Computational protocol: Monograph of Coccinia (Cucurbitaceae)

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Protocol publication

[…] For this monograph the phylogenetic data of ; ) were augmented with 20 new sequences from 8 accessions (GenBank accession numbers are given in Suppl. material ), and new phylogenies were calculated using RAxML v. 7.2.6 () and MrBayes v. 3.2 (). The substitution model was GTR+Γ as used before, and 1000 ML replicates were used to infer statistical support for the nodes via bootstrapping. For Bayesian analysis, four chains were run with 2,000,000 generations, with a sampling frequency of 1000. The first 25% of the trees were discarded as burn-in, and the rest were plotted as a 50% majority rule consensus tree using FigTree 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/). Gaps in the plastid matrix occurring in more than one accession were coded as “0”, “1”, or “?”, with “?” when data were missing or when shorter gaps were coded in the same place, but in different accessions. [...] Of the examined collections, 2024 were geo-referenced and mapped in Google Earth (Google Inc., Mountain View, CA, USA). Cultivated plants were geo-referenced according to the original collection site. If collecting sites were given as distances from locations, a path along major roads was used, beginning from the center of the starting location. Collecting sites were geo-referenced according to the description even if coordinates were given on the label, except for cases in which the coordinates were clearly derived from GPS or if the description did not allow further improvement. Location names were cross-validated from printed maps and then imported into DIVA-GIS 7.1.6.2 (http://www.diva-gis.org). If collecting sites of specimens appeared to be too useful to ignore in the distribution maps despite the large uncertainty of the position (radius > 5 km) or if the collecting site was only given as “nearby” a distinct locality, then geo-referenced coordinates are given in brackets. Political administrative borders were taken from GADM v.1 (Jan 2009) or v.2 (Jan 2012) (http://www.gadm.org/) and elevation data (1 km resolution) from CGIAR Consortium for Spatial Information (). The geodetic datum for the maps is WGS84; the projection in each case is equirectangular. Coordinates are given in decimal degrees in Suppl. material with WGS84 as geodetic datum. […]

Pipeline specifications

Software tools RAxML, MrBayes, FigTree, DIVA-GIS
Application Phylogenetics
Organisms Apis mellifera, Spinacia oleracea
Diseases Diabetes Mellitus, Fluorosis, Dental