Biology subjects

Prum, R. O.

Publications and source records attributed to Prum, R. O..

8 recordsLinked to original sources

bioRxiv2025

Developmental evolution of social signals in the delayed plumage maturation of manakins (Aves: Pipridae)

Avian plumage maturation involves replacing feathers, via discrete molts, until reaching an iteratively-regenerated definitive plumage. In most birds, this process takes about one year. In the Neotropical lekking manakins (Pipridae), males of most species exhibit delayed plumage maturation (DPM), passing through drab predefinitive plumages for two or three years before reaching a bright, sexually dimorphic, definitive plumage. We used a phylogenetic analysis to investigate the evolutionary history of DPM in manakins. Our unique comparative dataset derived characters from a graph structure representing the developmental schedules of individual, colorful plumage patches. We traced the origin of one-year DPM to the ancestor of sexually dichromatic Piprinae manakins, followed by three separate origins of prolonged, two-year DPM, plus one subsequent extension to three-year DPM. Consistent with social signaling hypotheses, prolonged DPM evolved to reveal and maintain signals of young male status. This interspecific pattern sheds light on the sociosexual development of lekking birds, a topic usually restricted to autecological field studies. By detailing heterochronic dynamics in manakin plumage evolution, we also show how the iterative regeneration of characters like bird feathers, insect instars, mammalian antlers, and angiosperm flowers can create multiple distinct levels of developmental homologies among bodies, sexes, and species.

evolutionary biology↗

bioRxiv2024

Genetic Characterization of the Cell Types of in Developing Feathers, and the Evolution of Feather Complexity

Feathers are the most complex and diverse epidermal appendages found in vertebrates. Their unique hierarchical organization and development is based on a diversity of cell types and morphologies. Despite being well characterized morphologically and extensive molecular developmental research focusing on candidate genes, little is known about the gene regulatory identities of these presumptive feather cell types. Here, we use single cell and single nuclear RNA sequencing with in situ hybridization to identify and characterize cells types in embryonic chicken feathers. We show that the distinct cell morphologies correspond to feather cell types with distinct gene expression profiles. We also describe a previously unidentified cell type, the basal barb ridge epithelium, which appears to play a role in signaling necessary for barb ridge differentiation and pulp cap production. We also analyze RNA velocity trajectories of developing feather cells, and find distinct developmental trajectories for epidermal cells that constitute the mature feather and those that function only in feather development. Finally, we produce an evolutionary tree of feather cell types based on transcription factor expression in order to test prior developmental hypotheses about feather evolution. Our tree is consistent with the developmental model of feather evolution, and sheds light on the influence of ancestral epidermal stratification on feather cell evolution. This transcriptomic approach to study feather cell types helps lay the ground work for understanding the developmental evolutionary complexity and diversity of feathers.

developmental biology↗

bioRxiv2023

Social context and the evolution of delayed reproduction in birds

One puzzling feature of avian life histories is that individuals in many different lineages delay reproduction for several years after they finish growing. Intraspecific field studies suggest that various complex social contexts--such as cooperative breeding groups, nesting colonies, and display leks--result in delayed reproduction because they require forms of sociosexual development that extend beyond physical maturation. Here, we explicitly propose this hypothesis and use a full suite of phylogenetic comparative methods to test it, analyzing the evolution of age at first reproduction (AFR) in females and males across 963 species of birds. Phylogenetic regressions support increased AFR in colonial females and males, cooperatively breeding males, and lekking males. Continuous Ornstein-Uhlenbeck models support distinct evolutionary regimes with increased AFR for all of cooperative, colonial, and lekking lineages. Discrete hidden state Markov models suggest a net increase in delayed reproduction for social lineages, even when accounting for hidden state heterogeneity and the potential reverse influence of AFR on sociality. Our results support the hypothesis that the evolution of social contexts reshapes the dynamics of life history evolution in birds. Comparative analyses of even the most broadly generalizable characters, such as AFR, must reckon with unique, heterogeneous, historical events in the evolution of individual lineages.

evolutionary biology↗

bioRxiv2022

Molecular early burst associated with the diversification of birds at the K-Pg boundary

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K- Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds [1-9]. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade [10]. Our approach identifies distinct and contrasting regimes of molecular evolution across exons, introns, untranslated regions, and mitochondrial genomes. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds [11-13]. Using simulation and machine learning techniques, we show that shifts in developmental mode [14] or adult body mass [4] best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass [15, 16]. In agreement with theoretical predictions, this scaling relationship appears to have weakened across the end-Cretaceous transition. Overall, our study provides evidence that the Chicxulub bolide impact [17] triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.

evolutionary biology↗

bioRxiv2022

Fighting isn't sexy in lekking Greater Sage-grouse (Centrocercus urophasianus)

In lekking systems, females can observe both male courtship displays and fights. It has been theorized that male-male agonism may function as a display, giving females more information about mate quality. However, males in many species, such as Greater Sage-grouse, often fight when females are absent, and can even attack during copulation attempts in seeming conflict with females choices. Traditional correlational approaches are inadequate to distinguish the underlying mechanisms of social interaction and can result in misleading associations between fighting and mating events. Using observations from a wild population, we posit a novel Relational Event Model that incorporates temporal dependencies of events among a network of individuals. We investigate how fighting among male sage-grouse predicts events such as future fights, copulation solicitations, and interrupted copulations. Our analysis reveals that fightings primary function is not to impress females. Indeed, males are less likely to start and more likely to leave fights with females present, plausibly to avoid entanglement in conflict that reduces availability to mate. Moreover, being drawn into these latter viscous cycles of combat and retribution constitutes a significant risk associated with initiating attacks on other males. However, fighting serves other roles, e.g., to deter copulation interruptions and rebuff competitors. Our findings suggest that social systems that regulate conflict and promote females choice based on display are likely fundamental to the stable evolution of leks.

animal behavior and cognition↗

bioRxiv2020

Single Gyroid and Inverse b.c.c. Photonic Crystals in Bird Feathers

Vivid, saturated structural colors are conspicuous and important features of many animals. A rich diversity of three-dimensional periodic photonic nanostructures is found in the chitinaceous exoskeletons of invertebrates. Three-dimensional photonic nanostructures have been described in bird feathers, but they are typically quasi-ordered. Here, we report bi-continuous single gyroid {beta}-keratin and air photonic crystal networks in the feather barbs of blue-winged leafbirds (Chloropsis cochinchinensis sensu lato), which have evolved from ancestral quasi-ordered channel-type nanostructures. Self-assembled avian photonic crystals may serve as inspiration for multi-functional applications, as they suggest efficient, alternative routes to single gyroid synthesis at optical length-scales, which has been experimentally elusive.

evolutionary biology↗

bioRxiv2019

Genomic phylogeography of the White Crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last [~]2.5 Ma.

evolutionary biology↗

bioRxiv2018

Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales

Birds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping scutate scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate reticulate scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many \"feather-specific genes\" are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers - and may represent an important mechanism for the origin of evolutionary novelties.

evolutionary biology↗