We also used the AU test to determine the influence of missing data on phylogenies inferred from the cpDNA and ITS datasets and to assess the degree of congruence between the phylogeny based on cpDNA loci and the phylogeny based on the complete data set.
Contrary to what was observed across microsatellites, the SGS analysis based on cpDNA did not show significant slopes within each one of the four Panamanian estuaries analyzed, perhaps due to limited sample size (Additional file 3).
Compared to the high genetic differentiation among populations between Yushan Mountain Range and the other mountain ranges based on cpDNA, nrDNA revealed much less differentiation among populations of different mountain ranges (FST = 0.02-0.08) (Tables 2, 3).
High levels of differentiation between Japan and China populations are detected for all comparisons, e.g., Fst of 0.115 (P < 0.01) between OK and FU based on mtDNA, and Fst = 0.159 between IR and FU (P < 0.01) based on cpDNA (Tables 4 and 5).
Intron sequences from Lychnis chalcedonica and Silene fruticosa did not show signs of elevated substitution rates relative to other cpDNA regions, and the phylogeny (Fig. 4B) is compatible with other Sileneae phylogenies based on cpDNA [18].
Another striking feature of F. suspensa was the marked group differentiation based on cpDNA (ΦCT = 0.793).
ranged from 4.36 to 29.21 MYA based on cpDNA, and from 8.72 to 58.42 MYA based on nrDNA.
(4.36-29.21 MYA) overlapped the estimates of divergence time (2.895-8.722 MYA) based on cpDNA, in which monophyly was attained.
To-date, based on cpDNA, T. pallescens is the closest extant species to the maternal ancestor of white clover.
Three of these losses are evident in our phylogeny based on cpDNA sequences (indicated by bars in Figs. 2, 3).
