Fig 1.
Unrooted phylogram of the RAxML maximum likelihood analysis.
Results of the RAxML maximum likelihood analysis of 149 ITS paralogs obtained from thirty-one species of Cycas (excluding 12 putative recombinants). A) Unrooted phylogram of all samples; B-E) magnified views of clades indicated in A).
Fig 2.
Rooted phylogram of the Bayesian analysis.
Bayesian 50% majority-rule consensus cladogram showing evolutionary relationships of 94 functional ITS paralogs and 4 pseudogenes (C. armstrongii_5, C. media_9, C. javana_5, and C. circinalis_11). Here C. circinalis_11 was chosen as an outgroup sample. Bayesian posterior probabilities (BPP), and bootstrap support values of ML (MLBS) analyses are shown above branches, respectively (BPP/ MLBS, dashes indicate BPP or MLBS values < 50%). Ancestral distribution inferred from Bayesian analysis with RASP were also labeled on the cladogram; pie charts beside internal branches represented ancestral distributions as probabilities coded as follows: A (South China), B (Indochina), C (Islands of Southeast Asia).
Fig 3.
Geographic distribution of Cycas species (adapted from [61]).
Data points were colored based on clade associations (Fig. 2).