Figure 3
From: Highlighting nonlinear patterns in population genetics datasets
PCA and ncMCE complementarity.
(a) PCA (left) provides a clear separation between the Yoruba (YRI), European (CEU) and Asian (CHB and JPT) samples but it is unable to detect the differences between the Chinese and Japanese individuals that form the Asian group. ncMCE (centre) clearly detected this difference over Dim2 and also provided an ordering over this dimension that was related to the organisation of these populations in a phylogenetic tree (right). (b) and (c): PCA (left) scattered the Malay and Singaporean individuals in a geographic manner. ncMCE (centre), just as in (a), clearly detected the genetic differences between individuals by separating ethnic groups over Dim2 and highlighting their phylogenetic relationships (right) over this same dimension. MY-MN and MY-KN are Malay Malay, MY-BD are Malay Bidayuh, MY-TM are Proto-Malay and MY-JH and MY-KS are Malay Negritos. SG-MY are Singaporean of Malay descent, SG-CH are Singaporean of Chinese descent and SG-ID are Singaporean of Indian descent.
