Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.

BACKGROUND: The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. RESULTS: HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20). CONCLUSIONS: Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.

Production of species-specific anthocyanins through an inducible system in plant hairy roots.

Anthocyanins are widely distributed pigments in flowering plants with red, purple or blue colours. Their properties in promoting heath make anthocyanins perfect natural colourants for food additives. However, anthocyanins with strong colour and stability at neutral pH, suitable as food colourants are relatively rare in nature. Acylation increases anthocyanin stability and confers bluer colour. In this study, we isolated two anthocyanin regulators SbMyb75 and SbDel from S. baicalensis, and showed that constitutive expression of the two TFs led to accumulation of anthocyanins at high levels in black carrot hairy roots. However, these hairy roots had severe growth problems. We then developed a ß-estradiol inducible system using XVE and a Lex-35S promoter, to initiate expression of the anthocyanin regulators and induced this system in hairy roots of black carrot, tobacco and morning glory. Anthocyanins with various decorations were produced in these hairy roots without any accompanying side-effects on growth. We further produced highly acylated anthocyanins with blue colour in a 5 L liquid culture in a bioreactor of hairy roots from morning glory. We provide here a strategy to produce highly decorated anthocyanins without the need for additional engineering of any of the genes encoding decorating enzymes. This strategy could be transferred to other species, with considerable potential for natural colourant production for the food industries.

Diving into the diversity of colour patterns in reef fishes.

Colours and associated patterns are probably some of the most obvious phenotypic traits in animals and reef teleost fishes are often cited as a textbook example for illustrating this type of diversity. Even if it is well established that colour patterns play a central role in the ecology and evolution of reef fishes, we still lack the necessary toolkits to fully grasp the mechanisms driving the diversification of this obvious phenotypic trait. On the one hand, genotyping power seems now limitless thanks to current DNA sequencing technologies. Today, entire genomes of fishes can be easily produced for large sets of species. On the other hand, the description of colour patterns and the quantification of their variation across reef fishes might be highly challenging. In a cover manuscript in this issue of Molecular Ecology, Coulmance et al. (2023) introduced an innovative approach for extracting and quantifying the major colour pattern elements present in the hamlets (Hypoplectrus spp., Serranidae), a recent reef fish radiation from the Caribbean. Then, they intelligently used the quantified colour pattern variation as a phenotypic trait for a genome-wide association study (GWAS). Interestingly, using a method that required no a priori knowledge, they were able to recover well-established marks (e.g., vertical bars) and to highlight less expected colour pattern elements (e.g., dark to light gradient on ventral part as well as caudal and anal fins), which show strong association peaks on linkage group (LG) 12 and 04. Beyond the demonstration of the potential of their new quantitative analysis of colour pattern variation in reef fishes combined with GWAS, their findings offer new perspectives on our understanding of the intrinsic and extrinsic factors generating this outstanding diversity of the fish world.

Emotions reflected in colours: experiences of nursing students during the COVID-19 period.

BACKGROUND: The aim of this study was to identify nursing students' fears and emotions and to concretise the metaphors they used to describe their feelings towards the COVID-19 pandemic. METHODS: This study was conducted with nursing students at a foundation university between December 2021 and February 2022 using a sequential mixed methods research design. In the quantitative part of the study, 323 nursing students answered the 'Positive and Negative Emotion Scale' and the 'COVID-19 Fear Scale'. In the qualitative part, students were asked to metaphorise COVID-19 with a colour and 21 in-depth interviews were conducted on the reasons for choosing this colour. RESULTS: The average age of the students participating in the study was 21.41 ± 1.97 years and 78% of them were female. It was observed that 15.8 of the students had previously tested positive for COVID-19. Most of the participants (98.5%) were vaccinated against COVID-19 and 31.9% had a relative who died due to COVID-19. When the participants were asked which colour they compared COVID-19 to, it was observed that more than half of them chose red (51.4%) among bright colours and 13% chose black among dark colours. In this study, it was determined that students who chose dark colours to describe COVID-19 had higher COVID-19 Fear and Negative Emotion Scale scores. In in-depth interviews, it was observed that students who chose dark colours were more deeply affected by the COVID-19 process, while students who chose light colours associated this period with negative emotions. CONCLUSION: In this study, it was observed that nursing students' feelings and thoughts about the COVID-19 period in line with their experiences affect the choice of colour in metaphorisation.

Colour-dependent dishonesty in a game of chance.

