Publications by authors named "Francois Besnier"

39 Publications

Geographic variation in gene flow from a genetically distinct migratory ecotype drives population genetic structure of coastal Atlantic cod ( L.).

Evol Appl 2022 Jul 21;15(7):1162-1176. Epub 2022 Jun 21.

Institute of Marine Research Bergen Norway.

Identifying how physical and biotic factors shape genetic connectivity among populations in time and space is essential to our understanding of the evolutionary trajectory as well as the management of marine species. Atlantic cod is a widespread and commercially important marine species displaying several ecotypes with different life history strategies. Using three sets of SNPs: neutral, informative, and genome-inversion linked, we studied population genetic structure of ~2500 coastal Atlantic cod (CC) from 40 locations along Norway's 2500 km coastline, including nine fjords. We observed: (1) a genetic cline, suggesting a mechanism of isolation by distance, characterized by a declining between CC and North East Arctic Cod (NEAC-genetically distinct migratory ecotype) with increasing latitude, (2) that in the north, samples of CC from outer-fjord areas were genetically more similar to NEAC than were samples of CC from their corresponding inner-fjord areas, (3) greater population genetic differentiation among CC sampled from outer-fjord areas along the coast, than among CC sampled from their corresponding inner-fjord areas, (4) genetic differentiation among samples of CC from both within and among fjords. Collectively, these results permit us to draw two main conclusions. First, that differences in the relative presence of the genetically highly distinct, migratory ecotype NEAC, declining from north to south and from outer to inner fjord, plays the major role in driving population genetic structure of the Norwegian CC. Second, that there is limited connectivity between CC from different fjords. These results suggest that the current management units implemented for this species in Norway should be divided into smaller entities. Furthermore, the situation where introgression from one ecotype drives population genetic structure of another, as is the case here, may exist in other species and geographical regions, thus creating additional challenges for sustainable fisheries management.
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http://dx.doi.org/10.1111/eva.13422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9309456PMC
July 2022

Introgression of domesticated salmon changes life history and phenology of a wild salmon population.

Evol Appl 2022 May 11;15(5):853-864. Epub 2022 Apr 11.

Institute of Marine Research Bergen Norway.

The release of domesticated conspecifics into the natural environment, whether deliberate or accidental, has the potential to alter the genetic integrity and evolutionary trajectory of wild populations. This widespread challenge is of particular concern for wild Atlantic salmon. By investigating phenotypic differences between the offspring of domesticated, hybrid, and wild Atlantic salmon released into the natural environment, earlier studies have documented the short-term consequences of introgression from domesticated fish into wild salmon populations. However, few studies have investigated the joined product of introgression and natural selection after several generations. Here, we investigated the phenotypic response of an Atlantic salmon population that has been subjected to an average of 24% genetic admixture by domesticated conspecifics escaping from fish farms over three decades (approximately 6-7 generations). Individual levels of admixture were positively correlated with increased size at the smolt and adult stages for both sexes, a decrease in the age of male smolts, and a decrease in the age at maturity for males. These life history changes are presumably the consequence of the well-documented directional selection for increased growth in domesticated salmon and are likely maladaptive. However, the most novel result of this study is that admixture was positively linked with delayed date of return to the river, with highly admixed fish arriving up to 26 days later than nonadmixed fish. Potentially, this phenological change provides admixed individuals with a survival advantage in the later phase of the life cycle as it reduces their period of exposure to selection through rod and line angling. We, therefore, conclude that while gene flow from domesticated conspecifics changes life history and phenological traits of wild Atlantic salmon populations, most of which are likely to be maladaptive, when pressured by additional anthropogenic challenges, some changes may confer a fitness advantage for a short part of the life cycle.
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http://dx.doi.org/10.1111/eva.13375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9108307PMC
May 2022

The salmon louse genome: Copepod features and parasitic adaptations.

Genomics 2021 11 14;113(6):3666-3680. Epub 2021 Aug 14.

Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway. Electronic address:

Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.
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http://dx.doi.org/10.1016/j.ygeno.2021.08.002DOI Listing
November 2021

Losing the 'arms race': multiresistant salmon lice are dispersed throughout the North Atlantic Ocean.

R Soc Open Sci 2021 May 26;8(5):210265. Epub 2021 May 26.

Department of Biology, Sea Lice Research Center, University of Bergen, PO Box 7803, 5020 Bergen, Norway.

