Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

Table 2 Impact of long-branch exclusion on full alignment, A ₁₃₆₆₆₅ and A ₁₃₃₀₆₅ data partitions

	Subsection Krempfianae ( P . *krempfii* )				*Pinus merkusii* / P . *latteri*				Subsection Contortae
	All	No non- *Pinus* outgroups	Subgenus only	Section + single outgroup	All	No non- *Pinus* outgroups	Subgenus only	Section + single outgroup	All	No non- *Pinus* outgroups	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)
Full Alignment	(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)
A₁₃₆₆₆₅	(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)
A₁₃₃₀₆₅	(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.

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