsatsen är tydlig. Sverige vidtar inte de åtgärder som krävs för att skydda barns och ungdomars rättigheter enligt Europakonventionen till skydd för de mänskliga rättigheterna. Detta medför allvarliga risker för liv och hälsa för unga generationer, människor i andra länder och särskilt utsatta grupper. Detta kan inte fortsätta. Därför ställer vi oss bakom Auroras krav att Sverige börjar göra sin rättvisa andel och omedelbart sätter igång ett omfattande och långtgående klimatarbete som vilar på vetenskaplig grund och sätter rättvisa i centrum.

ABSTRACT: BACKGROUND: Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics. RESULTS: We have used genome-wide strain-specific single nucleotide polymorphism data from 64 strains of budding yeast (Saccharomyces cerevisiae or Saccharomyces paradoxus) to determine whether adaptive positive selection is correlated with protein regions showing propensity for different classes of structure conformation. Data from phylogenetic and population genetic analysis of 3746 gene alignments consistently shows a significantly higher degree of positive Darwinian selection in intrinsically disordered regions of proteins compared to regions of alpha helix, beta sheet or tertiary structure. Evidence of positive selection is significantly enriched in classes of proteins whose functions and molecular mechanisms can be coupled to adaptive processes and these classes tend to have a higher average content of intrinsically unstructured protein regions. CONCLUSIONS: We suggest that intrinsically disordered protein regions may be important for the production and maintenance of genetic variation with adaptive potential and that they may thus be of central significance for the evolvability of the organism or cell in which they occur.

The preference of juvenile Arctic char [Salvelinus alpinus (L.)] for odors from siblings and nonsiblings with different major histocompability complex class II (MHC) genotypes was studied in two-choice fluviarium tests. In the first part of the study, test fish demonstrated no preference for water scented by a sibling with a MHC genotype different from its own versus water scented by a MHC identical nonsibling. When both donors were siblings with different MHC genotypes, however, the test fish chose the water scented by the fish with the same MHC type as the test fish. The results suggest that odors with information about kinship are dependent on MHC but also on other, unknown factors. In the second part of the study, we observed that fish isolated since fertilization did not show any behavioral discrimination towards siblings, based on MHC genotype. One reasonable explanation for this result is that Arctic char learn to discriminate between odors from individuals of different MHC types.

No difference in attraction was observed in sibling Artic charr Salvelinus alpinus between water scented by dominant or subordinate major histocompability complex (MHC) identical fish observed in a two-choice fluviarium. In a second experiment, MHC identical sibling donors were given different types of food pellets before the preference test. The test fish showed a significant attraction to the sibling given the same kind of food as the test fish itself during the first 6 h of the fluviarium tests. The results suggest that diet has an influence on the odours released and can, in addition to MHC related odours, be used for information relating to group member identity.

Kin recognition and discrimination are thought to occur in several species of various taxonomic groups. In salmonid fish, juveniles can discriminate between odours of siblings and nonsiblings from the same population even if the odour donors and the test fish have been reared separately since fertilization. This indicates that some genetic factor is important in the recognition process. The mechanisms behind kin recognition and discrimination have not yet been described. In the present study, we performed fluviarium tests to examine whether kin recognition and discrimination in juvenile Arctic charr are influenced by the major histocompatibility complex (MHC). Prior to the fluviarium tests, exon 2 of an MHC class II B gene in charr was analysed with denaturing gradient gel electrophoresis (DGGE) and individual genotypes were determined. In the fluviarium, when fish had the choice between water scented by an MHC identical sibling and a sibling with a different MHC genotype they preferred water from identical siblings. Moreover, water scented by an MHC different sibling was preferred to water from an MHC different nonsibling. However, we observed no discrimination when the test fish shared one allele with the nonsibling donor but no alleles with the sibling donor. Our results indicate that the MHC has a significant influence on the odours used for kin recognition and discrimination in juvenile Arctic charr.

Per- and polyfluoroalkyl substances (PFAS) are a group of thousands of highly persistent anthropogenic chemicals widely used in many industries. Therefore, they are, ubiquitously present in various types of environments. Despite their omnipresence, ecotoxicological studies of most PFAS are scarce, and those available often assess the effects of long chain PFAS. In this study, we present the results of an exposure experiment in which wild aquatic amphipod Gammarus spp. was exposed to the short chain perfluorinated substance perfluorobutanoic acid (PFBA) at very low and environmentally relevant concentrations of 0, 10 and 100 ng/L. The exposure lasted for 12 days, and food intake and non-reproductive behavior were analyzed. Exposure to 10 and 100 ng/L PFBA resulted in a lower consumption of food during exposure but no effect on behavior was found. 

