Computational protocol: Using Morphological, Molecular and Climatic Data to Delimitate Yews along the Hindu Kush-Himalaya and Adjacent Regions

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Protocol publication

[…] DNA was extracted from silica-gel dried leaf materials of all field-collected individuals and from leaves of selected herbarium specimens. DNA extraction, PCR amplification and sequencing of nrDNA ITS and cpDNA trnL-F followed Shah et al. . Sequences were edited and assembled using Sequencher 5.0 (Gene Codes Corp., Ann Arbor, MI, USA) and aligned with ClustalW in BioEdit followed by minor manual adjustments . Indels in the trnL-F matrix were coded according to the simple gap coding method . Maximum parsimony (MP) analysis was performed in PAUP 4.0b10 , using the heuristic search option with 1000 random additions and TBR swapping and MulTrees on. Branch support was provided by a bootstrap analysis of 10000 replicates of heuristic searches, with MulTrees on and TBR swapping off. Consistency indices (CI) and retention indices (RI) were obtained in PAUP. […]

Pipeline specifications

Software tools Sequencher, Clustal W, BioEdit, PAUP*
Application Phylogenetics
Organisms Taxus mairei