Computational protocol: Plant performance was greater in the soils of more distantly related plants for an herbaceous understory species

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Protocol publication

[…] To estimate phylogenetic distances among species in the experiment, and to ensure that results were robust, we compared two estimated phylogenies. First, we used a molecular phylogeny, estimated de novo for taxa in this experiment [see]. We aligned each DNA region separately in MUSCLE (Edgar ) in the MEGA platform (version 5.2.2) and concatenated four DNA regions for analysis [see ]. We conducted a maximum likelihood tree search in Garli (; version 0.951) and branch lengths are in substitutions per site (). The result is a phylogram with fine-scale variation in phylogenetic distances among species pairs. Second, we used phyloGenerator’s () congeneric.merge function, which matches species in our sampled species list to genera on the global angiosperm phylogeny of . Because the genus Anemonella was not present in this phylogeny, we used the synonym Anemone thalictoides, in place of the now accepted name Anemonella thalictroides when conducting this merging function. The result is an ultrametric tree, with branch lengths in approximate millions of years [see ]. The phylogenetic distance between species was calculated as the summed branch lengths between them on the phylogenies. The placement of Anemonella in the Ranunculaceae was different for these two approaches, and the typology of these phylogenies was otherwise congruent ([see]. Figure 2 […]

Pipeline specifications

Software tools MUSCLE, GARLI, phyloGenerator
Applications Phylogenetics, Nucleotide sequence alignment
Organisms cellular organisms