2019
DOI: 10.1111/2041-210x.13182
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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 org… Show more

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Cited by 98 publications
(87 citation statements)
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“…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).…”
Section: Discussionmentioning
confidence: 99%
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“…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).…”
Section: Discussionmentioning
confidence: 99%
“…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.…”
Section: Phylogenetic Datamentioning
confidence: 99%
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“…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.…”
Section: Methodsmentioning
confidence: 99%
“…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).…”
Section: Methodsmentioning
confidence: 99%