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Both softwares estimate the genome ancestry directly or indirectly.
Other computationally efficient approaches for solving the genome ancestry problem have largely ignored the breeding scheme.
The genome ancestry problem was modeled as a combinatorial optimization problem in Zhang et al. (2008).
We implement our model GAIN (Genome Ancestry with INbreeding) for CC using C++.
To sum up, even partial pedigree knowledge causes a big difference in analyzing genome ancestry.
Genome ancestry refers to the ancestry measured using the full set of SNPs in HapMap.
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It indicates that the AT and zebu genome ancestries have had time to 'diffuse' homogenously among the calves of our study population, while the level of European taurine introgression, of more recent origin, still needs to reach an equilibrium.
By "asymmetric gene flow" we believe the reviewers are referring to the fact that hybrid populations are skewed in their genome wide ancestry and that this requires some explanation.
Using this new dataset and the admixture model, ten parallel Markov chains were run for the correlated allele frequency models with a burn-in of 500,000 iterations and a run length of 10 iterations to estimate the proportion of every planted tree's genome possessing ancestry in each of K clusters [ 10, 32].
ADMIXTURE [ 27] was used to estimate genome-wide ancestry of the SAC study group.
Depending on dominance effects, this could explain why hybrid populations are skewed in genome-wide ancestry.
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