An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life

Abstract

Comprehensive, time‐scaled phylogenies provide a critical resource for many questions in ecology, evolution and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging. We introduce the Fish Tree of Life website and associated r package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations and diversification rate estimates for the most diverse group of vertebrate organisms, the ray‐finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the r package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyse the data. We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the r package. First, we test for the presence of long branch attraction artefacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package. This resource makes a large comparative vertebrate dataset easily accessible via the website, while the r package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other r packages and software for molecular biology and comparative methods.

Can ancestry and morphology be used as surrogates for species niche relationships?

“…Brownian motion simulations and phylomorphospace plots were carried in the package phytools (Revell, 2012), and the Abouheif's C mean index was calculated in the package adephylo (Jombart, Balloux, & Dray, 2010). Fish phylogeny was retrieved from the fishtree package (Chang et al, 2019).…”

“…Phylogenetic relationships were based on a supertree created from analysis of molecular data (multiple genes) from ca. 11,000 fish species (marine and freshwater species) and time-calibrated using fossil records (Chang, Rabosky, Smith, & Alfaro, 2019;Rabosky et al, 2018). For 21 out of 68 species in our dataset (~31%), genetic information was not available, and those species were not present in the published supertree.…”

“…Phylogenetic data available for download from the R package fishtree (Chang et al, 2019) and the website https://fisht reeof life.org/ (accessed on 10 November 2019). Average and standard deviation of isotopic ratios for each species can be found in the supplementary materials ( Figure S1).…”

Speciation rate and the diversity of fishes in freshwaters and the oceans

“…As a phylogenetic framework, I used the phylogeny of Actinopterygian fishes from Rabosky et al (2018), which was used to assess the relationship between latitude and speciation rate. This phylogeny is available through the R package 'fishtree' (Chang, Rabosky, Smith, & Alfaro, 2019) and is based on 11,638 species whose position was estimated from genetic data; the remaining 19,888 species were placed in the tree using stochastic polytomy resolution. The phylogeny was dated using 130 fossil calibration points.…”

The evolution of red blood cell shape in a continental radiation of fishes

“…This phylogeny was obtained from a fully-sampled topology for Actinopterygii recently published (Rabosky et al, 2018). Analysis was done in the fishtree package (Chang et al, 2019).…”