[GodGunsGuts]

Apparently you can’t even read phylogenetic trees. State CG allows for humans and chimps to have diverged from apes and NOT from each other. That means, even your co-religionists over at the Temple of Darwin are admitting that their human-chimp catechism may be wrong. LOL

[allmendream]

State CG was the exception not the rule. They accounted for all possible states and used a model that showed that state CG was much less prevalent than the states that grouped humans and chimps. Their data unambiguously showed that humans and chimps split more recently than gorillas split from the human chimp line, as they concluded with their estimate of 4 million years for the human-chimp split.

Your selective quoting just shows your desperation. The scientists you are quoting clearly concludes that chimps and humans are closer to each other than either is to a gorilla. Are the scientists in error over their own data GGG?

[allmendream]

"Analysis of such large fragments is challenging because different parts of the alignment will have different evolutionary histories (and thus different genealogies, see Figure 1) because of recombination [14,20]. Ideally, one would like to infer the genealogical changes directly from the data and then analyze each type of genealogy separately. A natural approach to this challenge is to move along the alignment, and simultaneously compute the probabilities of different relationships and speciation times. While recombination has been considered in previous likelihood models [14], the spatial information along the alignment has largely been ignored. In this paper we describe a hidden Markov model (HMM) that allows the presence of different genealogies along large multiple alignments. The hidden states are different possible genealogies (labeled HC1, HC2, HG, and CG in Figures 1 and 2). Parameters of the HMM include population genetics parameters such as the HC and human–chimp–gorilla (HCG) ancestral effective population sizes, NHC and NHCG, and speciation times τ1 and τ2 (see Figure 1). We therefore name our approach a coalescent HMM (coal-HMM)."