We report an odd result of a coin-flip experiment which incentivises dishonest behaviour. Participants of two treatments were asked to flip a coin in private, of which one side was WHITE and the other side BLACK, and report the colour shown by the coin. Payoff depended on the reported colour: in one treatment WHITE was the more profitable outcome whereas in the other treatment BLACK was more profitable. Surprisingly, the magnitude of cheating, as reflected by the difference between the frequency of reporting the more profitable colour and its statistical expectation (50%) was not, more or less, the same in both treatments. Rather, significantly more participants cheated when BLACK was the profitable outcome. This result reappeared in two variants of the coin-flip task. We suggest that a sense of entitlement triggered by a WHITE outcome may explain this behaviour.

Relationship between the colours of the rivers in the Amazon and the incidence of malaria.

BACKGROUND: Malaria is transmitted by different Anopheles species. In Brazil, the disease is concentrated in the Amazon region. Rivers play an important role in the life cycle of malaria since the vector reproduces in aquatic environments. The waters of the rivers in the Amazon have distinct chemical characteristics, which affect the colour of the water and therefore, the study analysed whether the colour of the waters of the rivers have an on influence the distribution of malaria. The goal of the study was to correlate the different colourations of the water (black, white and mixed water) and the malaria incidence in 50 municipalities of the Amazonas state, Brazil, and then test hypotheses about the characteristics of the colour of the rivers and disease incidence. METHODS: This study was conducted for a period of seventeen years (2003-2019) in 50 municipalities in the state of Amazonas, Brazil. A conditionally Gaussian dynamic linear model was developed to analyse the association of malaria incidence and three types of river colour: white, black and mixed. RESULTS: The analyses indicate that the distribution of malaria is related to the colouration of the rivers. The results showed that places located near black-water rivers have a higher malaria incidence when compared to places on the banks of white-water rivers. CONCLUSIONS: Historically, the hydrological regime has played an important role in the dynamics of malaria in the Amazon, but little is known about the relationship between river colours and the incidence of the disease. This research was carried out in a region with hydrographic characteristics that were heterogeneous enough to allow an analysis that contrasted different colours of the rivers and covered almost the whole of the state of Amazonas. The results help to identify the places with the highest risk of malaria transmission and it is believed that they will be able to contribute to more precise planning of actions aimed at controlling the disease in the region.

Iridescent scales signal male fighting ability to access females in the jewelled splitfin Xenotoca variata.

Jewelled splitfin males (Xenotoca variata) possess multi-colour iridescent scales (speckles) on the flanks. This study tested the hypothesis that the number of speckles could be a good proxy for predicting fighting ability in contests for access to females. The experiments consisted in observing and recording males' agonistic behaviour, courtship displays and mating attempts in mixed-sex groups. The data were analysed and presented based on a Bayesian approach, which revealed that the density (cm-2 ) of speckles was positively correlated with the increase observed in the proportional frequency of attacks. Similarly, the density of speckles was positively associated with the increase observed in the frequency of courtship behaviour and with the frequency of mating attempts. Male-male aggressions drastically diminished (by eightfold) when females were removed from the observation tanks. These results indicate that the number of speckles is a consistent predictor of successful access to females and therefore, speckled males are likely to be able to gain more mating opportunities. This finding highlights the ubiquitous role iridescent colours play in visual signalling.

Are fish communities on coral reefs becoming less colourful?

An organism's colouration is often linked to the environment in which it lives. The fishes that inhabit coral reefs are extremely diverse in colouration, but the specific environmental factors that support this extreme diversity remain unclear. Interestingly, much of the aesthetic and intrinsic value humans place on coral reefs (a core ecosystem service they provide) is based on this extreme diversity of colours. However, like many processes on coral reefs, the relationship between colouration and the environment is likely to be impacted by global environmental change. Using a novel community-level measure of fish colouration, as perceived by humans, we explore the potential links between fish community colouration and the environment. We then asked if this relationship is impacted by human-induced environmental disturbances, e.g. mass coral bleaching events, using a community-level dataset spanning 27 years on the Great Barrier Reef. We found that the diversity of colours found within a fish community is directly related to the composition of the local environment. Areas with a higher cover of structurally complex corals contained fish species with more diverse and brighter colourations. Most notably, fish community colouration contracted significantly in the years following the 1998 global coral bleaching event. Fishes with colouration directly appealing to human aesthetics are becoming increasingly rare, with the potential for marked declines in the perceived colour of reef fish communities in the near future. Future reefs may not be the colourful ecosystems we recognize today, representing the loss of a culturally significant ecosystem service.

Trees growing in Eastern North America experience higher autumn solar irradiation than their European relatives, but is nitrogen limitation another factor explaining anthocyanin-red autumn leaves?: A comment on Peña-Novas and Marchetti 2021 (https://doi.org/10.1111/jeb.13903).

