============================================================ Metadata associated with "Garrick_etal_2018b_Simulated_Data" ============================================================ These simple text (.txt) files contain DNA sequence datasets that were simulated in DIY-ABC v2.1.0 (Cornuet et al. 2014) using a HKY model of evolution (Hasegawa et al. 1985) with proportion of invariant sites = 10% and gamma = 2.0, and a mutation rate (µ) of 1×10-7 substitutions per site per generation. Each locus is selectively neutral, unlinked, has a diploid autosomal mode of inheritance, and an alignment length of 400-bp (no missing data, sequencing error, nor gaps). Each dataset was simulated with either 10 or 50 sampled diploid individuals (ind). Four lineage fusion scenarios (Scen), labeled A-D, were considered. The number of independent loci (Loc) contained within each dataset was either 1, 5, 25, 100 or 400. The following applies to all files, excluding those within the folder "ScenarioB_bottleneck": - Along all branches of the population tree within which simulations were performed, the effective population size (Ne) was set at either 1000 (1k), 10000 (10k) or 100000 (100k). At the moment of fusion, the relative genetic contribution of each fusing lineage (i.e., the mixing, Mx) was either symmetrical [1:1 ratio; i.e., 50% contribution from lineage 1 (50Mx)] or asymmetrical [1:3 ratio; i.e., 25% contribution from lineage 1 (25Mx)]. For each individual (ind) × lineage fusion scenario (Scen) x locus number (Loc) x effective population size (Ne) x mixing (Mx) combination, either 5 or 10 replicate (Rep) datasets were simulated. The following applies only to those files within the folder "ScenarioB_bottleneck": - Along branches of the population tree within which simulations were performed, the effective population size (Ne) was set in such a way as to force an instantaneous bottleneck (bott) at the moment of lineage divergence. Here, each sister lineage that descended from the shared common ancestor had its Ne reduced to half the size of ancestor's Ne (e.g., if the ancestor's Ne was 1000, then each sister lineage had a Ne of 500). Then, at the moment of fusion, the resulting admixed population instantaneously regained the Ne of the original ancestor (e.g., if the ancestor's Ne was 1000, then the fusion event gave rise to a population with an Ne of 1000). Effective population size (Ne) of the original ancestor was set at either 1000 (1k), 10000 (10k) or 100000 (100k). At the moment of fusion, the relative genetic contribution of each fusing lineage (i.e., the mixing, Mx) was either symmetrical [1:1 ratio; i.e., 50% contribution from lineage 1 (50Mx)] or asymmetrical [1:3 ratio; i.e., 25% contribution from lineage 1 (25Mx)]. For each individual (ind) × lineage fusion scenario (Scen) x locus number (Loc) x effective population size (Ne) x mixing (Mx) combination, either 5 replicate (Rep) datasets were simulated. File names reflect all of the above information. For example, the file named "10ind_ScenA_1Loc_10kNe_50Mx_Rep1.txt" contains data from 10 sampled individuals simulated under lineage fusion scenario A, it has 1 locus in the dataset, the effective population size along branches of the containing population tree was 10000, mixing upon fusion was symmetrical, and it is replicate dataset number 1 (also, no bottleneck event was enforced). ============================================================ References ============================================================ Cornuet J-M, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin J-M, Estoup A (2014) DIYABC v2.0: A software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics, 30, 1187–1189. Hasegawa M, Kishino K, Yano T. (1985). Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160–174.