human: A set of R objects containing observed data from three human populations, and simulated data under three different demographic models. The data set is used to illustrate model selection and parameter inference in an ABC framework (see the package's vignette for more details).

Description

data(human) loads in four R objects: stat.voight is a data frame with 3 rows and 3 columns and contains the observed summary statistics for three human populations, stat.3pops.sim is also a data frame with 150,000 rows and 3 columns and contains the simulated summary statistics, models is a vector of character strings of length 150,000 and contains the model indices, par.italy.sim is a data frame with 50,000 rows and 4 columns and contains the parameter values that were used to simulate data under a population bottleneck model. The corresponding summary statistics can be subsetted from the stat.3pops.sim object as

subset(stat.3pops.sim,
  subset=models=="bott")

Usage

data(human)

Arguments

source

The observed statistics were taken from Voight et al. 2005 (Table 1.). Also, the same input parameters were used as in Voight et al. 2005 to simulate data under the three demographic models. Simulations were performed using the software ms and the summary statistics were calculated using sample_stats (Hudson 1983).

Details

Data is provided to estimate the posterior probabilities of classical demographic scenarios in three human populations: Hausa, Italian, and Chinese. These three populations represent the three continents: Africa, Europe, Asia, respectively. par.italy.sim may then used to estimate the ancestral population size of the European population assuming a bottleneck model. It is generally believed that African human populations are expanding, while human populations from outside of Africa have gone through a population bottleneck. Tajima's D statistic has been classically used to detect changes in historical population size. A negative Tajima's D signifies an excess of low frequency polymorphisms, indicating population size expansion. While a positive Tajima's D indicates low levels of both low and high frequency polymorphisms, thus a sign of a population bottleneck. In constant size populations, Tajima's D is expected to be zero.

With the help of the human data one can reach these expected conclusions for the three human population samples, in accordance with the conclusions of Voight et al. (2005) (where the observed statistics was taken from), but using ABC.

References

B. F. Voight, A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson and A. Di Rienzo (2005) Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. PNAS 102, 18508-18513.