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    1. The green, blue and red lines highlights the same specific choices of ancestor used in Fig. 1.

      It would be helpful to define these colors in one or more of the figure captions. Currently they are only defined in the main text (not Fig 1) despite this pointing to Figure 1.

    2. Our analysis shows that the amount of diversity at a given evolutionary time depends strongly on the ancestor, due to highly non-trivial epistatic dynamical correlations. More epistatically constrained ancestors give rise to less diversity, thus allowing for reconstruction over longer evolutionary times (Fig. 8a). Yet, at comparable amount of diversity, more epistatic ancestors are more difficult to reconstruct (Fig. 8b), at least using the FastML algorithm that neglects correlations between sites

      This is a really intriguing finding. It would be interesting to look at the posterior probabilities of the FastML reconstructed ancestors for each level of epistasis. I am wondering if the posterior probabilities reflect the uncertainty you are observing here, or whether ASR algorithms are blind to them (because they are blind to epistasis). In other words, do the more epistatic ancestors produce ML ASR sequences with lower posterior probabilities or are the probabilities misleadingly high? If the latter, this work could have implications for the validity of ASR on sequences with high levels of epistasis since the posterior probabilities are generally used as a measure of confidence in the reconstructions.