Computational protocol: A phylogenetically informed delineation of floristic regions within a biodiversity hotspot in Yunnan, China

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Protocol publication

[…] We constructed a phylogenetic tree by grafting the genera present in the study area onto a backbone phylogenetic hypothesis using the online program Phylomatic. The backbone of the supertree was the Phylomatic tree version R20120829, based on Angiosperm Phylogeny Group's system. Branch lengths in the supertree were adjusted to match clade age estimates reported by Wikstrom using the BLADJ algorithm implemented in the software Phylocom. Given the scarcity of comprehensive time-calibrated phylogenies within families, we followed previous studies to treat genera as polytomies within families. [...] To quantify spatial turnover of Yunnan floristic assemblages in species composition and phylogenetic relationships between county-level floras, we calculated taxonomic beta diversity and phylogenetic beta diversity between localities. We used the Bray-Curtis index (Bbc) and the mean nearest phylogenetic neighbor index (Dnn) (see for equations) as our taxonomic and phylogenetic beta diversity measures, respectively, because they are both widely used and conceptually related. The average taxonomic and phylogenetic dissimilarity between the focal region and all other regions were mapped to visualize the distinctiveness of each county-level assemblage in relation to the rest of the region.Because phylogenetic beta diversity is likely to be related to taxonomic beta diversity, we used a null model analysis to test if county-level floras were more or less phylogenetically similar than expected by chance. A null distribution was generated for each county comparison by randomizing the names of the taxa on the phylogeny 999 times. This randomizes the phylogenetic beta diversity patterns between counties, while preserving the underlying taxonomic beta diversity differences between the samples. In each iteration, Dnn was calculated for each county comparison. The null distributions were used to calculate standardized effect sizes (SES_Dnn), where the mean of the null distribution was subtracted from the observed dissimilarity Dnn, and divided by the standard deviation of the null distribution. Positive standard effect size measures indicate greater phylogenetic beta diversity than expected based on random sampling of the regional flora; negative standard effect sizes indicate the opposite. We then averaged the SES_Dnn values for each county to all other counties and mapped the results to illustrate patterns of regional turnover of phylogenetic composition.Finally, we tested for correlations between species beta diversity, phylogenetic beta diversity and SES_Dnn using Mantel tests, which were used to analyze associations between distance matrices. Permutation tests were applied to assess the significance of the correlation by randomizing the distance matrix 999 times. Analyses were performed in R 2.15.3 software using the 'vegan' and 'picante' packages. […]

Pipeline specifications

Software tools Phylomatic, Phylocom, Picante
Application Phylogenetics