next on phyloseminar.org
Ancestral recombination graphs
An empirical view of the population pedigree
Often, the summary statistics of population genetics are framed in the setting of Kingman's coalescent or related models. These statistics can be alternatively thought of as descriptive statistics of the realized population pedigree-with-recombination, in a way that has become much more useful in the era of whole-genome sequencing. For instance, pairwise number of nucleotide differences is proportional to "effective population size", which is sometimes more usefully thought of as an estimate of the average length of the path through the pedigree to the most recent common ancestor at a randomly chosen locus (with an explicit standard error). Another example is the pairwise distribution of long tracts of IBD, which provides an estimate of a functional of the entire distribution of such paths.
A demography-aware conditional sampling distribution for inferring ancient demography and detecting introgression patterns
Complex demographic histories shape the genealogies of contemporary individuals and thus have a substantial impact on the genetic variation observed today. These genealogies are commonly modeled by the ancestral recombination graph (ARG), and we developed a novel demography-aware conditional sampling distribution (CSD) to approximate these ARGs under general demographic models. We apply this CSD in an expectation-maximization framework for demographic inference. We show that this method can accurately recover biologically relevant demographic parameters like population divergence times, migration rates, or ancestral population sizes from simulated datasets. Furthermore, we apply the CSD to detect tracts of genetic material that introgressed from Neanderthal into modern humans. Our results are in general agreement with previously published results, and we will discuss the similarities and differences, and their biological implications.