RT Journal Article
SR Electronic
T1 Gene flow biases population genetic inference of recombination rate
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.09.26.461846
DO 10.1101/2021.09.26.461846
A1 K. Samuk
A1 M.A.F. Noor
YR 2021
UL http://biorxiv.org/content/early/2021/09/26/2021.09.26.461846.abstract
AB Accurate estimates of the rate of recombination are key to understanding a host of evolutionary processes as well as the evolution of recombination rate itself. Model-based population genetic methods that infer recombination rates from patterns of linkage disequilibrium (LD) in the genome have become a popular method to estimate rates of recombination. However, these LD-based methods make a variety of simplifying assumptions about the populations of interest that are often not met in natural populations. One such assumption is the absence of gene flow from other populations. Here, we use forward-time population genetic simulations of isolation-with-migration scenarios to explore how gene flow affects the accuracy of LD-based estimators of recombination rate. We find that moderate levels of gene flow can result in either the overestimation or underestimation of recombination rates by up to 20-50% depending on the timing of divergence. We also find that these biases can affect the detection of interpopulation differences in recombination rate, causing both false positive and false negatives depending on the scenario. We discuss future possibilities for mitigating these biases and recommend that investigators exercise caution and confirm that their study populations meet assumptions before deploying these methods.Competing Interest StatementThe authors have declared no competing interest.