We approach the field of stress immunology from an ecological point of view and ask: why should a heavy physical workload, for example as a result of a high reproductive effort, compromise immune function? We argue that immunosuppression by neuroendocrine mechanisms, such as stress hormones, during heavy physical workload is adaptive, and consider two different ultimate explanations of such immunosuppression. First, several authors have suggested that the immune system is suppressed to reallocate resources to other metabolic demands. In our view, this hypothesis assumes that considerable amounts of energy or nutrients can be saved by suppressing the immune system; however, this assumption requires further investigation. Second, we suggest an alternative explanation based on the idea that the immune system is tightly regulated by neuroendocrine mechanisms to avoid hyperactivation and ensuing autoimmune responses. We hypothesize that the risk of autoimmune responses increases during heavy physical workload and that the immune system is suppressed to counteract this.

Genes of the major histocompatibility complex (MHC) are remarkably polymorphic. Several selection mechanisms have been invoked to account for this diversity, including disassortative mating preferences. In addition, eggs may discriminate between sperm based on MHC. To investigate the effects of MHC-genotype on fertilization success, we obtained mature gametes from ripe Arctic charr (Salvelinus alpinus) males and females captured on spawning grounds. The eggs of each female were divided into two batches, and by letting each of 2 males fertilize 1 of the batches, we obtained a total of 36 half-sibling batch-pairs. The semen was diluted to ensure that the two males in each half-sibling batch-pair contributed with the same number of sperm cells. We found that MHC-heterozygous males had significantly higher fertilization success than MHC-homozygous males and neither initial spermatocrit, sperm motility nor swimming velocity co-varied with difference in fertilization success. There was no effect of female genotype or female-male MHC-similarity on fertilization success. However, one MHC-allele was associated with increased fertilization success. It seems plausible that the difference in fertilization success between homo-and heterozygous males may be due to MHC-dependent sperm selection by the ovum.

Considering the rapid degradation of coral reefs, it is becoming increasingly important to assess factors such as levels of intraspecific genetic diversity and degree of connectivity between populations and reefs. In this study, five DNA microsatellite markers were used to infer migration patterns and levels of genetic diversity in ten populations of the faviid coral Platygyra daedalea along the coast of East Africa. Populations from reef-slopes and offshore islands had significantly greater genetic diversity, measured as expected heterozygosity and allelic richness than those of inshore lagoonal reefs. A combination of F-statistics and individual assignment tests indicated moderate to high levels of gene flow among lagoonal populations, and less migration between lagoonal sites and the reef-slope and island sites. These results suggest that reef-slope and island reefs could be important reservoirs of genetic diversity for this coral species.

This study showed that population differentiation in P. damicornis varied over spatial scales and that this variability occurred at both evolutionary and ecological time scales. This paradox is discussed in light of stochastic recruitment and small scale population structures found in other species of coral. The study also identifies potential source reefs, such as those within Mnemba Conservation area near Zanzibar and genetically isolated reefs such as those within Malindi Marine National Park and Reserve in northern Kenya.

Studies on genetic connectivity are essential for the design of management strategies for coral reef fisheries. In this study we used a mitochondrial DNA marker to investigate population structure of the reef-associated parrotfish, Scarus ghobban, from four countries, Kenya, Mauritius, Seychelles and Tanzania, in the western Indian Ocean. We obtained nucleotide sequences of the mitochondrial control region for 117 individuals. Measures of haplotype diversity were relatively high. Pairwise population differentiation (F (ST)) was low, but not always non-significant. Analysis of molecular variance (AMOVA) showed genetic differentiation between groups, when the data was partitioned into two groups consisting of samples from Mauritius and Tanzania in one group, and samples from Kenya and Seychelles in another group. Direction of gene flow was estimated using a Bayesian approach. Migration was sometimes asymmetric or directional, coinciding with the flow of major oceanic and coastal currents in the region. Mismatch distributions, based on the observed number of differences among haplotype pairs, produced a unimodal distribution, indicative of recent demographic expansion. Phylogenetic analyses revealed three clades without any geographic structure, suggesting recent migration between historically isolated lineages. We reconstructed the historical demography of S. ghobban and examined it in the context of Pleistocene climate stages and changes in relative sea level. Overall, these results showed that populations of S. ghobban are genetically diverse and have relatively high gene flow, with some genetic structuring in the western Indian Ocean.

The immune and the detoxication systems of animals are characterized by allelic polymorphisms, which underlie individual differences in ability to combat assaults from pathogens and toxic compounds. Previous studies have shown that females may improve offspring survival by selecting mates on the basis of sexual ornaments and signals that honestly reveal health. In many cases the expression of these ornaments appears to be particularly sensitive to oxidative stress. Activated immune and detoxication systems often generate oxidative stress by an extensive production of reactive metabolites and free radicals. Given that tolerance or resistance to toxic compounds and pathogens can be inherited, female choice should promote the evolution of male ornaments that reliably reveal the status of the bearers' level of oxidative stress. Hence, oxidative stress may be one important agent linking the expression of sexual ornaments to genetic variation in fitness-related traits, thus promoting the evolution of female mate choice and male sexual ornamentation, a controversial issue in evolutionary biology ever since Darwin.