Mapping different subfamilies and copy numbers to the phylogenetic tree. A) Based on the rag2 sequences, the phylogenetic tree of 17 fishes representing different tribes of Cyprinidae family was constructed using Bayesian inference. Among them, the rag2 sequences of three species Distoechodon hupeinensis, Shizothorax grahami, Barbodes opisthoptera was substituted by another closely related species in the same genus respectively, because the absence of their rag2 sequences in GenBank. The trees resulting from phylogenetic analyses of the RAG2 gene place the Danioninae as the basal-most group in the family and divide the remaining cyprinids into two divergent subfamilies Cyprininae and Leuciscinae. The arrow denoted the Xenocyprinidini clade, containing silver carp, bighead carp and their closely related species endemic to East Asia. B) This part listed the clone numbers of SINE and LINE isolated from each species and the copy numbers estimated by qRT-PCR. The mapping results shows the four subfamilies, as multiple active source genes, expanded preferentially in a certain lineage or the whole family of Cyprinidae. The star indicated that the whole clones contain 21 and 15 of HAmo type I reported previously. The seventh column (U) denoted the unidentified SINE sequences that cannot be classified into a kind of type.