List of haplotypes found in best reconstruction, with frequencies in parentheses. 1: T A T C G G A A G A C G G A A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A T T G C C (2) 2: A A C C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C A A T T G G T T A G T G C G (1) 3: A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C G (5) 4: T A T C G G A A G A C G G A C A G G C C C G G G C A A C C D A D G C G C T A C A G T C G G G D G G T G C G (1) 5: T A C C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C C A T T G G T T A G T G C G (1) 6: A G C C A G G G A G C G G G A A T A C C C G G G C T A C T D A T G A A C T G C A A T T G G T T A T T G C C (3) 7: T A T C G G A A G A C G G A C A G G C C C G G G C A A C C D A D G C G C T A C A A T T G G T T A G T G C G (2) 8: A G C C A G G G A G C G G G A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A T T G C C (4) 9: A G C C A G G G A G C G G G A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A G T G C G (1) 10: A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C A A T T G G T T A G T G C G (1) 11: T A T C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C A A T T G G T T A G T G C G (3) 12: T A T C G G A A G A T T G A C G G G C C A G G G C A A C C D A D G C A C T G C A A T T G G T T A T T G C C (1) 13: T A T C G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G T T A G T G C G (3) 14: A G C C G G A A G A T T G A A A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C G (3) 15: A G C T G G A A G A C T G A C A G G C C C G G G C A A C C D A D G C G C T G C A A T T G G T T A T T G C C (1) 16: T A T C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C A A T T G G T T A T T G C C (2) 17: A G C C G G A A G A T T G A C A G A C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C G (2) 18: A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C C (2) 19: A G C T G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G T T A G T G C G (1) 20: A G C C A G G G A G C G G G A A T G C C C G G G C T A C T D A T G A A C T G C A A T T G G T T A T T G C C (1) 21: T A T C G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G T T A T T G C C (1) 22: T A T C G G A A G A C T G A A A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G T T A G T G C G (1) 23: A G C C G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C A A T T G G T T A T T G C C (1) 24: T A T C G G A A G A C G G A A A G G C C C G G G C A A C C A A D G C G C T G C C G T C G A G D G G T G C G (1) 25: T A T C G G A A G A C G G A A G G A C C C G A A T A A A C D A D T C G C T G C A A T T G G T T A G T G C G (1) 26: T A T C G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C A C T G C A A T T G G T T A T T G C C (1) Summary of best reconstruction (numbers refer to the list of haplotypes given above) E001: (1,2) E002: (3,4) E003: (5,6) E004: (3,7) E005: (8,9) E006: (7,10) E007: (1,11) E008: (12,8) E009: (13,14) E010: (15,16) E011: (16,6) E012: (17,11) E013: (6,17) E014: (18,3) E015: (14,13) E016: (19,3) E017: (20,21) E018: (13,3) E019: (14,8) E020: (11,22) E021: (23,8) E022: (18,24) E023: (25,26) Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: E001 (T) A (T) C G G A A G A C G G A A G G A (C) C C G G G C A A C T D G D T C (A) C T G C A A T T G G T T A T T G C C (A) A (C) C G G A A G A C G G A A G G A (T) C C G A A T A A A C D A D T C (G) C T G C A A T T G G T T A G T G C G E002 A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T (G) C (C) G T C G (A) G D G G T G C G T A T C G G A A G A C G G A C A G G C C C G G G C A A C C D A D G C G C T (A) C (A) G T C G (G) G D G G T G C G E003 T A C C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C (C) A T T G G T T A G T G C G A G C C A G G G A G C G G G A A T A C C C G G G C T A C T D A T G A A C T G C (A) A T T G G T T A T T G C