The Early Origin of Feathers

From Bayes to Darwin: Evolutionary search as an exaptation from sampling-based Bayesian inference

Building on the algorithmic equivalence between finite population replicator dynamics and particle filtering based approximation of Bayesian inference, we design a computational model to demonstrate the emergence of Darwinian evolution over representational units when collectives of units are selected to infer statistics of high-dimensional combinatorial environments. The non-Darwinian starting point is two units undergoing a few cycles of noisy, selection-dependent information transmission, corresponding to a serial (one comparison per cycle), non-cumulative process without heredity. Selection for accurate Bayesian inference at the collective level induces an adaptive path to the emergence of Darwinian evolution within the collectives, capable of maintaining and iteratively improving upon complex combinatorial information. When collectives are themselves Darwinian, this mechanism amounts to a top-down (filial) transition in individuality. We suggest that such a selection mechanism can explain the hypothesized emergence of fast timescale Darwinian dynamics over a population of neural representations within animal and human brains, endowing them with combinatorial planning capabilities. Further possible physical implementations include prebiotic collectives of non-replicating molecules and reinforcement learning agents with parallel policy search.

How smart was T. rex? Testing claims of exceptional cognition in dinosaurs and the application of neuron count estimates in palaeontological research

Recent years have seen increasing scientific interest in whether neuron counts can act as correlates of diverse biological phenomena. Lately, Herculano-Houzel (2023) argued that fossil endocasts and comparative neurological data from extant sauropsids allow to reconstruct telencephalic neuron counts in Mesozoic dinosaurs and pterosaurs, which might act as proxies for behaviors and life history traits in these animals. According to this analysis, large theropods such as Tyrannosaurus rex were long-lived, exceptionally intelligent animals equipped with "macaque- or baboon-like cognition", whereas sauropods and most ornithischian dinosaurs would have displayed significantly smaller brains and an ectothermic physiology. Besides challenging established views on Mesozoic dinosaur biology, these claims raise questions on whether neuron count estimates could benefit research on fossil animals in general. Here, we address these findings by revisiting Herculano-Houzel's (2023) work, identifying several crucial shortcomings regarding analysis and interpretation. We present revised estimates of encephalization and telencephalic neuron counts in dinosaurs, which we derive from phylogenetically informed modeling and an amended dataset of endocranial measurements. For large-bodied theropods in particular, we recover significantly lower neuron counts than previously proposed. Furthermore, we review the suitability of neurological variables such as neuron numbers and relative brain size to predict cognitive complexity, metabolic rate and life history traits in dinosaurs, coming to the conclusion that they are flawed proxies for these biological phenomena. Instead of relying on such neurological estimates when reconstructing Mesozoic dinosaur biology, we argue that integrative studies are needed to approach this complex subject.

Bio-molecular analyses enable new insights into the taphonomy of feathers

Exceptionally preserved feathers from the Mesozoic era have provided valuable insights into the early evolution of feathers and enabled color reconstruction of extinct dinosaurs, including early birds. Mounting chemical evidence for the two key components of feathers-keratins and melanins-in fossil feathers has demonstrated that exceptional preservation can be traced down to the molecular level. However, the chemical changes that keratin and eumelanin undergo during fossilization are still not fully understood, introducing uncertainty in the identification of these two molecules in fossil feathers. To address this issue, we need to examine their taphonomic process. In this study, we analyzed the structural and chemical composition of fossil feathers from the Jehol Biota and compared them with the structural and chemical changes observed in modern feathers during the process of biodegradation and thermal degradation, as well as the structural and chemical characteristics of a Cenozoic fossil feather. Our results suggest that the taphonomic process of feathers from the Cretaceous Jehol Biota is mainly controlled by the process of thermal degradation. The Cretaceous fossil feathers studied exhibited minimal keratin preservation but retained strong melanin signals, attributed to melanin's higher thermal stability. Low-maturity carbonaceous fossils can indeed preserve biosignals, especially signals from molecules with high resistance to thermal degradation. These findings provide clues about the preservation potential of keratin and melanin, and serve as a reference for searching for those two biomolecules in different geological periods and environments.

The Limitations of Large Language Models for Understanding Human Language and Cognition

Researchers have recently argued that the capabilities of Large Language Models (LLMs) can provide new insights into longstanding debates about the role of learning and/or innateness in the development and evolution of human language. Here, we argue on two grounds that LLMs alone tell us very little about human language and cognition in terms of acquisition and evolution. First, any similarities between human language and the output of LLMs are purely functional. Borrowing the "four questions" framework from ethology, we argue that what LLMs do is superficially similar, but how they do it is not. In contrast to the rich multimodal data humans leverage in interactive language learning, LLMs rely on immersive exposure to vastly greater quantities of unimodal text data, with recent multimodal efforts built upon mappings between images and text. Second, turning to functional similarities between human language and LLM output, we show that human linguistic behavior is much broader. LLMs were designed to imitate the very specific behavior of human writing; while they do this impressively, the underlying mechanisms of these models limit their capacities for meaning and naturalistic interaction, and their potential for dealing with the diversity in human language. We conclude by emphasising that LLMs are not theories of language, but tools that may be used to study language, and that can only be effectively applied with specific hypotheses to motivate research.

