Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa

Abstract

Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.

Key questions and challenges in angiosperm macroevolution

“…Phylogenetic reconstruction is currently undergoing a revolution of its own, thanks to the generalization of genomic data to questions of all scales, but also to the development of powerful pipelines capable of building very large trees from available sequence data (Antonelli et al ., ; Smith & Brown, ). These ongoing developments will no doubt continue to play a very important role in providing the essential background for all comparative methods.…”

Ecological determinants of butterfly vulnerability across the European continent

“…However, in our comparative analysis, we require a single, composite estimate. We synthesized this following a two-step (2) occasional colonization events over <10 km, (3) urban areas and gardens, (4) occasional colonization events over >10 km, (5) rapid range expansions over >100 km in 10 years, (6) short-distance overseas dispersal-at sea records-island populations, (7) incidental long-distance (mass) movements, (8) regular reversed long distance migrations Voltinism Ordinal (1) 0.5, (2) 1, (3) 1-2, (4) 2, (5) 2-3, (6) 3-4 (generations per year) Overwintering Ordinal (1) Egg, (2) first instar larva, (3) half-grown, (4) last instar, (5) pupa, (6) adult, (7) Antonelli et al (2016), by first inferring a backbone tree and then grafting the trees for the monophyletic higher taxon partitions from Mutanen et al (2016) onto it. To obtain input data for backbone tree inference, we subsampled exemplar taxa from each of the higher taxon partitions and aligned their COI sequences using MUSCLE (Edgar 2004), under default settings.…”

OneTwoTree: An online tool for phylogeny reconstruction

“…In particular, the results obtained by PhyLoTa are taxonomically constrained; that is, all sequences of the most recent common ancestor are collected even if one specifies only part of a clade. SUPERSMART (Antonelli et al., ) offers a customized framework for the inference of dated phylogenies, given a set of taxa of interest and a list of calibration points. Supporting both a virtual machine Linux‐based platform and a Web server with simpler functionality, SUPERSMART relies on the data assembled by PhyLoTa for the clustering process.…”