Genetics of colouration in birds

Skin colour: A window into human phenotypic evolution and environmental adaptation

As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.

Transcriptome analysis of sexual dimorphism in dorsal down coloration in goslings

BACKGROUND

In day-old Hungarian white goose goslings, there is a noticeable difference in dorsal down coloration between males and females, with females having darker dorsal plumage and males having lighter plumage. The ability to autosex day-old goslings based on their dorsal down coloration is important for managing them efficiently and planning their nutrition in the poultry industry. The aim of this study was to determine the biological and genetic factors underlying this difference in dorsal down colorationthrough histological analysis, biochemical assays, transcriptomic profiling, and q‒PCR analysis.

RESULTS

Tissue analysis and biochemical assays revealed that compared with males, 17-day-old embryos and day-old goslings of female geese exhibited a greater density of melanin-containing feather follicles and a greater melanin concentration in these follicles during development. Both female and male goslings had lower melanin concentrations in their dorsal skin compared to 17-day-old embryos. Transcriptome analysis identified a set of differentially expressed genes (DEGs) (MC1R, TYR, TYRP1, DCT and MITF) associated with melanogenesis pathways that were downregulated or silenced specifically in the dorsal skin of day-old goslings compared to 17-day-old embryos, affecting melanin synthesis in feather follicles. Additionally, two key genes (MC1R and MITF) associated with feather coloration showed differences between males and females, with females having higher expression levels correlated with increased melanin synthesis and darker plumage.

CONCLUSION

The expression of multiple melanogenesis genes determines melanin synthesis in goose feather follicles. The dorsal down coloration of day-old Hungarian white goose goslings shows sexual dimorphism, likely due to differences in the expression of the MC1R and MITF genes between males and females. These results could help us better understand why male and female goslings exhibit different plumage patterns.

Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese

The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research.

Winter-ground microhabitat use by differently coloured phenotypes affects return rate in a long-distance migratory bird

Migratory bird populations are declining globally at alarming rates. Non-breeding site conditions affect breeding populations, but generalising non-breeding habitat conditions over large spatial regions cannot address potential fine-scale differences across landscapes or local populations. Plumage characteristics can mediate the effects of environmental conditions on individual fitness. However, whether different phenotypes use distinctive non-breeding sites, and whether they respond to non-breeding site conditions differently remains largely unknown. Stable isotopes (δ13C, δ15N, δ2H) of inert tissues are useful to infer habitat characteristics and geographic origins where those tissues were grown. We collected winter-grown feathers from pied flycatchers (Ficedula hypoleuca) on their breeding grounds over several years from males whose dorsal plumage colouration ranged continuously from brown to black and assessed their stable isotope values as proxies of local habitat conditions. Based on feather δ2H profiles we found that browner males spent their non-breeding season in drier habitats than black males. Assignment to origin analysis shows potential regional non-breeding ground separation between differently coloured males. High within-individual repeatability of both δ13C and δ15N indicate the pied flycatcher males return yearly to similar areas. Blacker males were more likely to return to the breeding grounds after dry years compared with brown males. The opposite was found in wet years. Our study demonstrates that different phenotypes are exposed to different non-breeding site conditions which can differentially affect individual survivorship. This has important ramifications for population dynamics under predicted climate change scenarios where especially brown phenotype pied flycatcher males may be under a risk of decreasing.

Comparison of gamithromycin residue depletion in yellow-feather and white-feather broilers after one single subcutaneous injection

This study aimed to compare the residue depletion of gamithromycin in yellow-feather and white-feather broilers, using Sanhuang and Arbor Acres chickens as typical examples, respectively. Each breed (54 chickens) received a single subcutaneous dose of gamithromycin at 7.5 mg/kg bodyweight (BW). Tissues, including muscle, skin + fat, liver, kidney, and injection site, were collected at 6 h, 3, 5, 7, 10, 14, 21, 28, and 35 d postdrug administration. Gamithromycin concentrations in these tissues were determined using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The kinetics of gamithromycin were analyzed in different tissues using a noncompartmental method in the Phoenix software. Differences were observed in gamithromycin concentrations and kinetic characteristics in both breeds of chickens, with higher residue concentrations and longer residue times found in yellow-feathered broilers. In Sanhuang broilers, the elimination rates of gamithromycin followed this order: injection site > muscle > liver > kidney > skin + fat. The corresponding elimination half-lives (t1/2λzs) in these samples were 1.22, 1.30, 1.71, 2.04, and 2.52 d, respectively. In contrast, in Arbor Acres broilers, a different order was noted: muscle > injection site > kidney > liver > skin + fat, with corresponding t1/2λzs of 1, 1.23, 1.88, 1.93, and 2.21 d, respectively. These differences may be related to variations in pigments in various tissues of chickens of the 2 breeds. However, further investigations are warranted to discern the underlying reasons.

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.

Convergent evolution of parrot plumage coloration

Parrots have remarkable plumage coloration that result in part from a unique ability to produce pigments called psittacofulvins that yield yellow to red feather colors. Little is known about the evolution of psittacofulvin-based pigmentation. Widespread color mutations of captive-bred parrots provide perfect opportunities to study the genetic basis of this trait. An earlier study on blue budgerigars, which do not possess psittacofulvins, reveals the involvement of an uncharacterized polyketide synthase (MuPKS) in yellow psittacofulvin synthesis. The blue phenotype had repeatedly appeared in different parrot species, similar to independent experimental replications allowing the study of convergent evolution and molecular mechanism of psittacofulvin-based pigmentation. Here, we investigated the genetic basis of the blue phenotypes in two species of Agapornis parrots, Fischer's lovebird (A. fischeri) and Yellow-collared lovebird (A. personatus). Using whole-genome data, we identified a single genomic region with size <2 Mb to be strongly associated with the color difference between blue and wild-type (WT) birds in both species. Surprisingly, we discovered that the mutation associated with the blue Agapornis phenotype was identical to the previously described substitution causing the functional change of MuPKS in budgerigars. Together with the evidence of shared blue-associated haplotypes and signatures of a selective sweep in this genomic region in both species, we demonstrated both de novo mutation and interspecific introgression play a role in the evolution of this trait in different Agapornis species. The convergent substitution in the same gene in both lovebirds and budgerigars also indicates a strong evolutionary constraint on psittacofulvin-based coloration.

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.

