Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns.
Traditionally nonrecombinant genome, i.e., mtDNA or Y chromosome, has been used for phylogeography, notably for ease of analysis. The topology of the phylogeny structure in this case is an acyclic graph, which is often a tree, is easy to comprehend and is somewhat easy to infer. However, recombination is an undeniable genetic fact for most part of the genome. Driven by the need for a more complete analysis, we address the problem of estimating the ancestral recombination graph (ARG) from a collection of extant sequences. We exploit the coherence that is observed in the human haplotypes as patterns and present a network model of patterns to reconstruct the ARG. We test our model on simulations that closely mimic the observed haplotypes and observe promising results.
Computational Biology Center, IBM TJ Watson Research, Yorktown Heights, NY 10598, USA. parida@us.ibm.com
Laxmi
L
Parida
Marta
M
Melé
Francesc
F
Calafell
Jaume
J
Bertranpetit
D000465:Algorithms; D041322:Chromosomes, Human, Y / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D006239:Haplotypes; D006801:Humans; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic
D004272:DNA, Mitochondrial