Trees growing at a particular latitude in Eastern North America (ENA) receive more autumn solar irradiation than do trees growing at the same latitude in Europe, a difference that could partly explain the higher percentage of anthocyanin-producing deciduous species in ENA compared with European floras. A proposed link between autumn light intensity and the production of anthocyanins is their function in photoprotection, which enables plants with red leaves to resorb nutrients for a longer time than can yellow or brown leaves. The innately 4-week-shorter foliage period of ENA trees compared with European ones may also play a role, as may stronger nitrogen limitation in poorer soils in ENA. We here test for a correlation between nitrogen access and fall anthocyanin in 126 species (55 genera, 22 families) from different temperate forests, using a Hierarchical Bayesian model and accounting for phylogenetic structure in the data. None of 81 species with nitrogen-fixing symbionts produce autumn anthocyanin, whereas 42% of non-nitrogen-fixers do. Thus, when ample nitrogen is available from symbionts, the benefits of anthocyanin-derived photoprotection apparently do not outweigh the costs of anthocyanin production. If nitrogen limitation indeed plays a role in the dominance of red-autumn-colouring trees in ENA floras - while European floras predominantly produce yellow autumn leaves - there might also be continental differences in the frequency or abundance of nitrogen-fixing trees and shrubs, a new hypothesis that deserves testing.

Combination of Spray-Chilling and Spray-Drying Techniques to Protect Carotenoid-Rich Extracts from Pumpkin (Cucurbita moschata) Byproducts, Aiming at the Production of a Powdered Natural Food Dye.

Reducing waste, using byproducts, and natural food additives are important sustainability trends. In this context, the aim of this study was to produce and evaluate a natural food dye, extracted from pumpkin byproducts, powdered and protected by spray-chilling (SC) and a combination of spray-drying and spray-chilling techniques (SDC). The extract was obtained using ethanol as solvent; vegetable fat and gum Arabic were used as carriers. Formulations were prepared with the following core:carrier ratios: SC 20 (20:80), SC 30 (30:70), SC 40 (40:60), SDC 5 (5:95), SDC 10 (10:90), and SDC 15 (15:85). The physicochemical properties of the formed microparticles were characterised, and their storage stability was evaluated over 90 days. The microparticles exhibited colour variation and size increase over time. SDC particles exhibited the highest encapsulation efficiency (95.2-100.8%) and retention of carotenoids in the storage period (60.8-89.7%). Considering the carotenoid content and its stability, the optimal formulation for each process was selected for further analysis. All of the processes and formulations produced spherical particles that were heterogeneous in size. SDC particles exhibited the highest oxidative stability index and the highest carotenoid release in the intestinal phase (32.6%). The use of combined microencapsulation technologies should be considered promising to protect carotenoid compounds.

A test of the photoprotection hypothesis for the evolution of autumn colours: Chlorophyll resorption, not anthocyanin production, is correlated with nitrogen translocation.

A prominent hypothesis for the adaptive value of anthocyanin production in the autumn leaves of trees and shrubs is that anthocyanins protect leaves from photooxidative stress at low temperatures, allowing a better resorption of nutrients-in particular, nitrogen-before leaf fall. While there is evidence that anthocyanins enable photoprotection, it is not clear whether this translates to improved nitrogen translocation and how this can explain inter-specific variation in autumn colours. A recent comparative analysis showed no correlation between temperature and anthocyanin production across species but did not analyse nitrogen content and nitrogen resorption efficiency. Here, we provide this comparison by analysing the nitrogen content of mature and senescent leaves and their autumn colours in 55 species of trees. We find no correlation between the presence of anthocyanins and the efficiency of nitrogen resorption. We find, instead, that nitrogen resorption is more efficient in species with yellow autumn colours, pointing to chlorophyll resorption, rather than anthocyanin synthesis, as the main determinant of nitrogen translocation efficiency. Hence, our results do not corroborate the photoprotection hypothesis for the evolution of autumn colours.

Synthesis and luminescence spectroscopy study of a novel orange-red colour emissions phosphor based on Tb3+ ion-doped Na2 ZnP2 O7.

