A roadmap for global synthesis of the plant tree of life

Abstract

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.

Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

“…For the five best-sampled families (Euphorbiaceae, Fabaceae, Passifloraceae, Brassicaceae, Cucurbitaceae), only 21.95% to 40.56% of species have one of the five loci. Hence, no large (> 1,000 species) family of rosids exceeds 45% species coverage, and most are below 30% coverage (Table S2), consistent with molecular sampling patterns across the angiosperms (Eiserhardt et al 2018, Folk et al, 2018).…”

“…34% estimated from Hinchliff et al, 2015) have any type of DNA data in GenBank (see also Folk et al, 2018), and after a series of filtering steps, our topology represents only 16.25% of all rosid species recorded in OTT (Table 1). This relative sampling level (less than 20%) typifies most major clades of flowering plants (Eiserhardt et al, 2018; Folk et al, 2018).…”

Using and navigating the plant tree of life

“…As one example, Eiserhardt et al. () provide a vision for the future of green plant phylogenetics that will lead to a global phylogenetic synthesis and an integrated, open, and continually updated green plant tree of life; we enthusiastically endorse their recommendations.…”

Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids

“…With recent advances in generating very large phylogenetic trees (e.g., Smith and O’Meara, 2012; Stamatakis, 2014; Hinchliff et al, 2015; Nguyen et al, 2015; Smith and Brown, 2018; Eiserhardt et al, 2018), and in analytical methods (Nee et al, 1994a,b; Pybus and Harvey, 200; Paradis et al, 2004; Alfaro et al, 2009; Stadler, 2011; Pennell et al, 2014; Rabosky, 2014; Morlon et al, 2016; Höhna et al, 2016), assessing macroevolutionary patterns for globally distributed clades with available biodiversity information has become common (e.g., Jetz et al, 2012; Morlon, 2014; Scholl and Wiens, 2016; Magallón et al, 2018; Rabosky et al, 2018; Upham et al, 2019). Analyses of diversification rates have shed light on potential drivers of diversity gradients across wide phylogenetic and geographic scales (Jetz et al, 2012; Rabosky et al, 2018; Landis et al, 2018).…”