Ornamental comb colour predicts T-cell-mediated immunity in male red grouse Lagopus lagopus scoticus

Translating conventional wisdom on chicken comb color into automated monitoring of disease-infected chicken using chromaticity-based machine learning models

Bacteria- or virus-infected chicken is conventionally detected by manual observation and confirmed by a laboratory test, which may lead to late detection, significant economic loss, and threaten human health. This paper reports on the development of an innovative technique to detect bacteria- or virus-infected chickens based on the optical chromaticity of the chicken comb. The chromaticity of the infected and healthy chicken comb was extracted and analyzed with International Commission on Illumination (CIE) XYZ color space. Logistic Regression, Support Vector Machines (SVMs), K-Nearest Neighbors (KNN), and Decision Trees have been developed to detect infected chickens using the chromaticity data. Based on the X and Z chromaticity data from the chromaticity analysis, the color of the infected chicken's comb converged from red to green and yellow to blue. The development of the algorithms shows that Logistic Regression, SVM with Linear and Polynomial kernels performed the best with 95% accuracy, followed by SVM-RBF kernel, and KNN with 93% accuracy, Decision Tree with 90% accuracy, and lastly, SVM-Sigmoidal kernel with 83% accuracy. The iteration of the probability threshold parameter for Logistic Regression models has shown that the model can detect all infected chickens with 100% sensitivity and 95% accuracy at the probability threshold of 0.54. These works have shown that, despite using only the optical chromaticity of the chicken comb as the input data, the developed models (95% accuracy) have performed exceptionally well, compared to other reported results (99.469% accuracy) which utilize more sophisticated input data such as morphological and mobility features. This work has demonstrated a new feature for bacteria- or virus-infected chicken detection and contributes to the development of modern technology in agriculture applications.

Identifying Signatures of Selection Related to Comb Development

The aim of this study was to identify genes involved in comb development to provide insights into the molecular mechanism of chickens' comb formation. Fixation index (FST) and average number of base differences (π) of males with large and small combs were calculated based on whole-genome resequencing data. Chromosome regions with larger FST values and smaller π were considered candidate selection regions. Through further annotation of gene functions and pathways, we sought to screen possible selected genes associated with comb development. By screening whole genome resequencing data, FST and π were calculated using a 40 Kb sliding window strategy and eight regions were identified. Quantitative trait loci (QTL; FOX1 gene) related to comb length were found on chromosome 1. QTL (GLP1R, BTBD9, MIR6633, and MDGA1 genes) related to comb weight were found on chromosome 3. QTL (ALDH1A1, TMC1, and ANXA1 genes) associated with comb area were found on the Z chromosome. Nineteen genes, Wnt signaling pathway and neuroactive ligand-receptor interaction signaling pathway directly or indirectly related to comb growth and development were found through functional annotation and GO analysis. Among the selected genes LYN, GLP1R, FOX1, TBK1, STRAP, ST6GALNAC, and Wnt signaling pathways were related to immunity. MDGA1, BTBD9, MTSS1, SrGAPs, and neuroactive ligand receptor interaction signaling pathways related to neural function were screened. ALDH1A1, ANXAl, THBS, HIF-1α, and ACTN1 genes were related to heat dissipation. Among the selected genes FOX1, MDGAl, and ANXAl associated with immunity, neurological function, and heat dissipation function coincided with genes affecting the length, weight, and area of the comb. Comprehensive analysis suggested that comb development was due to multiple genes and signaling pathways.

Immune challenges and visual signalling in tree frogs

In animals, mate-choice is often based on sexual signals that carry information and help the receiver make the best choice to improve the receiver's fitness. Orange visual sexual signals have been hypothesised to carry immune information because they are often due to carotenoid pigments which are also involved in immunity response. Although many studies have focused on the direct relationships between coloration and immunocompetence, few studies have simultaneously studied immunocompetent response and coloration variation after an immune challenge. We tested this hypothesis on starved and ad libitum-fed males of the European tree frog Hyla arborea. Our results show that male coloration is not a reliable indicator of its immune response capacity in this species. However, after an immune challenge induced by a PHA (Phaseolus vulgaris phytohaemagglutinin) injection, starved males presented a significant coloration loss and this alteration was related to the immune response intensity. Taken together, these results suggest that the brighter (lighter) coloration may be used as a cue by female to exclude males with a recent immune challenge, due to diseases or parasites for example.