Two High-Quality Cygnus Genome Assemblies Reveal Genomic Variations Associated with Plumage Color

As an exemplary model for examining molecular mechanisms responsible for extreme phenotypic variations, plumage color has garnered significant interest. The Cygnus genus features two species, Cygnus olor and Cygnus atratus, that exhibit striking disparities in plumage color. However, the molecular foundation for this differentiation has remained elusive. Herein, we present two high-quality genomes for C. olor and C. atratus, procured using the Illumina and Nanopore technologies. The assembled genome of C. olor was 1.12 Gb in size with a contig N50 of 26.82 Mb, while its counterpart was 1.13 Gb in size with a contig N50 of 21.91 Mb. A comparative analysis unveiled three genes (TYR, SLC45A2, and SLC7A11) with structural variants in the melanogenic pathway. Notably, we also identified a novel gene, PWWP domain containing 2A (PWWP2A), that is related to plumage color, for the first time. Using targeted gene modification analysis, we demonstrated the potential genetic effect of the PWWP2A variant on pigment gene expression and melanin production. Finally, our findings offer insight into the intricate pattern of pigmentation and the role of polygenes in birds. Furthermore, these two high-quality genome references provide a comprehensive resource and perspective for comparative functional and genetic studies of evolution within the Cygnus genus.

Pigment Identification and Gene Expression Analysis during Erythrophore Development in Spotted Scat (Scatophagus argus) Larvae

Red coloration is considered an economically important trait in some fish species, including spotted scat, a marine aquaculture fish. Erythrophores are gradually covered by melanophores from the embryonic stage. Despite studies of black spot formation and melanophore coloration in the species, little is known about erythrophore development, which is responsible for red coloration. 1-phenyl 2-thiourea (PTU) is a tyrosinase inhibitor commonly used to inhibit melanogenesis and contribute to the visualization of embryonic development. In this study, spotted scat embryos were treated with 0.003% PTU from 0 to 72 h post fertilization (hpf) to inhibit melanin. Erythrophores were clearly observed during the embryonic stage from 14 to 72 hpf, showing an initial increase (14 to 36 hpf), followed by a gradual decrease (36 to 72 hpf). The number and size of erythrophores at 36 hpf were larger than those at 24 and 72 hpf. At 36 hpf, LC-MS and absorbance spectrophotometry revealed that the carotenoid content was eight times higher than the pteridine content, and β-carotene and lutein were the main pigments related to red coloration in spotted scat larvae. Compared with their expression in the normal hatching group, rlbp1b, rbp1.1, and rpe65a related to retinol metabolism and soat2 and apoa1 related to steroid hormone biosynthesis and steroid biosynthesis were significantly up-regulated in the PTU group, and rh2 associated with phototransduction was significantly down-regulated. By qRT-PCR, the expression levels of genes involved in carotenoid metabolism (scarb1, plin6, plin2, apoda, bco1, and rep65a), pteridine synthesis (gch2), and chromatophore differentiation (slc2a15b and csf1ra) were significantly higher at 36 hpf than at 24 hpf and 72 hpf, except for bco1. These gene expression profiles were consistent with the developmental changes of erythrophores. These findings provide insights into pigment cell differentiation and gene function in the regulation of red coloration and contribute to selective breeding programs for ornamental aquatic animals.

Effects of SLC45A2 and GPNMB on Melanin Deposition Based on Transcriptome Sequencing in Chicken Feather Follicles

As an essential genetic and economic trait, chicken feather color has long been an important research topic. To further understand the mechanism of melanin deposition associated with coloration in chicken feathers, we selected feather follicle tissues from the neck and wings of chickens with differently colored feathers (yellow, sub-Columbian, and silver) for transcriptome analysis. We focused on genes that were expressed in both the wings and neck and were expressed with the same trends in breeds with two different plumage colors, specifically, SLC45A2, GPNMB, MLPH, TYR, KIT, WNT11, and FZD1. GO and KEGG enrichment analyses showed the DEGs were enriched in melanin-related pathways, such as tyrosine metabolic pathway and melanogenesis, and PPI analysis highlighted the genes SLC45A2 and GPNMB as associated with melanin deposition. Verification experiments in chicken melanocytes demonstrated that these two genes promote melanocyte melanin deposition. These data enrich our knowledge of the mechanisms that regulate chicken feather color.

The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken - a review

Chicken is a major source of protein for the increasing human population and is useful for research purposes. There are almost 1,600 distinct regional breeds of chicken across the globe, among which a large body of genetic and phenotypic variations has been accumulated due to extensive natural and artificial selection. Moreover, natural selection is a crucial force for animal domestication. Several approaches have been adopted to detect selection signatures in different breeds of chicken using whole genome sequencing (WGS) data including integrated haplotype score (iHS), cross-populated extend haplotype homozygosity test (XP-EHH), fixation index (F_ST), cross-population composite likelihood ratio (XP-CLR), nucleotide diversity (Pi), and others. In addition, gene enrichment analyses are utilized to determine KEGG pathways and gene ontology (GO) terms related to traits of interest in chicken. Herein, we review different studies that have adopted diverse approaches to detect selection signatures in different breeds of chicken. This review systematically summarizes different findings on selection signatures and related candidate genes in chickens. Future studies could combine different selection signatures approaches to strengthen the quality of the results thereby providing more affirmative inference. This would further aid in deciphering the importance of selection in chicken conservation for the increasing human population.

Color polymorphism in the Cuban endemic livebearing fish Limia vittata (Teloestei, Poeciliidae): Potential roles of sexual and natural selection

Color polymorphism can be maintained in natural populations by natural selection or sexual selection. In this study, we use two different approaches to test which of these evolutionary mechanisms may explain the presence of color polymorphism in the Cuban Limia (Limia vittata), an endemic livebearing fish from Cuba. First, we investigate the role of sexual selection using traditional binary choice tests looking at both female and male preferences relative to varying degrees of black spotting in stimulus mates. Second, we assess the role of natural selection by analyzing the frequency and geographic distribution of black-spotted and nonspotted morphs of L. vittata in natural populations from Cuba. The frequency of black-spotted morphs is significantly higher in brackish and saltwater environments compared with freshwater habitats, which could be related to higher predation pressure in coastal ecosystems compared with purely freshwater environments. Our results suggest that habitat variation is the most important factor in maintaining color polymorphism in L. vittata. Salinity levels could be indirectly responsible for maintaining different color morphs in this species, likely due to the regulatory effect of saline gradients on predation regimes.

Association between Synonymous SNPs of SOX10 and Plumage Color and Reproductive Traits of Ducks

Mutations in the SOX10 gene affect the plumage color of chickens and pigeons. The mutation also causes abnormal pigmentation of the skin and hair color, as well as postnatal growth retardation and reproduction problems in humans and mice. In this study, we investigated the association between the SOX10 gene and plumage color and reproductive traits of ducks using SNPs. We found six novel SNPs from 11 identified SNP sites using direct sequencing for PCR products from three different mixed DNA pools. We found two coding SNPs to be associated with the plumage color of ducks (ZJU1.0 Chr1. g.54065419C>T and g.54070844C>T), and found three coding SNPs associated with the reproductive traits of ducks (g.54065419C>T, g.54070844C>T, and g.54070904C>T), which were age at sexual maturity, body weight at sexual maturity, and the Haugh unit for egg quality traits and egg production in different productive periods. These results also indicated that the T alleles of the three SNPs of the coding region of SOX10 contribute to lower reproductive traits.

