TimeTree of Life
Supplementary newick tree files for the publication:
Tree of Life Reveals Clock-Like Speciation and Diversification
PDF | Supplement 1 | Supplement 2
S. Blair Hedges ^a–c,1, Julie Marin ^a–c, Michael Suleski ^a–c, Madeline Paymer ^a–c, and Sudhir Kumar ^a–c
a Center for Biodiversity, Temple University, Philadelphia, PA 19122, USA.
^b Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
^c Department of Biology, Temple University, Philadelphia, PA 19122, USA.
¹ To whom correspondence may be addressed. E-mail: sbh@temple.edu

NOTE: Before using the timetrees linked below, it is important to read the paper and understand the meaning of unsmoothed, smoothed, and interpolated timetrees. Briefly, smoothed means that the polytomies are resolved by random placement of branches, which is used sometimes in diversification analyses. Interpolated timetrees have species lacking any data and which are placed in the tree taxonomically (e.g., a dataless species added to a genus node), only for uses where complete species coverage is needed. If you want a “normal” phylogeny or timetree, use “unsmoothed”, although keep in mind it will have some polytomies.

Molecular Biology and Evolution, Mol. Biol. Evol. 32(4):835–845 (February, 2015).

Click on a link to download each tree file:

1. TTOL_all_unsmoothed
2. TTOL_all_smoothed
3. TTOL_animals_unsmoothed
4. TTOL_plants_unsmoothed
5. TTOL_fungi_unsmoothed
6. TTOL_birds_unsmoothed
7. TTOL_birds_smoothed_interpolated
8. TTOL_mammals_unsmoothed
9. TTOL_mammals_smoothed_interpolated
10. TTOL_squamates_unsmoothed
11. TTOL_amphibians_unsmoothed
12. TTOL_actinopterygians_unsmoothed
13. TTOL_arthropods_unsmoothed
14. TTOL_mollusks_unsmoothed
15. TTOL_cnidarians_unsmoothed
16. TTOL_ascomycetes_unsmoothed
17. TTOL_basidiomycetes_unsmoothed
18. TTOL_angiosperms_unsmoothed
19. TTOL_gymnosperms_unsmoothed
20. TTOL_moniliformopses_unsmoothed
21. TTOL_liverworts_unsmoothed
22. TTOL_mosses_unsmoothed
23. TTOL_chlorophytes_unsmoothed
24. TTOL_diatoms_unsmoothed
25. TTOL_phaeophyceans_unsmoothed
26. TTOL_eubacteria_unsmoothed
27. TTOL_archaebacteria_unsmoothed

NOTE: The last two files below provide consensus support values (number of trees supporting a node/count) where count is the total number trees potentially pertaining to the node (e.g., 5 of 5 study trees = 100%, 3 of 4 study trees = 75%). It is not the same as a bootstrap value. We list it here for general reference but recommend that you examine the original published studies if you need support values. For example, only 1 of 2 studies (50%) may support a node, but that single supporting study may be a genomic study with high nodal bootstrap support and the other study may report only weak evidence for an alternative topology, in which case the 50% consensus support value listed here underestimates the true support for the node. Also for 20% of nodes, no support values are given because the node was newly created using methods described in the paper (Hedges et al. 2015) and data from published studies. Be aware that some tree viewing software will show support values of zero for such nodes lacking information, but examination of the Newick file in a text editor will reveal the true value (= no value) of those nodes. For 3.5% of nodes, the support value is zero because the partition was resolved in the NCBI taxonomy tree but not in constituent studies.

28. TTOL_eukaryote_partition_consensus
    (support values only)
29. TTOL_eukaryote_partition_concensus_count
    (count values only)