DOI: 10.5061/dryad.4f4qrfjd3
title: Estimating the distribution of carotenoid coloration in skin and integumentary structures of birds and extinct dinosaurs

description: 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.
description: 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<i> Handbook of the Birds of the World
 </i>(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.