The Experts below are selected from a list of 297 Experts worldwide ranked by ideXlab platform
Leif Andersson - One of the best experts on this subject based on the ideXlab platform.
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genetic origin and salinity history influence the reproductive success of Atlantic Herring
Marine Ecology Progress Series, 2019Co-Authors: Florian Berg, Aril Slotte, Leif Andersson, Arild FolkvordAbstract:Atlantic Herring populations inhabit environments ranging in salinity from fully marine to nearly freshwater, but their relative reproductive success in these respective environments remains unclea ...
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moderate nucleotide diversity in the Atlantic Herring is associated with a low mutation rate
eLife, 2017Co-Authors: Chungang Feng, Leif Andersson, Arild Folkvord, Mats E Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Nima Rafati, Michele CasiniAbstract:Evolution by natural selection favours the survival of individuals that are well suited to their environment. This process depends on genetic differences between individuals that make some more able to survive than others. These genetic differences are the result of mutations in DNA of germ-line cells, that is, the cells that produce egg cells and sperm. These mutations mean that new offspring always have a few small differences in some of the genes they inherited from each of their parents. DNA contains strings of molecules known as bases. These act as individual “letters” in the genetic code of an individual. Rapid sequencing of DNA to find out the order of these bases makes it possible to study the rate of mutations within a species. This provides a way to measure how different an individual is from its parents and, by extension, the potential of the species to diversify and adapt to different environments. There are over a trillion Atlantic Herring in the Atlantic Ocean, so this fish is an ideal model to study the effects of germ-line mutations on genetic diversity. In 2016, a group of researchers reported that there is relatively little genetic diversity across Atlantic Herring. Given the large population, this suggested that the mutation rate in this species may be low. Feng, Pettersson, Lamichhaney et al. – who were also involved with the earlier work – sequenced the DNA of two families of Atlantic Herring raised in captivity to calculate the rate of germ-line mutations in this species. The results showed that, on average, two changes occur per one billion letters in the genetic code in each generation. That is one to two new mutations per egg cell or sperm. This is the lowest mutation rate yet recorded in any animal with a backbone and is around six times lower than the mutation rate in humans. Whilst the low mutation rate in Atlantic Herring means there are few differences between individual fish, the extremely large number of these fish on the planet still means that there is enough diversity across the population to allow the species to adapt to changing conditions. This work is important for conservation as it highlights the great variation in potential genetic diversity across species. Future work will need to examine why the mutation rate in Atlantic Herring is so low and compare it more widely to mutation rates in other species.
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moderate nucleotide diversity in the Atlantic Herring is associated with a low mutation rate
bioRxiv, 2017Co-Authors: Chungang Feng, Arild Folkvord, Mats E Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Nima Rafati, Michele Casini, Leif AnderssonAbstract:The Atlantic Herring (Clupea harengus) is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π=0.3%), only three-fold higher than in human. The expected nucleotide diversity for selectively neutral alleles is a function of population size and the mutation rate, and it is strongly affected by demographic history. Here, we present a pedigree-based estimation of the mutation rate in the Atlantic Herring. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 1.7 x 10-9 per base per generation. There was no significant difference in the frequency of paternal and maternal mutations (8 and 7, respectively). Furthermore, we observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development when we do not expect a strong gender effect. The now estimated mutation rate — the lowest among vertebrates analyzed to date — partially explains the discrepancy between the rather low nucleotide diversity in Herring and its huge census population size (>10^11). But our analysis indicates that a species like the Herring will never reach its expected nucleotide diversity for selectively neutral alleles primarily because of fluctuations in population size due to climate variation during the millions of years it takes to build up a high nucleotide diversity. In addition, background selection and selective sweeps lead to reductions in nucleotide diversity at linked neutral sites.
Catriona Clemmesen - One of the best experts on this subject based on the ideXlab platform.
