population bottleneck
Ragsdale AP & Gutenkunst RN 2017 Inferring demographic history using two-locus statistics. Genetics 206:1037-1048.
- methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful
- such methods ignore potentially informative patterns of linkage disequilibrium (LD) between neighboring loci
- two-locus statistics are more sensitive to demographic history than single-locus statistics
- two-locus statistics escape the notorious confounding of depth and duration of a bottleneck
- they provide a means to estimate effective population size based on the recombination rather than mutation rate
- we inferred a substantially lower ancestral effective population size than previous works and did not infer a bottleneck history
- disentangling the depth and duration of a bottleneck from allele frequency data are notoriously challenging (Keinan et al. 2007; Bunnefeld et al. 2015)
- jointly incorporating information about LD dramatically improves parameter identifiability
- inferring the parameters of a bottleneck model from single-locus data are notoriously difficult (Keinan et al. 2007)
- we were able to precisely and consistently recover the correct demographic parameters using two-locus statistics
- little power is lost when data are unphased and genotype frequencies are fit