Here, we report the synthesis and study of new orange-red (OR) colour-emitting phosphors Na2 ZnP2 O7 :xTb3+ (x = 1, 1.25, 1.5, and 1.75 mol%) using a conventional solid-state reaction. The sample crystallographic structures and their room temperature photoluminescence properties were measured using X-ray powder diffraction, excitation and emission spectra, as well as emission decay curves. X-ray diffraction analysis showed an isostructural tetragonal structure for all the doped materials with no impurities. Several colour emissions corresponding to 5 D4 →7 F6 (blue), 5 D4 →7 F5 (green), 5 D4 →7 F4 (orange) and 5 D4 →7 F3,2,0 (red) intraconfigurational transitions were observed and investigated. These colours were dominated by the OR colours. 5 D4 energy level lifetime was independent of Tb3+ concentration. Various radiative and luminescence parameters, such as experimental branching ratio, radiative decay rate, and luminescence quantum efficiencies, were calculated and discussed. Chromaticity diagram calculations illustrated an orange emission for all the studied materials.

Characterization of a Natural, Stable, Reversible and Colourful Anthocyanidin Network from Sphagnum Moss Based Mainly on the Yellow Trans-Chalcone and Red Flavylium Cation Forms.

Anthocyanins with various functions in nature are one of the most important sources of colours in plants. They are based on anthocyanidins or 3-deoxyanthocyanidins having in common a C15-skeleton and are unique in terms of how each anthocyanidin is involved in a network of equilibria between different forms exhibiting their own properties including colour. Sphagnorubin C (1) isolated from the cell wall of peat moss (Sphagnum sp.) was in fairly acidic and neutral dimethyl sulfoxide characterized by nuclear magnetic resonance (NMR) and ultraviolet-visible (UV-vis) absorption techniques. At equilibrium, the network of 1 behaved as a two-component colour system involving the reddish flavylium cationic and the yellow trans-chalcone forms. The additional D- and E-rings connected to the common C15-skeleton extend the π-conjugation within the molecule and provide both bathochromic shifts in the absorption spectra of the various forms as well as a low isomerization barrier between the cis- and trans-chalcone forms. The hemiketal and cis-chalcone forms were thus not observed experimentally by NMR due to their short lives. The stable, reversible network of 1 with good colour contrast between its two components has previously not been reported for other natural anthocyanins and might thus have potential in future photochromic systems. This is the first full structural characterization of any naturally occurring anthocyanin chalcone form.

A comparative analysis of the photoprotection hypothesis for the evolution of autumn colours.

The adaptive value of autumn colours-the seasonal production of red anthocyanins observed in many species of trees and shrubs-is still debated. According to the photoprotection hypothesis, anthocyanins protect leaves from photo-inhibition and photo-oxidation at low temperatures, enabling the tree to reabsorb nutrients more efficiently before leaf fall. Hence, the hypothesis predicts that autumn colours are more likely to evolve in species growing in colder environments. We tested this prediction by comparing the climatic parameters of 237 North American tree species. We found that, although species with yellow autumn leaves grow under lower minimum temperatures than species with green leaves, there is no significant difference in temperature between species with red autumn leaves and species with green or yellow autumn leaves. We conclude that, although reabsorbing chlorophyll in autumn, and the consequent unmasking of yellow carotenoids, may be an adaptation to cold temperatures, the production of red anthocyanins is not. Hence, our interspecific comparative analysis does not support the photoprotection hypothesis as an explanation for the evolution of autumn colours.

Segmentation, retardation and mass approximation of birefringent particles on a standard light microscope.

This study presents a simple technique for the approximation of retardation, thickness and mass of birefringent particles with a retardation from 8 to 231 nm retardation. Tuning of the imaging system (standard light microscope equipped with a left and a right circular polarizer) to match grey values of polymer retarder films of known retardation with rendered grey values allows for a robust calibration and accurate approximation of retardation. In addition, a technique for accurate particle segmentation using a Canny-Deriche algorithm was used to minimize the bias on mass estimated from different thresholding techniques. The technique was tested using microscopic calcitic plates called coccoliths produced by the marine algal group coccolithophores, and the results compare well with published coccolith mass estimates obtained from volumetric analysis. LAY DESCRIPTION: Material with certain optical properties display interference colours when observed in a light microscope under circular polarized light. This study presents a simple technique for measuring the thickness and retardation of small particles within the 8 to 231 nm retardation range based on the grey values of their interference colours. Retardation is a measure of the distance between waves of two mutually perpendicular polarized light waves after passing through material. The technique involves the tuning of a standard light microscope system equipped with a left and a right circular polarizer and a digital camera to match grey values of polymer retarder films with a known retardation with grey values of a digitially rendered Michel-Lévy chart. A technique for accurate isolation of particles from the image background using a Canny-Deriche algorithm is also described, which avoids possible biased results from thresholding. The techniques were tested using microscopic calcitic plates called coccoliths produced by the marine algal group coccolithophores, and the results compare well with published estimates obtained from volumetric analysis.