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the swimming kinematics and foraging behavior of larval Atlantic Herring clupea harengus l are unaffected by elevated pco2
Journal of Experimental Marine Biology and Ecology, 2015Co-Authors: Rommel Maneja, Arild Folkvord, Andrea Frommel, Howard I Browman, Audrey J Geffen, Uwe Piatkowski, Caroline M F Durif, Reidun M Bjelland, Anne Berit Skiftesvik, Catriona ClemmesenAbstract:Abstract The kinematics of swimming behavior of Atlantic Herring larvae cultured under three p CO 2 conditions (control — 370, medium — 1800, and high — 4200 μatm) were extracted at 34 days post-hatch (dph) from swim path recordings obtained using silhouette video photography. The swim paths were analyzed for move duration, speed and length, stop duration, and horizontal and vertical turn angles to determine the effects of elevated p CO 2 on fish larval behavior. The swimming kinematics and occurrence of S-postures in Atlantic Herring larvae that had survived to 34-dph were unaffected by extremely elevated levels of seawater p CO 2 , indicating that at least some larvae in the population are resilient to ocean acidification.
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the proteome of Atlantic Herring clupea harengus l larvae is resistant to elevated pco2
Marine Pollution Bulletin, 2014Co-Authors: Rommel Maneja, Andrea Frommel, Audrey J Geffen, Anne Berit Skiftesvik, Catriona Clemmesen, R Dineshram, Vengatesen Thiyagarajan, Howard I BrowmanAbstract:Abstract Elevated anthropogenic pCO2 can delay growth and impair otolith structure and function in the larvae of some fishes. These effects may concurrently alter the larva’s proteome expression pattern. To test this hypothesis, Atlantic Herring larvae were exposed to ambient (370 μatm) and elevated (1800 μatm) pCO2 for one-month. The proteome structure of the larvae was examined using a 2-DE and mass spectrometry. The length of Herring larvae was marginally less in the elevated pCO2 treatment compared to the control. The proteome structure was also different between the control and treatment, but only slightly: the expression of a small number of proteins was altered by a factor of less than 2-fold at elevated pCO2. This comparative proteome analysis suggests that the proteome of Herring larvae is resilient to elevated pCO2. These observations suggest that Herring larvae can cope with levels of CO2 projected for near future without significant proteome-wide changes.
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organ damage in Atlantic Herring larvae as a result of ocean acidification
Ecological Applications, 2014Co-Authors: Andrea Frommel, Arild Folkvord, Rommel Maneja, Audrey J Geffen, Uwe Piatkowski, D M Lowe, Christine Pascoe, Catriona ClemmesenAbstract:The dissolution of anthropogenically emitted excess carbon dioxide lowers the pH of the world's ocean water. The larvae of mass spawning marine fishes may be particularly vulnerable to such ocean acidification (OA), yet the generality of earlier results is unclear. Here we show the detrimental effects of OA on the development of a commercially important fish species, the Atlantic Herring (Clupea harengus). Larvae were reared at three levels of CO2: today (0.0385 kPa), end of next century (0.183 kPa), and a coastal upwelling scenario (0.426 kPa), under near-natural conditions in large outdoor tanks. Exposure to elevated CO2 levels resulted in stunted growth and development, decreased condition, and severe tissue damage in many organs, with the degree of damage increasing with CO2 concentration. This complements earlier studies of OA on Atlantic cod larvae that revealed similar organ damage but at increased growth rates and no effect on condition.
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effect of ocean acidification on early life stages of Atlantic Herring clupea harengus l
Biogeosciences, 2011Co-Authors: Andrea Franke, Catriona ClemmesenAbstract:Due to atmospheric accumulation of anthropogenic CO2 the partial pressure of carbon dioxide (pCO2) in surface seawater increases and the pH decreases. This process known as ocean acidification might have severe effects on marine organisms and ecosystems. The present study addresses the effect of ocean acidification on early developmental stages, the most sensitive stages in life history, of the Atlantic Herring (Clupea harengus L.). Eggs of the Atlantic Herring were fertilized and incubated in artificially acidified seawater (pCO2 1260, 1859, 2626, 2903, 4635 μatm) and a control treatment (pCO2 480 μatm) until the main hatch of Herring larvae occurred. The development of the embryos was monitored daily and newly hatched larvae were sampled to analyze their morphometrics, and their condition by measuring the RNA/DNA ratios. Elevated pCO2 neither affected the embryogenesis nor the hatch rate. Furthermore the results showed no linear relationship between pCO2 and total length, dry weight, yolk sac area and otolith area of the newly hatched larvae. For pCO2 and RNA/DNA ratio, however, a significant negative linear relationship was found. The RNA concentration at hatching was reduced at higher pCO2 levels, which could lead to a decreased protein biosynthesis. The results indicate that an increased pCO2 can affect the metabolism of Herring embryos negatively. Accordingly, further somatic growth of the larvae could be reduced. This can have consequences for the larval fish, since smaller and slow growing individuals have a lower survival potential due to lower feeding success and increased predation mortality. The regulatory mechanisms necessary to compensate for effects of hypercapnia could therefore lead to lower larval survival. Since the recruitment of fish seems to be determined during the early life stages, future research on the factors influencing these stages are of great importance in fisheries science.
