Hidden Markov Genomics

Asger Hobolth at North Carolina State University's Bioinformatics Research Center and his team used a hidden Markov model to estimate that chimps and humans diverged from a common ancestor only about 4.1 million years ago. ¹ Hobolth looked at the probability distribution of 1.9 billion DNA base pairs across humans, chimpanzees, gorillas, and orangutans, searching for differences in the historical sequences.

"Because recombination causes different parts of the genome to have different evolutionary histories, closely related species will have more recent common ancestry in some stretches of DNA than in others," according to Jeffrey Thorne, professor of Genetics and Statistics also at North Carolina State University, and a member of the Faculty of 1000. "Accounting for this variation of histories is particularly important when closely related species are compared, and the hidden Markov approach of Hobolth and collaborators does this."

"The specific estimated date for the human-chimpanzee divergence will require more scrutiny," says Thorne, "and the authors are aware that they can make future improvements to their statistical approach. I think the big contribution of this paper is that it introduces a statistical tool for studying how long ago did the genetic lineages of different species split. It doesn't matter if it's human-chimp relationship or other biologically related species. If you have some genomic data, you could use the statistical technique introduced in this paper and apply it."