Nothing lasts forever, including the effect of chemicals aimed to control pests in food production. As old pesticides have been compromised by emerging resistance, new ones have been introduced and turned the odds back in our favour. With time, however, some pests have developed multi-pesticide resistance, challenging our ability to control them. In salmonid aquaculture, the ectoparasitic salmon louse has developed resistance to most of the available delousing compounds. The discovery of genetic markers associated with resistance to organophosphates and pyrethroids made it possible for us to investigate simultaneous resistance to both compounds in approximately 2000 samples of salmon lice from throughout the North Atlantic in the years 2000-2016. We observed widespread and increasing multiresistance on the European side of the Atlantic, particularly in areas with intensive aquaculture. Multiresistant lice were also found on wild Atlantic salmon and sea trout, and also on farmed salmonid hosts in areas where delousing chemicals have not been used. In areas with intensive aquaculture, there are almost no lice left that are sensitive to both compounds. These results demonstrate the speed to which this parasite can develop widespread multiresistance, illustrating why the aquaculture industry has repeatedly lost the arms race with this highly problematic parasite.
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http://dx.doi.org/10.1098/rsos.210265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8150044PMC
May 2021

Genetic response to human-induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway.

Ecol Evol 2021 Feb 18;11(4):1691-1718. Epub 2021 Jan 18.

Institute of Marine Research Bergen Norway.

Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation ( ) between marine and brackish sprat is larger in the comparison Norway-Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.
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http://dx.doi.org/10.1002/ece3.7160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7882954PMC
February 2021

Genomic analysis reveals neutral and adaptive patterns that challenge the current management regime for East Atlantic cod .

Evol Appl 2020 Dec 5;13(10):2673-2688. Epub 2020 Sep 5.

Department of Animal and Aquaculture Sciences Faculty of Biosciences Centre for Integrative Genetics Norwegian University of Life Sciences Ås Norway.

Challenging long-held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod () is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north-east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank.
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http://dx.doi.org/10.1111/eva.13070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7691467PMC
December 2020

Autosomal Pseudogenes Explain Discordances Between Phenotypic Sex and DNA Marker for Sex Identification in Atlantic Salmon.

Front Genet 2020 14;11:544207. Epub 2020 Oct 14.

Institute of Marine Research, Bergen, Norway.

Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are among the best studied fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome () has been identified. However, displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of recent transposition events in this species. We hypothesized the existence of an autosomal copy of , causing apparent discordance between phenotypic and genetic sex, that is transmitted in accordance with autosomal inheritance. To test this, we developed a qPCR methodology to detect the total number of copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2,025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomal copies of in addition to the Y-specific copy present in males. Patterns across families were highly consistent with autosomal inheritance. These autosomal copies appear to have lost the ability to function as a sex determining gene and were only occasionally assigned to the actual sex chromosome in any of the affected families.
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http://dx.doi.org/10.3389/fgene.2020.544207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591749PMC
October 2020

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations.

BMC Genet 2020 10 9;21(1):118. Epub 2020 Oct 9.

Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.

Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies.

Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global F among these populations was 0.015-0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (F > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species' Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean F = 0.065, F = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin.

Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
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http://dx.doi.org/10.1186/s12863-020-00921-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7547435PMC
October 2020

"A cleaner break": Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse ().

Ecol Evol 2020 Jun 5;10(12):6120-6135. Epub 2020 Jun 5.

Institute of Marine Research Bergen Norway.

Capture and long-distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg-laying species. Wrasse from Galicia were highly differentiated from all Scandinavian locations, but more similar to northwestern than southeastern locations. Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographic patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture-mediated translocation of ballan wrasse from Sweden and southern Norway to western and middle Norway has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice.
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http://dx.doi.org/10.1002/ece3.6404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319121PMC
June 2020

Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface.

BMC Genet 2020 02 7;21(1):13. Epub 2020 Feb 7.

Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.

Background: Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations.

Results: After rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets.

Discussion: The observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.
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http://dx.doi.org/10.1186/s12863-020-0816-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006396PMC
February 2020

Evolutionary drivers of kype size in Atlantic salmon (): domestication, age and genetics.

R Soc Open Sci 2019 Apr 17;6(4):190021. Epub 2019 Apr 17.

Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway.