Arild Folkvord - One of the best experts on this subject based on the ideXlab platform.
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genetic origin and salinity history influence the reproductive success of Atlantic Herring
Marine Ecology Progress Series, 2019Co-Authors: Florian Berg, Aril Slotte, Leif Andersson, Arild FolkvordAbstract:Atlantic Herring populations inhabit environments ranging in salinity from fully marine to nearly freshwater, but their relative reproductive success in these respective environments remains unclea ...
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moderate nucleotide diversity in the Atlantic Herring is associated with a low mutation rate
eLife, 2017Co-Authors: Chungang Feng, Leif Andersson, Arild Folkvord, Mats E Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Nima Rafati, Michele CasiniAbstract:Evolution by natural selection favours the survival of individuals that are well suited to their environment. This process depends on genetic differences between individuals that make some more able to survive than others. These genetic differences are the result of mutations in DNA of germ-line cells, that is, the cells that produce egg cells and sperm. These mutations mean that new offspring always have a few small differences in some of the genes they inherited from each of their parents. DNA contains strings of molecules known as bases. These act as individual “letters” in the genetic code of an individual. Rapid sequencing of DNA to find out the order of these bases makes it possible to study the rate of mutations within a species. This provides a way to measure how different an individual is from its parents and, by extension, the potential of the species to diversify and adapt to different environments. There are over a trillion Atlantic Herring in the Atlantic Ocean, so this fish is an ideal model to study the effects of germ-line mutations on genetic diversity. In 2016, a group of researchers reported that there is relatively little genetic diversity across Atlantic Herring. Given the large population, this suggested that the mutation rate in this species may be low. Feng, Pettersson, Lamichhaney et al. – who were also involved with the earlier work – sequenced the DNA of two families of Atlantic Herring raised in captivity to calculate the rate of germ-line mutations in this species. The results showed that, on average, two changes occur per one billion letters in the genetic code in each generation. That is one to two new mutations per egg cell or sperm. This is the lowest mutation rate yet recorded in any animal with a backbone and is around six times lower than the mutation rate in humans. Whilst the low mutation rate in Atlantic Herring means there are few differences between individual fish, the extremely large number of these fish on the planet still means that there is enough diversity across the population to allow the species to adapt to changing conditions. This work is important for conservation as it highlights the great variation in potential genetic diversity across species. Future work will need to examine why the mutation rate in Atlantic Herring is so low and compare it more widely to mutation rates in other species.
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moderate nucleotide diversity in the Atlantic Herring is associated with a low mutation rate
bioRxiv, 2017Co-Authors: Chungang Feng, Arild Folkvord, Mats E Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Nima Rafati, Michele Casini, Leif AnderssonAbstract:The Atlantic Herring (Clupea harengus) is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π=0.3%), only three-fold higher than in human. The expected nucleotide diversity for selectively neutral alleles is a function of population size and the mutation rate, and it is strongly affected by demographic history. Here, we present a pedigree-based estimation of the mutation rate in the Atlantic Herring. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 1.7 x 10-9 per base per generation. There was no significant difference in the frequency of paternal and maternal mutations (8 and 7, respectively). Furthermore, we observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development when we do not expect a strong gender effect. The now estimated mutation rate — the lowest among vertebrates analyzed to date — partially explains the discrepancy between the rather low nucleotide diversity in Herring and its huge census population size (>10^11). But our analysis indicates that a species like the Herring will never reach its expected nucleotide diversity for selectively neutral alleles primarily because of fluctuations in population size due to climate variation during the millions of years it takes to build up a high nucleotide diversity. In addition, background selection and selective sweeps lead to reductions in nucleotide diversity at linked neutral sites.