Candidate pigmentation genes related to feather color variation in an indigenous chicken breed revealed by whole genome data

Chicken plumage color is an inheritable phenotype that was naturally and artificially selected for during domestication. The Baicheng You chicken is an indigenous Chinese chicken breed presenting three main feather colors, lavender, black, and yellow plumages. To explore the genetic mechanisms underlying the pigmentation in Baicheng You chickens, we re-sequenced the whole genome of Baicheng You chicken with the three plumage colors. By analyzing the divergent regions of the genome among the chickens with different feather colors, we identified some candidate genomic regions associated with the feather colors in Baicheng You chickens. We found that EGR1, MLPH, RAB17, SOX5, and GRM5 genes were the potential genes for black, lavender, and yellow feathers. MLPH, GRM5, and SOX5 genes have been found to be related to plumage colors in birds. Our results showed that EGR1 is a most plausible candidate gene for black plumage, RAB17, MLPH, and SOX5 for lavender plumage, and GRM5 for yellow plumage in Baicheng You chicken.

Canalised and plastic components of melanin-based colouration: a diet-manipulation experiment in house sparrows

Whether melanin-based plumage colouration accurately reflects a bird's quality is still controversial. To better understand potential mechanisms behind the observed variation in plumage colouration, we shifted our attention from a high-level expression of colour to low-level physiological phenomena by targeting the microstructure and pigment content of the feather. In a well-studied model system, the house sparrow (Passer domesticus), we combined an experimental manipulation of birds' physiological condition and availability of resources that are key to the production of the studied colouration (phenylalanine and tyrosine (PT). We found that feathers from sparrows fed with the control diet had noticeably lower values of brightness, suggesting a higher quality of the ornamental "blackness" in comparison to those sampled from birds fed with a PT-reduced diet. Electron paramagnetic resonance (EPR) spectroscopy detected higher melanin concentrations in samples from the control than the PT-reduced group. Our multi-level analysis excluded mechanisms such as barbule density and melanosomes' distribution, clearly pointing to the finest-level proxy of colour: the concentration of melanin in melanosomes themselves. Despite melanins being manufactured by birds endogenously, the efficiency of melanogenesis can be noticeably limited by diet. As a result, the birds' plumage colouration is affected, which may entail consequences in social signalling.

Phenotypic and genetic diversity of the Anjian chicken in China

The Anjian chicken is a local breed in Hotan, Xinjiang, China. Herein, we studied the morphological characteristics and genetic diversity of the Anjian chicken population. The findings of this study could inform the genetic improvement strategy of this breed. Phenotypic characteristics investigated included the diversity in the general appearance, feather color, and crowing length of the Anjian cocks. The population structure of the Anjian chicken and its relationship with other chicken breeds were also assessed based on mitochondrial DNA (mtDNA) D-loop sequence analysis. Phenotypically, the feather color of the Anjian chicken varied considerably. The sequence diversity analysis revealed the following: nucleotide diversity (Pi) was 0.00618, haplotype diversity (Hd) was 0.776, the average number of nucleotide differences (k) was 7.631, and Tajima’s (D) was −0.00407, indicating that Anjian chicken is moderately genetically diverse. Further phylogenetic analysis revealed that the Anjian chicken breed has 10 haplotypes clustered into two branches. Genetic distance and median network analysis showed that the mtDNA D-loop sequence of the Anjian chicken was distributed in many different clusters of the tree. These data demonstrate that even though the Anjian chicken mainly originated from red jungle fowl, it has multiple maternal origins. In conclusion, the Anjian chicken is highly genetically diverse.

Association of MC1R variation and plumage color diversity of Nigerian domestic pigeon (Columba livia domestica)

OBJECTIVES

Domestic pigeons (Columba livia domestica) have diverse plumage pigmentations. Melanocortin 1 receptor (MC1R) gene variation has been correlated with color traits. The association between MC1R and plumage coloration in African domestic pigeons is yet to be investigated.

MATERIALS AND METHODS

Herein, we report the relationships between single nucleotide polymorphisms (SNPs) in MC1R and plumage of 35 domestic pigeons from Nigeria with 4 different plumage phenotypes plus 37 published MC1R sequences from France (n = 14) and Russia (n = 11).

RESULTS

We obtained 14 SNP sites among 72 individuals. Missense mutations C206T (Ser69Leu) and G253A (Val85Met) were observed in 16 and 8 Nigerian pigeons, respectively. The chi-squared test (p < 0.05) for C206T, G253A, and A520G has the advantage of homozygous genotypes CC, GG, and AA, respectively. The association of C206T loci showed the advantage of CC genotype in ash-red, spread, and white pigeons, and TT in blue-bar, spread, and white feather pigeons. For G253A and A520G loci, GG and AA were dominant in all plumages except for genotype AA in G253A, which was prominent in ash-red, spread, and white plumages. The three SNPs were assigned to seven haplotypes. The median-joining network revealed 20 haplotypes, including 5 in Nigeria and 2 shared.

CONCLUSION

This study provides an insight into the association of MC1R variation and plumage diversity in Nigerian domestic pigeons. However, due to the limitation of the current data, we could not make further conclusions; this necessitates the need for more genomics studies on Nigerian pigeons.

Genome-Wide Association Study Identifies Candidate Genes for Stripe Pattern Feather Color of Rhode Island Red Chicks

Feather colors of chickens are not only characteristics of breeds but also as phenotypic markers in chicken breeding. Pure-bred Rhode Island Red (RIR) chicks have a stripe pattern and a non-stripe pattern on the back. The stripe pattern of RIR is generally shown as four longitudinal black stripes on the back and is more likely to appear in females. In this study, we performed a genome-wide association study (GWAS) to identify candidate genes controlling the stripe pattern of RIR chicks, and then, based on physical location and biological functions, quantitative RT-PCR analysis was used to validate the differential expression of candidate genes between stripe pattern and non-stripe pattern back skin tissue. The GWAS showed that a major signal contains 768 significant single nucleotide polymorphisms (SNPs) and 87 significant small insertions-deletions (INDELs) spanning 41.78 to 43.05 Mb (~1.27 Mb) on GGA1, corresponding to 16 genes associated with stripe pattern phenotype. Among these 16 genes, KITLG and TMTC3 could be considered candidate genes as they showed different expressions between back skin tissues of stripe pattern and non-stripe pattern chicks in value (p = 0.062) and the significant level (p < 0.05), respectively. This study provided novel insight into the mechanisms underlying feather pigmentation and stripe formation in RIR chicks.

