Interface to the Fish Tree of Life API

An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.

BuildStatus CRANstatus

The goal of fishtree is to provide an easy interface to the Fish Tree of Life API, to download taxonomies, phylogenies, diversification rate information, and other data for ray-finned fishes.


See a list of taxa available to download.

tax <- fishtree_taxonomy()
#>         rank        name
#> 1      class Actinopteri
#> 2      class   Cladistia
#> 3   subclass Chondrostei
#> 4   subclass Neopterygii
#> 5 infraclass    Holostei
#> 6 infraclass   Teleostei

Retrieve a phylogeny for the surgeonfishes and plot the phylogeny and lineage through time plot.

phy <- fishtree_phylogeny(rank = "Acanthuridae")
#> Phylogenetic tree with 67 tips and 66 internal nodes.
#> Tip labels:
#>  Acanthurus_mata, Acanthurus_blochii, Acanthurus_xanthopterus, Acanthurus_bariene, Acanthurus_dussumieri, Acanthurus_leucocheilus, ...
#> Rooted; includes branch lengths.
par(mfrow=c(2, 1))
plot(phy, show.tip.label = FALSE)


You can install the released version of fishtree from CRAN with:


Alternatively, download the development version with devtools:



The manuscript for this package is currently in review.


withr::with_envvar(c("NOT_CRAN" = "true"), devtools::release())


fishtree 0.2.0

  • New function: fishtree_rogues, identifies rogue/intruder taxa that break the monophyly of a selected group.

  • fishtree_phylogeny now permits downloads of MRCA trees for paraphyletic groups. Suggested by an anonymous reviewer.

  • fishtree_taxonomy revamped. It now takes a single argument ranks = ... where you can retrieve taxonomic information for any valid taxonomic rank in our taxonomy. Calling it without arguments returns a data frame of all valid taxa names. Suggested by an anonymous reviewer.

fishtree 0.1.0

Initial release.

Reference manual

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0.3.4 by Jonathan Chang, a year ago,

Report a bug at

Browse source code at

Authors: Jonathan Chang [aut, cre] , Michael E Alfaro [ctb] , Daniel L Rabosky [ctb] , Stephen A Smith [ctb]

Documentation:   PDF Manual  

BSD_2_clause + file LICENSE license

Imports ape, jsonlite, memoise, parallel, rlang, utils

Suggests diversitree, geiger, hisse, knitr, markdown, phytools, picante, rfishbase, rmarkdown, spelling, testthat

Imported by FishPhyloMaker.

See at CRAN