Response to "No evidence that transmissible cancer has shifted from emergence to endemism in Tasmanian devils"

Herein, we rebut the critique of Patton et al. 2020, entitled, No evidence that a transmissible cancer has shifted from emergence to endemism, by Stammnitz et al. 2024. First and foremost, the authors do not conduct any phylogenetic or epidemiological analyses to rebut the inferences from or data. Additionally, Stammnitz et al. 2024 present a phylogenetic tree based on only 32 copy number variants in an effort to rebut our tree that was inferred from 436.1 kb of sequence data and nearly two orders of magnitude more parsimony-informative sites; 2520 SNPs. As such it is not surprising that their phylogeny did not have a similar branching pattern to ours, given that support for each branch of their tree was weak and essentially formed a polytomy. While the authors are correct that we used suboptimal filtering of our raw whole genome sequencing data, re-analyses of the data with 30X coverage, as suggested, resulted in a mutation rate similar to that reported in Stammnitz et al. 2024. Most importantly, when we re-analyzed our data, as well as Stammnitz et al. own data, the results of the Patton et al. (2020) article are supported with both datasets. That is, the effective transmission rate of DFTD has transitioned over time to approach one, suggesting endemism; and, the spread of DFTD is rapid and omnidirectional despite the observed east-to-west wave of spread. Overall, Stammnitz et al. 2024 not only fail to provide evidence to contradict the findings of Patton et al. 2020, but instead help support the results with their own data.