Sex Identification of Feather Color in Geese and the Expression of Melanin in Embryonic Dorsal Skin Feather Follicles

In production practice, we have found that the gray and black down on the backs of the Holdobaggy goslings is usually darker in females than in males. Melanin is the key pigment affecting the color of poultry plumage. Therefore, to determine whether the darkness of the dorsal plumage of the Holdobaggy goslings is related to sex, we study the melanin in the feather follicles of the dorsal skin during the embryonic period. The feather follicle structure and melanin distribution on the dorsal surface of the goose embryo is observed by HE staining and melanin-specific staining. The melanin content in the feather follicles of the dorsal skin of goslings is determined by ELISA. The results showed that the melanin content is higher in female geese than in males (p < 0.05). In addition, we also analyze the mRNA and protein expression levels of melanin-related genes (TYRP1 and ASIP) by quantitative real-time PCR and Western blotting analysis. The results show that the mRNA expression level of TYRP1 is significantly higher in the females’ dorsal skin feather follicles (p < 0.05), while the mRNA expression level of ASIP is significantly higher in the dorsal skin feather follicles of male geese (p < 0.05). In conclusion, the difference between males and females in the color of the black feathers on the dorsal track of the Holdobaggy goslings is verified, and it is feasible to identify the sex by the initial plumage color.

Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern

A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools for delimiting species and understanding their evolutionary relationships. This allows for a more accurate and detailed view on conservation status compared with other, traditionally used, methods. However, from a practical and ethical perspective, gathering sufficient samples for endangered taxa may be difficult. Here, we use museum specimens to trace the evolutionary history and species boundaries in an Asian oriole clade. The endangered silver oriole has long been recognized as a distinct species based on its unique coloration, but a recent study suggested that it might be nested within the maroon oriole-species complex. To evaluate species designation, population connectivity, and the corresponding conservation implications, we assembled a de novo genome and used whole-genome resequencing of historical specimens. Our results show that the silver orioles form a monophyletic lineage within the maroon oriole complex and that maroon and silver forms continued to interbreed after initial divergence, but do not show signs of recent gene flow. Using a genome scan, we identified genes that may form the basis for color divergence and act as reproductive barriers. Taken together, our results confirm the species status of the silver oriole and highlight that taxonomic revision of the maroon forms is urgently needed. Our study demonstrates how genomics and Natural History Collections (NHC) can be utilized to shed light on the taxonomy and evolutionary history of natural populations and how such insights can directly benefit conservation practitioners when assessing wild populations.

Pig pigmentation: testing Gloger’s rule

Comparative studies indicate that several mammalian clades obey Gloger’s rule in that they exhibit darker coloration in humid warm climates, although the mechanisms responsible for this association still are poorly understood. We surveyed external appearances of a single species, the feral pig (Sus scrofa), shot at 48 hunting lodges across North America and matched these to potential abiotic drivers, namely: relative humidity, temperature, precipitation, and ultraviolet (UV) radiation, and to biotic factors of habitat shade and predation pressure. We found that darker animals occupy locations of greater precipitation and warmer temperatures, as expected from Gloger’s rule. The recent range expansion of S. scrofa implies selection for pelage coloration has occurred very rapidly. Separating pelage coloration into eumelanin- and phaeomelanin-based pigmentation, we found more pronounced eumelanin-based pelage in areas of higher rainfall and temperatures and UV radiation, whereas pelage phaeomelanin is related to cool dry climates with lower UV radiation. This implies that humidity or UV protection but not crypsis are the mechanisms underlying Gloger’s rule in this species and the factors driving eumelanin and phaeomelanin expression in mammalian pelage are different, reinforcing new interpretations of this venerable rule.

Fur colour in the Arctic fox: genetic architecture and consequences for fitness

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.

Variability, heritability and condition-dependence of the multidimensional male colour phenotype in a passerine bird

Elaborate ornamental traits are commonly assumed to be honest signals of individual quality, owing to the presumed costs involved in their production and/or maintenance. Such traits are often highly variable, possibly because of condition-dependence and/or high underlying genetic variation, and it has been suggested that their expression should be more sensitive to condition and/or more heritable than non-ornamental traits. Many bird species display colourful plumage with multiple distinct patches of different developmental origins, forming complex colour phenotypes. Despite this complexity, colourful ornaments are often studied in isolation, without comparison to suitable non-ornamental controls. Based on plumage reflectance data collected over 8 years, we assessed the signalling potential of the multidimensional male colour phenotype in a tropical bird: the purple-crowned fairy-wren Malurus coronatus. Specifically, we tested the predictions that the expression of putative ornamental colours (purple and black - the breeding colours - and blue) is (1) more variable, (2) more heritable and (3) more condition-dependent compared to year-round non-ornamental colours (buff-white and brown). Our results show that ornamental colours exhibit greater levels of variability, and some chromatic components of purple and blue colouration appear slightly heritable (h² = 0.19-0.30). However, contrary to predictions of heightened condition-dependence in ornaments, only brightness of the buff-white and brown colouration increased with male body condition, although brightness of the purple colouration was related to male age as expected. Despite partial support for predictions, the lack of consistent patterns illustrates the complexity of visual signals and highlights the need to study colour phenotypes in their entirety.

Avian Coloration Genetics: Recent Advances and Emerging Questions

The colorful phenotypes of birds have long provided rich source material for evolutionary biologists. Avian plumage, beaks, skin, and eggs-which exhibit a stunning range of cryptic and conspicuous forms-inspired early work on adaptive coloration. More recently, avian color has fueled discoveries on the physiological, developmental, and-increasingly-genetic mechanisms responsible for phenotypic variation. The relative ease with which avian color traits can be quantified has made birds an attractive system for uncovering links between phenotype and genotype. Accordingly, the field of avian coloration genetics is burgeoning. In this review, we highlight recent advances and emerging questions associated with the genetic underpinnings of bird color. We start by describing breakthroughs related to 2 pigment classes: carotenoids that produce red, yellow, and orange in most birds and psittacofulvins that produce similar colors in parrots. We then discuss structural colors, which are produced by the interaction of light with nanoscale materials and greatly extend the plumage palette. Structural color genetics remain understudied-but this paradigm is changing. We next explore how colors that arise from interactions among pigmentary and structural mechanisms may be controlled by genes that are co-expressed or co-regulated. We also identify opportunities to investigate genes mediating within-feather micropatterning and the coloration of bare parts and eggs. We conclude by spotlighting 2 research areas-mechanistic links between color vision and color production, and speciation-that have been invigorated by genetic insights, a trend likely to continue as new genomic approaches are applied to non-model species.

Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in ducks

Background

Birds have various plumage color patterns, and spot is a common phenotype. Herein, we conducted genome-wide association studies (GWAS) in a population of 225 ducks with different sized black spots to reveal the genetic basis of this phenomenon.

