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Ronald C Ydenberg - One of the best experts on this subject based on the ideXlab platform.
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genome wide single nucleotide polymorphism Analysis reveals recent genetic introgression from domestic pigs into northwest european wild boar populations
Molecular Ecology, 2013Co-Authors: Daniel J Goedbloed, Hendrikjan Megens, J Herreromedrano, Panoraia Alexandri, W.f. Van Hooft, Spike E Van Wieren, Richard P. M. A. Crooijmans, Martien A. M. Groenen, W. Lutz, Ronald C YdenbergAbstract:Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele Frequency Spectrum Analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP Analysis is a promising tool to quantify recent hybridization in free-living populations.
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genome wide snp Analysis reveals recent genetic introgression from domestic pigs into northwest european wild boar populations
Molecular Ecology, 2013Co-Authors: Daniel J Goedbloed, Hendrikjan Megens, J Herreromedrano, Panoraia Alexandri, W.f. Van Hooft, Spike E Van Wieren, Richard P. M. A. Crooijmans, Martien A. M. Groenen, W. Lutz, Ronald C YdenbergAbstract:Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele Frequency Spectrum Analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP Analysis is a promising tool to quantify recent hybridization in free-living populations.
Daniel J Goedbloed - One of the best experts on this subject based on the ideXlab platform.
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genome wide single nucleotide polymorphism Analysis reveals recent genetic introgression from domestic pigs into northwest european wild boar populations
Molecular Ecology, 2013Co-Authors: Daniel J Goedbloed, Hendrikjan Megens, J Herreromedrano, Panoraia Alexandri, W.f. Van Hooft, Spike E Van Wieren, Richard P. M. A. Crooijmans, Martien A. M. Groenen, W. Lutz, Ronald C YdenbergAbstract:Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele Frequency Spectrum Analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP Analysis is a promising tool to quantify recent hybridization in free-living populations.
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genome wide snp Analysis reveals recent genetic introgression from domestic pigs into northwest european wild boar populations
Molecular Ecology, 2013Co-Authors: Daniel J Goedbloed, Hendrikjan Megens, J Herreromedrano, Panoraia Alexandri, W.f. Van Hooft, Spike E Van Wieren, Richard P. M. A. Crooijmans, Martien A. M. Groenen, W. Lutz, Ronald C YdenbergAbstract:Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele Frequency Spectrum Analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP Analysis is a promising tool to quantify recent hybridization in free-living populations.
W R Babbitt - One of the best experts on this subject based on the ideXlab platform.
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spectral hole burning for wideband high resolution radio Frequency Spectrum Analysis
Optics Letters, 2005Co-Authors: Friso Schlottau, Max Colice, Kelvin H Wagner, W R BabbittAbstract:We present experimental results for what is to our knowledge the first spectral-hole-burning based rf Spectrum analyzer to cover 10 GHz of rf Analysis bandwidth. The rf signal of interest is modulated onto an optical carrier, and the resultant optical sidebands are burned into the inhomogeneously broadened absorption band of a Tm3+:YAG crystal. At the same time a second, Frequency-swept laser reads out the absorption profile, which is a double-sideband replica of the rf Spectrum, and thus the rf Spectrum can be deduced after spectral calibration of the nonlinear readout chirp. This initial demonstration shows spectral Analysis covering 10 GHz of bandwidth with >5500 spectral channels and provides 43 dB of dynamic range.
George N Kiladis - One of the best experts on this subject based on the ideXlab platform.
