[This is a review of the original version. See Text S1 for the version history. The authors’ responses are included in line and are reflected in the published version.]

This Topic Page presents a competent and useful overview of phylodynamics as applied to viruses. The authors have themselves made significant contributions to this field and can thus draw from extensive experience and insightful case studies.

My comments are relatively minor and mainly represent suggestions for improving structure and clarity:

A major hallmark of phylodynamic approaches is the attempt to link observed phylogenetic patterns to the underlying biological mechanisms, often through mathematical models. However, it is important to emphasise that there often is a one-to-many relationship between pattern and process. While the ladder-like tree shown in figure 1 for example is consistent with an effect of selection, similarly imbalanced trees may also as a result due to other processes involving serial population bottlenecks. Overcoming these problems, often by drawing on data other than viral sequences alone, represents one of the major current challenges and is an active area of research (as nicely illustrated much later in the influenza case example).

Response: Using epidemiological and ecological data in combination with viral phylogenies is the most promising way to resolve identifiability issues related to phylodynamic inference. We have included a discussion of these identifiability issues at the end of the #Sources_of_phylodynamic_variation section.

I find that the distinction made in the application section into 'dating origins' and 'epidemiological' doesn't work particularly well, partly because the two parts are of very uneven length but also because arguably all viral phylodynamic studies relate to epidemiological processes. That subsection could be broken further for example into 'structured populations', 'within-host dynamics', 'linking different scales' etc. Alternatively, the section could just give an overview without subsections, since many of these themes are also later discussed in the case examples.

Response: We agree that the headings of 'dating origins' and 'epidemiological' didn't make sense as application categories. We have reorganized this section into 'Viral origins', 'Viral spread' and 'Viral control efforts'.

The term coalescence is used in the subsection on epidemiological applications without further explanation. A link to the section further below, explaining this concept, may be helpful at that point.

Response: As the paragraph is discussing rates of evolution, we've removed the reference to "coalescence" to improve clarity.

For the figures, the authors chose to focus exclusively on phylogenetic patterns rather than the dynamical processes they relate to but many of these could also be represented graphically such as migration, transmission chains, or changes in population size.

Response: We've revised figures 1 and 2 to better illustrate the underlying the process that is being revealed in the phylogeny. In the case of figure 1, changes in population size, and in figure 2 population structure.

Adding panels to figures 1-3 labeled a) and b) would help to refer to specific pattern in the text. It would also be useful to explain (for example in the section on coalescent theory) that actual phylogenies tend to look very different from the depicted caricatures due to the stochastic nature of the coalescent.

Response: We've added panels to figures 1-3 and revised the text to make it clear that the figures are caricatures.

While phylodynamics has so far been synonymous with viruses, this is about to change with advent of novel sequencing technologies, making the phylodynamic approaches discussed here applicable to a much wider range of pathogens (such as bacteria for example). This would be worth pointing out.

Response: We have included a new section ('Future directions') at the end of the manuscript discussing advances in sequencing technologies and the application of phylodynamic techniques to a diversity of pathogenic organisms.

Typo in Applications/Epidemiological - "geographic movement of human THE influenza virus"

Response: Fixed.

Reference 22 looks wrong.

Response: We apologize for this oversight. These citations have been replaced with a reference to Anderson and May, based on a recommendation by reviewer 1.