Imperfect past and present progressive: beak color reflects early-life and adult exposure to antigen

Secondary sexual traits may convey information about individual condition. We assessed the capacity for immune challenge with lipopolysaccharide (LPS) or keyhole limpet hemocyanin (KLH) during the prenatal and early postnatal stages to impact beak color development and expression in captive zebra finches. In addition, we tested whether adult immune challenge impacted beak color, and if early-life experience was influential. Immune challenge with KLH early in life slowed development of red beak coloration, and males challenged with KLH as nestlings had reduced red coloration as adults. Following adult KLH challenge, males exhibited a decline in beak redness. Birds challenged with KLH during development produced more anti-KLH antibodies after adult challenge. There was a significant interaction between young treatment and anti-KLH antibody production; for males not challenged with KLH early in life, individuals that mounted a weaker antibody response lost more red coloration after challenge than males mounting a stronger antibody response. Based on models of avian vision, these differences in beak coloration should be detectable to the finches. In contrast to previous studies, we found no effect of early-life or adult challenge with LPS on any aspects of beak coloration. These results provide evidence that beak color reflects developmental and current conditions, and that the signal is linked to critical physiological processes.

Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica)

Epigenetic modification of cytosine methylation states can be elicited by environmental stresses and may be a key process affecting phenotypic plasticity and adaptation. Parasites are potent stressors with profound physiological and ecological effects on their host, but there is little understanding in how parasites may influence host methylation states. Here, we estimate epigenetic diversity and differentiation among 21 populations of red grouse (Lagopus lagopus scotica) in north-east Scotland and test for association of gastrointestinal parasite load (caecal nematode Trichostrongylus tenuis) with hepatic genome-wide and locus-specific methylation states. Following methylation-sensitive AFLP (MSAP), 129 bands, representing 73 methylation-susceptible and 56 nonmethylated epiloci, were scored across 234 individuals. The populations differed significantly in genome-wide methylation levels and were also significantly epigenetically (F_SC = 0.0227; P < 0.001) and genetically (F_SC = 0.0058; P < 0.001) differentiated. Parasite load was not associated with either genome-wide methylation levels or epigenetic differentiation. Instead, we found eight disproportionately differentiated epilocus-specific methylation states (F_ST outliers) using bayescan software and significant positive and negative association of 35 methylation states with parasite load from bespoke generalized estimating equations (GEE), simple logistic regression (sam) and Bayesian environmental analysis (bayenv2). Following Sanger sequencing, genome mapping and geneontology (go) annotation, some of these epiloci were linked to genes involved in regulation of cell cycle, signalling, metabolism, immune system and notably rRNA methylation, histone acetylation and small RNAs. These findings demonstrate an epigenetic signature of parasite load in populations of a wild bird and suggest intriguing physiological effects of parasite-associated cytosine methylation.

Cellular respiration: the nexus of stress, condition, and ornamentation

A fundamental hypothesis for the evolution and maintenance of ornamental traits is that ornaments convey information to choosing females about the quality of prospective mates. A diverse array of ornaments (e.g., colors, morphological features, and behaviors) has been associated with a wide range of measures of individual quality, but decades of study of such indicator traits have failed to produce general mechanisms of honest signaling. Here, I propose that efficiency of cellular respiration, as a product of mitochondrial function, underlies the associations between ornamentation and performance for a broad range of traits across taxa. A large biomedical literature documents the fundamental biochemical links between oxidative phosphorylation (OXPHOS) and the production of reactive oxygen species (ROS), the process of metabolism, the function of the immune system, the synthesis of proteins, and the development and function of the nervous system. The production of virtually all ornaments whose expressions have been demonstrated to be condition-dependent is directly affected by the efficiency of cellular respiration, suggesting that the signaling of respiratory efficiency may be the primary function of such traits. Furthermore, the production of ornaments links to stress-response systems, including particularly the neuroendocrine system, through mitochondrial function, thereby makes ornamental traits effective signals of the capacity to withstand environmental perturbations. The identification of a unifying mechanism of honest signaling holds the potential to connect many heretofore-disparate fields of study related to stress and ornamentation, including neuroendocrinology, respiratory physiology, metabolic physiology, and immunology.

