population expansion - senecio7の日記

Ragsdale AP & Gravel S 2019 Models of archaic admixture and recent history from two-locus statistics. PLoS Genet 15:e1008204.

human expansion models underestimate LD between low frequency variants
the demographic model for human out-of-Africa (OOA) expansion proposed and inferred by Gutenkunst et al. [2] has been widely used for subsequent simulation studies
parameter estimates have been refined as more data became available [3, 35, 38]
we generalized the Gutenkunst model with a number of additional parameters accounting for recent events, including size changes in the YRI population, recent admixture between populations, and substructure within each continental population
none of these modifications provided satisfactory fit to the data and some did not converge to biologically realistic parameters

Fig 3
(A) we fit the 13-parameter Gutenkunst et al. model to statistics in the two-locus, multi-population Hill-Robertson system
most statistics were accurately predicted by this model, including
(B) the decays of E[D²] in each population
(C) the decay of the covariance of D between populations
(E) the joint heterozygosity E[π₂(i)]
(D) E[D_i(1 − 2p_i)(1 − q_i)] was fit poorly by this model
we were unable to find a three-population model that recovered these observed statistics, including with additional periods of growth, recent admixture between human populations, or substructure within modern populations

Table 1
we fit the commonly used 13-parameter model to the multi-population Hill-Robertson statistics
the best fit parameters shown here were fit to the set of statistics without the E[Dz] terms
inclusion of those terms led to runaway parameter behavior in the optimization
this is often a sign of model mis-specification
the same 13-parameter model is augmented by the inclusion of two deeply diverged branches, putatively Neanderthal and an unknown lineage within Africa
these branches split from the branch leading to modern humans roughly 460 – 650 kya, and contributed migrants until quite recently (~ 19 kya)
times reported here assume a generation time of 29 years and are calibrated by the recombination (rather than mutation) rate

Fig 4
inferred OOA model with archaic admixture
(A) we fit a model for out-of-Africa expansion related to the standard model in Fig 3A
we also include two branches with deep split from the ancestral population to modern humans
(B-E) this model fits the data much better than the model without archaic admixture, and especially for the Dz statistics (D)

beyond the classical recursions for E[D] and E[D²] [12, 14], two-locus statistics are difficult to compute for non-equilibrium, multi-population demographic models
Sved [53] proposed an IBD based recursion to compute E[r²] across subdivided populations
its accuracy and interpretation remain debated [12]