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the swimming kinematics and foraging behavior of larval Atlantic Herring clupea harengus l are unaffected by elevated pco2
Journal of Experimental Marine Biology and Ecology, 2015Co-Authors: Rommel Maneja, Arild Folkvord, Andrea Frommel, Howard I Browman, Audrey J Geffen, Uwe Piatkowski, Caroline M F Durif, Reidun M Bjelland, Anne Berit Skiftesvik, Catriona ClemmesenAbstract:Abstract The kinematics of swimming behavior of Atlantic Herring larvae cultured under three p CO 2 conditions (control — 370, medium — 1800, and high — 4200 μatm) were extracted at 34 days post-hatch (dph) from swim path recordings obtained using silhouette video photography. The swim paths were analyzed for move duration, speed and length, stop duration, and horizontal and vertical turn angles to determine the effects of elevated p CO 2 on fish larval behavior. The swimming kinematics and occurrence of S-postures in Atlantic Herring larvae that had survived to 34-dph were unaffected by extremely elevated levels of seawater p CO 2 , indicating that at least some larvae in the population are resilient to ocean acidification.
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organ damage in Atlantic Herring larvae as a result of ocean acidification
Ecological Applications, 2014Co-Authors: Andrea Frommel, Arild Folkvord, Rommel Maneja, Audrey J Geffen, Uwe Piatkowski, D M Lowe, Christine Pascoe, Catriona ClemmesenAbstract:The dissolution of anthropogenically emitted excess carbon dioxide lowers the pH of the world's ocean water. The larvae of mass spawning marine fishes may be particularly vulnerable to such ocean acidification (OA), yet the generality of earlier results is unclear. Here we show the detrimental effects of OA on the development of a commercially important fish species, the Atlantic Herring (Clupea harengus). Larvae were reared at three levels of CO2: today (0.0385 kPa), end of next century (0.183 kPa), and a coastal upwelling scenario (0.426 kPa), under near-natural conditions in large outdoor tanks. Exposure to elevated CO2 levels resulted in stunted growth and development, decreased condition, and severe tissue damage in many organs, with the degree of damage increasing with CO2 concentration. This complements earlier studies of OA on Atlantic cod larvae that revealed similar organ damage but at increased growth rates and no effect on condition.
Carl André - One of the best experts on this subject based on the ideXlab platform.
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Temporally stable genetic structure of Atlantic Herring (Clupea harengus) in Swedish waters but indications of small local effective population size
2020Co-Authors: Lena C. Larsson, Linda Laikre, Carl André, Thomas G. Dahlgren, Nils RymanAbstract:Genes are the foundation of evolution and biodiversity. The genetic structure of natural populations needs to be understood to maintain exploited resources rationally. This thesis focuses on genetic variability and methods to determine spatial and temporal genetic heterogeneities. Intense human exploitation generates particular challenges to conserve genetic diversity of fishes since it has genetic effects. My research concerns one of our most valuable fish species: the Atlantic Herring (Clupea harengus).I analyzed Atlantic Herring samples from the North and Baltic Seas. The objectives were to determine: 1) spatial genetic structure, 2) whether allozymes and microsatellites provide similar descriptions of the differentiation pattern, or 3) if they are influenced by selection, 4) factors affecting statistical power when testing for genetic differentiation, and 5) the temporal stability of the genetic structure.The results show: 1) very low levels of spatial genetic differentiation in Atlantic Herring; a major component is a difference between the Baltic and North Seas, 2) a concordant pattern with allozymes and microsatellites, 3) that selection influences a microsatellite locus, which can be a low salinity adaptation, 4) that statistical power is substantial for frequently used sample sizes and markers; the difference in power between organelle and nuclear loci is partly dependent on the populations’ stage of divergence, and 5) no changes in amount of genetic variation or spatial genetic structure over a 24-year period; the selection pattern in one microsatellite locus remained.The notion that the large population sizes make Herring unlikely to lose genetic diversity may be disputed. I found small local effective population sizes, and the evidence of selection hints of a distinct evolutionary lineage in the Baltic. When Atlantic Herring is managed as very large units, there can be detrimental genetic effects if certain population segments are excessively harvested.
