| 1. |
- Bernatchez, Louis, et al.
(författare)
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Harnessing the Power of Genomics to Secure the Future of Seafood
- 2017
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Ingår i: Trends in Ecology and Evolution. - : Elsevier BV. - 0169-5347. ; 32:9, s. 665-680
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Forskningsöversikt (refereegranskat)abstract
- Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward. Advancements of genetic technologies now allow the collection of genome-wide data in nonmodel species in a cost-effective manner. These genomic-informed technologies allow addressing a comprehensive spectrum of needs and applications relevant to fisheries, aquaculture, and biosecurity. Genomics tools also improve our understanding of how aquatic organisms adapt and respond to the environment, and improve our ability to monitor environmental variation and exploited species. Genomic approaches are now rapidly replacing traditional genetic markers, but their application in fisheries and aquaculture management has stagnated when compared to agriculture where they have long been used for improved production. There is no reason to further delay the application of genomic tools in fisheries management and aquaculture production.
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| 2. |
- Backström, Niclas, et al.
(författare)
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A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution
- 2008
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 179, s. 1479-1495
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Tidskriftsartikel (refereegranskat)abstract
- By taking advantage of a recently developed reference markerset for avian genome analysis we have constructed a gene-basedgenetic map of the collared flycatcher, an important "ecologicalmodel" for studies of life-history evolution, sexual selection,speciation, and quantitative genetics. A pedigree of 322 birdsfrom a natural population was genotyped for 384 single nucleotidepolymorphisms (SNPs) from 170 protein-coding genes and 71 microsatellites.Altogether, 147 gene markers and 64 microsatellites form 33linkage groups with a total genetic distance of 1787 cM. Malerecombination rates are, on average, 22% higher than femalerates (total distance 1982 vs. 1627 cM). The ability to anchorthe collared flycatcher map with the chicken genome via thegene-based SNPs revealed an extraordinary degree of both syntenyand gene-order conservation during avian evolution. The greatmajority of chicken chromosomes correspond to a single linkagegroup in collared flycatchers, with only a few cases of inter-and intrachromosomal rearrangements. The rate of chromosomaldiversification, fissions/fusions, and inversions combined isthus considerably lower in birds (0.05/MY) than in mammals (0.6–2.0/MY).A dearth of repeat elements, known to promote chromosomal breakage,in avian genomes may contribute to their stability. The degreeof genome stability is likely to have important consequencesfor general evolutionary patterns and may explain, for example,the comparatively slow rate by which genetic incompatibilityamong lineages of birds evolves.
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| 3. |
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| 4. |
- Johansson, Markus, et al.
(författare)
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Does habitat fragmentation reduce fitness and adaptability? : A case study of the common frog (Rana temporaria)
- 2007
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 16:13, s. 2693-2700
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Tidskriftsartikel (refereegranskat)abstract
- Studies examining the effects of anthropogenic habitat fragmentation on both neutral and adaptive genetic variability are still scarce. We compared tadpole fitness-related traits (viz. survival probability and body size) among populations of the common frog (Rana temporaria) from fragmented (F) and continuous (C) habitats that differed significantly in population sizes (C > F) and genetic diversity (C > F) in neutral genetic markers. Using data from common garden experiments, we found a significant positive relationship between the mean values of the fitness related traits and the amount of microsatellite variation in a given population. While genetic differentiation in neutral marker loci (F-ST) tended to be more pronounced in the fragmented than in the continuous habitat, genetic differentiation in quantitative traits (Q(ST)) exceeded that in neutral marker traits in the continuous habitat (i.e. Q(ST) > F-ST), but not in the fragmented habitat (i.e. Q(ST) approximate to F-ST). These results suggest that the impact of random genetic drift relative to natural selection was higher in the fragmented landscape where populations were small, and had lower genetic diversity and fitness as compared to populations in the more continuous landscape. The findings highlight the potential importance of habitat fragmentation in impairing future adaptive potential of natural populations.
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| 5. |
- Johansson, Markus, 1974-
(författare)
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Effects of Agriculture on Abundance, Genetic Diversity and Fitness in the Common Frog, Rana temporaria
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aims of this thesis were to evaluate the effects of agriculture on amphibians in terms of (i) population genetic consequences of agriculture-induced spatial changes of the landscape and (ii) local adaptation and tolerance to frequently used agrochemicals. The study was performed using the common frog Rana temporaria as a model. Abundance, occurrence, genetic diversity and gene flow were negatively affected by agriculture in southern Sweden, but unaffected or even positively affected by agriculture in the central and northern regions, respectively. These test parameters correlated positively with landscape diversity both in the south and in the north. Moreover, the size and occurrence of R. temporaria populations decreased towards the north i.e. the margin of the species’ distribution range. In accordance with theoretical expectations, genetic variability decreased and population substructuring increased as a negative function of (effective) population size. Southern Swedish common frogs are naturally exposed to higher levels of nitrates, and thus have a higher tolerance to high nitrate levels than their northern conspecifics. This suggests local adaptation to naturally varying nitrate levels. Consequently, increased anthropogenic supplementation of nitrate could impact more the northern than the southern Swedish common frog populations. Exposure to the pesticides azoxystrobin, cyanazine and permethrin at ecologically relevant concentrations had small or no effects on R. temporaria tadpoles. The populations with lowest microsatellite variation (fragmented populations) in southern Sweden had considerably lower fitness in terms of survival and growth as compared to those with the highest genetic variability (non-fragmented populations). The results indicate that populations with low levels of neutral genetic variability were phenotypically less differentiated than populations with higher levels of variability. One possible explanation for this is that the degree of population differentiation in low variability populations has been constrained due to lack of suitable genetic variation or inefficiency of selection relative to genetic drift.