The diversity of reproduction and associated mating patterns in Atlantic salmon () has long captivated evolutionary biologists. exhibit strategies involving migration, bold mating behaviours and radical morphological and physiological change. One such radical change is the elongation and curvature of the lower jaw in sexually mature males into a hook-like appendage called the kype. The kype is a secondary sexual characteristic used in mating hierarchies and a prime candidate for sexual selection. As one of the core global aquaculture fish species, however, mate choice, and thus sexual selection, has been replaced by industrial artificial fertilization seeking to develop more commercially viable strains. Removal of mate choice provides a unique opportunity to examine the kype over successive generations in the absence of sexual selection. Here we use a large-scale common-garden experiment, incorporating six experimental strains (wild, farmed and wild × farmed hybrids), experiencing one to three sea winters, to assess the impact of age and genetic background. After controlling for allometry, fork length-adjusted kype height (AKH) was significantly reduced in the domesticated strain in comparison to two wild strains. Furthermore, genetic variation at a locus on linkage group SSA1 was associated with kype height, and a locus on linkage group SSA23 was associated with fork length-adjusted kype length (AKL). The reduction in fork length-AKH in domesticated salmon suggests that the kype is of importance in mate choice and that it has decreased due to relaxation of sexual selection. Fork length-AKL showed an increase in domesticated individuals, highlighting that it may not be an important cue in mate choice. These results give us insight into the evolutionary significance of the kype, as well as implications of genetic induced phenotypic change caused by domesticated individuals escaping into the natural environment.
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http://dx.doi.org/10.1098/rsos.190021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6502380PMC
April 2019

An extensive common-garden study with domesticated and wild Atlantic salmon in the wild reveals impact on smolt production and shifts in fitness traits.

Evol Appl 2019 Jun 6;12(5):1001-1016. Epub 2019 Mar 6.

Institute of Marine Research Nordnes, Bergen Norway.

Interactions between domesticated escapees and wild conspecifics represent a threat to the genetic integrity and fitness of native populations. For Atlantic salmon, the recurrent presence of large numbers of domesticated escapees in the wild makes it necessary to better understand their impacts on native populations. We planted 254,400 eggs from 75 families of domesticated, F1-hybrid, and wild salmon in a river containing up- and downstream traps. Additionally, 41,630 hatchery smolts of the same pedigrees were released into the river. Over 8 years, 6,669 out-migrating smolts and 356 returning adults were recaptured and identified to their families of origin with DNA. In comparison with wild salmon, domesticated fish had substantially lower egg to smolt survival (1.8% vs. 3.8% across cohorts), they migrated earlier in the year (11.8 days earlier across years), but they only displayed marginally larger smolt sizes and marginally lower smolt ages. Upon return to freshwater, domesticated salmon were substantially larger at age than wild salmon (2.4 vs. 2.0, 4.8 vs. 3.2, and 8.5 vs. 5.6 kg across sexes for 1, 2, and 3 sea-winter fish) and displayed substantially lower released smolt to adult survival (0.41% vs. 0.94% across releases). Overall, egg-to-returning adult survival ratios were 1:0.76:0.30 and 1:0.44:0.21 for wild:F1-hybrid:domesticated salmon, respectively, using two different types of data. This study represents the most updated and extensive analysis of domesticated, hybrid, and wild salmon in the wild and provides the first documentation of a clear genetic difference in the timing of smolt migration-an adaptive trait presumed to be linked with optimal timing of entry to seawater. We conclude that spawning and hybridization of domesticated escapees can lead to (i) reduced wild smolt output and therefore wild adult abundance, through resource competition in freshwater, (ii) reduced total adult abundance due to freshwater competition and reduced marine survival of domesticated salmon, and (iii) maladaptive changes in phenotypic traits.
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http://dx.doi.org/10.1111/eva.12777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503829PMC
June 2019

Cryptic introgression: evidence that selection and plasticity mask the full phenotypic potential of domesticated Atlantic salmon in the wild.

Sci Rep 2018 09 18;8(1):13966. Epub 2018 Sep 18.

Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway.