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oceanographic connectivity and environmental correlates of genetic structuring in Atlantic Herring in the baltic sea
Evolutionary Applications, 2013Co-Authors: Amber G F Teacher, Carl André, Per R Jonsson, Juha MerilaAbstract:Marine fish often show little genetic structuring in neutral marker genes, and Atlantic Herring (Clupea harengus) in the Baltic Sea are no exception; historically, very low levels of population differentiation (FST ≈ 0.002) have been found, despite a high degree of interpopulation environmental heterogeneity in salinity and temperature. Recent exome sequencing and SNP studies have however shown that many loci are under selection in this system. Here, we combined population genetic analyses of a large number of transcriptome-derived microsatellite markers with oceanographic modelling to investigate genetic differentiation and connectivity in Atlantic Herring at a relatively fine scale within the Baltic Sea. We found evidence for weak but robust and significant genetic structuring (FST = 0.008) explainable by oceanographic connectivity. Genetic differentiation was also associated with site differences in temperature and salinity, with the result driven by the locus Her14 which appears to be under directional selection (FST = 0.08). The results show that Baltic Herring are genetically structured within the Baltic Sea, and highlight the role of oceanography and environmental factors in explaining this structuring. The results also have implications for the management of Herring fisheries, the most economically important fishery in the Baltic Sea, suggesting that the current fisheries management units may be in need of revision.
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whole mitochondrial genome scan for population structure and selection in the Atlantic Herring
BMC Evolutionary Biology, 2012Co-Authors: Carl André, Amber G F Teacher, Juha Merila, Christopher W WheatAbstract:Background Marine fish, such as the Atlantic Herring (Clupea harengus), often show a low degree of differentiation over large geographical regions. Despite strong environmental gradients (salinity and temperature) in the Baltic Sea, population genetic studies have shown little genetic differentiation among Herring in this area, but some evidence for environmentally-induced selection has been uncovered. The mitochondrial genome is a likely target for selection in this system due to its functional role in metabolism.
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temporally stable genetic structure of heavily exploited Atlantic Herring clupea harengus in swedish waters
Heredity, 2010Co-Authors: Lena C. Larsson, Linda Laikre, Carl André, Thomas G. Dahlgren, Nils RymanAbstract:Information on the temporal stability of genetic structures is important to permit detection of changes that can constitute threats to biological resources. Large-scale harvesting operations are known to potentially alter the composition and reduce the variability of populations, and Atlantic Herring (Clupea harengus) has a long history of heavy exploitation. In the Baltic Sea and Skagerrak waters, the census population sizes have declined by 35–50% over the last three decades. We compared the genetic structure of Atlantic Herring in these waters sampled at least two different times between 1979 and 2003 by assaying 11 allozyme and nine microsatellite loci. We cannot detect any changes in the amount of genetic variation or spatial structure, and differentiation is weak with overall FST ¼ 0.003 among localities for the older samples and FST ¼ 0.002 for the newer ones. There are indications of temporal allele frequency changes, particularly in one of five sampling localities that is reflected in a relatively small local Ne estimate of c. 400. The previously identified influence of selection at the microsatellite locus Cpa112 remains stable over the 24-year period studied here. Despite little genetic differentiation, migration among localities appears small enough to permit demographic independence between populations.
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biocomplexity in a highly migratory pelagic marine fish Atlantic Herring
Proceedings of The Royal Society B: Biological Sciences, 2006Co-Authors: Daniel E Ruzzante, Carl André, Thomas G. Dahlgren, Stefano Mariani, Dorte Bekkevold, Henrik Mosegaard, Law Clausen, William F Hutchinson, Emc Hatfield, Else TorstensenAbstract:The existence of biologically differentiated populations has been credited with a major role in conferring sustainability and in buffering overall productivity of anadromous fish population complexes where evidence for spatial structure is uncontroversial. Here, we describe evidence of correlated genetic and life history (spawning season linked to spawning location) differentiation in an abundant and highly migratory pelagic fish, Atlantic Herring, Clupea harengus, in the North Sea (NS) and adjacent areas. The existence of genetically and phenotypically diverse stocks in this region despite intense seasonal mixing strongly implicates natal homing in this species. Based on information from genetic markers and otolith morphology, we estimate the proportional contribution by NS, Skagerrak (SKG) and Kattegat and western Baltic (WBS) fish to mixed aggregations targeted by the NS fishery. We use these estimates to identify spatial and temporal differences in life history (migratory behaviour) and habitat use among genetically differentiated migratory populations that mix seasonally. Our study suggests the existence of more complex patterns of intraspecific diversity than was previously recognized. Sustainability may be compromised if such complex patterns are reduced through generalized management (e.g. area closures) that overlooks population differences in spatial use throughout the life cycle.