Results

First, we quantified the black spot phenotype within the duck population. The results showed that the uncolored area of the body surface first appeared on the ventral side. With increasing duck age, the area of the black spots was highly conserved across the whole body surface. The GWAS results identified a 198 kb (Chr4: 10,149,651 bp to 10,348,068 bp) genetic region that was significantly associated with the black spot phenotype. The conditional GWAS and linkage disequilibrium (LD) analysis further narrowed the ultimate candidate region to 167 kb (Chr4: 10,180,939 bp to 10,348,068 bp). A key gene regulating melanoblast migration and differentiation, EDNRB2 (Endothelin B receptor-like), was found in the candidate region and having significant mRNA expression level changes in embryonic duck skin tissue with different spot sizes. The significant SNPs (single nucleotide polymorphisms) associated with the EDNRB2 gene were annotated, and two mutations (Chr4: 10,180,939 T > C and Chr4: 10,190,671 A > T) were found to result in the loss of binding sites for two trans-factors, XBP1 and cMYB. The phenotypic effect of these two mutations suggested that they can regulate the size of black spots in a dose-dependent manner, and Chr4: 10,180,939 T > C was the major allele locus.

Conclusions

Our results revealed that EDNRB2 was the gene responsible for the variation in duck body surface spot size. Chr4: 10,180,939 T > C was the major allele that explained 49.5 % (dorsal side) and 32.9 % (ventral side) of the variation in duck body surface spot size, while 32.1 % (dorsal side) and 19.1 % (ventral side) of the variation could be explained by Chr4: 10,190,671 A > T. The trans-factor prediction also suggested that XBP1 and cMYB have the potential to interact with EDNRB2, providing new insights into the mechanism of action of these genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07719-7.

Genomic scan revealed KIT gene underlying white/gray plumage color in Chinese domestic geese

Goose is an important type of domesticated poultry. The wild geese that are regarded as the ancestors of modern domestic geese present gray plumage. Domesticated, geese have both white and gray feathers. To elucidate the genetic mechanisms underlying the formation of white and gray plumage in geese, we resequenced the whole genome of 18 geese from six populations including white and gray goose breeds. The average sequencing depth per individual was 9.81× and the average genome coverage was 96.8%. A total of 346 genes were detected in the top 1% of F_ST scores of gray- and white-feathered geese, and a significant F_ST site was located in the intron region within the KIT gene, the 18 bp deletion in KIT having the strongest potential association with white feathers. It has been reported that a number of genes are associated with plumage colors in birds. However, no studies have identified the relationship between KIT and plumage color in birds at present, although the white coat can be attributed to mutations in KIT in some mammals. Our study showed that that KIT is a plausible candidate gene for white/gray plumage color in Chinese domestic geese.

Adaptive coloration in pied flycatchers (Ficedula hypoleuca)-The devil is in the detail

Understanding the origin and persistence of phenotypic variation within and among populations is a major goal in evolutionary biology. However, the eagerness to find unadulterated explanatory models in combination with difficulties in publishing replicated studies may lead to severe underestimations of the complexity of selection patterns acting in nature. One striking example is variation in plumage coloration in birds, where the default adaptive explanation often is that brightly colored individuals signal superior quality across environmental conditions and therefore always should be favored by directional mate choice. Here, we review studies on the proximate determination and adaptive function of coloration traits in male pied flycatchers (Ficedula hypoleuca). From numerous studies, we can conclude that the dark male color phenotype is adapted to a typical northern climate and functions as a dominance signal in male-male competition over nesting sites, and that the browner phenotypes are favored by relaxed intraspecific competition with more dominant male collared flycatchers (Ficedula albicollis) in areas where the two species co-occur. However, the role of avoidance of hybridization in driving character displacement in plumage between these two species may not be as important as initially thought. The direction of female choice on male coloration in pied flycatchers is not simply as opposite in direction in sympatry and allopatry as traditionally expected, but varies also in relation to additional contexts such as climate variation. While some of the heterogeneity in the observed relationships between coloration and fitness probably indicate type 1 errors, we strongly argue that environmental heterogeneity and context-dependent selection play important roles in explaining plumage color variation in this species, which probably also is the case in many other species studied in less detail.

A variety-specific arrangement of histone H1 subtype (H1.b and H1.z) polymorphic variants in differently plumaged quails

1. This study was undertaken to evaluate genetic diversity among three varieties of Japanese quail (British Range, English White and Tuxedo) differing in plumage colour. The level of genetic variation was rated through the histone H1 polymorphic loci (H1.b and H1.z) containing quantitatively similar (P > 0.05) isoforms (H1.b1, H1.b2 and H1.z1, H1.z2) that form both homozygous (b1, b2 and z1, z2) and heterozygous (b1b2 and z1z2) phenotypes.2. The complete set of histone H1 phenotypes were characteristic of the British Range and Tuxedo varieties. Phenotypes b2 and z2 were not detected in the English White variety. A lack of the former phenotypes resulted in excess of heterozygotes at loci H1.b (F = -0.563) and H1.z (F = -0.562), pointing to the presence of outbreeding.3. The English White variety deviated from Hardy-Weinberg proportions (H1.b - Χ² = 7.61, P < 0.05 and H1.z - Χ² = 5.84, P < 0.05), in contrast to the British Range variety (H1.b - Χ² = 0.86, P > 0.05 and H1.z - Χ² = 0.86, P > 0.05) and Tuxedo (H1.b - Χ² = 1.6, P > 0.05 and H1.z - Χ² = 1.6, P > 0.05). The estimated values of the F_ST index for loci H1.b (0.073) and H1.z (0.099) indicate a moderate genetic diversity of the quail population.4. The distinct array and distribution of histone H1 phenotypes among quail varieties suggested that histone H1 allelic variants might have an individual impact on characteristic pigmentation of poultry.

Melanin-based ornament darkness positively correlates with across-season nutritional condition

Sexually dimorphic ornamental traits are widely regarded as indicators of nutritional condition. However, variation of nutritional condition outside the reproductive and the ornament production seasons has rarely been considered, although it affects the generality of information content, especially for ornaments that may be used across the year. We measured several indicators of migratory and molt condition in male and female blackcaps (Sylvia atricapilla) during their autumn migration, and quantified their crown reflectance. We detected robust correlations between migratory and molt condition indices, and the correlation structure was similar in the two sexes. Furthermore, the across-season measure of body condition was positively related to the darkness of the black crown in males, while being unrelated to reflectance traits of the reddish crown in females. Our results reinforce the possibility that some melanin-based ornaments may be year-round indicators of individual quality via their dependence on nutritional condition.

