The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae)

How and why certain groups become speciose is a key question in evolutionary biology. Novel traits that enable diversification by opening new ecological niches are likely important mechanisms. However, ornamental traits can also promote diversification by opening up novel sensory niches and thereby creating novel inter-specific interactions. More specifically, ornamental colors may enable more precise and/or easier species recognition and may act as key innovations by increasing the number of species-specific patterns and promoting diversification. While the influence of coloration on diversification is well-studied, the influence of the mechanisms that produce those colors (e.g., pigmentary, nanostructural) is less so, even though the ontogeny and evolution of these mechanisms differ. We estimated a new phylogenetic tree for 121 sunbird species and combined color data of 106 species with a range of phylogenetic tools to test the hypothesis that the evolution of novel color mechanisms increases diversification in sunbirds, one of the most colorful bird clades. Results suggest that: (1) the evolution of novel color mechanisms expands the visual sensory niche, increasing the number of achievable colors, (2) structural coloration diverges more readily across the body than pigment-based coloration, enabling an increase in color complexity, (3) novel color mechanisms might minimize trade-offs between natural and sexual selection such that color can function both as camouflage and conspicuous signal, and (4) despite structural colors being more colorful and mobile, only melanin-based coloration is positively correlated with net diversification. Together, these findings explain why color distances increase with an increasing number of sympatric species, even though packing of color space predicts otherwise.

Dorsal and Ventral Plumage Coloration Evolve as Distinct Modules with Different Environmental Correlations

AbstractMany animals exhibit contrast between their dorsal coloration and their ventral coloration. If selection acts differently on dorsal versus ventral coloration, ancestral covariance between these traits should break down, eventually leading to independent modules of trait evolution. Here, we compare the evolution of feather color across body regions for a clade of Australasian songbirds (Meliphagoidea). We find evidence for three modules of covarying color regions. Among these modules, ventral feathers evolve with high lability, evolving at three times the rate of dorsal plumage and 20 times the rate of flight feathers. While both dorsal plumage and ventral plumage are darker in areas with more precipitation and vegetation, we find that dorsal plumage is twice as similar to colors in satellite photos of background substrates. Overall, differential selection on ventral and dorsal colors likely maintains these as distinct modules over evolutionary timescales-a novel explanation for dorsoventral contrast in pigmentation.

Recent genetic, phenetic and ecological divergence across the Mesoamerican highlands: a study case with Diglossa baritula (Aves: Thraupidae)

The topographical, geological, climatic and biodiversity complexity of Mesoamerica has made it a primary research focus. The Mesoamerican highlands is a region with particularly high species richness and within-species variation. The Cinnamon-bellied Flowerpiercer, Diglossa baritula (Wagler, 1832), is a species endemic to the Mesoamerican highlands, with three allopatric subspecies currently recognized. To characterize divergence within this species, we integrated genomics, morphology, coloration and ecological niche modeling approaches, obtained from sampling individuals across the entire geographic distribution of the species. Our results revealed a clear genomic divergence between the populations to the east versus the west of the Isthmus of Tehuantepec. In contrast to the genomic results, morphology and coloration analyses showed intermediate levels of differentiation, indicating that population groups within D. baritula have probably been under similar selective pressures. Our morphology results indicated that the only sexually dimorphic morphological variable is the wing chord, with males having a longer wing chord than females. Finally, ecological data indicated that there are differences in ecological niche within D. baritula. Our data suggest that D. baritula could contain two or more incipient species at the intermediate phase of the speciation continuum. These results highlight the importance of the geographical barrier of the Isthmus of Tehuantepec and Pleistocene climatic events in driving isolation and population divergence in D. baritula. The present investigation illustrates the speciation potential of the D. baritula complex and the capacity of Mesoamerican highlands to create cryptic biodiversity and endemism.

Ecological factors drive the divergence of morphological, colour and behavioural traits in cactus wrens (Aves, Troglodytidae)

The study of ecological mechanisms influencing organisms' phenotypic variation is a central subject of evolutionary biology. In this study, we characterized morphological, plumage colour and acoustic variation in cactus wrens Campylorhynchus brunneicapillus throughout its distribution. We assessed whether Gloger's, Allen's and Bergmann's ecogeographical rules, and the acoustic adaptation hypothesis relate to geographical trait variation. We analysed specimen coloration in belly and crown plumage, beak shape and structural song characteristics. We tested whether the subspecific classification or the peninsular/mainland groups mirrored the geographical variation in phenotypes and whether ecological factors were associated with patterns of trait variation. Our results suggest that colour, beak shape and acoustic traits varied across the range, in agreement with two lineages described by genetics. The simple versions of Gloger's and Allen's rules are related to variations in colour traits and morphology. Conversely, patterns of phenotypic variation did not support Bergmann's rule. The acoustic adaptation hypothesis supported song divergence for frequency-related traits. Phenotypic variation supports the hypothesis of two taxa: C. affinis in the Baja California peninsula and C. brunneicapillus in the mainland. The ecological factors are associated with phenotypic trait adaptations, suggesting that divergence between lineages could result from ecological divergence.

Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

Colorful signals in nature provide some of the most stunning examples of rapid phenotypic evolution. Yet, studying color pattern evolution has been historically difficult owing to differences in perceptual ability of humans and analytical challenges with studying how complex color patterns evolve. Island systems provide a natural laboratory for testing hypotheses about the direction and magnitude of phenotypic change. A recent study found that plumage colors of island species are darker and less complex than continental species. Whether such shifts in plumage complexity are associated with increased rates of color evolution remains unknown. Here, we use geometric morphometric techniques to test the hypothesis that plumage complexity and insularity interact to influence color diversity in a species-rich clade of colorful birds-kingfishers (Aves: Alcedinidae). In particular, we test three predictions: (1) plumage complexity enhances interspecific rates of color evolution, (2) plumage complexity is lower on islands, and (3) rates of plumage color evolution are higher on islands. Our results show that more complex plumages result in more diverse colors among species and that island species have higher rates of color evolution. Importantly, we found that island species did not have more complex plumages than their continental relatives. Thus, complexity may be a key innovation that facilitates evolutionary response of individual color patches to distinct selection pressures on islands, rather than being a direct target of selection itself. This study demonstrates how a truly multivariate treatment of color data can reveal evolutionary patterns that might otherwise go unnoticed.

Feather function and the evolution of birds

The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life-history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.

Evolution of female colours in birds: The role of female cost of reproduction and paternal care

Female ornamentation is frequently observed in animal species and is sometimes found as more evolutionary labile than male ornamentation. A complex array of factors may explain its presence and variation. Here we assessed the role of female cost of reproduction and paternal care. Both factors have been pinpointed as important by theoretical studies but have not been investigated yet in details at the interspecific level. We worked on 133 species of North temperate Passeriformes bird species for which both the clutch volume - here taken as the proxy of female cost of reproduction - and amount of paternal care are relatively well known. Using spectrometry, we measured the whole-body coloured plumage patches and quantified three metrics corresponding to brightness (i.e. achromatic component), colour chromaticity (i.e. intensity) and colour volume (i.e. diversity). We found a strong association between male and female colour metrics. Controlling for this association, we found additional small but detectable effects of both cost of reproduction and paternal care. First, females of species with more paternal care were slightly brighter. Second, the interaction between the level of paternal care and egg volume was correlated with female colour intensity: females with more paternal care were more chromatic, with this association mostly present when their investment in reproduction was low. Together these results suggest that female cost of reproduction and paternal care are part of the multiple factors explaining variation of female coloration, besides the strong covariation between male and female coloration.

The evolution of sex similarities in social signals: Climatic seasonality is associated with lower sexual dimorphism and greater elaboration of female and male signals in antbirds (Thamnophilidae)

Selection on signals that mediate social competition varies with resource availability. Climate regulates resource availability, which may affect the strength of competition and selection on signals. Traditionally, this meant that more seasonal, colder, or dryer-overall harsher-environments should favor the elaboration of male signals under stronger male-male competition, increasing sexual dimorphism. However, females also use signals to compete; thus, harsher environments could strengthen competition and favor elaboration of signals in both sexes, decreasing sexual dimorphism. Alternatively, harsher environments could decrease sexual dimorphism due to scarcer resources to invest in signal elaboration in both sexes. We evaluated these contrasting hypotheses in antbirds, a family of Neotropical passerines that varies in female and male signals and occurs across diverse climatic regimes. We tested the association of sexual dimorphism of plumage coloration and songs with temperature, precipitation, and their seasonality. We found that greater seasonality is associated with lower sexual dimorphism in plumage coloration and greater elaboration of visual signals in both sexes, but not acoustic signals. Our results suggest that greater seasonality may be associated with convergent elaboration of female and male visual signals, highlighting the role of signals of both sexes in the evolution of sexual dimorphism.