Sangeet Lamichhaney - One of the best experts on this subject based on the ideXlab platform.
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moderate nucleotide diversity in the Atlantic Herring is associated with a low mutation rate
eLife, 2017Co-Authors: Chungang Feng, Leif Andersson, Arild Folkvord, Mats E Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Nima Rafati, Michele CasiniAbstract:Evolution by natural selection favours the survival of individuals that are well suited to their environment. This process depends on genetic differences between individuals that make some more able to survive than others. These genetic differences are the result of mutations in DNA of germ-line cells, that is, the cells that produce egg cells and sperm. These mutations mean that new offspring always have a few small differences in some of the genes they inherited from each of their parents. DNA contains strings of molecules known as bases. These act as individual “letters” in the genetic code of an individual. Rapid sequencing of DNA to find out the order of these bases makes it possible to study the rate of mutations within a species. This provides a way to measure how different an individual is from its parents and, by extension, the potential of the species to diversify and adapt to different environments. There are over a trillion Atlantic Herring in the Atlantic Ocean, so this fish is an ideal model to study the effects of germ-line mutations on genetic diversity. In 2016, a group of researchers reported that there is relatively little genetic diversity across Atlantic Herring. Given the large population, this suggested that the mutation rate in this species may be low. Feng, Pettersson, Lamichhaney et al. – who were also involved with the earlier work – sequenced the DNA of two families of Atlantic Herring raised in captivity to calculate the rate of germ-line mutations in this species. The results showed that, on average, two changes occur per one billion letters in the genetic code in each generation. That is one to two new mutations per egg cell or sperm. This is the lowest mutation rate yet recorded in any animal with a backbone and is around six times lower than the mutation rate in humans. Whilst the low mutation rate in Atlantic Herring means there are few differences between individual fish, the extremely large number of these fish on the planet still means that there is enough diversity across the population to allow the species to adapt to changing conditions. This work is important for conservation as it highlights the great variation in potential genetic diversity across species. Future work will need to examine why the mutation rate in Atlantic Herring is so low and compare it more widely to mutation rates in other species.
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moderate nucleotide diversity in the Atlantic Herring is associated with a low mutation rate
bioRxiv, 2017Co-Authors: Chungang Feng, Arild Folkvord, Mats E Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Nima Rafati, Michele Casini, Leif AnderssonAbstract:The Atlantic Herring (Clupea harengus) is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π=0.3%), only three-fold higher than in human. The expected nucleotide diversity for selectively neutral alleles is a function of population size and the mutation rate, and it is strongly affected by demographic history. Here, we present a pedigree-based estimation of the mutation rate in the Atlantic Herring. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 1.7 x 10-9 per base per generation. There was no significant difference in the frequency of paternal and maternal mutations (8 and 7, respectively). Furthermore, we observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development when we do not expect a strong gender effect. The now estimated mutation rate — the lowest among vertebrates analyzed to date — partially explains the discrepancy between the rather low nucleotide diversity in Herring and its huge census population size (>10^11). But our analysis indicates that a species like the Herring will never reach its expected nucleotide diversity for selectively neutral alleles primarily because of fluctuations in population size due to climate variation during the millions of years it takes to build up a high nucleotide diversity. In addition, background selection and selective sweeps lead to reductions in nucleotide diversity at linked neutral sites.