A quantitative trait locus on chromosome 2 was identified that accounts for a substantial proportion of phenotypic variance of the yellow plumage color in chicken

Chicken plumage color is an important economical trait in poultry breeding, as triple-yellow indigenous broilers are preferred over western commercial broilers in the Chinese market. However, the studies on the pigmentation of plumage coloration are relatively rare at present. Here, we performed a genome-wide mapping study on an F₂ intercross, whose 2 founders were one hybrid commercial line “High Quality chicken Line A” that originated from the Anak red chicken and one indigenous line “Huiyang Beard” chicken that is a classical “triple-yellow” Chinese indigenous breed. Moreover, we used an automatic colorimeter that can quantitatively assess the colorations in L∗, a∗, and b∗ values. One major quantitative trait locus (QTL) on chromosome 2 was thus identified by both genome-wide association and linkage analyses, which could explain 10 to 20% of the total phenotypic variance of the b∗ measurements of the back plumage color. Using linkage analysis, 2 additional QTL on chromosome 1 and 20 were also found to be significantly associated with the plumage coloration in this cross. With additional samples from Anak red and Huiyang Beard chickens as well as pooled resequencing data from the 2 founders of this cross, we then further narrowed down the QTL regions and identified several candidate genes, such as CABLES1, CHST11, BCL2L1, and CHD22. As the effects of QTL found in this study were substantial, quantitatively measuring the coloration rather than the descriptive measurements provides stronger statistical power for the analyses. In addition, this major QTL on chromosome 2 that was associated with feather pigmentation at the genome-wide level will facilitate the future chicken breeding for yellow plumage color. In conclusions, we mapped 3 associated QTL on chromosome 1, 2, and 20. The candidate genes identified in this study shed light in the genetic basis of yellow plumage color in chicken.

A 14-bp insertion in endothelin receptor B-like (EDNRB2) is associated with white plumage in Chinese geese

BACKGROUND

Gang goose is a native species with gray plumage in Sichuan, China. As a result of overhunting, the number of gray Gang geese has decreased dramatically. To keep the species from extinction, conservation work for Gang geese was undertaken. In the process of pure breeding of gray Gang geese, approximately 2% of the offspring of each generation were white. This study aims to explain the genetic mechanism of this phenomenon and provide reliable molecular markers for goose-related plumage color breeding.

RESULTS

We used the method of pooled whole genome sequencing and Fst (fixation statistics) to identify the differentiation degree of alleles between gray Gang geese and white Gang geese from their offspring. In this way, EDNRB2, a key gene that affects the migration of melanoblasts, was identified. Then, the transcriptome was sequenced for the two geese plumage color populations, and the DEGs (differentially expressed genes) were analyzed. The results indicated that EDNRB2, as a possible candidate gene, had a significantly differential mRNA expression. In addition, a 14-bp insertion (NW_013185915.1: g. 750,748-750,735 insertion. CACAGGTGAGCTCT) in exon 3 of EDNRB2 was analyzed and found to have a significant association between gray geese and Chinese white breeds (P = 0.00), while this mutation was not found in European geese. Meanwhile, the insertion was homozygous in all the white geese we detected and heterozygous in gray geese, indicating that this mutation is recessive. Furthermore, this 14-bp insertion leads to a frameshift mutation in the EDNRB2 coding region and nonsense-mediated mRNA decay.

CONCLUSION

Our study strongly suggests that the 14-bp insertion in exon 3 of the EDNRB2 gene is associated with the white plumage phenotype in Chinese geese. This study is the first to investigate the relationship between EDNRB2 and white plumage in geese.

Integrated Analysis of mRNA Expression, CpG Island Methylation, and Polymorphisms in the MITF Gene in Ducks (Anas platyrhynchos)

Microphthalmia-associated transcription factor (MITF) is a key regulator for the development and function of melanocytes in skin, eye, and plumage pigmentations. Thus, the MITF was selected as a candidate gene associated with plumage coloration in ducks. This study analyzed the mRNA expression, promoter methylation, and polymorphisms in the MITF gene in ducks with different plumage colors (Putian Black, Putian White, Liancheng White, and Longsheng Jade-green). No expression of the MITF melanin-specific isoform (MITF-M) was detected in white feather bulbs. By contrast, the mRNA expression levels of MITF-M were high in black feather bulbs. Bioinformatics analysis showed that two CpG islands were present in the promoter region of the MITF gene. The methylation level of the second CpG island was significantly lower in black feather bulbs than in white feather bulbs. However, the methylation level of the first CpG island was not different among the feather bulbs with various colors except Liancheng White feather bulbs. The methylation status of the whole CpG island significantly and negatively correlated with the mRNA expression of MITF-M (P < 0.05). Furthermore, four novel SNPs (single nucleotide polymorphisms) were identified in the 5′UTR, exon 4, intron 7, and intron 8 of the MITF gene. Allele T in g.39807T>G and allele G in g.40862G>A were the predominant alleles only found in Putian White, whereas the variant A allele in g.32813G>A exhibited a high allele frequency in Liancheng White. Collectively, these results contributed to the understanding of the function of the MITF gene in duck plumage coloration.

Multiple components of feather microstructure contribute to structural plumage colour diversity in fairy-wrens

Closely related species often differ in coloration. Understanding the mechanistic bases of such differences can reveal whether evolutionary changes in colour are driven by single key mechanisms or changes in multiple pathways. Non-iridescent structural plumage colours in birds are a good model in which to test these questions. These colours result from light absorption by pigments, light scattering by the medullary spongy layer (a nanostructure found within barbs) and contributions from other structural elements. Fairy-wrens (Malurus spp.) are a small clade of closely related birds that display a large diversity of ornamental structural colours. Using spectrometry, electron microscopy and Fourier analysis, we show that 30 structural colours, varying from ultraviolet to blue and purple, share a similar barb morphology. Despite this similarity, we find that at the microscopic scale, variation across multiple structural elements, including the size and density of the keratin cortex, spongy layer and melanin, explains colour diversity. These independent axes of morphological variation together account for sizeable amounts of structural colour variability (R2 = 0.21–0.65). The coexistence of many independent, evolutionarily labile mechanisms that generate colour variation suggests that the diversity of structural colours in this clade could be mediated by many independent genetic and environmental factors.

Bar, stripe and spot development in sand-dwelling cichlids from Lake Malawi

Background

Melanic patterns such as horizontal stripes, vertical bars and spots are common among teleost fishes and often serve roles in camouflage or mimicry. Extensive research in the zebrafish model has shown that the development of horizontal stripes depends on complex cellular interactions between melanophores, xanthophores and iridophores. Little is known about the development of horizontal stripes in other teleosts, and even less is known about bar or spot development. Here, we compare chromatophore composition and development of stripes, bars and spots in two cichlid species of sand-dwellers from Lake Malawi—Copadichromis azureus and Dimidiochromis compressiceps.