A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait

The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations. Understanding the genetic mechanism underpinned feathered-foot development in wild birds is still in its infancy. Here, we assembled a chromosome-level genome of the Asian house martin (Delichon dasypus) using the long-read High Fidelity sequencing approach to initiate the search for genes associated with its feathered feet. We employed the whole-genome alignment of D. dasypus with other swallow species to identify high-SNP regions and chromosomal inversions in the D. dasypus genome. After filtering out variations unrelated to D. dasypus evolution, we found six genes related to feather development near the high-SNP regions. We also detected three feather development genes in chromosomal inversions between the Asian house martin and the barn swallow genomes. We discussed their association with the wingless/integrated (WNT), bone morphogenetic protein, and fibroblast growth factor pathways and their potential roles in feathered-foot development. Future studies are encouraged to utilize the D. dasypus genome to explore the evolutionary process of the feathered-foot trait in avian species. This endeavor will shed light on the evolutionary path of feathers in birds.

Cellular structure of dinosaur scales reveals retention of reptile-type skin during the evolutionary transition to feathers

Fossil feathers have transformed our understanding of integumentary evolution in vertebrates. The evolution of feathers is associated with novel skin ultrastructures, but the fossil record of these changes is poor and thus the critical transition from scaled to feathered skin is poorly understood. Here we shed light on this issue using preserved skin in the non-avian feathered dinosaur Psittacosaurus. Skin in the non-feathered, scaled torso is three-dimensionally replicated in silica and preserves epidermal layers, corneocytes and melanosomes. The morphology of the preserved stratum corneum is consistent with an original composition rich in corneous beta proteins, rather than (alpha-) keratins as in the feathered skin of birds. The stratum corneum is relatively thin in the ventral torso compared to extant quadrupedal reptiles, reflecting a reduced demand for mechanical protection in an elevated bipedal stance. The distribution of the melanosomes in the fossil skin is consistent with melanin-based colouration in extant crocodilians. Collectively, the fossil evidence supports partitioning of skin development in Psittacosaurus: a reptile-type condition in non-feathered regions and an avian-like condition in feathered regions. Retention of reptile-type skin in non-feathered regions would have ensured essential skin functions during the early, experimental stages of feather evolution.

From emotional signals to symbols

The quest for the origins of language is a diverse enterprise, where research from a variety of disciplines brings area-specific ideas and area-specific terminology to bear. This variety often results in misunderstandings and misconceptions about communication in various species. In the present paper, we argue for focus on emotional systems as the primary motivators for social signals in animals in general. This focus can help resolve discrepancies of interpretation among different areas of inquiry and can illuminate distinctions among different social signals as well as their phylogenetic origins in animals and especially in humans. We advocate, following Jaak Panksepp, a view wherein the Seeking System, the endogenous tendency to search and explore, is the most fundamental emotional motivation. The Seeking System forms the basis for flexible, voluntary, and exploratory control of motor systems and makes much of learning possible. The relative lack of vocal learning and expression in nonhuman primates contrasted with extensive vocal learning and expression in humans began, we propose, with the evolution in ancient hominins of a necessary foundation for the many subsequent capabilities required for language. That foundation was, according to the reasoning, naturally selected in the form of neurological connections between the Seeking System and mechanisms of glottal/phonatory control. The new connections allowed ancient hominins to develop flexible, endogenous vocal fitness signals produced at very high rates and including large numbers of discrete syllables, recombinable to form syllable combinations with many prosodic variations. The increasing sociality of hominins supported evolution of massive expansion in the utilization of these flexible vocal forms to allow development of words and sentences.

The avian ectodermal default competence to make feathers

Feathers originate as protofeathers before birds, in pterosaurs and basal dinosaurs. What characterizes a feather is not only its outgrowth, but its barb cells differentiation and a set of beta-corneous proteins. Reticula appear concomitantly with feathers, as small bumps on plantar skin, made only of keratins. Avian scales, with their own set of beta-corneous proteins, appear more recently than feathers on the shank, and only in some species. In the chick embryo, when feather placodes form, all the non-feather areas of the integument are already specified. Among them, midventral apterium, cornea, reticula, and scale morphogenesis appear to be driven by negative regulatory mechanisms, which modulate the inherited capacity of the avian ectoderm to form feathers. Successive dermal/epidermal interactions, initiated by the Wnt/β-catenin pathway, and involving principally Eda/Edar, BMP, FGF20 and Shh signaling, are responsible for the formation not only of feather, but also of scale placodes and reticula, with notable differences in the level of Shh, and probably FGF20 expressions. This sequence is a dynamic and labile process, the turning point being the FGF20 expression by the placode. This epidermal signal endows its associated dermis with the memory to aggregate and to stimulate the morphogenesis that follows, involving even a re-initiation of the placode.