Carotenoid-based coloration, condition, and immune responsiveness in the nestlings of a sexually dimorphic bird of prey

In many birds, nestlings exhibit brightly colored traits that are pigmented by carotenoids. Carotenoids are diet limited and also serve important health-related physiological functions. The proximate mechanisms behind the expression of these carotenoid-pigmented traits are still poorly known, especially in nestlings with sexual size dimorphism. In these nestlings, intrabrood competition levels and growth strategies likely differ between sexes, and this may in turn influence carotenoid allocation rules. We used dietary carotenoid supplementation to test whether wild marsh harrier (Circus aeruginosus) nestlings were carotenoid limited and whether carotenoid allocation strategies varied between sexes, which differ in their size and growth strategies. When supplemented, nestlings used the supplemental carotenoids to increase their coloration independently of their sex. We showed that the condition dependence of the carotenoid level and the response to an immune challenge (phytohemagglutinin test) differed between sexes, possibly because sexual size dimorphism influences growth strategies and/or intrabrood competition levels and access to different types of food. In this species, which often feeds on mammals, a trade-off likely exists between food quantity (energy) and quality (carotenoid content). Finally, carotenoid-based coloration expressed in marsh harrier nestlings appeared to be indicative of immune responsiveness rather than condition, therefore potentially advertising to parents nestling quality or value rather than nutritional need.

Differential effects of testosterone, dihydrotestosterone and estradiol on carotenoid deposition in an avian sexually selected signal

Recent studies have demonstrated that carotenoid-based traits are under the control of testosterone (T) by up-regulation of carotenoid carriers (lipoproteins) and/or tissue-specific uptake of carotenoids. T can be converted to dihydrotestosterone (DHT) and estradiol (E2), and variation in conversion rate may partly explain some contradictory findings in the literature. Moreover, most studies on the effect of T on sexual signals have focused on the male sex only, while in many species females show the same signal, albeit to a lesser extent. We studied the effects of T, DHT, and E2 treatment in male and female diamond doves Geopelia cuneata in which both sexes have an enlarged red eye ring, which is more pronounced in males. We first showed that this periorbital ring contains very high concentration of carotenoids, of which most are lutein esters. Both T and DHT were effective in enhancing hue, UV-chroma and size in both sexes, while E2 was ineffective. However, E2 dramatically increased the concentration of circulating lipoproteins. We conclude that in both sexes both color and size of the secondary sexual trait are androgen dependent. The action of androgens is independent of lipoproteins regulation. Potential mechanisms and their consequences for trade-off are discussed.

Ecological immunology of bird-ectoparasite systems

Ecological immunology is a rapidly expanding field of research that attempts to explain variation in immune function across individuals, populations and species. Birds and ectoparasitic arthropods have frequently been used in attempts to measure the cost of immune function in relation to adult condition, nestling growth and other life history challenges. Unfortunately, most studies in ecological immunology have relied on assays of general immunocompetence that are not connected to actual parasites. A summary of potential interactions between the avian immune system and ectoparasites is provided and methods that can be used to test ecological questions in the context of naturally occurring host-parasite interactions are proposed.

Cell-mediated immune activation rapidly decreases plasma carotenoids but does not affect oxidative stress in red-legged partridges (Alectoris rufa)

In animals yellow-orange-red sexual traits pigmented by carotenoids have been suggested to act as signals of current health. Because carotenoids have important physiological functions, individuals might trade-off allocating these pigments to self-maintenance versus coloration. Carotenoids may act as scavengers of free radicals that are released during an immune response. Here, we experimentally assessed whether a local cell-mediated immune response affects circulating carotenoids, antioxidant status, oxidative damage and the expression of a carotenoid-based trait. Male red-legged partridges (Alectoris rufa) were subcutaneously injected with phytohaemagglutinin (PHA) or with phosphate buffer solution (controls). The effect of the treatment on circulating carotenoids, total plasma antioxidant status (TAS), lipid oxidative damage in erythrocytes (TBARS) and ornamentation was assessed. Immune challenge induced a 13% decrease in circulating carotenoids within 24 h. However, this treatment did not affect TAS, TBARS or coloration. Coloration, circulating carotenoids and cell-mediated immune response were positively correlated, but these were not related to TAS or TBARS. Carotenoids were only weakly related to TAS after controlling for the effect of uric acid levels. These results suggest that carotenoid-based ornaments may honestly indicate immunocompetence but probably not antioxidant capacity in this species, and that carotenoids might be relatively weak antioxidants in the plasma. Furthermore, even a relatively harmless and locally elicited immune challenge had important effects on circulating carotenoids, but this effect did not appear to be associated with oxidative stress. Alternative mechanisms linking carotenoids to immunity (not necessarily relying on the use of these pigments as antioxidants) should be considered in future studies on birds.