Urban past predicts contemporary genetic structure in city rats
Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa)
Recommendation: posted 11 May 2020, validated 11 May 2020
DiLeo, M. (2020) Urban past predicts contemporary genetic structure in city rats. Peer Community in Ecology, 100044. 10.24072/pci.ecology.100044
Urban areas are expanding worldwide, and have become a dominant part of the landscape for many species. Urbanization can fragment pre-existing populations of vulnerable species leading to population declines and the loss of connectivity. On the other hand, expansion of urban areas can also facilitate the spread of human commensals including pests. Knowledge of the features of cityscapes that facilitate gene flow and maintain diversity of pests is thus key to their management and eradication.
Cities are complex mosaics of natural and manmade surfaces, and habitat quality is not only influenced by physical aspects of the cityscape but also by socioeconomic factors and human behaviour. Constant development means that cities also change rapidly in time; contemporary urban life reflects only a snapshot of the environmental conditions faced by populations. It thus remains a challenge to identify the features that actually drive ecology and evolution of populations in cities . While several studies have highlighted strong urban clines in genetic structure and adaption , few have considered the influence of factors beyond physical aspects of the cityscape or historical processes.
In this paper, Stragier et al.  sought to identify the current and past features of the cityscape and socioeconomic factors that shape genetic structure and diversity of the house mouse (Mus musculus domesticus) in Dakar, Senegal. The authors painstakingly digitized historical maps of Dakar from the time of European settlement in 1862 to present. The authors found that the main spatial genetic cline was best explained by historical cityscape features, with higher apparent gene flow and genetic diversity in areas that were connected earlier to initial European settlements. Beyond the main trend of spatial genetic structure, they found further evidence that current features of the cityscape were important. Specifically, areas with low vegetation and poor housing conditions were found to support large, genetically diverse populations. The authors demonstrate that their results are reproducible using several statistical approaches, including modeling that explicitly accounts for spatial autocorrelation.
The work of Stragier et al.  thus highlights that populations of city-dwelling species are the product of both past and present cityscapes. Going forward, urban evolutionary ecologists should consider that despite the potential for rapid evolution in urban landscapes, the signal of a species’ colonization can remain for generations.
 Rivkin, L. R., Santangelo, J. S., Alberti, M. et al. (2019). A roadmap for urban evolutionary ecology. Evolutionary Applications, 12(3), 384-398. doi: 10.1111/eva.12734
 Miles, L. S., Rivkin, L. R., Johnson, M. T., Munshi‐South, J. and Verrelli, B. C. (2019). Gene flow and genetic drift in urban environments. Molecular ecology, 28(18), 4138-4151. doi: 10.1111/mec.15221
 Stragier, C., Piry, S., Loiseau, A., Kane, M., Sow, A., Niang, Y., Diallo, M., Ndiaye, A., Gauthier, P., Borderon, M., Granjon, L., Brouat, C. and Berthier, K. (2020). Interplay between historical and current features of the cityscape in shaping the genetic structure of the house mouse (Mus musculus domesticus) in Dakar (Senegal, West Africa). bioRxiv, 557066, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/557066
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/557066
Version of the preprint: 2 (October 3, 2019)
Author's Reply, 29 Jan 2020
Decision by Michelle DiLeo, posted 05 Dec 2019
First, I would like to sincerely apologise for the delay in handling your manuscript. The revision came in while I was out of office, and finding a third reviewer to evaluate the methodological additions to the manuscript took longer than expected.
I have now received three reviews on the revised manuscript. I applaud the authors on the thoroughness of this revision. It is clear that a tremendous amount of work went into this, and I believe that the new analyses show that the results are relatively robust, and also introduce approaches that I have not seen used elsewhere in landscape-genetic studies. The reviewers for the most part share my enthusiasm, however, I agree with reviewer 3 that the extensive additions have now led to a decrease in readability. I unfortunately I cannot recommend the manuscript at this time, however I believe only minor changes are needed before the manuscript can be accepted. The suggested changes do not require new analyses, and can be addressed through additional clarification and by moving some of the new methods and results to the supplementary material.
I invite the authors to respond carefully to all reviewer comments. In particular, please work on increasing the readability. For example, both the RF methods produced similar results, so please only present one and move the methods and results of the other to the supplement. Similarly, the authors can consider omitting the model selection on the INLA results and instead just present the full model, with interpretation following from a comparison of coefficients.
Thank you and I look forward to seeing the revised manuscript.
Sincerely, Michelle DiLeo
Reviewed by anonymous reviewer 1, 19 Nov 2019
Reviewed by , 25 Oct 2019
Reviewed by Torsti Schulz, 28 Nov 2019
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/557066
Author's Reply, 03 Oct 2019
Decision by Michelle DiLeo, posted 02 Apr 2019
I have now received two reviews on your manuscript. In general, both reviewers were positive about the potential of this manuscript to make an interesting contribution, and I share their enthusiasm. That said, the reviewers had concerns and suggest several areas for improvement, which I would like to see addressed before I consider recommendation. While I would like to see replies to all of the reviewers concerns, below I highlight the areas that I think need the most work.
In particular, I share the concern that the site-level sampling strategy is perhaps not ideal, and that the implications of this should be discussed. It seems that MAPI is more suited to individual-based sampling (or at least finer-scale sampling) and I am interested to know if the results are sensitive to the resolution of the generated MAPI surface. How do the results of MAPI compare to analyses done with only the fourteen sampled sites?
Second, I echo the reviewer comment about the ability to tease apart the effects of historical versus contemporary aspects of the cityscape. It seems that these variables would be correlated, and it should be made abundantly clear to the reader how this problem was considered. I suspect that if there were no problems with collinearity, this might be easily addressed by reporting pairwise correlations and variance inflation factors for all variables.
Third, I agree that the discussion could use some work and that too much space is reserved for discussing the colonization history, which in my opinion is not the main or most interesting message of the paper.
Finally, I would be interested to see if genetic diversity correlates with the same aspects of the cityscape compared to genetic differentiation. Genetic diversity and differentiation can be driven by different processes and I think both are important when considering the practical applications of this work. I understand that with 14 sites you are limited to what can be included in a single model, but does genetic diversity show any strong univariate relationships with cityscape features beyond just the European settlement vs ancient village dichotomy?
Thank you for this interesting submission and I look forward to seeing your revision.
Sincerely, Michelle DiLeo