| 1. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 3. |
- Jonker, R.M., et al.
(författare)
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Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis
- 2013
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 22:23, s. 5835-5847
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Tidskriftsartikel (refereegranskat)abstract
- Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions, new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of the Barnacle Goose to evaluate the consequences of altered migratory traditions. We used a set of 358 single nucleotide polymorphism (SNP) markers to genotype 418 individuals from breeding populations in Greenland, Spitsbergen, Russia, Sweden and the Netherlands, the latter two being newly emerged populations. We used discriminant analysis of principal components, FST, linkage disequilibrium and a comparison of geneflow models using MIGRATE-N to show that there is significant population structure, but that relatively many pairs of SNPs are in linkage disequilibrium, suggesting recent admixture between these populations. Despite the assumed traditions of migration within populations, we also show that genetic exchange occurs between all populations. The newly established nonmigratory population in the Netherlands is characterized by high emigration into other populations, which suggests more exploratory behaviour, possibly as a result of shortened parental care. These results suggest that migratory traditions in populations are subject to change in geese and that such changes have population genetic consequences. We argue that the emergence of nonmigration probably resulted from developmental plasticity.
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| 4. |
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| 5. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 6. |
- Frantz, Laurent A. F., et al.
(författare)
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Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:35, s. 17231-17238
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Tidskriftsartikel (refereegranskat)abstract
- Archaeological evidence indicates that pig domestication had begun by similar to 10,500 y before the present ( BP) in the Near East, and mitochondrial DNA ( mtDNA) suggests that pigs arrived in Europe alongside farmers similar to 8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
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| 7. |
- Söderquist, Pär, et al.
(författare)
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Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)
- 2017
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Ingår i: European Biophysics Journal. - : Springer Verlag (Germany). - 0175-7571 .- 1432-1017. ; 63
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Tidskriftsartikel (refereegranskat)abstract
- Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.
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| 8. |
- Söderquist, Pär, et al.
(författare)
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Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos)
- 2017
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Ingår i: European Biophysics Journal. - : Springer Verlag. - 0175-7571 .- 1432-1017. ; 63:6
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Tidskriftsartikel (refereegranskat)abstract
- Disruption of naturally evolved spatial patterns of genetic variation and local adaptations is a growing concern in wildlife management and conservation. During the last decade, releases of native taxa with potentially non-native genotypes have received increased attention. This has mostly concerned conservation programs, but releases are also widely carried out to boost harvest opportunities. The mallard, Anas platyrhynchos, is one of few terrestrial migratory vertebrates subjected to large-scale releases for hunting purposes. It is the most numerous and widespread duck in the world, yet each year more than three million farmed mallard ducklings are released into the wild in the European Union alone to increase the harvestable population. This study aimed to determine the genetic effects of such large-scale releases of a native species, specifically if wild and released farmed mallards differ genetically among subpopulations in Europe, if there are signs of admixture between the two groups, if the genetic structure of the wild mallard population has changed since large-scale releases began in the 1970s, and if the current data matches global patterns across the Northern hemisphere. We used Bayesian clustering (Structure software) and Discriminant Analysis of Principal Components (DAPC) to analyze the genetic structure of historical and present-day wild (n = 171 and n = 209, respectively) as well as farmed (n = 211) mallards from six European countries as inferred by 360 single-nucleotide polymorphisms (SNPs). Both methods showed a clear genetic differentiation between wild and farmed mallards. Admixed individuals were found in the present-day wild population, implicating introgression of farmed genotypes into wild mallards despite low survival among released farmed mallards. Such cryptic introgression would alter the genetic composition of wild populations and may have unknown long-term consequences for conservation.
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| 9. |
- Elmberg, Johan, et al.
(författare)
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Farmed European mallards are genetically different and cause introgression in the wild population following releases
- 2016
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Konferensbidrag (refereegranskat)abstract
- The practice of restocking already viable populations to increase harvest potential has since long been common in forestry, fisheries and wildlife management. The potential risks of restocking native species have long been overshadowed by the related issue of invasive alien species. However, during the last decade releases of native species with potentially non-native genome have received more attention. A suitable model to study genetic effects of large-scale releases of native species is the Mallard Anas platyrhynchos, being the most widespread duck in the world, largely migratory, and an important quarry species. More than 3 million unfledged hatchlings are released each year around Europe to increase local harvest. The aims of this study were to determine if wild and released farmed Mallards differ genetically, if there are signs of previous or ongoing introgression between wild and farmed birds, and if the genetic structure of the wild Mallard population has changed since large-scale releases started in Europe in the 1970s. Using 360 Single Nucleotide Polymorphisms (SNPs) we found that the genetic structure differed among historical wild, present-day wild, and farmed Mallards in Europe. We also found signs of introgression in the wild Mallard population, that is, individuals with a genetic background of farmed stock are part of the present free-living population. Although only a small proportion of the released Mallards appears to survive to merge with the free-living breeding population, their numbers are still so large that the genetic impact may have significance for the wild population in terms of individual survival and longterm fitness.
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| 10. |
- Elmberg, Johan, et al.
(författare)
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Farmed European mallards are genetically different and cause introgression in the wild population following releases
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The practice of restocking already viable populations to increase harvest potential has since long been common in forestry, fisheries and wildlife management. The potential risks of restocking native species have long been overshadowed by the related issue of invasive alien species. However, during the last decade releases of native species with potentially non-native genome have received more attention. A suitable model to study genetic effects of large-scale releases of native species is the Mallard Anas platyrhynchos, being the most widespread duck in the world, largely migratory, and an important quarry species. More than 3 million unfledged hatchlings are released each year around Europe to increase local harvest. The aims of this study were to determine if wild and released farmed Mallards differ genetically, if there are signs of previous or ongoing introgression between wild and farmed birds, and if the genetic structure of the wild Mallard population has changed since large-scale releases started in Europe in the 1970s. Using 360 Single Nucleotide Polymorphisms (SNPs) we found that the genetic structure differed among historical wild, present-day wild, and farmed Mallards in Europe. We also found signs of introgression in the wild Mallard population, that is, individuals with a genetic background of farmed stock are part of the present free-living population. Although only a small proportion of the released Mallards appears to survive to merge with the free-living breeding population, their numbers are still so large that the genetic impact may have significance for the wild population in terms of individual survival and longterm fitness.
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