C E004 A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C G T A T C G G A A G A C G G A C A G G C C C G G G C A A C C D A D G C G C T A C A A T T G G T T A G T G C G E005 A G C C A G G G A G C G G G A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A (T) T G C C A G C C A G G G A G C G G G A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A (G) T G C G E006 T A T C G G A A G A C G G A C A G G C C C G G G C A A C C D A D G C G C T A C A A T T G G T T A G T G C G A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C A A T T G G T T A G T G C G E007 T A T C G G A A G A C G G A A G G A (C) C C G G G C A A C T D G D T C (A) C T G C A A T T G G T T A T T G C C T A T C G G A A G A C G G A A G G A (T) C C G A A T A A A C D A D T C (G) C T G C A A T T G G T T A G T G C G E008 T A T C G G A A G A T T G A C G G G C C A G G G C A A C C D A D G C A C T G C A A T T G G T T A T T G C C A G C C A G G G A G C G G G A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A T T G C C E009 T A T C G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G [(T)] T A G T G C G A G C C G G A A G A T T G A A A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A [(G)] D G G T G C G E010 A G C (T) G G A A G A C T G A C A G G C C C G G G C A A C C D A D G C G C T G C A A T T G G T T A T T G C C T A T (C) G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C A A T T G G T T A T T G C C E011 T A T C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C A A T T G G T T A T T G C C A G C C A G G G A G C G G G A A T A C C C G G G C T A C T D A T G A A C T G C A A T T G G T T A T T G C C E012 A G C C G G A A G A T T G A C A G A C C C G G G C A A C C D A D G C G C T G C C G T C G A [G] D G G T G C G T A T C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C A A T T G G T T A G T G C G E013 A G C C A G G G A G C G G G A A T [A] C C C G G G C T A C T D A T G A A C T G C A A T T G G T T A T T G C C A G C C G G A A G A T T G A C A G A C C C G G G C A A C C D A D G C G C T G C C G T C G A [G] D G G T G C G E014 A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C C A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C G E015 A G C C G G A A G A T T G A A A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A [(G)] D G G T G C G T A T C G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G [(T)] T A G T G C G E016 A G C T G G A A G A T T G A C A G G C C (A) G G G C A A C C D A D G C G C T G C A A T T G G T T A G T G C G A G C T G G A A G A T T G A C A G G C C (C) G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C G E017 A G C C A G G G A G C G G G A A T G C C C G G G C T A C T D A T G A (A) C T G C A A T T G G T T A T T G C C T A T C G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C (G) C T G C A A T T G G T T A T T G C C E018 T A T C G G A A G A T T G A C A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G [T] T A G T G C G A G C T G G A A G A T T G A C A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A G D G G T G C G E019 A G C C G G A A G A T T G A A A G G C C C G G G C A A C C D A D G C G C T G C C G T C G A [G] D G G T G C G A G C C A G G G A G C G G G A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A T T G C [C] E020 T A T C G G A A G A C G G A A G G A T C C G A A T A A A C D A D T C G C T G C A A T T G G T T A G T G C G T A T C G G A A G A C T G A A A G G C C A G G G C A A C C D A D G C G C T G C A A T T G G T T A G T G C G E021 A G C C G G A A G A (T) T G A C A G G C C C G G G C A A C C D A D G C G C T G C A A T T G G T T A T T G C C A G C C A G G G A G (C) G G G A G G A C C C G G G C A A C T D G D T C A C T G C A A T T G G T T A T T G C C E022 A G C T G G A A G A T T G A (C) A G G C C C G G G C A A C C (D) A D G C G C T G C C G T C G A G D G G T G C (C) T A T C G G A A G A C G G A (A) A