clootl: an R package for accessing and manipulating a complete, versioned avian phylogeny

Birds are frequently used as a focal taxon for evolutionary and ecological studies. Thousands of papers a year are published using birds as study systems. Hundreds more are published clarifying the evolutionary relationships among clades or regionally circumscribed sets of bird species. Up to date phylogenies are essential for informing and guiding avian studies, controlling for the expectation of shared trait evolution, and for science communication, among other applications. However, employing up to date phylogenies to address these questions has proven challenging for a number of reasons. First, individually published phylogenies are often hard to access in a usable manner. For example, sequences are usually made available, and an image of the phylogeny is published, but the actual phylogeny data product is often not digitally available. Second, published phylogenies often do not include all taxa of interest or have branch lengths in units of time. Third, taxonomic mismatches between phylogenies and existing datasets can complicate analyses. We address these issues by sharing an R package, clootl, that wraps together a new, complete, dated bird phylogeny with easy to use tools to extract trees for taxa of interest and sample over uncertainty. The phylogeny incorporates information from more than 300 individually published bird phylogenies. The R package includes tools to help appropriately cite these input studies. This software will enable users to smoothly integrate accurate evolutionary information into any analyses on birds.