Genomic basis of melanin-associated phenotypes suggests colour-specific environmental adaptations in tawny owls

Feathers comprise a series of evolutionary innovations but also harbour colour, a key biological trait known to co-vary with life history or complex traits. Those relationships are particularly true in melanin-based pigmentation species due to known pleiotropic effects of the melanocortin pathway - originating from melanin-associated phenotypes. Here, we explore the molecular basis of melanin colouration and expected co-variation at the molecular level in the melanin-based, colour polymorphic system of the tawny owl (Strix aluco). An extensive body of literature has revealed that grey and brown tawny owl colour morphs differ in a series of life history and behavioural traits. Thus, it is plausible to expect co-variation also at molecular level between colour morphs. To investigate this possibility, we assembled the first draft genome of the species against which we mapped ddRADseq reads from 220 grey and 150 brown morphs - representing 10 years of pedigree data from a population in Southern Finland - and explored genome-wide associations with colour phenotype. Our results revealed putative molecular signatures of cold adaptation strongly associated with the grey phenotype, namely, a non-synonymous substitution in MCHR1, plus 2 substitutions in non-coding regions of FTCD and FAM135A whose genotype combinations obtained a predictive power of up to 100% (predicting grey colour). These suggest a molecular basis of cold environment adaptations predicted to be grey-morph specific. Our results potentially reveal part of the molecular machinery of melanin-associated phenotypes and provide novel insights towards understanding the functional genomics of colour polymorphism in melanin-based pigmented species.

Drug Repurposing in the Chemotherapy of Infectious Diseases

Repurposing is a universal mechanism for innovation, from the evolution of feathers to the invention of Velcro tape. Repurposing is particularly attractive for drug development, given that it costs more than a billion dollars and takes longer than ten years to make a new drug from scratch. The COVID-19 pandemic has triggered a large number of drug repurposing activities. At the same time, it has highlighted potential pitfalls, in particular when concessions are made to the target product profile. Here, we discuss the pros and cons of drug repurposing for infectious diseases and analyze different ways of repurposing. We distinguish between opportunistic and rational approaches, i.e., just saving time and money by screening compounds that are already approved versus repurposing based on a particular target that is common to different pathogens. The latter can be further distinguished into divergent and convergent: points of attack that are divergent share common ancestry (e.g., prokaryotic targets in the apicoplast of malaria parasites), whereas those that are convergent arise from a shared lifestyle (e.g., the susceptibility of bacteria, parasites, and tumor cells to antifolates due to their high rate of DNA synthesis). We illustrate how such different scenarios can be capitalized on by using examples of drugs that have been repurposed to, from, or within the field of anti-infective chemotherapy.

Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts

Most vertebrate species undergo tooth replacement throughout adult life. This process is marked by the shedding of existing teeth and the regeneration of tooth organs. However, little is known about the genetic circuitry regulating tooth replacement. Here, we tested whether fish orthologs of genes known to regulate mammalian hair regeneration have effects on tooth replacement. Using two fish species that demonstrate distinct modes of tooth regeneration, threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), we found that transgenic overexpression of four different genes changed tooth replacement rates in the direction predicted by a hair regeneration model: Wnt10a and Grem2a increased tooth replacement rate, whereas Bmp6 and Dkk2 strongly inhibited tooth formation. Thus, similar to known roles in hair regeneration, Wnt and BMP signals promote and inhibit regeneration, respectively. Regulation of total tooth number was separable from regulation of replacement rates. RNA sequencing of stickleback dental tissue showed that Bmp6 overexpression resulted in an upregulation of Wnt inhibitors. Together, these data support a model in which different epithelial organs, such as teeth and hair, share genetic circuitry driving organ regeneration.

Origins and Functional Significance of Eukaryotic Protein Folds

Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.

The selfish preen: absence of allopreening in Palaeognathae and its socio-cognitive implications

Preening behaviours are widespread in extant birds. While most birds appear to autopreen (self-directed preening), allopreening (preening directed at conspecifics) seems to have emerged only in certain species, but across many families. Allopreening has been hypothesised to reinforce mutual relationships and cooperation between individuals, and to underpin various socio-cognitive abilities. Palaeognathae is a bird group exhibiting neurocognitively plesiomorphic traits compared to other birds. They share many features with non-avian paravian dinosaurs and are thus important for the study of cognitive evolution in birds. Despite this, and the important correlation of allopreening with many complicated social behaviours, allopreening has not been systematically studied in Palaeognathae. Therefore, we examined the preening behaviours in four species of palaeognaths: common ostriches (Struthio camelus), greater rheas (Rhea americana), emus (Dromaius novaehollandiae), and elegant crested tinamous (Eudromia elegans). We compared findings with common ravens (Corvus corax), a neognath species known for its allopreening and complex social cognition. We found autopreening, but no allopreening, in the palaeognath species, while both autopreening and allopreening was found in common ravens. The absence of allopreening in Palaeognathae suggests an emergence of this behaviour within Neognathae. We contextualise our results in relation to the socio-cognitive underpinnings of allopreening and its implications for the understanding of the evolution of socio-cognitive abilities in non-avian paravian dinosaurs and early birds.

