This website, fishtreeoflife.org, is a community resource providing phylogenetic, taxonomic, and other information about ray-finned fishes, the most species-rich group of vertebrates.

We also offer an R package that provides programmatic access to the data products on this website, fishtree. The web documentation for fishtree contains a reference and usage examples in its vignettes. The R package uses our internal API, which is publicly available but intentionally undocumented, as the only supported access is through the R package.

We track your usage of our services using Google Analytics and the CRANlogs database. As we lack the funding to conduct user studies or other detailed survey instruments, this is the only way to measure our impact to ask for future funding or sponsorships.

Citing

If you use any phylogenetic products derived from this website, including taxonomic resources and fossil calibration constraints, please cite:

Daniel L. Rabosky*, Jonathan Chang*, Pascal O. Title*, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll, Michael E. Alfaro* (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714), 392–395 doi:10.1038/s41586-018-0273-1

If you use the R package or web API, please cite:

Jonathan Chang, Daniel L. Rabosky, Stephen A. Smith, Michael E. Alfaro (2019). An R package and online resource for macroevolutionary studies using the ray‐finned fish tree of life. Methods in Ecology and Evolution, 10:1118–1124 doi:10.1111/2041-210x.13182

We have also released a set of enhanced ATA trees; the details on how these ATA distributions differ are detailed in Rabosky et al. 2018 update. The original set of ATA phylogenies are available via Dryad. The taxonomic addition algorithm using stochastic polytomy resolution (TACT: Taxonomic Addition for Complete Trees) that generated these ATA phylogenies was published as:

Jonathan Chang, Daniel L. Rabosky, Michael E. Alfaro (2019). Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology, doi:10.1093/sysbio/syz081

Contact

For issues or feature requests for the website, please contact Jonathan Chang.

Significant contributors to this website and its data sources include:

Other critical contributors include:

Future updates

We are also interested in fixing any phylogenetic and taxonomic errors in a future revision of the Fish Tree of Life, especially rogue taxa that break the monophyly of well-studied lineages. Known issues include:

  • Total group Hippocampus age should be 11 Ma
  • Relationships within Cichlidae are not quite correct
  • Chlorurus gibbus has rogue behavior
  • Takifugu fasciatus is actually T. obscurus
  • Sister relationship of Salvelinus
  • Thalassenchelys coheni = Congriscus megastomus (Kurogi et al 2015)
  • Adding tip rate information for the following species:
    Species list
    • Acheilognathus tabira erythropterus
    • Acheilognathus tabira jordani
    • Acheilognathus tabira nakamurae
    • Acheilognathus tabira tohokuensis
    • Anguilla australis schmidtii
    • Anguilla bicolor pacifica
    • Aphanius dispar richardsoni
    • Aphredoderus gib
    • Arctogadus borisovi
    • Astronotus sp
    • Astyanax hubbsi
    • Astyanax sp
    • Cheilopogon antoncichi
    • Chirocentrus sp
    • Cobitis sp
    • Cyprinodon variegatus ovinus
    • Elacatinus digueti
    • Enigmapercis sp
    • Esox americanus vermiculatus
    • Etheostoma binotatum
    • Etheostoma mediae
    • Forbesichthys papilliferus
    • Glyptothorax longinema
    • Gobionotothen acuticeps
    • Gymnotus sp
    • Hemichromis sp
    • Hypostomus panamensis
    • Mastacembelus signatus
    • Mastacembelus stappersii
    • Melanotaenia splendida inornata
    • Melanotaenia splendida tatei
    • Mugil gyrans
    • Mugil soiuy
    • Paraneetroplus melanurus
    • Percina cf
    • Phoxinus lumaireul
    • Plecoglossus altivelis ryukyuensis
    • Pseudocrenilabrus sp
    • Pseudophoxinus chaignoni
    • Rhamdia cabrerae
    • Rutilus ohridanus
    • Rutilus prespensis
    • Salvelinus leucomaenis imbrius
    • Salvelinus leucomaenis pluvius
    • Sarcocheilichthys nigripinnis morii
    • Sarcocheilichthys sinensis fukiensis
    • Schizothorax yunnanensis paoshanensis
    • Schizothorax yunnanensis weiningensis
    • Scleromystax kronei
    • Simochromis pleurospilus
    • Takifugu fasciatus

If you identify any issues, please fill out this survey so we can collate all fixes for a future revision. Thanks!

Source code

The source code for this website is available on GitHub: jonchang/fishtreeoflife.org.

Funding

Development of this website was supported in part by NSF grant DEB-1256330 (to D.L.R.) and DEB-1601830 (to J.C. and M.E.A.), an Encyclopedia of Life Rubenstein Fellowship EOL-33066-13 (to J.C.), the David and Lucile Packard Foundation (to D.L.R.), the Gaylord Donnelley Postdoctoral Environment Fellowship and the ARC Centre of Excellence for Coral Reef Studies (to P.F.C.).

This website’s maintenance is not currently not supported by any grant or organization. Please consider sponsoring it via a recurring donation.