Domesticated Atlantic salmon grow much faster than wild salmon when reared together in fish tanks under farming conditions (size ratios typically 1:2-3). In contrast, domesticated salmon only display marginally higher growth than wild salmon when reared together in rivers (size ratios typically 1:1-1.2). This begs the question why? Is this a difference in the plastic response driven by divergent energy budgets between the two environments, or is it a result of selection, whereby domesticated salmon that display the greatest growth-potential are those at greatest risk of mortality in the wild? We reared domesticated, hybrid and wild salmon in a river until they smoltified at age 2 or 4, and thereafter in fish tanks for a further 2 years. In the river, there was no difference in the mean size between the groups. In contrast, after being transferred from the river to fish tanks, the domesticated salmon significantly outgrew the wild salmon (maximum size ratio of ~1:1.8). This demonstrates that selection alone cannot be responsible for the lack of growth differences observed between domesticated and wild salmon in rivers. Nevertheless, the final size ratios observed after rearing in tanks were lower than expected in that environment, thus suggesting that plasticity, as for selection, cannot be the sole mechanism. We therefore conclude that a combination of energy-budget plasticity, and selection via growth-potential mortality, cause the differences in growth reaction norms between domesticated and wild salmon across these contrasting environments. Our results imply that if phenotypic changes are not observed in wild populations following introgression of domesticated conspecifics, it does not mean that functional genetic changes have not occurred in the admixed population. Clearly, under the right environmental conditions, the underlying genetic changes will manifest themselves in the phenotype.
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http://dx.doi.org/10.1038/s41598-018-32467-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6143624PMC
September 2018

Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway's coastline.

BMC Genet 2018 07 9;19(1):42. Epub 2018 Jul 9.

Institute of Marine Research (IMR), Postbox 1870, N-5817, Bergen, Norway.

Background: Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated. We sampled > 4000 cod from 55 spawning sites. All fish were genotyped with 6 microsatellite markers and Pan I (Dataset 1). A sub-set of the samples (1295 fish from 17 locations) were also genotyped with an additional 9 microsatellites (Dataset 2). Otoliths were read in order to exclude North East Arctic Cod (NEAC) from the analyses, as and where appropriate.

Results: We found no difference in genetic diversity, measured as number of alleles, allelic richness, heterozygosity nor effective population sizes, in the north-south gradient. In both data sets, weak but significant population genetic structure was revealed (Dataset 1: global F = 0.008, P < 0.0001. Dataset 2: global F = 0.004, P < 0.0001). While no clear genetic groups were identified, genetic differentiation increased among geographically-distinct samples. Although the locus Gmo132 was identified as a candidate for positive selection, possibly through linkage with a genomic region under selection, overall trends remained when this locus was excluded from the analyses. The most common allele in loci Gmo132 and Gmo34 showed a marked frequency change in the north-south gradient, increasing towards the frequency observed in NEAC in the north.

Conclusion: We conclude that Norwegian coastal cod displays significant population genetic structure throughout its entire range, that follows a trend of isolation by distance. Furthermore, we suggest that a gradient of genetic introgression between NEAC and NCC contributes to the observed population genetic structure. The current management regime for coastal cod in Norway, dividing it into two stocks at 62°N, represents a simplification of the level of genetic connectivity among coastal cod in Norway, and needs revision.
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http://dx.doi.org/10.1186/s12863-018-0625-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6036686PMC
July 2018

Judging a salmon by its spots: environmental variation is the primary determinant of spot patterns in Salmo salar.

BMC Ecol 2018 04 12;18(1):14. Epub 2018 Apr 12.

Institute of Marine Research, Postboks 1870, Nordnes, 5817, Bergen, Norway.

Background: In fish, morphological colour changes occur from variations in pigment concentrations and in the morphology, density, and distribution of chromatophores in the skin. However, the underlying mechanisms remain unresolved in most species. Here, we describe the first investigation into the genetic and environmental basis of spot pattern development in one of the world's most studied fishes, the Atlantic salmon. We reared 920 salmon from 64 families of domesticated, F1-hybrid and wild origin in two contrasting environments (Hatchery; tanks for the freshwater stage and sea cages for the marine stage, and River; a natural river for the freshwater stage and tanks for the marine stage). Fish were measured, photographed and spot patterns evaluated.

Results: In the Hatchery experiment, significant but modest differences in spot density were observed among domesticated, F1-hybrid (1.4-fold spottier than domesticated) and wild salmon (1.7-fold spottier than domesticated). A heritability of 6% was calculated for spot density, and a significant QTL on linkage group SSA014 was detected. In the River experiment, significant but modest differences in spot density were also observed among domesticated, F1-hybrid (1.2-fold spottier than domesticated) and wild salmon (1.8-fold spottier than domesticated). Domesticated salmon were sevenfold spottier in the Hatchery vs. River experiment. While different wild populations were used for the two experiments, on average, these were 6.2-fold spottier in the Hatchery vs. River experiment. Fish in the Hatchery experiment displayed scattered to random spot patterns while fish in the River experiment displayed clustered spot patterns.