Revisiting Nature's "Unifying Patterns": A Biological Appraisal

Effective bioinspiration requires dialogue between designers and biologists, and this dialogue must be rooted in a shared scientific understanding of living systems. To support learning from "nature's overarching design lessons" the Biomimicry Institute has produced ten "Unifying Patterns of Nature". These patterns have been developed to engage with those interested in finding biologically inspired solutions to human challenges. Yet, although well-intentioned and appealing, they are likely to dishearten biologists. The aim of this paper is to identify why and propose alternative principles based on evolutionary theory.

Allometric wing growth links parental care to pterosaur giantism

Pterosaurs evolved a broad range of body sizes, from small-bodied early forms with wingspans of mostly 1-2 m to the last-surviving giants with sizes of small airplanes. Since all pterosaurs began life as small hatchlings, giant forms must have attained large adult sizes through new growth strategies, which remain largely unknown. Here we assess wing ontogeny and performance in the giant Pteranodon and the smaller-bodied anurognathids Rhamphorhynchus, Pterodactylus and Sinopterus. We show that most smaller-bodied pterosaurs shared negative allometry or isometry in the proximal elements of the fore- and hindlimbs, which were critical elements for powering both flight and terrestrial locomotion, whereas these show positive allometry in Pteranodon. Such divergent growth allometry typically signals different strategies in the precocial-altricial spectrum, suggesting more altricial development in Pteranodon. Using a biophysical model of powered and gliding flight, we test and reject the hypothesis that an aerodynamically superior wing planform could have enabled Pteranodon to attain its larger body size. We therefore propose that a shift from a plesiomorphic precocial state towards a derived state of enhanced parental care may have relaxed the constraints of small body sizes and allowed the evolution of derived flight anatomies critical for the flying giants.

Evo Devo of the Vertebrates Integument

All living jawed vertebrates possess teeth or did so ancestrally. Integumental surface also includes the cornea. Conversely, no other anatomical feature differentiates the clades so readily as skin appendages do, multicellular glands in amphibians, hair follicle/gland complexes in mammals, feathers in birds, and the different types of scales. Tooth-like scales are characteristic of chondrichthyans, while mineralized dermal scales are characteristic of bony fishes. Corneous epidermal scales might have appeared twice, in squamates, and on feet in avian lineages, but posteriorly to feathers. In contrast to the other skin appendages, the origin of multicellular glands of amphibians has never been addressed. In the seventies, pioneering dermal-epidermal recombination between chick, mouse and lizard embryos showed that: (1) the clade type of the appendage is determined by the epidermis; (2) their morphogenesis requires two groups of dermal messages, first for primordia formation, second for appendage final architecture; (3) the early messages were conserved during amniotes evolution. Molecular biology studies that have identified the involved pathways, extending those data to teeth and dermal scales, suggest that the different vertebrate skin appendages evolved in parallel from a shared placode/dermal cells unit, present in a common toothed ancestor, c.a. 420 mya.

Metabolic rate, sleep duration, and body temperature in evolution of mammals and birds: the influence of geological time of principal groups divergence

This study contains an analysis of basal metabolic rate (BMR) in 1817 endothermic species. The aim was to establish how metabolic scaling varies between the main groups of endotherms during evolution. The data for all the considered groups were combined and the common exponent in the allometric relationship between the BMR and body weight was established as b = 0.7248. Reduced to the common slope, the relative metabolic rate forms the following series: Neognathae – Passeriformes – 1.00, Neognathae – Non-Passeriformes – 0.75, Palaeognathae – 0.53, Eutheria – 0.57, Marsupialia – 0.44, and Monotremata – 0.26. The main finding is that the metabolic rate in the six main groups of mammals and birds consistently increases as the geological time of the group’s divergence approaches the present. In parallel, the average body temperature in the group rises, the duration of sleep decreases and the duration of activity increases. BMR in a taxon correlates with its evolutionary age: the later a clade diverged, the higher is its metabolic rate and the longer is its activity period; group exponents decrease as group divergence nears present times while with increase metabolic rate during activity, they not only do not decrease but can increase. Sleep duration in mammals was on average 40% longer than in birds while BMR, in contrast, was 40% higher in birds. The evolution of metabolic scaling, body temperature, sleep duration, and activity during the development of endothermic life forms is demonstrated, allowing for a better understanding of the underlying principles of endothermy formation.