Drivers of phenotypic divergence in a Mesoamerican highland bird

Animals derive their coloration from a variety of pigments as well as non-pigmentary structural features. One of the most widespread types of pigments are carotenoids, which are used by all invertebrate taxa and most vertebrate orders to generate red, pink, orange and yellow coloration. Despite their widespread use by diverse animal groups, animals obligately obtain carotenoid pigments from diet. Carotenoid-based coloration is therefore modulated by evolutionary and ecological processes that affect the acquisition and deposition of these pigments into tegumentary structures. The Flame-colored Tanager (Piranga bidentata) is a highland songbird in the cardinal family (Cardinalidae) that is distributed from Mexican sierras through Central America up to western Panama. While female plumage throughout its entire range is predominantly yellow, males exhibit a noticeable split in ventral plumage color, which is bright orange on the West slope and the Tres Marias Islands and blood red in Eastern Mexico and Central America. We used Multiple Regression on Matrices (MRM) to evaluate the relative contributions of geographic distance, climate and genetic distance on color divergence and body differences between geographically disjunct populations. We found that differentiation in carotenoid plumage coloration was mainly explained by rainfall differences between disjunct populations, whereas body size differences was best explained by variation in the annual mean temperature and temperature of coldest quarter. These results indicate that climate is a strong driver of phenotypic divergence in Piranga bidentata.

Ecology and behavior predict an evolutionary trade-off between song complexity and elaborate plumages in antwrens (Aves, Thamnophilidae)

The environment can impose constraints on signal transmission properties such that signals should evolve in predictable directions (Sensory Drive Hypothesis). However, behavioral and ecological factors can limit investment in more than one sensory modality leading to a trade-off in use of different signals (Transfer Hypothesis). In birds, there is mixed evidence for both sensory drive and transfer hypothesis. Few studies have tested sensory drive while also evaluating the transfer hypothesis, limiting understanding of the relative roles of these processes in signal evolution. Here, we assessed both hypotheses using acoustic and visual signals in male and female antwrens (Thamnophilidae), a species-rich group that inhabits diverse environments and exhibits behaviors, such as mixed-species flocking, that could limit investment in different signal modalities. We uncovered significant effects of habitat (sensory drive) and mixed-species flocking behavior on both sensory modalities, and we revealed evolutionary trade-offs between song and plumage complexity, consistent with the transfer hypothesis. We also showed sex- and trait-specific responses in visual signals that suggest both natural and social selection play an important role in the evolution of sexual dimorphism. Altogether, these results support the idea that environmental (sensory drive) and behavioral pressures (social selection) shape signal evolution in antwrens.

Speciation rates are positively correlated with the rate of plumage color evolution in hummingbirds

A fascinating pattern in nature is the uneven distribution of biodiversity among clades, some with low species richness and phenotypic variation in contrast to others with remarkable species richness and phenotypic diversity. In animals, communication signals are crucial for intra- and interspecific interactions and are likely an important factor in speciation. However, evidence for the association between the evolution of such signals and speciation is mixed. In hummingbirds, plumage coloration is an important communication signal, particularly for mate selection. Here, using reflectance data for 237 hummingbird species (∼66% of total diversity), we demonstrate that color evolution rates are associated with speciation rates, and that differences among feather patches are consistent with an interplay between natural and sexual selection. We found that female color evolution rates of multiple plumage elements, including the gorget, were similar to those of males. Although male color evolution in this patch was associated with speciation, female gorget color evolution was not. In other patches, the relationship between speciation and color evolution rates was pervasive between sexes. We anticipate that future studies on animal communication will likely find that evolution of signaling traits of both sexes has played a vital role in generating signal and species diversity.

Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae)

Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps-a widespread forest songbird that occurs in the lowlands of Central America, Chocó and Amazonia-using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.

Evolutionary history of mental glands in turtles reveals a single origin in an aquatic ancestor and recurrent losses independent of macrohabitat

Despite the relevance of chemical communication in vertebrates, comparative examinations of macroevolutionary trends in chemical signaling systems are scarce. Many turtle and tortoise species are reliant on chemical signals to communicate in aquatic and terrestrial macrohabitats, and many of these species possess specialized integumentary organs, termed mental glands (MGs), involved in the production of chemosignals. We inferred the evolutionary history of MGs and tested the impact of macrohabitat on their evolution. Inference of ancestral states along a time-calibrated phylogeny revealed a single origin in the ancestor of the subclade Testudinoidea. Thus, MGs represent homologous structures in all descending lineages. We also inferred multiple independent losses of MGs in both terrestrial and aquatic clades. Although MGs first appeared in an aquatic turtle (the testudinoid ancestor), macrohabitat seems to have had little effect on MG presence or absence in descendants. Instead, we find clade-specific evolutionary trends, with some clades showing increased gland size and morphological complexity, whereas others exhibiting reduction or MG loss. In sister clades inhabiting similar ecological niches, contrasting patterns (loss vs. maintenance) may occur. We conclude that the multiple losses of MGs in turtle clades have not been influenced by macrohabitat and that other factors have affected MG evolution.