Conclusions: These data demonstrate that while genetics plays an underlying role, environmental variation represents the primary determinant of spot pattern development in Atlantic salmon.
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http://dx.doi.org/10.1186/s12898-018-0170-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897946PMC
April 2018

A pedigree-based experiment reveals variation in salinity and thermal tolerance in the salmon louse, .

Evol Appl 2017 12 16;10(10):1007-1019. Epub 2017 Aug 16.

Institute of Marine Research Bergen Norway.

The salmon louse is a highly abundant ectoparasitic copepod of salmonids in the North Pacific and Atlantic. Widespread and rapid development of resistance to chemical agents used to delouse salmonids on marine farms is now threatening the continued development of the aquaculture industry and have served as a potent catalyst for the development of alternative pest management strategies. These include freshwater and warm-water treatments to which the louse is sensitive. However, given the well-documented evolutionary capacity of this species, the risk of developing tolerance towards these environmental treatments cannot be dismissed. Two common-garden experiments were performed using full-sibling families of lice identified by DNA parentage testing to investigate whether one of the fundamental premises for evolution, in this context genetic variation in the capacity of coping with fresh or warm water, exists within this species. Significant differences in survival were observed among families in both experiments, although for the salinity experiment, it was not possible to unequivocally disentangle background mortality from treatment-induced mortality. Thus, our data demonstrate genetic variation in tolerance of warm water and are suggestive of genetic variation in salinity tolerance. We conclude that extensive use of these environmental-based treatments to delouse salmonids on commercial farms may drive lice towards increased tolerance.
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http://dx.doi.org/10.1111/eva.12505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680634PMC
December 2017

The Phe362Tyr mutation conveying resistance to organophosphates occurs in high frequencies in salmon lice collected from wild salmon and trout.

Sci Rep 2017 10 27;7(1):14258. Epub 2017 Oct 27.

University of Bergen, Department of Biology, Sea Lice Research Center, P.O. Box 7803, N-5020, Bergen, Norway.

The parasitic salmon louse, and its resistance to chemical delousing agents, represents one of the largest challenges to the salmon aquaculture industry. We genotyped lice sampled from wild salmon and sea trout throughout Norway with the recently identified Phe362Tyr mutation that conveys resistance to organophosphates. These results were compared to data from lice sampled on farmed salmon in the same regions. The resistant (R) allele was observed in salmon lice from wild salmon and sea trout throughout Norway, although its frequency was highest in farming-intense regions. In most regions, the frequency of the R allele was higher in lice collected from wild sea trout than wild Atlantic salmon, and in all regions, the frequency of the R allele was similar in lice collected from wild sea trout and farmed Atlantic salmon. The R allele is only selected for in fish-farms where organophosphates are used for delousing. Therefore, our results suggest extensive exchange of lice between farmed and wild hosts, and indicate that in farming-dense regions in Norway, aquaculture represents a major driver of salmon louse population structure. Finally, these data suggest that the wild hosts within the regions studied will not delay the spread of resistance when organophosphates are used.
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http://dx.doi.org/10.1038/s41598-017-14681-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660183PMC
October 2017

The mechanism (Phe362Tyr mutation) behind resistance in Lepeophtheirus salmonis pre-dates organophosphate use in salmon farming.

Sci Rep 2017 09 27;7(1):12349. Epub 2017 Sep 27.

NMBU School of Veterinary Science, Sea Lice Research Centre, PO Box 8146 Dep., NO-0033, Oslo, Norway.

The salmon louse is an ectoparasitic copepod of salmonids in the marine environment, and represents a global challenge to salmon aquaculture. A major issue is the reliance of the industry on a limited number of chemicals to delouse salmonids on farms, and the high levels of resistance that lice have developed to all of these agents. However, for most of these chemicals, resistance and dispersal mechanisms are unknown. We recently demonstrated that the Phe362Tyr mutation is the primary cause of organophosphate resistance in lice collected on Norwegian farms. In the present study, we genotyped >2000 lice collected throughout the entire North Atlantic in the period 1998-2016, using Phe362Tyr and nine tightly linked SNPs. Our results showed that the Phe362Tyr mutation is strongly linked to lice survival following chemical treatment on farms located throughout the North Atlantic, demonstrating for the first time, that this mutation represents the primary mechanism for organophosphate resistance in salmon lice across the North Atlantic. Additionally, we observed multiple and diverse high frequency haplotypes linked with the allele conveying resistance to organophosphate. We, therefore, conclude that Phe362Tyr is not a de novo mutation, but probably existed in salmon lice before the introduction of organophosphates in commercial aquaculture.
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http://dx.doi.org/10.1038/s41598-017-12384-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617835PMC
September 2017

Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species.