Rebuilding ships while at sea-Character individuality, homology, and evolutionary innovation

How novel traits originate in evolution is still one of the most perplexing questions in Evolutionary Biology. Building on a previous account of evolutionary innovation, I here propose that evolutionary novelties are those individualized characters that are not homologous to any characters in the ancestor. To clarify this definition, I here provide a detailed analysis of the concepts of "character individuality" and "homology" first, before addressing their role for our understanding of evolutionary innovation. I will argue (1) that functional as well as structural considerations are important for character individualization; and (2) that compositional (structural) and positional homology need to be clearly distinguished to properly describe the evolutionary transformations of hierarchically structured characters. My account will therefore integrate functional and structural perspectives and put forward a new multi-level view of character identity and transformation.

Establishment of a culture model for the prolonged maintenance of chicken feather follicles structure in vitro

Protocols allowing the in vitro culture of human hair follicles in a serum free-medium up to 9 days were developed 30 years ago. By using similar protocols, we achieved the prolonged maintenance in vitro of juvenile feather follicles (FF) microdissected from young chickens. Histology showed a preservation of the FF up to 7 days as well as feather morphology compatible with growth and/or differentiation. The integrity of the FF wall epithelium was confirmed by transmission electron microscopy at Day 5 and 7 of culture. A slight elongation of the feathers was detected up to 5 days for 75% of the examined feathers. By immunochemistry, we demonstrated the maintenance of expression and localization of two structural proteins: scaffoldin and fibronectin. Gene expression (assessed by qRT-PCR) of NCAM, LCAM, Wnt6, Notch1, and BMP4 was not altered. In contrast, Shh and HBS1 expression collapsed, DKK3 increased, and KRT14 transiently increased upon cultivation. This indicates that cultivation modifies the mRNA expression of a few genes, possibly due to reduced growth or cell differentiation in the feather, notably in the barb ridges. In conclusion, we have developed the first method that allows the culture and maintenance of chicken FF in vitro that preserves the structure and biology of the FF close to its in vivo state, despite transcriptional modifications of a few genes involved in feather development. This new culture model may serve to study feather interactions with pathogens or toxics and constitutes a way to reduce animal experimentation.

Transcriptional Characteristics Showed That miR-144-y/FOXO3 Participates in Embryonic Skin and Feather Follicle Development in Zhedong White Goose

Simple Summary

Feather is one of the most valuable and economical products in goose farming and plays a crucial physiological role in birds. For avian biology and the poultry industry, it is essential to comprehend and regulate how skin and feather follicles develop during embryogenesis. This study showed that several key regulatory genes (FOXO3, CTGF, and PTCH1, among others) and miRNAs (miR-144-y) participated in the developmental process of the skin and feather follicles in Zhedong white goose. Our findings are particularly important because they will serve as a valuable resource for upcoming studies on down feathers in agricultural economic growth regarding complex molecular mechanisms and breeding techniques.

Abstract

Skin and feather follicle development are essential processes for goose embryonic growth. Transcriptome and next-generation sequencing (NGS) network analyses were performed to improve the genome of Zhedong White goose and discover the critical genes, miRNAs, and pathways involved in goose skin and feather follicle morphogenesis. Sequencing output generated 6,002,591,668 to 8,675,720,319 clean reads from fifteen libraries. There were 1234, 3024, 4416, and 5326 different genes showing differential expression in four stages, E10 vs. E13, E10 vs. E18, E10 vs. E23, and E10 vs. E28, respectively. The differentially expressed genes (DEGs) were found to be implicated in multiple biological processes and pathways associated with feather growth and development, such as the Wnt signaling pathway, cell adhesion molecules, ECM–receptor interaction signaling pathways, and cell cycle and DNA replication pathways, according to functional analysis. In total, 8276 DEGs were assembled into twenty gene profiles with diverse expression patterns. The reliability of transcriptome results was verified by real-time quantitative PCR by selecting seven DEGs and five miRNAs. The localization of forkhead box O3 (FOXO3), connective tissue growth factor (CTGF), protein parched homolog1 (PTCH1), and miR-144-y by in situ hybridization showed spatial-temporal expression patterns and that FOXO3 and miR-144-y have an antagonistic targeting relationship. The correlation coefficient of FOXO3 and miR-144-y was -0.948, showing a strong negative correlation. Dual-luciferase reporter assay results demonstrated that miR-144-y could bind to the expected location to suppress the expression of FOXO3, which supports that there is a targeting relationship between them. The detections in this report will provide critical insight into the complex molecular mechanisms and breeding practices underlying the developmental characteristics of skin and feather follicles in Zhedong white geese.

