This manuscript addresses an interesting question: did Indigenous peoples intentionally spread sunchokes across North America during the development of the Eastern Agricultural Complex around 4000 years ago, or were the plants already naturally widespread? The complex ploidy of sunchokes makes direct population genomic genetic analyses difficult. Instead, the authors studied a specialist parasitic fly that only lives on sunchokes as a proxy to address this question.

Overall, I really enjoyed reading this manuscript. I commend the authors on their clarity of writing and I appreciate the provided detail and transparency throughout the manuscript. Their approach and experimental design are well justified and the authors are cautious in their language and openly acknowledge caveats and limitations. That said, while I agree with the authors that their data are consistent with anthropogenic range expansion, the data supporting this conclusion are rather weak.

More specifically, the authors place a lot of weight on their nucleotide diversity estimates (e.g., abstract: “…we find S. longitudinalis nucleotide diversity is highest in the Ohio Valley, indicating this area as a pre-cultivation range for sunchoke.”). Indeed, the results prominently reported in the main text (Fig. 2A,B) would support that, but as the authors fairly acknowledge, this effect completely disappears when the analyses are based on sample-size-standardized estimates of nucleotide diversity (Fig. S2). Again, I really appreciate the authors openly reporting this result, but I think they should consequently re-evaluate and de-emphasize their nucleotide diversity-based results. I note that while estimates of haplotype richness and IMa3 population size estimates are higher for Ohio Valley than East and West, consistent with the main conclusion, the effect size is very small. The authors already suggest that more samples would be valuable for future studies (ll. 442-443), but I would advise that they more critically assess the current support for their main conclusions or, if possible, collect more data now.

Minor comments:
l. 61: “of” missing in “much that range”
ll. 297-314: consider using common names or remind readers of which species is your focal organisms. Keeping track of binomial species names for the host and parasitic fly is a bit cumbersome
ll. 321-322: I suggest following standard practice and report both contig and scaffold N50 here
Fig. S5: the resolution is rather bad

I am pleased to see that the authors have considered my concerns and incorporated recommendations by me and Reviewer 2. From my side, all issues have been addressed satisfactorily and I think the manuscript is now suitable for publication. Congratulations to the authors on this fine work.