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Thanks for the article link! >"Our estimated location of pandemic origin explains the observation that Kinshasa exhibits more contemporary HIV-1 genetic divers

Thanks for the article link! >"Our estimated location of pandemic origin explains the observation that Kinshasa exhibits more contemporary HIV-1 genetic diversity than anywhere else" >This is totally circular. As shown in their figure S2, they used genetic diversity in a region as an indication of earlier presence. It seems like they also used phylogenetic history. Diversity alone is not a sufficient to identify origination. >A very high genetic diversity of HIV-1 has been reported, not only in Kinshasa and the north and south of the DRC (12, 13, 31, 32), but also in Brazzaville in the RC and, to a lesser extent, in the Mayombe area of RC near Pointe-Noire, all of which have been suggested as potential source locations of the pandemic (22, 33, 34). We therefore performed phylogeographic analyses of viruses collected in both the DRC and RC (table S1) and compared sequence sampling locations with phylogenetic history to formally test hypotheses concerning the location of ancestral viral lineages (30). Our analyses robustly place the spatial origin of the HIV-1 group M pandemic in Kinshasa [posterior probability (PP) = 0.99] They could have used "consistent with" rather than "explains", though that may be a bit pedantic and debatable and we wouldn't be in the sorry state of science education/trust if all researchers would communicate like Neil deGrasse Tyson.

nonbel 11y ago
Well I know that information about genetic diversity was used to generate the phylogenetic tree since the same sequences are used to determine both, therefore there is data leakage. So I am sure it is circular, it is only a matter of how circular. I think totally circular. Perhaps I am misunderstanding their model, but look at figure S2. It shows the less closely related the sequences at each location, the more likely that was the originating region relative to the others. See how the leafs of the right tree corresponding to location B are more widely distributed (indicating diversity) than those for location A or C (which are more clustered within the tree)?

nonbel 11y ago

Well I know that information about genetic diversity was used to generate the phylogenetic tree since the same sequences are used to determine both, therefore there is data leakage. So I am sure it is circular, it is only a matter of how circular. I think totally circular. Perhaps I am misunderstanding their model, but look at figure S2. It shows the less closely related the sequences at each location, the more likely that was the originating region relative to the others. See how the leafs of the right tree corresponding to location B are more widely distributed (indicating diversity) than those for location A or C (which are more clustered within the tree)?