Arctic ice and the ecological rise of the dinosaurs

Abundant lake ice-rafted debris in Late Triassic and earliest Jurassic strata of the Junggar Basin of northwestern China (paleolatitude ~71°N) indicates that freezing winter temperatures typified the forested Arctic, despite a persistence of extremely high levels of atmospheric Pco2 (partial pressure of CO2). Phylogenetic bracket analysis shows that non-avian dinosaurs were primitively insulated, enabling them to access rich deciduous and evergreen Arctic vegetation, even under freezing winter conditions. Transient but intense volcanic winters associated with massive eruptions and lowered light levels led to the end-Triassic mass extinction (201.6 Ma) on land, decimating all medium- to large-sized nondinosaurian, noninsulated continental reptiles. In contrast, insulated dinosaurs were already well adapted to cold temperatures, and not only survived but also underwent a rapid adaptive radiation and ecological expansion in the Jurassic, taking over regions formerly dominated by large noninsulated reptiles.

Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations

Highly diversified astigmatic mites comprise many medically important human household pests such as house dust mites causing ∼1–2% of all allergic diseases globally; however, their evolutionary origin and diverse lifestyles including reversible parasitism have not been illustrated at the genomic level, which hampers allergy prevention and our exploration of these household pests. Using six high-quality assembled and annotated genomes, this study not only refuted the monophyly of mites and ticks, but also thoroughly explored the divergence of Acariformes and the diversification of astigmatic mites. In monophyletic Acariformes, Prostigmata known as notorious plant pests first evolved, and then rapidly evolving Astigmata diverged from soil oribatid mites. Within astigmatic mites, a wide range of gene families rapidly expanded via tandem gene duplications, including ionotropic glutamate receptors, triacylglycerol lipases, serine proteases and UDP glucuronosyltransferases. Gene diversification after tandem duplications provides many genetic resources for adaptation to sensing environmental signals, digestion, and detoxification in rapidly changing household environments. Many gene decay events only occurred in the skin-burrowing parasitic mite Sarcoptes scabiei. Throughout the evolution of Acariformes, massive horizontal gene transfer events occurred in gene families such as UDP glucuronosyltransferases and several important fungal cell wall lytic enzymes, which enable detoxification and digestive functions and provide perfect drug targets for pest control. This comparative study sheds light on the divergent evolution and quick adaptation to human household environments of astigmatic mites and provides insights into the genetic adaptations and even control of human household pests.

Environmental Factors Affecting Feather Taphonomy

The exceptional preservation of feathers in the fossil record has led to a better understanding of both phylogeny and evolution. Here we address factors that may have contributed to the preservation of feathers in ancient organisms using experimental taphonomy. We show that the atmospheres of the Mesozoic, known to be elevated in both CO2 and with temperatures above present levels, may have contributed to the preservation of these soft tissues by facilitating rapid precipitation of hydroxy- or carbonate hydroxyapatite, thus outpacing natural degradative processes. Data also support that that microbial degradation was enhanced in elevated CO2, but mineral deposition was also enhanced, contributing to preservation by stabilizing the organic components of feathers.

Pterosaur melanosomes support signalling functions for early feathers

Remarkably well-preserved soft tissues in Mesozoic fossils have yielded substantial insights into the evolution of feathers¹. New evidence of branched feathers in pterosaurs suggests that feathers originated in the avemetatarsalian ancestor of pterosaurs and dinosaurs in the Early Triassic², but the homology of these pterosaur structures with feathers is controversial^3,4. Reports of pterosaur feathers with homogeneous ovoid melanosome geometries^2,5 suggest that they exhibited limited variation in colour, supporting hypotheses that early feathers functioned primarily in thermoregulation⁶. Here we report the presence of diverse melanosome geometries in the skin and simple and branched feathers of a tapejarid pterosaur from the Early Cretaceous found in Brazil. The melanosomes form distinct populations in different feather types and the skin, a feature previously known only in theropod dinosaurs, including birds. These tissue-specific melanosome geometries in pterosaurs indicate that manipulation of feather colour-and thus functions of feathers in visual communication-has deep evolutionary origins. These features show that genetic regulation of melanosome chemistry and shape^7-9 was active early in feather evolution.

Morphology and distribution of scales, dermal ossifications, and other non-feather integumentary structures in non-avialan theropod dinosaurs

