SUPERSMART - a self-updating software platform for inferring phylogenetic trees

Elucidating evolutionary relationships and processes through a new big-data framework for phylogenetic tree generation

Data resources used via GBIF : 724,002 species occurrences
Phoenix canariensis
Phoenix canariensis by Steven Kurniawidjaja via iNaturalist. Photo licensed under CC BY-NC 4.0.

Phylogenetic trees based on molecular and fossil data can be powerful tools for biogeographical analyses seeking to explain macroevolutionary processes such as migration, speciation, diversification and niche evolution.

In this paper, researchers presents a new conceptual and bioinformatic approach to inferral of dated phylogenies called SUPERSMART (conveniently short for Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa). The open source modular framework which relies on GenBank sequence data can be freely installed and run on Linux systems by anyone.

The authors demonstrate the functionality of SUPERSMART on two distinct clades: the very-well sequenced Primates order, and the much larger, however, less studied family of Arecaceae (palms). They validate the latter tree through biogeographic analysis using GBIF-mediated occurrences by estimating ancestral ranges and calculating dispersal events, showing that SUPERSMART is a fully functional tool capable of dealing with vast amounts of data for producing time-calibrated species phylogenies.

Citations

Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B and Vos RA (2016) Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa. Systematic Biology. Oxford University Press (OUP) syw066. Available at: https://doi.org/10.1093/sysbio/syw066.

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