The taxonomic status of Taxus in Pakistan was confused and uncertain due to opposing views about specimen identities. We used 27 morphological characters of 62 selected herbarium specimens of T. baccata, T. wallichiana and tentatively identified T. fuana to investigate the taxonomic status of Taxus in Pakistan by principal component analysis (PCA). Three discrete clusters representing the three species were identified in the PCA scatter plot. Character combinations allowed the reliable identification of specimens of T. fuana, T. baccata and T. wallichiana. Sequence data of nuclear ribosomal DNA ITS and the chloroplast trnL-F region were used to further delimitate T. baccata, T. wallichiana and T. fuana. Using maximum parsimony analysis three distinct clades were obtained representing the three species with strong bootstrap support. Based on both morphological and molecular sequence data, the Taxus species occurring in the western Himalaya including Pakistan was shown to be T. fuana and not T. wallichiana or T. baccata. The distinct species status of T. fuana, T. baccata and T. wallichiana was also well supported and found to be well correlated with their geographic distributions. The geographic ranges of the three species were updated based on the present study.
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