Modern birds are typified by the presence of feathers, complex evolutionary innovations that were already widespread in the group of theropod dinosaurs (Maniraptoriformes) that include crown Aves. Squamous or scaly reptilian-like skin is, however, considered the plesiomorphic condition for theropods and dinosaurs more broadly. Here, we review the morphology and distribution of non-feathered integumentary structures in non-avialan theropods, covering squamous skin and naked skin as well as dermal ossifications. The integumentary record of non-averostran theropods is limited to tracks, which ubiquitously show a covering of tiny reticulate scales on the plantar surface of the pes. This is consistent also with younger averostran body fossils, which confirm an arthral arrangement of the digital pads. Among averostrans, squamous skin is confirmed in Ceratosauria (Carnotaurus), Allosauroidea (Allosaurus, Concavenator, Lourinhanosaurus), Compsognathidae (Juravenator), and Tyrannosauroidea (Santanaraptor, Albertosaurus, Daspletosaurus, Gorgosaurus, Tarbosaurus, Tyrannosaurus), whereas dermal ossifications consisting of sagittate and mosaic osteoderms are restricted to Ceratosaurus. Naked, non-scale bearing skin is found in the contentious tetanuran Sciurumimus, ornithomimosaurians (Ornithomimus) and possibly tyrannosauroids (Santanaraptor), and also on the patagia of scansoriopterygids (Ambopteryx, Yi). Scales are surprisingly conservative among non-avialan theropods compared to some dinosaurian groups (e.g. hadrosaurids); however, the limited preservation of tegument on most specimens hinders further interrogation. Scale patterns vary among and/or within body regions in Carnotaurus, Concavenator and Juravenator, and include polarised, snake-like ventral scales on the tail of the latter two genera. Unusual but more uniformly distributed patterning also occurs in Tyrannosaurus, whereas feature scales are present only in Albertosaurus and Carnotaurus. Few theropods currently show compelling evidence for the co-occurrence of scales and feathers (e.g. Juravenator, Sinornithosaurus), although reticulate scales were probably retained on the mani and pedes of many theropods with a heavy plumage. Feathers and filamentous structures appear to have replaced widespread scaly integuments in maniraptorans. Theropod skin, and that of dinosaurs more broadly, remains a virtually untapped area of study and the appropriation of commonly used techniques in other palaeontological fields to the study of skin holds great promise for future insights into the biology, taphonomy and relationships of these extinct animals.

Infrared antenna-like structures in mammalian fur

Many small animals, including shrews, most rodents and some marsupials, have fur composed of at least four types of hair, all with distinctive and complex anatomy. A ubiquitous and unexplained feature is periodic, internal banding with spacing in the 6-12 µm range that hints at an underlying infrared function. One bristle-like form, called guard hair, has the correct shape and internal periodic patterns to function as an infrared antenna. Optical analysis of guard hair from a wide range of species shows precise tuning to the optimum wavelength for thermal imaging. For heavily predated, nocturnal animals the ability to sense local infrared sources has a clear survival advantage. The tuned antennae, spectral filters and waveguides present in guard hair, all operating at a scale similar to the infrared wavelength, could be a rich source of bio-inspiration in the field of photonics. The tools developed in this work may enable us to understand the other hair types and their evolution.

Estimating the distribution of carotenoid coloration in skin and integumentary structures of birds and extinct dinosaurs

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, nonpasserine species (n = 4022) 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 nonplumage keratin has a 50% 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 nonpasserine neognaths, consistent with previous studies. Although our data do not support a strict sequence of tissue expression in nonpasserine birds, we find support that expression of carotenoid-consistent color in nonplumage 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 nonavian 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.

Making region-specific integumentary organs in birds: evolution and modifications

Birds are the most diversified terrestrial vertebrates due to highly diverse integumentary organs that enable robust adaptability to various eco-spaces. Here we show that this complexity is built upon multi-level regional specifications. Across-the-body (macro-) specification includes the evolution of beaks and feathers as new integumentary organs that are formed with regional specificity. Within-an-organ (micro-) specification involves further modifications of organ shapes. We review recent progress in elucidating the molecular mechanisms underlying feather diversification as an example. (1) β-Keratin gene clusters are regulated by typical enhancers or high order chromatin looping to achieve macro- and micro-level regional specification, respectively. (2) Multi-level symmetry-breaking of feather branches confers new functional forms. (3) Complex color patterns are produced by combinations of macro-patterning and micro-patterning processes. The integration of these findings provides new insights toward the principle of making a robustly adaptive bio-interface.

Cretaceous amniote integuments recorded through a taphonomic process unique to resins

Fossil records of vertebrate integuments are relatively common in both rocks, as compressions, and amber, as inclusions. The integument remains, mainly the Mesozoic ones, are of great interest due to the panoply of palaeobiological information they can provide. We describe two Spanish Cretaceous amber pieces that are of taphonomic importance, one bearing avian dinosaur feather remains and the other, mammalian hair. The preserved feather remains originated from an avian dinosaur resting in contact with a stalactite-shaped resin emission for the time it took for the fresh resin to harden. The second piece shows three hair strands recorded on a surface of desiccation, with the characteristic scale pattern exceptionally well preserved and the strands aligned together, which can be considered the record of a tuft. These assemblages were recorded through a rare biostratinomic process we call "pull off vestiture" that is different from the typical resin entrapment and embedding of organisms and biological remains, and unique to resins. The peculiarity of this process is supported by actualistic observations using sticky traps in Madagascar. Lastly, we reinterpret some exceptional records from the literature in the light of that process, thus bringing new insight to the taphonomic and palaeoecological understanding of the circumstances of their origins.