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convectively coupled equatorial waves Analysis of clouds and temperature in the wavenumber Frequency domain
Journal of the Atmospheric Sciences, 1999Co-Authors: Matthew C Wheeler, George N KiladisAbstract:A wavenumber-Frequency Spectrum Analysis is performed for all longitudes in the domain 158S‐158N using a long (;18 years) twice-daily record of satellite-observed outgoing longwave radiation (OLR), a good proxy for deep tropical convection. The broad nature of the Spectrum is red in both zonal wavenumber and Frequency. By removing an estimated background Spectrum, numerous statistically significant spectral peaks are isolated. Some of the peaks correspond quite well to the dispersion relations of the equatorially trapped wave modes of shallow water theory with implied equivalent depths in the range of 12‐50 m. Cross-Spectrum Analysis with the satellite-based microwave sounding unit deep-layer temperature data shows that these spectral peaks in the OLR are ‘‘coupled’’ with this dynamical field. The equivalent depths of the convectively coupled waves are shallower than those typical of equatorial waves uncoupled with convection. Such a small equivalent depth is thought to be a result of the interaction between convection and the dynamics. The convectively coupled equatorial waves identified correspond to the Kelvin, n 5 1 equatorial Rossby, mixed Rossby-gravity, n 5 0 eastward inertiogravity, n 5 1 westward inertio-gravity (WIG), and n 5 2 WIG waves. Additionally, the Madden‐Julian oscillation and tropical depression-type disturbances are present in the OLR spectra. These latter two features are unlike the convectively coupled equatorial waves due to their location away from the equatorial wave dispersion curves in the wavenumber-Frequency domain. Extraction of the different convectively coupled disturbances in the time‐longitude domain is performed by filtering the OLR dataset for very specific zonal wavenumbers and frequencies. The geographical distribution of the variance of these filtered data gives further evidence that some of the spectral peaks correspond to particular equatorial wave modes. The results have implications for the cumulus parameterization problem, for the excitation of equatorial waves in the lower stratosphere, and for extended-range forecasting in the Tropics.
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convectively coupled equatorial waves Analysis of clouds and temperature in the wavenumber Frequency domain
Journal of the Atmospheric Sciences, 1999Co-Authors: Matthew C Wheeler, George N KiladisAbstract:Abstract A wavenumber-Frequency Spectrum Analysis is performed for all longitudes in the domain 15°S–15°N using a long (∼18 years) twice-daily record of satellite-observed outgoing longwave radiation (OLR), a good proxy for deep tropical convection. The broad nature of the Spectrum is red in both zonal wavenumber and Frequency. By removing an estimated background Spectrum, numerous statistically significant spectral peaks are isolated. Some of the peaks correspond quite well to the dispersion relations of the equatorially trapped wave modes of shallow water theory with implied equivalent depths in the range of 12–50 m. Cross-Spectrum Analysis with the satellite-based microwave sounding unit deep-layer temperature data shows that these spectral peaks in the OLR are “coupled” with this dynamical field. The equivalent depths of the convectively coupled waves are shallower than those typical of equatorial waves uncoupled with convection. Such a small equivalent depth is thought to be a result of the interacti...
W. Lutz - One of the best experts on this subject based on the ideXlab platform.
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genome wide single nucleotide polymorphism Analysis reveals recent genetic introgression from domestic pigs into northwest european wild boar populations
Molecular Ecology, 2013Co-Authors: Daniel J Goedbloed, Hendrikjan Megens, J Herreromedrano, Panoraia Alexandri, W.f. Van Hooft, Spike E Van Wieren, Richard P. M. A. Crooijmans, Martien A. M. Groenen, W. Lutz, Ronald C YdenbergAbstract:Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele Frequency Spectrum Analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP Analysis is a promising tool to quantify recent hybridization in free-living populations.
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genome wide snp Analysis reveals recent genetic introgression from domestic pigs into northwest european wild boar populations
Molecular Ecology, 2013Co-Authors: Daniel J Goedbloed, Hendrikjan Megens, J Herreromedrano, Panoraia Alexandri, W.f. Van Hooft, Spike E Van Wieren, Richard P. M. A. Crooijmans, Martien A. M. Groenen, W. Lutz, Ronald C YdenbergAbstract:Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele Frequency Spectrum Analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP Analysis is a promising tool to quantify recent hybridization in free-living populations.