BMC Genomics 2017 01 13;18(1):76. Epub 2017 Jan 13.

Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway.

Background: In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An example of this can be seen in the minke whale species complex. Antarctic minke whales are genetically and morphologically distinct from the common minke found in the north Atlantic and Pacific oceans, and the two species are estimated to have been isolated from each other for 5 million years or more. Recent atypical migrations from the southern to the northern hemisphere have been documented and fertile hybrids and back-crossed individuals between both species have also been identified. However, it is not known whether this represents a contemporary event, potentially driven by ecosystem changes in the Antarctic, or a sporadic occurrence happening over an evolutionary time-scale. We successfully used whole genome resequencing to identify a panel of diagnostic SNPs which now enable us address this evolutionary question.

Results: A large number of SNPs displaying fixed or nearly fixed allele frequency differences among the minke whale species were identified from the sequence data. Five panels of putatively diagnostic markers were established on a genotyping platform for validation of allele frequencies; two panels (26 and 24 SNPs) separating the two species of minke whale, and three panels (22, 23, and 24 SNPs) differentiating the three subspecies of common minke whale. The panels were validated against a set of reference samples, demonstrating the ability to accurately identify back-crossed whales up to three generations.

Conclusions: This work has resulted in the development of a panel of novel diagnostic genetic markers to address inter-oceanic and global contact among the genetically isolated minke whale species and sub-species. These markers, including a globally relevant genetic reference data set for this species complex, are now openly available for researchers interested in identifying other potential whale hybrids in the world's oceans. The approach used here, combining whole genome resequencing and high-throughput genotyping, represents a universal approach to develop similar tools for other species and population complexes.
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http://dx.doi.org/10.1186/s12864-016-3416-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5237217PMC
January 2017

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance.

Biol Lett 2015 Oct;11(10)

Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK

Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10(-7) mutations/site/year (95% confidence interval 3.75 × 10(-8)-1.12 × 10(-6)). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.
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http://dx.doi.org/10.1098/rsbl.2015.0561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650172PMC
October 2015

Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis.

BMC Genomics 2014 Oct 26;15:937. Epub 2014 Oct 26.

Institute of Marine Research, Nordnes, Bergen, Norway.

Background: The salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. Lice control on farms is reliant upon a few groups of pesticides that have all shown time-limited efficiency due to resistance development. However, to date, this example of human-induced evolution is poorly documented at the population level due to the lack of molecular tools. As such, important evolutionary and management questions, linked to the development and dispersal of pesticide resistance in this parasite, remain unanswered. Here, we introduce the first Single Nucleotide Polymorphism (SNP) array for the salmon louse, which includes 6000 markers, and present a population genomic scan using this array on 576 lice from twelve farms distributed across the North Atlantic.

Results: Our results support the hypothesis of a single panmictic population of lice in the Atlantic, and importantly, revealed very strong selective sweeps on linkage groups 1 and 5. These sweeps included candidate genes potentially connected to pesticide resistance. After genotyping a further 576 lice from 12 full sibling families, a genome-wide association analysis established a highly significant association between the major sweep on linkage group 5 and resistance to emamectin benzoate, the most widely used pesticide in salmonid aquaculture for more than a decade.

Conclusions: The analysis of conserved haplotypes across samples from the Atlantic strongly suggests that emamectin benzoate resistance developed at a single source, and rapidly spread across the Atlantic within the period 1999 when the chemical was first introduced, to 2010 when samples for the present study were obtained. These results provide unique insights into the development and spread of pesticide resistance in the marine environment, and identify a small genomic region strongly linked to emamectin benzoate resistance. Finally, these results have highly significant implications for the way pesticide resistance is considered and managed within the aquaculture industry.
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http://dx.doi.org/10.1186/1471-2164-15-937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223847PMC
October 2014

Genetic influences on brain gene expression in rats selected for tameness and aggression.

Genetics 2014 Nov 3;198(3):1277-90. Epub 2014 Sep 3.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany Department of Human Genetics, Gonda Center, University of California, Los Angeles, California 90095

Interindividual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior toward humans for >64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40, and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals.
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http://dx.doi.org/10.1534/genetics.114.168948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224166PMC
November 2014

Clinical presentation of dengue by serotype and year of epidemic in Martinique.

