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Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction.

We also revealed this relationship with analyses of data matrices by removing unreliable aligned regions, substitution saturation genes and rapidly evolving sites or coalescent phylogenetic reconstruction on 82 aligned PCGs.

The branch lengths of J and C were significantly reduced in these analyses (Fig. The branch length ratios of J and C relative to HCX in analyses of resolved J (C, HCX) were all much smaller than those in analyses of resolved HCX (J, C) (Fig. The LBA between subclades J and C and ancient rapid divergence [within 4.15 My between 46.16 and 50.31 Ma for J (C, HCX), or within 1.15 My between 48.79 and 47.64 Ma for HCX (J, C)] among three subclades (Fig. S5; Supplementary Table S4) should jointly explain the long controversy about their relationships.

Species of Cupressoideae are important in the North Hemisphere forest, and many are constructive and dominant species.

Many species are also economically important as timber sources, especially species of Calocedrus, Chamaecyparis, Cupressus and Thuja.

The right HCX (J, C) was supported by analyses of PCG, PCG12, AA, PCG-GB-relaxed, PCG-GB-default, PCG-Iss-9, PCG-slope-12, PCG-R-11, PCG-OV-fast-partition, PCG-TIGER-fast-partition and PCG-GTR-CAT, and bootstrap values are shown on branches. The numbers above bars are the branch length ratio for each of three subclades relative to HCX. By the PCG-Iss-73 matrix, the divergence time between subclades J and C-HCX was estimated at 50.31 million years ago (Ma; 46.84 to 53.34 Ma), and the split between C and HCX at 46.16 Ma (42.45 to 50.24 Ma) (Fig. By the PCG matrix, the divergence of subclades J-C from HCX was estimated at 48.79 Ma (47.48 to 50.29 Ma) and between subclades J and C at 47.64 Ma (46.16 to 48.87 Ma) (Supplementary Fig. Our divergence time estimations are robust to topology differences.

Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA.In this study, data filtering by Gblocks was efficient in reducing the LBA artifact.Rapidly evolving sites could accumulate multiple mutations, which tend to be saturated and contribute to LBA.Our analyses of PCG-GB-strict, PCG-Iss-73, PCG-slope-70, PCG-R-71, PCG-OV/TIGER-medium-partition, PCG-OV-sorted and PCG-ASTRAL resolved a relationship of J (C, HCX) (Figs 2 and 3; Supplementary Fig. This result agrees with previous analyses of plastid markers.This topology was also recovered by some of our analyses involving original or slightly modified matrices or more complex models (Figs 1 and 3; Supplementary Fig. A relationship C (J, HCX) was also resolved by nr ITS revealed a relationship J (C, HCX).The ML analysis of the PCG matrix fully resolved the intergeneric relationships of Cupressoideae (Fig. Thuja-Thujopsis was resolved as the first diverged clade, and Chamaecyparis-Fokienia as second, then sister pairs of Calocedrus-Platycladus and J-C-HCX.

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