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.
Parida
Laxmi
L
Computational Biology Center, IBM TJ Watson Research, Yorktown Heights, NY 10598, USA. parida@us.ibm.com
Melé
Marta
M
Calafell
Francesc
F
Bertranpetit
Jaume
J
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