Computational protocol: Pterislatipinna sp. nov. (Pteridaceae), a new species segregated from Pterisfauriei

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Protocol publication

[…] To clarify the phylogenetic relationships of the undescribed plants, 34 other Pteris taxa with bipinnatifid laminae were sampled. Three Pteris species, P. grevilleana, P. longipinna, and P. venusta, were used as outgroups. These bipinnatifid and outgroup species belong to clades A1 and A2, respectively, according to the phylogenetic tree of Pteris (). Vouchers and GenBank accession numbers are listed in Appendix . Total genomic DNA was extracted from young fronds, following a modified cetyltrimethylammonium bromide (CTAB) method (). Two chloroplast genes, rbcL and matK, were amplified using the PCR primers for rbcL and matK as per . Alignment was performed with ClustalW () and manually edited using BioEdit 7.1.3 (). Gaps were treated as missing data.Maximum likelihood (ML) analyses were performed using GARLI v.2.0.1019 (). Ten independent runs were conducted using automatic termination following 10,000 generations without a significant (lnL increase of 0.01) change in topology. To calculate ML bootstrap support for each node, 1,000 bootstrap replicates were performed with automatic termination at 10,000 generations, under one run. […]

Pipeline specifications

Software tools Clustal W, BioEdit, GARLI
Application Phylogenetics