Fig. 1

HGT identification pipeline. From the pair-wise alignment data, we extracted the human genome regions that were conserved between 12 non-mammalian vertebrates and the human genome. A human genome region is called a non-mammal conserved region if this region is aligned to at least two non-mammal genomes with an identity no less than 40%. These regions were then compared to the mammalian genomes. For these non-mammal conserved regions, if a region can be aligned to at most eight (<20%) of the 41 mammals with an alignment identity ≥40% and length of the aligned region longer than 40% of the human region, this region is defined as a predicted HGT region. We choose the predicted HGT regions which lengths are longer than 1000 bps to analyze