Genomic Triangulation Method

Method
The genomic triangulation method was applied to the human, chimpanzee and rhesus genomes in order to reconstuct ancestral genome structures.

The paper Human-Specific Changes of Genome Structure Detected by Genomic Triangulation summarizes the method and characterizes detected human-specific rearrangements.

Rhesus breakpoints are included in the paper Evolutionary and Biomedical Insights from the Rhesus Macaque Genome.




Genomic Triangulation Method:
Input:	genomes and other available genomic data from at least three species, two of which form a monophyletic group with the other one serving as an outgroup.
Output:	reconstruction of the ancestral genome of the monophyletic group and a map of the breakpoints in specific branches of an unrooted phylogenetic tree.


Steps
	1. Blockset Construction Produces blocks consisting of pairs of orthologous chromosomal segments unbroken by large-scale rearrangements Each block corresponds to a segment of the monophyletic group Blocks are inferred from collinear orthologous anchors derived from: Genome assembly comparisons Large-insert clone mappings Comparative linkage maps Radiation hybrid maps

	2. Ancestral Threading Reconstructs ancestral genome structure from blocksets in a process similar to genome assembly Overlap of blocks from different blocksets is deduced from overlaps of positional coordinates of the blocks within a single species Overlapping blocks from the pairwise blocksets are threaded into scaffolds of an ancestral genome

	3. Ancestral Gapset Construction Infers ancestral gapsets from ancestral blocksets Every breakpoint is flanked by two blocks Every pair of adjacent blocks defines a gap

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