Hellow
The reviewer expressed concerns regarding the use of the software to estimate absolute recombination rates in populations with drastically different nucleotide diversity and demographic histories.
While the software might handle demographic misspecification to some extent, it is limited to inferring relative recombination rates at hotspots, not absolute rates. Accurate absolute recombination maps require pedigree studies or sperm-typing.
Additionally, the reviewer pointed out that the software trained the neural network using an equilibrium demographic model, which does not account for the bottleneck and admixture histories of domestic breeds.
This leads to inaccurate estimates of absolute recombination rates, despite the authors placing significant weight on these inferred values.
In response, I added results from smc++, using the --demographicHistory WL_smc++_plot.csv. However, the recombination rate calculated for all chromosomes across all breeds is 0.
**I would appreciate your guidance on how to resolve this issue or how I should respond to the reviewer’s comments?**
Thank you again!
Hellow
The reviewer expressed concerns regarding the use of the software to estimate absolute recombination rates in populations with drastically different nucleotide diversity and demographic histories.
While the software might handle demographic misspecification to some extent, it is limited to inferring relative recombination rates at hotspots, not absolute rates. Accurate absolute recombination maps require pedigree studies or sperm-typing.
Additionally, the reviewer pointed out that the software trained the neural network using an equilibrium demographic model, which does not account for the bottleneck and admixture histories of domestic breeds.
This leads to inaccurate estimates of absolute recombination rates, despite the authors placing significant weight on these inferred values.
In response, I added results from smc++, using the --demographicHistory WL_smc++_plot.csv. However, the recombination rate calculated for all chromosomes across all breeds is 0.