Table 2

Impact of long-branch exclusion on full alignment, A136665 and A133065 data partitions
SubsectionKrempfianae(P. krempfii) Pinus merkusii/P. latteri SubsectionContortae
All No non-Pinusoutgroups Subgenus only Section + single outgroup All No non-Pinusoutgroups Subgenus only Section + single outgroup All No non-Pinusoutgroups Subgenus only Section + single outgroup
Full Alignment (K + G) + S (K + G) + S (K + G) + S (K + G) + S (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus C + (A + P) C + (A + P) C + (A + P) C + (A + P)
(79) (61) (79) (79) (53) (53) (54) (78) (100) (100) (100) (100)
A136665 (K + G) + S (K + G) + S (K + G) + S (K + G) + S (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus C + (A + P) C + (A + P) C + (A + P) C + (A + P)
(71) (70) (71) (54) (43) (46) (47) (68) (100) (100) (100) (100)
A133065 (K + G) + S (K + G) + S (K + G) + S (K + G) + S (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus (M/L + Pina.) + Pinus P + (C + A) P + (C + A) P + (C + A) C + (A + P)
(97) (97) (97) (98) (99) (100) (100) (99) (37/42) (31/36) (35/42) (84)

For each combination, supported topology is given with maximum likelihood bootstrap support underneath in parentheses. Subsection and species abbreviations are as follows: A = Australes , C = Contortae , G = Gerardianae , K = P. krempfii , M/L = P. merkusii /P. latteri , P = Ponderosae, Pinast. = Pinaster , S = Strobus . Single outgroups used in most exclusive groups are described Methods and Materials.

Parks et al.

Parks et al. BMC Evolutionary Biology 2012 12:100   doi:10.1186/1471-2148-12-100

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