Down feather morphology reflects adaptation to habitat and thermal conditions across the avian phylogeny

Down feathers are the first feather types that appear in both the phylogenetic and the ontogenetic history of birds. Although it is widely acknowledged that the primary function of downy elements is insulation, little is known about the interspecific variability in the structural morphology of these feathers, and the environmental factors that have influenced their evolution. Here, we collected samples of down and afterfeathers from 156 bird species and measured key morphological characters that define the insulatory properties of the downy layer. We then tested if habitat and climatic conditions could explain the observed between-species variation in down feather structure. We show that habitat has a very strong and clearly defined effect on down feather morphology. Feather size, barbule length and nodus density all decreased from terrestrial toward aquatic birds, with riparian species exhibiting intermediate characters. Wintering climate, expressed as windchill (a combined measure of the ambient temperature and wind speed) had limited effects on down morphology, colder climate only being associated with higher nodus density in dorsal down feathers. Overall, an aquatic lifestyle selects for a denser plumulaceous layer, while the effect of harsh wintering conditions on downy structures appear limited. These results provide key evidence of adaptations to habitat at the level of the downy layer, both on the scale of macro- and micro-elements of the plumage. Moreover, they reveal characters of convergent evolution in the avian plumage and mammalian fur, that match the varying needs of insulation in terrestrial and aquatic modes of life.

Volant Fossil Vertebrates: Potential for Bioinspired Flight Technology

Animal flight is ecologically important and has a long evolutionary history. It has evolved independently in many distantly related clades of animals. Powered flight has evolved only three times in vertebrates, making it evolutionarily rare. Major recent fossil discoveries have provided key data on fossil flying vertebrates and critical insights regarding the evolution and different arrangements of animal flight surfaces. Combined with new methodologies, these discoveries have paved the way for potentially expanding biomimetic and biologically inspired designs to incorporate lessons from fossil taxa. Here, we review the latest knowledge and literature regarding flight performance in fossil vertebrates. We then synthesise key elements to provide an overview of those cases where fossil flyers might provide new insights for applied sciences.

The Making of a Flight Feather: Bio-architectural Principles and Adaptation

The evolution of flight in feathered dinosaurs and early birds over millions of years required flight feathers whose architecture features hierarchical branches. While barb-based feather forms were investigated, feather shafts and vanes are understudied. Here, we take a multi-disciplinary approach to study their molecular control and bio-architectural organizations. In rachidial ridges, epidermal progenitors generate cortex and medullary keratinocytes, guided by Bmp and transforming growth factor β (TGF-β) signaling that convert rachides into adaptable bilayer composite beams. In barb ridges, epidermal progenitors generate cylindrical, plate-, or hooklet-shaped barbule cells that form fluffy branches or pennaceous vanes, mediated by asymmetric cell junction and keratin expression. Transcriptome analyses and functional studies show anterior-posterior Wnt2b signaling within the dermal papilla controls barbule cell fates with spatiotemporal collinearity. Quantitative bio-physical analyses of feathers from birds with different flight characteristics and feathers in Burmese amber reveal how multi-dimensional functionality can be achieved and may inspire future composite material designs. VIDEO ABSTRACT.

Evaluation of the effectiveness of cryptic coloration of the Carolina anole’s skin

Cryptic coloration of animals’ integument is one of the effective adaptations that allow them to lead an active lifestyle while being protected from natural enemies due to visual disguise. This is achieved by the similarity of body color of a particular individual to the background of various substrates in its environment. The morphological and functional basis of cryptic coloration in vertebrates, including reptiles, is ensured by the skin pigmentation. Using bioinformatic methods, we calculated the skin camouflage index of the Carolina anole (Anolis carolinensis Voigt, 1832) in various conditions of its habitat. The skin camouflage index (Ic) is the ratio of the sum of the average values of rgb coordinates of the skin color to the sum of the average values of rgb coordinates of the color of the external substrate. Ic satisfies the effective level of adaptation to habitat conditions if it falls within the range of 0.80–1.20. It has been shown that rgb-values of the dominant color of the dorsal skin of green anoles slightly differ from the similar parameters characteristic of the deciduous habitat, which is reflected by Ic of its skin (0.94). In the brown anoles on a background of woody substrate, the Ic value of its skin (0.88) is also optimal, since it exceeds the lower limit (0.80), which indicates close values of the sums of the rgb coordinates of the skin color and the color of the external background. In the mixed green-brown anoles, the deciduous habitat is preferable to the woody one. In the first case, Ic (1.11) is in the optimum zone, and in the second case, Ic (0.70) goes beyond the lower limit of the optimum, which indicates a greater vulnerability of the animal to external threats. We have confirmed the relativity of visual hiding of the skin that is effective only in the habitat conditions in which the camouflage abilities of the skin manifest as fully as possible.