Fig. 6.

A multiple-species alignment showing indels identified by Champagne in the pig, cow, and dog genomes, using human as reference species. (A) An illustration of the real pig, cow, and dog chains that align with a 14-Mb section of the human chromosome 2. Indels identified by Champagne in this section of the reference genome are shown: “I” indicates shared insertions, and “D” indicates shared deletions. On this stretch, we find five indels that are shared by pig and cow, supporting the most parsimonious topology ((pig, cow), dog), and only 1 (shown with a dashed arc) that is shared by dog and cow, possibly due to ILS. (B) A multiple sequence alignment of an 81-bp deletion shared by pig and cow, but not dog (leftmost deletion in panel A).