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This is consistent with our experience from a different admixture study [ 26] in which large numbers of subsets of 10 animals per ancestral breed were used.
Results agree with an island model of speciation where the brown Hanwoo represents the ancestral breed, whilst the Jeju Black and Chikso diverge from this common ancestor, following different evolutionary trajectories.
A clear Merino genetic component was detected in several breeds at K = 10 in the ADMIXTURE analysis, which provides evidence for an extensive circulation of Merino genetic material as previously reported by Kijas et al. [ 12], but confounds a reconstruction of ancestral breed relationships.
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Our primary goal is the identification of small panels of AIMs that achieve accurate assignment of individuals to breeds, using the reported ancestral breeds in the Bovine HapMap dataset [19] as reference.
A tremendous loss of SNP genetic diversity has been observed in chicken with significant absence of rare alleles (50% or more) in commercial breeds compared to ancestral breeds [ 10].
It is thought that the breed is descended from the same ancestral stock as the other Scottish terriers the Dandie Dinmont, Scottish, and cairn terriers.
Or how can it sometimes be beneficial for a few individuals to breed preferentially among themselves rather than with the rest of the population, in others words with the ancestral stock?
Another result of industrialisation was the greatest decline in domestic chicken diversity in history, with half or more of all ancestral chicken breeds now lost.
The proportional contributions of the inferred ancestral populations per breed are in Additional file 5: Table S3 for K = 12.
Assessing both the presence of these regions in other breeds and their genetic content can provide information on how they affect the phenotype and relate to the ancestral origin of breeds.
To gain additional insights into population structure, the fractional contributions of ancestral populations to each breed were converted into genetic distances among breeds and represented in UPGMA trees for K = 3 (see Additional file 7: Figure S3) and K = 12 (Fig. 3), as described by Cañón et al. [ 24] and García et al. [ 25].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com