From Davis and Clarke: Color expression was recorded for all extant, non-passerine bird species (n = 4,022, based on the species list in Jetz et al. (2012)) and 12 outgroup species (members of Testudines, Crocodilia; see Supplemental Data). We included outgroup species from across the two major extant clades of turtles (Cryptodira and Pleurodira), and the three major extant clades within Crocodylia (Alligatoridae, Crocodylidae, and Gavialidae), and sampled a number of species proportional to the size of each outgroup clade. For the sampled birds, the iris, beak keratin, face skin, neck skin, fleshy head and neck skin (i.e., a wattle, crop, or pouch), leg skin, leg scales, and plumage were considered in mature males and females. For seasonal color variants, color was scored as present if it was expressed by a species during some stage of the annual cycle. Data on carotenoid-consistent plumage color and other pigments assessed via Raman spectroscopy were available from Thomas et al. (2014a) and were modified only in consideration of subsequent stud ies (see Supplemental Data for citations by species). Other non-feather coloration was scored from open-source photographs of each species and verified using the Handbook of the Birds of the World (now: Birds of the World; del Hoyo et al., 2019; Billerman et al., 2020); in cases where species were split or subspecies were listed in the Handbook but not the Jetz et al. (2012) list, all subspecies were considered for scoring the Jetz species. When possible, known pigment use was taken from the literature (see AllBirds Dataset). We collected diet data from the literature for the 61 species and used the diet characterizations of Olson (2006) to assign each a minimum, maximum, and average dietary carotenoid content value based on dietary information collected on each species (see Supplemental Data for references by species). We used Olson's coarse classification scheme, in which dietary items are quantified, placed into general categories, and then ranked from least to most carotenoid rich (Olson 2006 p 622; summarized in Table S1). This allowed us to analyze diet as both a continuous trait based on estimated absolute carotenoid content and as a discrete category of least to most carotenoid rich (see Olson 2006). We calculated an average expected dietary carotenoid content for each species and used both that value and the log-transformed value in our analyses. To further investigate a potential relationship between the extent of coloration and diet type, we also categorized the dietary content of the 61 birds generally as either primarily vegetarian, carnivorous, or omnivorous. We then categorized birds by the total number of tissue categories that express color (skin, keratinous, or plumage) as well as by the total number of individual body regions (beak, face, neck, leg skin, leg scales, and plumage) that express color.

Carotenoids are pigments responsible for most bright yellow, red, and orange hues in birds. Their distribution has been investigated in avian plumage, but the evolution of their expression in skin and other integumentary structures has not been approached in detail. Here, we investigate the expression of carotenoid-consistent coloration across tissue types in all extant, non-passerine species (n= 4,022) and archelosaur outgroups in a phylogenetic framework. We collect dietary data for a subset of birds and investigate how dietary carotenoid intake may relate to carotenoid expression in various tissues. We find that carotenoid-consistent expression in skin or non-plumage keratin has a 50 percent probability of being present in the most recent common ancestor of Archosauria. Skin expression has a similar probability at the base of the avian crown clade, but plumage expression is unambiguously absent in that ancestor and shows hundreds of independent gains within non-passerine neognaths, consistent with previous studies. Although our data do not support a strict sequence of tissue expression in non-passerine birds, we find support that expression of carotenoid-consistent color in non-plumage integument structures might evolve in a correlated manner and feathers are rarely the only region of expression. Taxa with diets high in carotenoid content also show expression in more body regions and tissue types. Our results may inform targeted assays for carotenoids in tissues other than feathers, and expectations of these pigments in non-avian dinosaurs. In extinct groups, bare-skin regions and the rhamphotheca, especially in species with diets rich in plants, may express these pigments, which are not expected in feathers or feather homologues.

Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: GRFP