A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data

Supporting Information

Supporting Information

  • Supporting Information - File S1, Tables S1-S2, and Figures S1-S9 (PDF, 2 MB)
  • File S1 - Scripts to generate simulated data sets. (PDF, 468 KB)
  • Table S1 - List of putative loci under incomplete selective sweeps in D. melanogaster Rwanda population inferred from iHS test. (PDF, 469 KB)
  • Table S2 - List of putative loci under incomplete selective sweeps in D. melanogaster Rwanda population inferred from nSL test. (PDF, 42 KB)
  • Figure S1 - Joint sampling probability under incomplete selective sweep for n1 = n2 = 10 and r/s = 0.01 or 0.04. (PDF, 519 KB)
  • Figure S2 - Composite likelihood ratio calculated for a simulated data set of 20 DNA sequences of 100kb long (R = 4,000). (PDF, 556 KB)
  • Figure S3 - Distributions of maximum CLR for samples generated under different demographic models. (PDF, 515 KB)
  • Figure S4 - Changes in the distributions of T0 with varying recombination rates in different demographic models. (PDF, 522 KB)
  • Figure S5 - Genome-wide empirical distribution of derived-allele frequency in the Rwanda D. melanogaster sample (22 sequences) in comparison with the standard neutral distribution for a sample of same size. (PDF, 558 KB)
  • Figure S6 - Composite Likelihood Ratio (T1x) calculated for chromosome 2R. (PDF, 489 KB)
  • Figure S7 - Polymorphism pattern surrounding the site of strongest signal detected by CLR test within each cluster listed in Table 2. (PDF, 974 KB)
  • Figure S8 - Polymorphism patterns of genome areas surrounding the putative site under selection detected exclusively by iHS or nSL method. (PDF, 751 KB)
  • Figure S9 - Deterministic changes in pA, the frequency of a linked neutral derived allele in the subpopulation of chromosomes carrying the ancestral allele of the S locus during the course of a selective sweep. (PDF, 506 KB)