Am J Trop Med Hyg 2014 Jul 27;91(1):138-45. Epub 2014 May 27.

Emergency and Intensive Care Department, University Hospital, Fort-de-France, Martinique; Laboratory of Virology and Immunology, University Hospital, Fort-de-France, Martinique; Regional office (Cire) of the French Institute for Public Health Surveillance, Fort-de-France, Martinique; Department of Infectious and Tropical Diseases and CIC-EC (Inserm CIE 802), University Hospital, Fort-de-France, Martinique.

During the last decade Martinique experienced four dengue epidemics, each characterized by the predominance of 1 or 2 serotypes. In this retrospective database analysis, we investigated the relationship between dengue serotype and disease severity. Data on dengue were collected from 715 patients (male/female ratio 0.87), 14 to 91 years of age (median 35 years) examined in the adult emergency department between 2005 and 2010. In this series, DENV-4 infections more frequently had a milder clinical presentation. The DENV-2 infections were most often secondary infections admitted at the critical phase of dengue illness with signs of plasma leakage. The DENV-1 infections were disabling, particularly in females, and most often led to disease of intermediate severity, without overt plasma leakage. These data were consistent with there being differences in virulence between serotypes, regardless of the host's immune status. However, secondary DENV-2 infections showed an increased risk of plasma leakage.
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http://dx.doi.org/10.4269/ajtmh.13-0595DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080553PMC
July 2014

MAPfastR: quantitative trait loci mapping in outbred line crosses.

G3 (Bethesda) 2013 Dec 9;3(12):2147-9. Epub 2013 Dec 9.

Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden.

MAPfastR is a software package developed to analyze quantitative trait loci data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate quantitative trait loci analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7.
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http://dx.doi.org/10.1534/g3.113.008623DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852377PMC
December 2013

Atlantic salmon populations invaded by farmed escapees: quantifying genetic introgression with a Bayesian approach and SNPs.

BMC Genet 2013 Aug 23;14:74. Epub 2013 Aug 23.

Section of Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway.

Background: Many native Atlantic salmon populations have been invaded by domesticated escapees for three decades or longer. However, thus far, the cumulative level of gene-flow that has occurred from farmed to wild salmon has not been reported for any native Atlantic salmon population. The aim of the present study was to investigate temporal genetic stability in native populations, and, quantify gene-flow from farmed salmon that caused genetic changes where they were observed. This was achieved by genotyping historical and contemporary samples from 20 populations covering all of Norway with recently identified single nucleotide polymorphism markers that are collectively diagnostic for farmed and wild salmon. These analyses were combined with analysis of farmed salmon and implementation of Approximate Bayesian computation based simulations.

Results: Five of the populations displayed statistically significant temporal genetic changes. All five of these populations became more similar to a pool of farmed fish with time, strongly suggesting introgression of farmed fish as the primary cause. The remaining 15 populations displayed weak or non-significant temporal genetic changes. Estimated introgression of farmed fish ranged from 2-47% per population using approximate Bayesian computation. Thus, some populations exhibited high degrees of farmed salmon introgression while others were more or less unaffected. The observed frequency of escapees in each population was moderately correlated with estimated introgression per population R² = 0.47 P < 0.001. Genetic isolation by distance existed within the historical and contemporary data sets, however, the among-population level of divergence decreased with time.

Conclusions: This is the first study to quantify cumulative introgression of farmed salmon in any native Atlantic salmon population. The estimations demonstrate that the level of introgression has been population-specific, and that the level of introgression is not solely predicted by the frequency of escapees observed in the population. However, some populations have been strongly admixed with farmed salmon, and these data provide policy makers with unique information to address this situation.
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http://dx.doi.org/10.1186/1471-2156-14-74DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765417PMC
August 2013

ParallelStructure: a R package to distribute parallel runs of the population genetics program STRUCTURE on multi-core computers.

PLoS One 2013 29;8(7):e70651. Epub 2013 Jul 29.

Department of Population Genetics, Institute of Marine Research, Bergen, Norway.

This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070651PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726640PMC
August 2014

Three decades of farmed escapees in the wild: a spatio-temporal analysis of Atlantic salmon population genetic structure throughout Norway.

PLoS One 2012 15;7(8):e43129. Epub 2012 Aug 15.