Results

(1) In D. compressiceps, stripes are made of dense melanophores underlaid by xanthophores and overlaid by iridophores. Melanophores and xanthophores are either loose or absent in interstripes, and iridophores are dense. In C. azureus, spots and bars are composed of a chromatophore arrangement similar to that of stripes but are separated by interbars where density of melanophores and xanthophores is only slightly lower than in stripes and iridophore density appears slightly greater. (2) Stripe, bar and spot chromatophores appear in the skin at metamorphosis. Stripe melanophores directly differentiate along horizontal myosepta into the adult pattern. In contrast, bar number and position are dynamic throughout development. As body length increases, new bars appear between old ones or by splitting of old ones through new melanophore appearance, not migration. Xanthophore and iridophore distributions follow melanophore patterns. (3) Metamorphic pigmentation arises in cichlids in a fashion similar to that described in zebrafish: melanophore progenitors derived from the medial route of neural crest migration migrate from the vicinity of the neural tube to the skin during metamorphosis.

Conclusion

The three pigment cell types forming stripes, bars and spots arise in the skin at metamorphosis. Stripes develop by differentiation of melanophores along horizontal myosepta, while bars do not develop along patent anatomical boundaries and increase in number in relation with body size. We propose that metamorphic melanophore differentiation and migratory arrest upon arrival to the skin lead to stripe formation, while bar formation must be supported by extensive migration of undifferentiated melanophores in the skin.

Red carotenoids and associated gene expression explain colour variation in frillneck lizards

A long-standing hypothesis in evolutionary ecology is that red-orange ornamental colours reliably signal individual quality owing to limited dietary availability of carotenoids and metabolic costs associated with their production, such as the bioconversion of dietary yellow carotenoids to red ketocarotenoids. However, in ectothermic vertebrates, these colours can also be produced by self-synthesized pteridine pigments. As a consequence, the relative ratio of pigment types and their biochemical and genetic basis have implications for the costs and information content of colour signals; yet they remain poorly known in most taxonomic groups. We tested whether red- and yellow-frilled populations of the frillneck lizard, Chlamydosaurus kingii, differ in the ratio of different biochemical classes of carotenoid and pteridine pigments, and examined associated differences in gene expression. We found that, unlike other squamate reptiles, red hues derive from a higher proportion of ketocarotenoids relative to both dietary yellow carotenoids and to pteridines. Whereas red frill skin showed higher expression of several genes associated with carotenoid metabolism, yellow frill skin showed higher expression of genes associated with steroid hormones. Based on the different mechanisms underlying red and yellow signals, we hypothesize that frill colour conveys different information in the two populations. More generally, the data expand our knowledge of the genetic and biochemical basis of colour signals in vertebrates.

Colour plasticity in response to social context and parasitic infection in a self-fertilizing fish

Many animal species rely on changes in body coloration to signal social dominance, mating readiness and health status to conspecifics, which can in turn influence reproductive success, social dynamics and pathogen avoidance in natural populations. Such colour changes are thought to be controlled by genetic and environmental conditions, but their relative importance is difficult to measure in natural populations, where individual genetic variability complicates data interpretation. Here, we studied shifts in melanin-related body coloration in response to social context and parasitic infection in two naturally inbred lines of a self-fertilizing fish to disentangle the relative roles of genetic background and individual variation. We found that social context and parasitic infection had a significant effect on body coloration that varied between genetic lines, suggesting the existence of genotype by environment interactions. In addition, individual variation was also important for some of the colour attributes. We suggest that the genetic background drives colour plasticity and that this can maintain phenotypic variation in inbred lines, an adaptive mechanism that may be particularly important when genetic diversity is low.

Molecular-genetic bases of plumage coloring in chicken

The color of plumage in birds is an important feature, often determining descent to a particular species or breed. It serves as a key factor in the interaction of birds with each other due to their well-developed visual perception of the surrounding world. In poultry including chickens, the color of the plumage can be treated as a genetic marker, useful for identifying breeds, populations and breeding groups with their specific traits. The origin of diverse color plumage is the result of two interrelated physical processes, chemical and optical, due to which pigment and structural colors in the color are formed. The pigment melanin, which is presented in two forms, eumelanin and pheomelanin, is widely spread in birds. The basis for the formation of melanin is the aromatic amino acid tyrosine. The process of melano-genesis involves many loci, part of the complex expression of plumage color genes. In birds, the solid black color locus encodes the melanocortin 1 receptor (MC1R), mutations in which lead to a change in receptor activation and form different variants of the E locus. Using the GWAS analysis, possible genes affecting the formation of color in chickens were detected. The biosynthesis and types of melanin are affected by the activity of the enzyme tyrosine, and mutations in the tyrosinase gene (TYR) cause albinism in different species. The formation mechanism of brown, silver, gold, lavender and a number of other shades is determined by the influence on the work of the MC1R genes and TYR specific modifier genes. Thus, locus I currently associated with the PMEL17 gene inhibits the expression of eumelanin, and the MLPH gene affects tyrosinase function. Research on the mechanisms of formation of the secondary coloring of plumage in chickens is being actively conducted nowadays. The formation of a marble feather pattern is associated with the mutation of the endothelin B2 receptor (EDNRB2), in the coding part of the gene of which a polymorphism is found associated with the mo locus. The molecular base that causes the feather banding (locus B and autosomal recessive banding) is identified. Today, only some genes that determine the color of the plumage of chickens are studied and described. Different genes can produce similar plumage patterns, and different phenotypes can be determined by the polymorphism of a single gene. Using molecular methods, you can more accurately identify these differences. This overview shows the nature of melanin coloration in birds using the example of chickens of various breeds and also attempts to systematize knowledge about the molecular-genetic mechanisms of the appearance of various types of coloration.

Diversity in warning coloration: selective paradox or the norm?

Aposematic theory has historically predicted that predators should select for warning signals to converge on a single form, as a result of frequency-dependent learning. However, widespread variation in warning signals is observed across closely related species, populations and, most problematically for evolutionary biologists, among individuals in the same population. Recent research has yielded an increased awareness of this diversity, challenging the paradigm of signal monomorphy in aposematic animals. Here we provide a comprehensive synthesis of these disparate lines of investigation, identifying within them three broad classes of explanation for variation in aposematic warning signals: genetic mechanisms, differences among predators and predator behaviour, and alternative selection pressures upon the signal. The mechanisms producing warning coloration are also important. Detailed studies of the genetic basis of warning signals in some species, most notably Heliconius butterflies, are beginning to shed light on the genetic architecture facilitating or limiting key processes such as the evolution and maintenance of polymorphisms, hybridisation, and speciation. Work on predator behaviour is changing our perception of the predator community as a single homogenous selective agent, emphasising the dynamic nature of predator-prey interactions. Predator variability in a range of factors (e.g. perceptual abilities, tolerance to chemical defences, and individual motivation), suggests that the role of predators is more complicated than previously appreciated. With complex selection regimes at work, polytypisms and polymorphisms may even occur in Müllerian mimicry systems. Meanwhile, phenotypes are often multifunctional, and thus subject to additional biotic and abiotic selection pressures. Some of these selective pressures, primarily sexual selection and thermoregulation, have received considerable attention, while others, such as disease risk and parental effects, offer promising avenues to explore. As well as reviewing the existing evidence from both empirical studies and theoretical modelling, we highlight hypotheses that could benefit from further investigation in aposematic species. Finally by collating known instances of variation in warning signals, we provide a valuable resource for understanding the taxonomic spread of diversity in aposematic signalling and with which to direct future research. A greater appreciation of the extent of variation in aposematic species, and of the selective pressures and constraints which contribute to this once-paradoxical phenomenon, yields a new perspective for the field of aposematic signalling.

