Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates

We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.,Microsatellite genotypes of Alpine ibex demes in the Swiss AlpsThis file contains raw data (genotypes of 37 microsatellites) of 954 individuals sampled in 31 Alpine ibex demes in the Swiss Alps. These data were collected and processed between 2005 and 2008 by Iris Biebach ([email protected]) and collaborators in the lab of Lukas Keller ([email protected]) at the University of Zurich, Switzerland. The content of this file has the following format: First line: number of loci (37). Lines 2 to n-1 (one line per individual): deme_id allele1_of_locus1; allele2_of_locus1; allele1_of_locus2; allele2_of_locus2. Names of demes (deme_id; first column in lines 2 to n-1) correspond to those given in Table S1 in the Supporting Information.genotypes_neutral_Aug10_geneflow_all_casus_37loci.txtCensus sizes of Alpine ibex demes in the Swiss AlpsThis file contains census population sizes of Alpine ibex in the Swiss Alps from 1906 to 2007.census_sizes.csvTransfer by humans of Alpine ibexThis file contains numbers of male and female Alpine ibex transferred by humans between demes during the process of reintroduction into the Swiss Alps. The entries cover the time between 1906 and 1993.transfers.csv,