Section of Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway.

Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world's largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15-30 years. In order to study the potential genetic impact, we conducted a spatio-temporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970-2010. Based upon the analysis of 22 microsatellites, individual admixture, F(ST) and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P=0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global F(ST) =0.038) and contemporary data sets (global F(ST) =0.030), although significantly reduced with time (P=0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global F(ST) dropped from 0.058 to 0.039, P=0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043129PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419752PMC
January 2013

Clinical presentation of dengue among patients admitted to the adult emergency department of a tertiary care hospital in Martinique: implications for triage, management, and reporting.

Ann Emerg Med 2012 Jan 8;59(1):42-50. Epub 2011 Sep 8.

Emergency and Intensive Care Department, University Hospital, Fort-de-France, Martinique.

Study Objective: During dengue epidemics, emergency physicians face large numbers of patients with acute febrile illness. Triage algorithms and appropriate reporting systems are useful to manage patients and prioritize resources. We identify possible adaptations to these systems to improve the management of patients during epidemics.

Methods: In a prospective observational study in the adult emergency department (ED) of a tertiary care hospital, we enrolled all patients with febrile illness and a confirmed diagnosis of dengue (ribonucleic acid identification). We then retrospectively classified cases according to the initial clinical presentation at the ED.

Results: We enrolled 715 patients (332 male patients), aged 14 to 91 years (median 35 years). Severe illness was documented in 332 cases (46.4%) and was mostly caused by serotype 2, or a secondary infection of any serotype. Severe forms included dengue hemorrhagic fever or dengue shock syndrome (104/332; 31.3%), severe bleeding (9/332; 2.7%), and acute organ failure (56/332; 16.9%). The other patients with severe illness (171/332; 51.5%) presented with symptoms of presyncope, intense weakness, prolonged gastrointestinal symptoms, and hypotension. This presentation was common during epidemics and appeared to be associated with dehydration and electrolyte loss that improved markedly within 24 hours with saline solution infusion. This group did not have evidence of plasma leakage, although similar features were observed in patients with dengue hemorrhagic fever/dengue shock syndrome.

Conclusion: Dengue has a wide range of clinical presentations in the ED. Many patients who appear seriously ill on presentation will respond to intravenous fluids.
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http://dx.doi.org/10.1016/j.annemergmed.2011.08.010DOI Listing
January 2012

Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.

PLoS Genet 2011 Jul 21;7(7):e1002180. Epub 2011 Jul 21.

Department of Animal Breeding and Genetics, Swedish University of Agriculture Sciences (SLU), Uppsala, Sweden.

Dissection of the genetic architecture of complex traits persists as a major challenge in biology; despite considerable efforts, much remains unclear including the role and importance of genetic interactions. This study provides empirical evidence for a strong and persistent contribution of both second- and third-order epistatic interactions to long-term selection response for body weight in two divergently selected chicken lines. We earlier reported a network of interacting loci with large effects on body weight in an F(2) intercross between these high- and low-body weight lines. Here, most pair-wise interactions in the network are replicated in an independent eight-generation advanced intercross line (AIL). The original report showed an important contribution of capacitating epistasis to growth, meaning that the genotype at a hub in the network releases the effects of one or several peripheral loci. After fine-mapping of the loci in the AIL, we show that these interactions were persistent over time. The replication of five of six originally reported epistatic loci, as well as the capacitating epistasis, provides strong empirical evidence that the originally observed epistasis is of biological importance and is a contributor in the genetic architecture of this population. The stability of genetic interaction mechanisms over time indicates a non-transient role of epistasis on phenotypic change. Third-order epistasis was for the first time examined in this study and was shown to make an important contribution to growth, which suggests that the genetic architecture of growth is more complex than can be explained by two-locus interactions only. Our results illustrate the importance of designing studies that facilitate exploration of epistasis in populations for obtaining a comprehensive understanding of the genetics underlying a complex trait.
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http://dx.doi.org/10.1371/journal.pgen.1002180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140984PMC
July 2011

Fine mapping and replication of QTL in outbred chicken advanced intercross lines.

Genet Sel Evol 2011 Jan 17;43(1). Epub 2011 Jan 17.

Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F(2) populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F(2) animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.

Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F(2) population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.

Results: Five of the nine QTL detected with the original F(2) population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.

Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.
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http://dx.doi.org/10.1186/1297-9686-43-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3034666PMC
January 2011
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