Rethinking Gloger's Rule: Climate, Light Environments, and Color in a Large Family of Tropical Birds (Furnariidae)

AbstractEcogeographic rules provide a framework within which to test evolutionary hypotheses of adaptation. Gloger's rule predicts that endothermic animals should have darker colors in warm/rainy climates. This rule also predicts that animals should be more rufous in warm/dry climates, the so-called complex Gloger's rule. Empirical studies frequently demonstrate that animals are darker in cool/wet climates rather than in warm/wet climates. Furthermore, sensory ecology predicts that, to enhance crypsis, animals should be darker in darker light environments. We aimed to disentangle the effects of climate and light environments on plumage color in the large Neotropical passerine family Furnariidae. We found that birds in cooler and rainier climates had darker plumage even after controlling for habitat type. Birds in darker habitats had darker plumage even after controlling for climate. The effects of temperature and precipitation interact so that the negative effect of precipitation on brightness is strongest in cool temperatures. Finally, birds tended to be more rufous in warm/dry habitats but also, surprisingly, in cool/wet locales. We suggest that Gloger's rule results from complementary selective pressures arising from myriad ecological factors, including crypsis, thermoregulation, parasite deterrence, and resistance to feather abrasion.

Evolution of breeding plumages in birds: A multiple-step pathway to seasonal dichromatism in New World warblers (Aves: Parulidae)

Many species of birds show distinctive seasonal breeding and nonbreeding plumages. A number of hypotheses have been proposed for the evolution of this seasonal dichromatism, specifically related to the idea that birds may experience variable levels of sexual selection relative to natural selection throughout the year. However, these hypotheses have not addressed the selective forces that have shaped molt, the underlying mechanism of plumage change. Here, we examined relationships between life-history variation, the evolution of a seasonal molt, and seasonal plumage dichromatism in the New World warblers (Aves: Parulidae), a family with a remarkable diversity of plumage, molt, and life-history strategies. We used phylogenetic comparative methods and path analysis to understand how and why distinctive breeding and nonbreeding plumages evolve in this family. We found that color change alone poorly explains the evolution of patterns of biannual molt evolution in warblers. Instead, molt evolution is better explained by a combination of other life-history factors, especially migration distance and foraging stratum. We found that the evolution of biannual molt and seasonal dichromatism is decoupled, with a biannual molt appearing earlier on the tree, more dispersed across taxa and body regions, and correlating with separate life-history factors than seasonal dichromatism. This result helps explain the apparent paradox of birds that molt biannually but show breeding plumages that are identical to the nonbreeding plumage. We find support for a two-step process for the evolution of distinctive breeding and nonbreeding plumages: That prealternate molt evolves primarily under selection for feather renewal, with seasonal color change sometimes following later. These results reveal how life-history strategies and a birds' environment act upon multiple and separate feather functions to drive the evolution of feather replacement patterns and bird coloration.

Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae)

The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.

A simple index to quantify and compare the magnitude of intraspecific geographic plumage colour variation in typical antbirds (Aves: Passeriformes: Thamnophilidae)

Intraspecific geographic phenotypic variation is a crucial theme in evolutionary biology. Comparing its magnitude across species can provide insights into its ecological and genetic correlates. Here, we developed an index, which we dub the V index, to quantify intraspecific plumage colour variation in typical antbirds (Thamnophilidae), a family which has long interested ornithologists due to a high prevalence of intraspecific variation. The V index is based on a bivariate colour space defined by brightness and redness. Its value for each species equals the mean area occupied by each of its subspecies in that colour space, divided by the area of the species. Lower values indicate greater intraspecific geographic variation. Based on this index, Thamnophilus caerulescens (Variable Antshrike) was exceptionally geographically variable compared to other thamnophilids, as previously suggested based on qualitative evidence. In general, we found that the most variable species had disjunct distributions and deep phylogeographic structure, suggesting an effect of historical population dynamics in producing geographic variation. The V index can be adapted for use with other taxa, traits, and taxonomic levels, and we expect it will instigate novel ways of thinking about phenotypic variation in birds and other animals.

A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.