Therefore, by comparing the PTX files from the two coding programs we could detect the bottleneck that causes the speed reduction.
Detecting the bottleneck depends on the chance to sample a sufficient number of pairs of alleles corresponding to the second class: the bottleneck must be strong enough (large F2 value) and not too old (small or intermediate F1).
Although the reliability of various bottleneck tests to detect the occurrence and timing of genetic bottlenecks has been questioned, particularly the M-ratio test (Peery et al. 2012), we used multiple approaches and found concordant results across these approaches.
To detect the presence of possible population bottlenecks, genotype data were analyzed in the computer program B OTTLENECK[ 36] using the stepwise mutation model (SMM) and two-phase model (TPM) at 95% stepwise and 70% stepwise.
These data sets were then used to evaluate the performances of two recently developed population genetics methods, BayesAss+, that estimates recent migration rates among populations, and Bottleneck, that detects the occurrence of recent bottlenecks.
The Bottleneck analysis suggested both the Manhole Sacramento and Zoo populations have experienced bottlenecks, but also detected the signature of a bottleneck in several other populations that would not be expected to have them.
We used our C. remanei generated data sets to evaluate the performances of two recently developed population genetics methods, implemented in the programs BayessAss+ [7], that estimates recent migration rates among populations, and Bottleneck [20], that detects the occurrence of recent bottlenecks.
BOTTLENECK v. 1. 2. 02 [ 33] was used to detect recent bottlenecks under the assumptions of the infinite allele mutation model (IAM), and the Wilcoxon signed rank test was applied.
Interestingly, the power to detect bottlenecks with the SFS does not decrease monotonically with respect to the start time, T 1.
The Garza-Williamsion index is more powerful to detect genetic bottlenecks if the bottleneck lasted several generations or if the population made a rapid demographic recovery [ 67].