G G C C C G G G C A A C C (A) A D G C G C T G C C G T C G A G D G G T G C (G) E023 T A T C G G A A G A C G G A A (G) G A C C C G A A T A A A C D A D T C (G) C T G C A A T T G G T T A (G) T G C (G) T A T C G G A A G A T T G A C (A) G G C C A G G G C A A C C D A D G C (A) C T G C A A T T G G T T A (T) T G C (C) Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = E001 (T) ? (T) = = = = = = = = = ? = = = = ? (C) = = = G G C = = C ? = G = = = (A) = = = = = = = = = = = = = T = = = C (A) ? (C) = = = = = = = = = ? = = = = ? (T) = = = A A T = = A ? = A = = = (G) = = = = = = = = = = = = = G = = = G E002 A G C T = = = = = = T T = = = = = = = = = = = = = = = = = = = = = = = = = (G) = (C) = = = = (A) = = = = = = = = T A T C = = = = = = C G = = = = = = = = = = = = = = = = = = = = = = = = = (A) = (A) = = = = (G) = = = = = = = = E003 T A = = G = A A G A = = = A = G G = T = = = A A T A = A C = = D T C G = = = = (C) = = = = = = = = G = = = G A G = = A = G G A G = = = G = A T = C = = = G G C T = C T = = T G A A = = = = (A) = = = = = = = = T = = = C E004 A G C ? = = = = = = T T = = = = = = = = = = = = = = = = = = = = = = = = = G = C G = C = ? ? D G = = = = = T A T ? = = = = = = C G = = = = = = = = = = = = = = = = = = = = = = = = = A = A A = T = ? ? T A = = = = = E005 = = = = = = ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = C = = = = = = ? = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = G E006 T A T C = = = = = = C G ? = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = A G C T = = = = = = T T ? = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = E007 = = = = = = = = = = = = = = = = = = (C) = = = G G C ? ? C T = G = = = (A) = = = = = = = = = = = = = T = = = C = = = = = = = = = = = = = = = = = = (T) = = = A A T ? ? A C = A = = = (G) = = = = = = = = = = = = = G = = = G E008 T A T = G = A A G A T T = A C = = G = = A = = = = = = = C = A = G = = = = = ? = = = = = = = = = = = = = = A G C = A = G G A G C G = G A = = A = = C = = = = = = = T = G = T = = = = = ? = = = = = = = = = = = = = = E009 T A T = = = = = = = = = = = C = = = = = A = = = = = = = = = = = = = = = = = = A A = T = ? ? T A = = = = = A G C = = = = = = = = = = = A = = = = = C = = = = = = = = = = = = = = = = = = C G = C = ? ? D G = = = = = E010 A G C (T) = = = = = = = T ? = C ? = ? C = = = G G C = = C = = = = G = = = = = = = = = = = = = = = = = = = = T A T (C) = = = = = = = G ? = A ? = ? T = = = A A T = = A = = = = T = = = = = = = = = = = = = = = = = = = = E011 T A T = G = A A G A = = = A = G G = T = = = A A T A = A C = = D T C G = = = = = = = = = = = = = = = = = = A G C = A = G G A G = = = G = A T = C = = = G G C T = C T = = T G A A = = = = = = = = = = = = = = = = = = E012 A G C = = = = = = = T T = = C A = = C = = = G G C = = C = = = = G = = = = = = C G = C = A ? D G = = = = = T A T = = = = = = = C G = = A G = = T = = = A A T = = A = = = = T = = = = = = A A = T = G ? T A = = = = = E013 = = = = A = G G A G C G = G A = T ? = = = = = = = T = = T = = T = A A = = = = A A = T = ? ? T A T = = = C = = = = G = A A G A T T = A C = G ? = = = = = = = A = = C = = D = C G = = = = C G = C = ? ? D G G = = = G E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G E015 A G C = = = = = = = = = = = A = = = = = C = = = = = = = = = = = = = = = = = = C G = C = A ? D G = = = = = T A T = = = = = = = = = = = C = = = = = A = = = = = = = = = = = = = = = = = = A A = T = G ? T A = = = = = E016 = = = = = = = = = = = = = = = = = ? ? ? (A) = = = = = = = = = = = = = = = = = ? A A = T = G ? T A = = = = = = = = = = = = = = = = = = = = = = ? ? ? (C) = = = = = = = = = = = = = = = = = ? C G = C = A ? D G = = = = = E017 A G C = A = G G A G C G ? G A = T = = = C = = = = T = = T = = T = A (A) = = = = = = = ? = = = = = = = = = = T A T = G = A A G A T T ? A C = G = = = A = = = = A = = C = = D = C (G) = = = = = = = ? = = = = = = = = = = E018 T A T C = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = A A = T = ? ? T A = = = = = A G C T = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = C G = C = ? ? D G = = = = = E019 = = = = G = A A G A T ? ? A = A = G = = = = = = = = = = C = A = G = G = = = = C G = C = A ? D G G = = ? ? = = = = A = G G A G C ? ? G = G = A = = = = = = = = = = T = G = T = A = = = = A A = T = G ? T A T = = ? ? E020 = = = = = = = = = = = G = = = G = ? T = C = A A T = = A = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = A = ? C = A = G G C = = C = = = = G = = = = = = = = = = = = = = = = = = = = E021 = = = = G = A A G A (T) T = A C A = G = = = = = = = = = = C = A = G = G = = = = = = = = = = = = = = = = = = = = = = A = G G A G (C) G = G A G = A = = = = = = = = = = T = G = T = A = = = = = = = = = = = = = = = = = = E022 A G C T = = = = = = T T = = (C) = = ? ? ? = = = = = = = = = (D) = = = = = = = = = = = = = = = = = = = = = = (C) T A T C = = = = = = C G = = (A) = = ? ? ? = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = (G) E023 = = = = = = = = = = C G = = A (G) = ? = = C = A A T = = A = = = = T = (G) = = = = = = = = = = = = = (G) = = = (G) = = = = = = = = = = T T = = C (A) = ? = = A = G G C = = C = = = = G = (A) = = = = = = = = = = = = = (T) = = = (C) Phase probabilities at each site with phase known positions indicated by = 0.56 = 0.74 = = = = = = = = = = = = = = = 0.85 = = = 1 1 1 = = 1 = = 1 = = = 0.87 = = = = = = = = = = = = = 1 = = = 1 1 1 1 0.98 = = = = = = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = 0.8 = 0.8 = = = = 0.75 = = = = = = = = 0.91 1 = = 1 = 1 1 1 1 = = = 1 = 1 1 = 0.99 = = = 1 1 1 1 = 1 1 = = 1 1 1 1 = = = = 0.58 = = = = = = = = 1 = = = 1 1 1 1 = = = = = = = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = 1 = 1 1 = 1 = = = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.67 = = = 1 1 1 1 0.98 = = = = = = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.85 = = = 1 1 1 = = 1 0.99 = 1 = = = 0.87 = = = = = = = = = = = = = 1 = = = 1 1 1 1 = 1 = 1 1 1 1 0.97 1 = 1 1 = = 1 = = 1 = = = = = = = 1 = 1 = 1 = = = = = = = = = = = = = = = = = = = = 1 1 1 = = = = = = = = = = = 1 = = = = = 1 = = = = = = = = = = = = = = = = = = 1 1 = 1 = = = 1 1 = = = = = 1 1 1 0.59 = = = = = = = 1 = = 1 = = = 0.99 = = = 1 1 1 = = 1 = = = = 1 = = = = = = = = = = = = = = = = = = = = 0.99 1 1 = 1 = 1 1 1 1 = = = 1 = 0.99 1 = 0.98 = = = 1 1 1 1 = 1 1 = = 1 1 1 0.99 = = = = = = = = = = = = = = = = = = 1 1 1 = = = = = = = 1 1 = = 0.99 1 = = 1 = = = 1 1 1 = = 1 = = = = 1 = = = = = = 1 1 = 1 = 0.99 = 1 1 = = = = = = = = = 1 = 1 1 1 1 1 1 = 1 0.97 = 1 = = = = = = = = 1 = = 1 = = 1 = 1 0.99 = = = = 1 1 = 1 = = = 1 1 1 = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 1 1 1 = = = = = = = = = = = 1 = = = = = 1 = = = = = = = = = = = = = = = = = = 1 1 = 1 = 0.98 = 1 1 = = = = = = = = = = = = = = = = = = = = = = = = = 0.51 = = = = = = = = = = = = = = = = = = 1 1 = 1 = 1 = 1 1 = = = = = 1 1 1 = 1 = 1 1 1 1 1 1 = 1 0.99 = 1 = = = 1 = = = = 1 = = 1 = = 1 = 1 0.64 = = = = = = = = = = = = = = = = = = 1 1 1 1 = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = 1 1 = 1 = = = 1 1 = = = = = = = = = 1 = 1 1 1 1 1 = = 1 = 1 = 1 = = = = = = = = = = 1 = 1 = 1 = 1 = = = = 1 1 = 1 = 0.99 = 1 1 0.99 = = = = = = = = = = = = = = = 1 = = = 1 = = 0.99 = 1 = 1 1 1 = = 1 = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = 1 = 1 1 1 1 0.58 1 = 1 1 0.99 = 0.99 = = = = = = = = = = 1 = 1 = 1 = 1 = = = = = = = = = = = = = = = = = = 0.97 0.98 0.97 0.93 = = = = = = 0.97 0.98 = = 0.7 = = = = = = = = = = = = = = 0.73 = = = = = = = = = = = = = = = = = = = = = = 0.88 = = = = = = = = = = 1 1 = = 1 0.87 = = = = 1 = 1 1 1 = = 1 = = = = 1 = 0.64 = = = = = = = = = = = = = 0.84 = = = 0.84