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Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization

Six selected weedy Amaranthus genotypes (three accessions from each species of A. viridis and A. spinosus ) were evaluated in terms of nutrients, minerals, antioxidant constituents and antioxidant activity for the possibilities of weedy species as a vegetable cultivar in a randomized complete block design with three replications. As leafy vegetable, Weedy Amaranthus has remarkable protein, dietary fiber, carbohydrates, Ca, K, Mg, P, S, Fe, Mn, Cu, Zn, Na, Mo, B, chlorophylls, β-cyanins, β-xanthins, betalains, β-carotene, vitamin C, TPC, TFC, and TAC (DPPH and ABTS + ) compared to any cultivated species. The A. viridis genotype WAV7 and A. spinosus genotype WAS13 had the highest nutrients, pigments, vitamins, phenolics, flavonoids, and antioxidant. Hence, these two weedy accessions could be used as an antioxidant profile enriched cultivar with high nutritional and antioxidant activity. Pigments, β-carotene, vitamin C, phenolics, and flavonoids had strong antioxidant activity and played a vital role in the antioxidant activity of weedy Amaranthus genotypes. Weedy species are an excellent source of phenolics, flavonoids, and antioxidants that have many pharmacological and medicinal effects of their traditional applications and detoxify ROS and offered huge prospects for feeding the antioxidant-deficient community to cope with the hidden hunger and attaining nutritional and antioxidant sufficiency.

A complete pre-agricultural European human genome from a ∼7,000-year-old Mesolithic skeleton suggests the existence of a common genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic, and ancestral alleles in several skin pigmentation genes suggest that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Last of the hunter-gatherers The emergence of agriculture is thought to have caused many of the evolutionary changes in human physiology evident in the fossil record. Precisely which changes it is hard to say in the absence of a baseline — a record of human physiology just before the advent of farming. We may now have that in the form of a genome of a Mesolithic hunter-gatherer from Spain, described by Carles Lalueza-Fox and colleagues this week. The genes of this male, who lived around 7,000 years ago, had more in common with ancient genomes from Siberia than with other Europeans, suggesting a wide if thinly spread genetic continuity across Eurasia. He would have been lactose intolerant and less able to digest starchy foods than Neolithic farming people, suggesting that these changes came in with agriculture. He would also have had the unusual combination of dark skin and blue eyes, suggesting that in Mesolithic times, the transition to a lighter, more modern European skin tone was incomplete and that changes in eye colour came first. Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe 1 , 2 , 3 . The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet 4 . However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12 , HMG20B , OCA2 , MITF , LEF1 , TRPS1 , BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF , LEF1 and TRPS1 , which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution. Massively parallel reporter assays identify 165 functional variants associated with skin pigmentation in ethnically diverse Africans. Functional characterization of eight variants demonstrates their impact in regulating melanin levels and validates CYB561A3 as a novel gene involved in melanogenesis and pigmentation.

The ultraviolet (UV) radiation triggers a pigmentation response in human skin, wherein, melanocytes rapidly activate divergent maturation and proliferation programs. Using single-cell sequencing, we demonstrate that these 2 programs are segregated in distinct subpopulations in melanocytes of human and zebrafish skin. The coexistence of these 2 cell states in cultured melanocytes suggests possible cell autonomy. Luria–Delbrück fluctuation test reveals that the initial establishment of these states is stochastic. Tracking of pigmenting cells ascertains that the stochastically acquired state is faithfully propagated in the progeny. A systemic approach combining single-cell multi-omics (RNA+ATAC) coupled to enhancer mapping with H3K27 acetylation successfully identified state-specific transcriptional networks. This comprehensive analysis led to the construction of a gene regulatory network (GRN) that under the influence of noise, establishes a bistable system of pigmentation and proliferation at the population level. This GRN recapitulates melanocyte behaviour in response to external cues that reinforce either of the states. Our work highlights that inherent stochasticity within melanocytes establishes dedicated states, and the mature state is sustained by selective enhancers mark through histone acetylation. While the initial cue triggers a proliferation response, the continued signal activates and maintains the pigmenting subpopulation via epigenetic imprinting. Thereby our study provides the basis of coexistence of distinct populations which ensures effective pigmentation response while preserving the self-renewal capacity.

The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the  Id locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the Id locus, its precise location and functional details remain elusive. Our study aims to precisely locate the Id locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the Id locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the Id locus to a ~1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the Id locus shares a common ancestry across all BBC breeds, much like the Fm locus. Selection signatures and highly differentiated BBC-specific SNPs within the MTAP gene position it as the prime candidate for the Id locus with CCDC112 and additional genes, suggesting a possible polygenic nature. Our results suggest that the Id locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.

