Fig. 2

Example gain and loss inferences based on ancestral state reconstruction. a Example sequence loss in the target species based on presence in the most-recent common ancestor (MRCA), at the root of the tree. b Example sequence gain in the query species. Sequence absence is the most parsimonious inferred ancestral state as it invokes two independent sequence gains rather than three independent losses necessary to explain the observed data. d The phylogeny in C may be resolved by choosing an unambiguous state from one of the two nodes directly above the root. In the case of the tree shown, this is equivalent to pruning the outermost outgroup and rerooting the tree. The inferred ancestral state, then, is presence of an orthologous sequence and sequence loss in the target species is called. e UCSC Genome Browser track for a region in the human genome (hg19 build) labelled by MapGL as a human-specific gain. The region contains a CTCF binding annotation residing in a primate-specific insertion of an L2a LINE transposable element. f UCSC Genome Browser track for a region in the human genome labelled by MapGL as a mouse-specific loss. This region also contains a CTCF binding site residing within an L2a LINE element, but one that was inserted prior to divergence of Atlantogenata and Boreoeutheria species