TimeTree 5: An Expanded Resource for Species Divergence Times

Abstract

We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the timetree of life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible to all. Using the TToL5 web portal, users can retrieve published studies and divergence times between species, the timeline of a species' evolution beginning with the origin of life, and the timetree for a given evolutionary group at the desired taxonomic rank. TToL5 contains divergence time information on 137,306 species, 41% more than the previous edition. The TToL5 web interface is now ADA-compliant and mobile-friendly, a result of comprehensive source code refactoring. TToL5 also offers programmatic access to species divergence times and timelines through an application programming interface, which is accessible at timetree.temple.edu/api. TToL5 is publicly available at timetree.org.

Fig. 1.

Results produced by TToL5 web portal. (A) The divergence time of mice and humans produced by the “Get Divergence Time” search function. The median time and its confidence interval are derived from the TToL5 database. Solar luminosity (furthest left, red), global CO₂ levels (second from left, orange), O₂ levels (thirds from left, yellow), and major earth impact events (circles) are also shown and may be toggled by the user. (B) The evolutionary timeline of Homo sapiens from the origin of all cellular life is produced by the “Get an Evolutionary Timeline” function. Each divergence starting from the root of the timetree of life to Hominidae, the youngest named divergence preceding Homo sapiens, is aligned on the evolutionary timescale. Hollow circles indicate divergences without any names in the NCBI database.

Fig. 2.

Timetrees produced by the “Build a Timetree” feature in TToL5 to present an overview of the global timetree. Timetrees of (A) Animal phyla, (B) Animal classes, and (C) mammalian orders are shown. Tip labels are removed due to space constraints, and the timescale is shown in millions of years. Blue dots on nodes can be clicked to view the NCBI name, taxonomic rank, median time, and confidence interval around the median. Polytomies reflect phylogenetic uncertainties caused by conflicting resolutions of species relationships and divergence times among published studies included in TToL5. Users can interact with the timetree display in numerous ways (Kumar et al. 2017) and download the resulting timetree in a Newick or graphic format. One can also view individual timetrees and openly download individual published timetrees used in building the global timetree.

Fig. 3.

Numbers of species, genera, families, classes, and phyla in TToL5. Orange pies show increased taxonomic representation in this edition compared to the previous edition published in 2017 (blue pies). The grey pies correspond to the number of taxa missing from the global timetree at the given taxonomic level. While the NCBI taxonomy database (Schoch et al. 2020) has over 1.3 million taxa, our count of 429,141 only included species whose names followed binomial nomenclature. This means that species whose whole names included abbreviations such as “sp.” and were marked as environmental samples were excluded. Notably, the number of species with binomial nomenclature fluctuated considerably in NCBI over the last few months (429,141–510,722). We note that 124,654 species names follow the binomial nomenclature in TToL5.

Fig. 4.

The number of studies informing divergence times for nodes in the TToL5. Divergence times for a vast majority of nodes (n, y-axis) are informed by only one study (s, x-axis). Their power relationship decays quickly (n = 2.17 × 10⁵s^–3.015; R² = 0.99), suggesting that only a very small number of node dates are based on many studies, while the vast majority of nodes are only informed by a single article, as shown by the inset pie chart. Species pairs for which the largest number of studies contains the divergence time estimates are the human-chimpanzee comparison (81), mouse-rat and human-old monkey [Old world] comparisons (76), human-mouse comparison (65), and the human-orangutan comparison (62).