List of haplotypes found in best reconstruction, with frequencies in parentheses. 1: C G A A G G C C G A G G C T (4) 2: A G A G G A A G C A G T T C (3) 3: C A A G G G C G G A G G C C (7) 4: C G A G G A A G C A G T T C (2) 5: C G A G G G C G G A G G C C (5) 6: C A A G G A A G C A G T T C (4) 7: C G A G G A A G G A G T T C (13) 8: C A A G G G C G G T G G C C (3) 9: C G T G G A A G C A G T T C (4) 10: C G T G G A A G G A G T T C (2) 11: A G A A G G C C G A G G C T (1) Summary of best reconstruction (numbers refer to the list of haplotypes given above) D001: (1,1) D002: (2,2) D003: (3,3) D004: (3,3) D005: (4,4) D006: (5,5) D007: (5,5) D008: (6,6) D009: (7,7) D010: (7,3) D011: (1,1) D012: (3,7) D013: (7,7) D014: (7,7) D015: (8,8) D016: (7,9) D033: (3,7) D034: (9,7) D035: (10,2) D036: (9,6) D037: (7,8) D038: (7,9) D039: (6,10) D040: (5,11) Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: D001 [C] G A A G G C C G A G G C T [C] G A A G G C C G A G G C T D002 A G A G G A A G C A G T T C A G A G G A A G C A G T T C D003 C A A G G G C G G A G G C C C A A G G G C G G A G G C C D004 C A A G G G C G G A G G C C C A A G G G C G G A G G C C D005 C G A G G A A G C A G T T C C G A G G A A G C A G T T C D006 C G A G G G C G G A G G C C C G A G G G C G G A G G C C D007 C G A G G G C G G A G G C C C G A G G G C G G A G G C C D008 C A A G G A A G C A G T T C C A A G G A A G C A G T T C D009 C G A G G A A G G A G T T C C G A G G A A G G A G T T C D010 C G A G G A A G G A G T T C C A A G G G C G G A G G C C D011 C G A A G G C C G A G G C T C G A A G G C C G A G G C T D012 C A A G G G C G G A G G C C C G A G G A A G G A G T T C D013 C G A G G A A G G A G T T C C G A G G A A G G A G T T C D014 C G A G G A A G G A G T T C C G A G G A A G G A G T T C D015 C A A G G G C G G T G G C C C A A G G G C G G T G G C C D016 C G A G G A A G (G) A G T T C C G T G G A A G (C) A G T T C D033 C A A G G G C G G A G G C C C G A G G A A G G A G T T C D034 C G (T) G G A A G C A G T T C C G (A) G G A A G G A G T T C D035 C G (T) G G A A G (G) A G T T C A G (A) G G A A G (C) A G T T C D036 C (G) T G G A A G C A G T T C C (A) A G G A A G C A G T T C D037 C G A G G A A G G A G T T C C A A G G G C G G T G G C C D038 C G A G G A A G (G) A G T T C C G T G G A A G (C) A G T T C D039 C (A) A G G A A G (C) A G T T C C (G) T G G A A G (G) A G T T C D040 (C) G A G G G C G G A G G C C (A) G A A G G C C G A G G C T Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = D001 ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = D002 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D003 = = = = = = = = = = = = ? = = = = = = = = = = = = = ? = D004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D007 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D010 = G = = = A A = = = = T T = = A = = = G C = = = = G C = D011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D012 ? A = = = G C = = = = G C = ? G = = = A A = = = = T T = D013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = D016 = = A = = = = = (G) = = = = = = = T = = = = = (C) = = = = = D033 = A = = = G C = = = = G C = = G = = = A A = = = = T T = D034 = = (T) = = = = = C = = = = = = = (A) = = = = = G = = = = = D035 C = (T) = = = = = (G) = = = = = A = (A) = = = = = (C) = = = = = D036 = (G) T = = = = = = = = = = = = (A) A = = = = = = = = = = = D037 ? G = = = A A = = A = T T = ? A = = = G C = = T = G C = D038 = = A = = = = = (G) = = = = = = = T = = = = = (C) = = = = = D039 = (A) A = = = = = (C) = = = = = = (G) T = = = = = (G) = = = = = D040 (C) = = G = = = G = = = = = C (A) = = A = = = C = = = = = T Phase probabilities at each site with phase known positions indicated by = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = = 1 1 = = = = 1 1 = = = = = = = = = = = = = = = = 0.98 = = = 1 1 = = = = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = 0.87 = = = = = = 0.98 = = = 1 1 = = = = 1 1 = = = 0.87 = = = = = 1 = = = = = 1 = 0.75 = = = = = 0.77 = = = = = = 0.89 1 = = = = = = = = = = = = 1 = = = 1 1 = = 0.98 = 1 1 = = = 1 = = = = = 0.87 = = = = = = 0.7 1 = = = = = 0.52 = = = = = 0.67 = = 1 = = = 1 = = = = = 1