population bottleneck
Bunnefeld L, Frantz LAF & Lohse K 2015 Inferring bottlenecks from genome-wide samples of short sequence blocks. Genetics 201:1157-1169.
- we extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks
- using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference
- the PSMC relies on an approximation to the coalescent
- it makes use of long-range linkage information
- [it] requires fairly well-assembled reference genomes
- the SFS throws away all linkage information
- Bhaskar and Song (2014) showed that for the piecewise constant models of population size change, the SFS is a sufficient statistic given enough data
- Terhorst and Song (2015) show that the error of SFS-based estimates converges at rate 1/logs
- s is the number of segregating sites
- this could be remedied by incorporating linkage information.
- an alternative set of methods bases inference on many short loci (blocks of sequence) without requiring the long-range linkage information necessary for the PSMC
- considering linked sites within sequence "blocks" exploits the demographic information contained in the distribution of genealogical branches while still avoiding the need to model the ancestral recombination graph
- this class of methods assumes that intrablock recombination can be ignored
- runs of homozygosity contain valuable information about demography
