Define the genetic structure of populations by simulated annealing ------------------------------- SAMOVA 2.0 implements an approach to define groups of populations that are geographically homogeneous and maximally differentiated from each other. The method is based on a simulated annealing procedure that aims at maximizing the proportion of total genetic variance due to differences between groups of populations (SAMOVA, Spatial Analysis of MOlecular VAriance). SAMOVA 2.0 can also be used to identify groups of populations that are maximally differentiated without geographical constraint (the populations in the groups are not necessarily adjacent) ------------------------------- --------------------------------- Reading the geographic input file ! "Sample 1" 0.0481282 0.699552 "Sample 2" 0.0103132 0.745391 "Sample 3" 0.037815 0.775286 "Sample 4" 0 0.829098 "Sample 5" 0.543161 0.906826 "Sample 6" 0.321805 0.877987 "Sample 7" 0.264224 0.706886 "Sample 8" 0.317268 0.896901 "Sample 9" 0.610059 0.845162 "Sample 10" 0.659768 0.902422 "Sample 11" 0.411805 0.920777 "Sample 12" 0.266458 0.693214 "Sample 13" 0.79604 0.824534 "Sample 14" 0.641239 0.971659 "Sample 15" 0.738011 0.930324 "Sample 16" 0.494586 0.907404 "Sample 17" 0.6619 0.890483 "Sample 18" 0.905875 0.847593 "Sample 19" 0.641823 0.938695 "Sample 20" 0.817766 0.960698 "Sample 21" 0.970229 0.822541 "Sample 22" 0.716835 0.884803 "Sample 23" 1 0.86583 "Sample 24" 0.644539 0.923249 "Sample 25" 0.939668 1 --------------------------------- Random generator initialized with : 66 --------------------------------- Searching the genetic structure automatically Number of groups = 2 Number of independent SA processes = 10 Number of steps in SA process = 10000 Exp. factor in SA process = 0.915811 DataType = 0 Molecular distance = 5 Gamma a value = 0.17 --------------------------------- Comparing input files Number of samples matches : (25) and (25) --------------------------------- Groups found below are geographically homogeneous -------- WITH GEO -------- SA process: 0 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 23 24 Group 1: 22 initFCT: -0.0431749 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 1 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 Group 1: 19 initFCT: -0.0171426 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 SA process: 2 Group 0: 0 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 6 initFCT: 0.132425 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 3 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 23 24 Group 1: 21 initFCT: -0.0531706 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 4 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 23 24 Group 1: 22 initFCT: -0.0431749 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 5 Group 0: 0 1 2 3 4 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 5 initFCT: -0.0682854 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 6 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18 19 20 21 22 23 24 Group 1: 16 initFCT: 0.0242943 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 7 Group 0: 0 1 2 3 4 5 6 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 7 initFCT: -0.038454 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 8 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 21 22 23 24 Group 1: 20 initFCT: 0.0226193 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 9 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 19 20 21 22 23 24 Group 1: 18 initFCT: -0.0633171 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 --------------------------------- Final configuration of groups Group 0 1 0 Group 1 24 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 0.220161 --------------------------------- Groups found below are NOT geographically homogeneous -------- NO GEO -------- SA process: 0 Group 0: 0 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 1 initFCT: -0.0170859 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 SA process: 1 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 15 16 17 18 19 20 21 22 23 24 Group 1: 14 initFCT: 0.122311 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 SA process: 2 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 23 24 Group 1: 22 initFCT: -0.0431749 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 SA process: 3 Group 0: 0 1 2 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 3 initFCT: 0.0374312 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 SA process: 4 Group 0: 0 1 2 3 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 4 initFCT: 0.0156026 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 5 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Group 1: 24 initFCT: 0.037429 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 6 Group 0: 0 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 6 initFCT: 0.132425 Group 0: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Group 1: 0 bestFCT: 0.220161 SA process: 7 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 24 Group 1: 23 initFCT: -0.0623563 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 SA process: 8 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 23 24 Group 1: 22 initFCT: -0.0431749 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 SA process: 9 Group 0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 21 22 23 24 Group 1: 19 initFCT: -0.0171426 Group 0: 0 Group 1: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 bestFCT: 0.220161 --------------------------------- Final configuration of groups (no geo) Group 0 1 0 Group 1 24 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 0.220161