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the genetic basis for ecological adaptation of the Atlantic Herring revealed by genome sequencing
eLife, 2016Co-Authors: Alvaro Martinez Barrio, Sangeet Lamichhaney, Nima Rafati, Mats Pettersson, He Zhang, Jacques Dainat, Diana Ekman, Marc P HoppnerAbstract:The Atlantic Herring is one of the most common fish in the world and has been a crucial food resource in northern Europe. One school of Herring may comprise billions of fish, but previous studies had only revealed very few genetic differences in Herring from different geographic regions. This was unexpected since Atlantic Herring is one of the few marine species that can reproduce throughout the brackish Baltic Sea, which can be about a tenth as salty as the Atlantic Ocean. This unexpected finding could be explained in at least two different ways. Firstly, perhaps Atlantic Herring are flexible enough to adapt to very different environments (i.e. high or low salinity) without much genetic change. Secondly, the previous studies only looked at a handful of sites in the Atlantic Herring’s genome and so it is possible that genetic differences at other genes control this fish’s adaptation instead. Now, Martinez Barrio, Lamichhaney, Fan, Rafati et al. have sequenced entire genomes from groups of Atlantic Herring and revealed hundreds of sites that are associated with adaptation to the Baltic Sea. The analysis also identified a number of genes that control when these fish reproduce by comparing Herring that spawn in the autumn with those that spawn in spring. This is important because natural populations must carefully time when they reproduce to maximize the survival of their young. These new findings provide compelling evidence that changes in protein-coding genes and stretches of DNA that regulate the expression of other genes both contribute to adaptation in Herrings. The analysis also clearly shows that variants of genes that contribute to adaptation were likely to evolve over time by accumulating multiple sequence changes affecting the same gene. Furthermore, these gene variants essentially form a rich “tool-box” that underlies the Atlantic Herring’s adaptation to its environment, and different subpopulations of Herring were found to have their own optimal sets of gene variants. For instance, autumn-spawning Herring and spring-spawning Herring from the Baltic Sea both have gene variants that favor adaptation to low salinity. However, autumn-spawning Baltic Herring also share gene variants that favor spawning in the autumn with autumn-spawning Herring from the North Sea, but not with spring-spawning Baltic Herring. The next step will be to study how the 500 or so genes identified affect adaptation at the molecular level. This will likely involve experiments with other model fish such as zebrafish and sticklebacks. Finally, these new findings can be directly applied to monitor stocks of Herring to make Herring fisheries more sustainable.
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De novo characterization of skeletal muscle transcriptome of Atlantic Herring (Clupea harengus) using Next Generation Sequencing NGS)
2013Co-Authors: Sangeet LamichhaneyAbstract:Atlantic Herring (Clupea harengus), one of the most abundant fish species on earth is an economically important marine species that is found in the Baltic Sea and on both sides of the Atlantic Ocean. Although it has been a popular species for marine fish population studies since long, yet the genomic information for Atlantic Herring is scarce. Recent developments in ultra high throughput RNA sequencing methods has allowed rapid and cost effective generation of large sequence information, which can be used to characterize the transcriptome in any non-model species even when no reference sequence is available. Transcriptome sequencing from the skeletal muscle of a single specimen of Atlantic Herring was performed using Illumina HiSeq 2000 platform that generated approximately 116 million reads (with 101 bp length). These short reads were trimmed for quality and were assembled into 115,046 contigs with an average length of 291 bp and N50 of 375 bp, thereby producing a draft transcriptome assembly with total size of 33.51 Mb. With the e-value threshold set to 10-4, 46,979 contigs (40.84%) were identified to have matches against GenBank non-redundant (NR) proteins and Zebrafish unigenes database. Using the annotated transcriptome resource, 25,431 putative allelic variants (24,351 SNPs and 1080 indels) were identified. The present study provides a comprehensive muscle transcriptome resource which will be particularly useful for the validation of draft genome assembly of Atlantic Herring that is currently being established within our group.
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population scale sequencing reveals genetic differentiation due to local adaptation in Atlantic Herring
Proceedings of the National Academy of Sciences of the United States of America, 2012Co-Authors: Sangeet Lamichhaney, Carljohan Rubin, Nima Rafati, Alvaro Martinez Barrio, Linda Laikre, Gorel Sundstrom, Elizabeth R Gilbert, Jonas Berglund, Anna Wetterbom, Matthew T WebsterAbstract:The Atlantic Herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled a muscle transcriptome and then aligned genomic reads to the transcripts, creating an “exome assembly,” capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index FST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic Herring as a model for population genetic studies of adaptation and natural selection.
