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Drawing a NJ tree of individuals did not show clear clustering patterns except for wild populations and did not provide further information on weedy populations' relationships (not shown).
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The study of population is also closely related to human ecology and environmental sociology, which studies a populations relationship with the surrounding environment and often overlaps with urban or rural sociology.
However, for the present analysis using samples from four HapMap populations, relationship estimation will be biased unless the population structure is considered.
For each of the five populations, relationship matrices were estimated from random subsets of markers, with the shrinkage intensity chosen to minimize the expected MSE.
This finding suggests that in comparison with small populations, relationship assignments of samples originating from large populations potentially may require more loci for similar correct classification rate and/or certain categories may not reach satisfactory correct classification rates.
Our results provide theoretical guidance for interpreting the pattern of PC plot in terms of population relationships.
To visualize the population relationships, we performed a non-parametric multidimensional scaling (MDS) on the pairwise FST statistics (figure 9).
However, it can be difficult to make appropriate inference about population relationships from the principal component (PC) scatter plot.
High correlation between phylogenetic tree, or population relationships, and linguistic tree, can be created during demographic expansions [14].
Here, we illustrate, by using examples, how the pattern of the representative points can be used to infer population relationships.
PCA method is applied to large-scale association studies based on SNP both to quantify population relationships and to correct for population stratification [21], [22].
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