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| 8. |
- Kjaerner-Semb, Erik, et al.
(författare)
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Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere
- 2021
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Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 14:2, s. 446-461
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Tidskriftsartikel (refereegranskat)abstract
- Most Atlantic salmon (Salmo salarL.) populations follow an anadromous life cycle, spending early life in freshwater, migrating to the sea for feeding, and returning to rivers to spawn. At the end of the last ice age similar to 10,000 years ago, several populations of Atlantic salmon became landlocked. Comparing their genomes to their anadromous counterparts can help identify genetic variation related to either freshwater residency or anadromy. The objective of this study was to identify consistently divergent loci between anadromous and landlocked Atlantic salmon strains throughout their geographical distribution, with the long-term aim of identifying traits relevant for salmon aquaculture, including fresh and seawater growth, omega-3 metabolism, smoltification, and disease resistance. We used a Pool-seq approach (n = 10-40 individuals per population) to sequence the genomes of twelve anadromous and six landlocked Atlantic salmon populations covering a large part of the Northern Hemisphere and conducted a genomewide association study to identify genomic regions having been under different selection pressure in landlocked and anadromous strains. A total of 28 genomic regions were identified and includedcadm1on Chr 13 andppargc1aon Chr 18. Seven of the regions additionally displayed consistently reduced heterozygosity in fish obtained from landlocked populations, including the genes gpr132, cdca4, and sertad2 on Chr 15. We also found 16 regions, includingigf1on Chr 17, which consistently display reduced heterozygosity in the anadromous populations compared to the freshwater populations, indicating relaxed selection on traits associated with anadromy in landlocked salmon. In conclusion, we have identified 37 regions which may harbor genetic variation relevant for improving fish welfare and quality in the salmon farming industry and for understanding life-history traits in fish.
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| 9. |
- Lehtonen, Paula K., et al.
(författare)
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Geographic patterns of genetic differentiation and plumage colour variation are different in the pied flycatcher (Ficedula hypoleuca)
- 2009
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Ingår i: Molecular Ecology. - 0962-1083. ; 18:21, s. 4463-4476
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Tidskriftsartikel (refereegranskat)abstract
- The pied flycatcher is one of the most phenotypically variable bird species in Europe. The geographic variation in phenotypes has often been attributed to spatial variation in selection regimes that is associated with the presence or absence of the congeneric collared flycatcher. Spatial variation in phenotypes could however also be generated by spatially restricted gene flow and genetic drift. We examined the genetic population structure of pied flycatchers across the breeding range and applied the phenotypic Q(ST) (P(ST))-F(ST) approach to detect indirect signals of divergent selection on dorsal plumage colouration in pied flycatcher males. Allelic frequencies at neutral markers were found to significantly differ among populations breeding in central and southern Europe whereas northerly breeding pied flycatchers were found to be one apparently panmictic group of individuals. Pairwise differences between phenotypic (P(ST)) and neutral genetic distances (F(ST)) were positively correlated after removing the most differentiated Spanish and Swiss populations from the analysis, suggesting that genetic drift may have contributed to the observed phenotypic differentiation in some parts of the pied flycatcher breeding range. Differentiation in dorsal plumage colouration however greatly exceeded that observed at neutral genetic markers, which indicates that the observed pattern of phenotypic differentiation is unlikely to be solely maintained by restricted gene flow and genetic drift.
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| 10. |
- Palo, Jukka, et al.
(författare)
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Latitudinal divergence of common frog (Rana temporaria) life-history traits by natural selection : evidence for a comparison of molecular and quantitative genetic data
- 2003
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 12:7, s. 1963-1978
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Tidskriftsartikel (refereegranskat)abstract
- The relative roles of natural selection and direct environmental induction, as well as of natural selection and genetic drift, in creating clinal latitudinal variation in quantitative traits have seldom been assessed in vertebrates. To address these issues, we compared molecular and quantitative genetic differentiation between six common frog (Rana temporaria) populations along an approximately 1600 km long latitudinal gradient across Scandinavia. The degree of population differentiation (QST approximately 0.81) in three heritable quantitative traits (age and size at metamorphosis, growth rate) exceeded that in eight (neutral) microsatellite loci (FST = 0.24). Isolation by distance was clear for both neutral markers and quantitative traits, but considerably stronger for one of the three quantitative traits than for neutral markers. QST estimates obtained using animals subjected to different rearing conditions (temperature and food treatments) revealed some environmental dependency in patterns of population divergence in quantitative traits, but in general, these effects were weak in comparison to overall patterns. Pairwise comparisons of FST and QST estimates across populations and treatments revealed that the degree of quantitative trait differentiation was not generally predictable from knowledge of that in molecular markers. In fact, both positive and negative correlations were observed depending on conditions where the quantitative genetic variability had been measured. All in all, the results suggest a very high degree of genetic subdivision both in neutral marker genes and genes coding quantitative traits across a relatively recently (< 9000 years) colonized environmental gradient. In particular, they give evidence for natural selection being the primary agent behind the observed latitudinal differentiation in quantitative traits.
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