Determining the mechanistic and genetic basis of animal coloration is essential to understand the costs and constraints on color production, and the evolution and maintenance of phenotypic variation. However, genes underlying structural color and widespread pigment classes apart from melanin remain largely uncharacterized, in part due to restricted taxonomic focus. We combined liquid chromatography-mass spectrometry and RNA-seq gene expression analyses to characterize the pigments and genes associated with skin color in the polymorphic lizard, Ctenophorus decresii. Throat coloration in male C. decresii may be a combination of orange, yellow, grey, or ultra-violet blue. We confirmed the presence of two biochemically different pigment classes, pteridines (self-synthesized) and carotenoids (acquired through the diet), in all skin colors. Orange skin had the highest levels of pteridine pigments while yellow skin tended to have higher levels of carotenoids, of which the vitamin A precursors β-carotene and β-cryptoxanthin have not been previously confirmed in reptiles. These results were confirmed by gene expression analyses, which detected 489 genes differentially expressed between the skin colors, including genes associated with pteridine production, provitamin A carotenoid metabolism, iridophore-specific synthesis, melanin synthesis, and steroid hormone pathways. For the majority of these 489 genes, however, our study reveals a new association with color production in vertebrates. These data represent a significant contribution to understanding the genetic basis of color variation in vertebrates and a rich resource for further studies.

Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B , which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates.

As a main part of pigmentation disorders, skin depigmentation diseases such as vitiligo and achromic naevus are very common and get more attention now. The pathogenesis of depigmentation includes melanocyte dysfunction and loss, which are possibly caused by heredity, autoimmunity and oxidative stress. Among them, oxidative stress plays a key role; however, few clinical treatments can deal with oxidative stress. As reported, Cistanche deserticola polysaccharide (CDP) is an effective antioxidant; based on that, we evaluated its role in melanocyte and further revealed the mechanisms. In this study, we found that CDP could promote melanogenesis in human epidermal melanocytes (HEMs) and mouse melanoma B16F10 cells, it also induced pigmentation in zebrafish. Furthermore, CDP could activate mitogen‐activated protein kinase (MAPK) signal pathway, then up‐regulated the expression of microphthalmia‐associated transcription factor (MITF) and downstream genes TYR, TRP1, TRP2 and RAB27A. Otherwise, we found that CDP could attenuate H2O2‐induced cytotoxicity and apoptosis in melanocytes. Further evidence revealed that CDP could enhance NRF2/HO‐1 antioxidant pathway and scavenge intracellular ROS. In summary, CDP can promote melanogenesis and prevent melanocytes from oxidative stress injury, suggesting that CDP helps maintain the normal status of melanocytes. Thus, CDP may be a novel drug for the treatment of depigmentation diseases. Cistanche deserticola polysaccharide (CDP) promotes melanogenesis in human epidermal melanocytes via activating mitogen‐activated protein kinase (MAPK) signal pathway, then up‐regulates the expression of MITF, TYR, TRP1, TRP2, and RAB27A. Otherwise, CDP can attenuate H2O2‐induced oxidative stress in melanocytes via enhancing NRF2/HO‐1 antioxidant pathway and scavenge intracellular ROS.

Oujiang color common carp display four striking varieties of pigmentation, but their epigenetic basis is unclear. We integrated genome-wide DNA methylation (MBD-seq) and transcriptomes (RNA-seq) from dorsal skin of four Oujiang color common carp varieties with three biological replicates. Black-spotted groups (RB, WB) showed approximately 6% higher global methylation than non-black-spotted groups (WR, WW), with differential methylation enriched in introns (>23%) and intergenic regions (>47%). Integrative analyses revealed a strong inverse association between promoter methylation and gene expression; 96 pigmentation-related genes were identified, spotlighting genes such as ASIP and frmA as key epigenetically silenced regulators in black-spotted carp. RT-qPCR confirmed directional concordance with RNA-seq for ASIP, frmA, DGAT2, SCARB1, and FOSB. Pathway enrichment implicated melanogenesis metabolism, tyrosine metabolism, lipid metabolism, and fatty acid metabolism, suggesting an interplay between pigment deposition and metabolic regulation. Collectively, the findings present an exploratory view of epigenetic control of coloration and underscore promoter methylation as a core layer influencing color diversity in Oujiang color common carp.