Heritability of plumage colour morph variation in a wild population of promiscuous, long-lived Australian magpies

Colour polymorphisms have evolutionary significance for the generation and maintenance of species diversity. Demonstrating heritability of polymorphic traits can be challenging for wild populations of long-lived species because accurate information is required on trait expression and familial relationships. The Australian magpie Cracticus tibicen has a continent-wide distribution featuring several distinct plumage morphs, differing primarily in colour of back feathers. Black or white-backed morphs occur in eastern Australia, with intermediate morphs common in a narrow hybrid zone where the two morphs meet. This study investigated heritability of back colour phenotypes in a hybrid zone population (Seymour, Victoria) based on long-term observational data and DNA samples collected over an 18 year period (1993-2010). High extra-pair paternity (~ 36% offspring), necessitated verification of parent-offspring relationships by parentage analysis. A total of 538 birds (221 parents and 317 offspring) from 36 territories were analysed. Back colour was a continuous trait scored on a five-morph scale in the field (0-4). High and consistent estimates of back colour heritability (h²) were obtained via weighted mid-parent regression (h² = 0.94) and by animal models (h² = 0.92, C.I. 0.80-0.99). Single-parent heritability estimates indicated neither maternal nor paternal non-genetic effects (e.g., parent body condition) played a large role in determining offspring back colour, and environmental effects of territory group and cohort contributed little to trait heritability. Distinctive back colouration of the Australian magpie behaves as a quantitative trait that is likely polygenic, although mechanisms responsible for maintaining these geographically structured morphs and the hybrid zone where they meet are unknown.

Plasticity for colour adaptation in vertebrates explained by the evolution of the genes pomc, pmch and pmchl

Different camouflages work best with some background matching colour. Our understanding of the evolution of skin colour is based mainly on the genetics of pigmentation ("background matching"), with little known about the evolution of the neuroendocrine systems that facilitate "background adaptation" through colour phenotypic plasticity. To address the latter, we studied the evolution in vertebrates of three genes, pomc, pmch and pmchl, that code for α-MSH and two melanin-concentrating hormones (MCH and MCHL). These hormones induce either dispersion/aggregation or the synthesis of pigments. We find that α-MSH is highly conserved during evolution, as is its role in dispersing/synthesizing pigments. Also conserved is the three-exon pmch gene that encodes MCH, which participates in feeding behaviours. In contrast, pmchl (known previously as pmch), is a teleost-specific intron-less gene. Our data indicate that in zebrafish, pmchl-expressing neurons extend axons to the pituitary, supportive of an MCHL hormonal role, whereas zebrafish and Xenopus pmch+ neurons send axons dorsally in the brain. The evolution of these genes and acquisition of hormonal status for MCHL explain different mechanisms used by vertebrates to background-adapt.

Testing the potential mechanisms for the maintenance of a genetic color polymorphism in bluefin killifish populations

The maintenance of genetic variation in the face of natural selection is a long-standing question in evolutionary biology. In the bluefin killifish Lucania goodei, male coloration is polymorphic. Males can produce either red or yellow coloration in their anal fins, and both color morphs are present in all springs. These 2 morphs are heritable and how they are maintained in nature is unknown. Here, we tested 2 mechanisms for the maintenance of the red/yellow color morphs. Negative frequency-dependent mating success predicts that rare males have a mating advantage over common males. Spatial variation in fitness predicts that different color morphs have an advantage in different microhabitat types. Using a breeding experiment, we tested these hypotheses by creating populations with different ratios of red to yellow males (5 red:1 yellow; 1 red:5 yellow) and determining male mating success on shallow and deep spawning substrates. We found no evidence of negative frequency-dependent mating success. Common morphs tended to have higher mating success, and this was particularly so on shallow spawning substrates. However, on deep substrates, red males enjoyed higher mating success than yellow males, particularly so when red males were rare. However, yellow males did not have an advantage at either depth nor when rare. We suggest that preference for red males is expressed in deeper water, possibly due to alterations in the lighting environment. Finally, male pigment levels were correlated with one another and predicted male mating success. Hence, pigmentation plays an important role in male mating success.

Mutations in the melanocortin-1 receptor (MC1R) gene have no influence on the distinct patterns of melanic plumage found in the manakins of the genus Antilophia (Aves: Pipridae)

The melanocortin-1 receptor gene is the most widely-used marker for the investigation of the genetic determination of melanic plumage patterns. Studies of a number of wild bird species have shown an association between non-synonymous mutations of the MC1R gene and the presence of melanic variants. The genus Antilophia (Pipridae) includes only two manakin species (A. galeata and A. bokermanni), which are distinguished primarily by the differences in the pattern of melanic coloration of the plumage of the mantle in the adult males. In A. galeata, this plumage is black, while in A. bokermanni, it is predominantly white. This study investigates the possible association between mutations of the MC1R marker and the variation in plumage coloration observed in the two species. The MC1R sequences of the two species was analyzed, and the observed nucleotide variation was compared. Six polymorphic sites were identified, representing seven distinct genotypes. Five of these polymorphic mutations were non-synonymous, but were not related to the different phenotypes. Neutral evolution and the absence of any systematic association between the variants of the MC1R and plumage coloration in the Antilophia species indicate that alternative mechanisms regulate the expression of the coloration of the plumage in the adult males.

Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration

Background

As one of the most recognizable characteristics in birds, plumage color has a high impact on understanding the evolution and mechanisms of coloration. Feather and skin are ideal tissues to explore the genomics and complexity of color patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst's pheasant (Chrysolophus amherstiae), exhibit brilliant colors in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage coloration mechanisms in birds.

Results

We sequenced and assembled a genome of golden pheasant with high coverage and annotated 15,552 protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons were conducted to investigate the complex features of plumage coloration. By identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant against different backgrounds, we found that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively. In addition, a study among 47 birds showed some candidate genes related to carotenoid coloration in a broad range of birds. The transcriptome data further reveal important regulators of the two colorations, particularly one splicing transcript of the microphthalmia-associated transcription factor gene for pheomelanin synthesis.

Conclusions

Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage coloration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity.

Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon

Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.