Brilliant angle-independent structural colours preserved in weevil scales from the Swiss Pleistocene.

Extant weevils exhibit a remarkable colour palette that ranges from muted monochromatic tones to rainbow-like iridescence, with the most vibrant colours produced by three-dimensional photonic nanostructures housed within cuticular scales. Although the optical properties of these nanostructures are well understood, their evolutionary history is not fully resolved, in part due to a poor knowledge of their fossil record. Here, we report three-dimensional photonic nanostructures preserved in brightly coloured scales of two weevils, belonging to the genus Phyllobius or Polydrusus, from the Pleistocene (16-10 ka) of Switzerland. The scales display vibrant blue, green and yellow hues that resemble those of extant Phyllobius/Polydrusus. Scanning electron microscopy and small-angle X-ray scattering analyses reveal that the subfossil scales possess a single-diamond photonic crystal nanostructure. In extant Phyllobius/Polydrusus, the near-angle-independent blue and green hues function primarily in crypsis. The preservation of far-field, angle-independent structural colours in the Swiss subfossil weevils and their likely function in substrate matching confirm the importance of investigating fossil and subfossil photonic nanostructures to understand the evolutionary origins and diversification of colours and associated behaviours (e.g. crypsis) in insects.

Lights and colours: Science, Techniques and Surveillance for the Future - 4th IC3EM 2020, Caparica, Portugal.

•Special Issue on 4th IC3EM 2020.•Science, Techniques, Surveillance.•The importance of Science.•Fluorescent dyes.

Colour pattern divergence in reef fish species is rapid and driven by both range overlap and symmetry.

Signal divergence is an important process underpinning the diversification of lineages. Research has shown that signal divergence is greatest in species pairs that possess high geographic range overlap. However, the influence of range-size differences within pairs is less understood. We investigated how these factors have shaped signal divergence within brightly coloured coral reef butterflyfishes (genus: Chaetodon). Using a novel digital imaging methodology, we quantified both colouration and pattern using 250 000 sample points on each fish image. Surprisingly, evolutionary age did not affect colour pattern dissimilarity between species pairs, with average differences arising in just 300 000 years. However, the effect of range overlap and range symmetry was significant. Species-pair colour patterns become more different with increasing overlap, but only when ranges are similar in size. When ranges differ markedly in area, species-pair colour patterns become more similar with increasing overlap. This suggests that species with small ranges may maintain non-colour-based species boundaries.

Origins of a pervasive, erroneous idea: The "green birefringence" of Congo red-stained amyloid.

Congo red was discovered to stain amyloid by accident in 1922, and Congo red-stained amyloid was shown to be birefringent on polarization microscopy in 1927. Colours, namely green and yellow, were reported under these conditions in 1945, although these are only two of various anomalous colours that may be seen, depending on the optical set-up. In 1953 there began a dogmatic insistence that in Congo red-stained amyloid between crossed polarizer and analyser green alone should be seen, and the finding of any other colour was a mistake. The idea that green, and only green, is essential for the diagnosis of amyloid has persisted almost universally, and virtually all mentions of Congo red-stained amyloid say that it just shows "green birefringence" or "apple-green birefringence." This idea is wrong and is contrary to everyday experience, because green is seldom seen on its own under these conditions of microscopy, and often, there is no green at all. How observers maintain this unscientific position is explained by a study of its historical origins. Most of the early literature was in German or French and was usually quoted in English at second hand, which meant that misquotations, misattributions and misunderstandings were common. Few workers reported their findings accurately, hardly any attempted to explain them, and until 2008, none gave a completely satisfactory account of the physical optics. The history of Congo red-stained amyloid is an instructive example of how an erroneous belief can become widely established even when it is contradicted by simple experience.

Diffusive structural colour in Hoplia argentea.

Nature's nanostructures can bring about vivid and iridescent colours seen in many insects, notably in beetles and butterflies. While the intense structural colours can be advantageous for display purposes, they may also be appealing to predators and therefore constitute an evolutionary disadvantage. Animals often employ absorption and scattering in order to reduce the directionality of the reflected light and thereby enhance their camouflage. Here, we investigated the monkey beetle Hoplia argentea using microspectrophotometry, electron microscopy, fluorimetry and optical modelling. We show that the dull green dorsal colour comes from the nanostructured scales on the elytra. The nanostructure consists of a multi-layered photonic structure covered by a filamentous layer. The filamentous layer acts as a spatial diffuser of the specular reflection from the multilayer and suppresses the iridescence. This combination leads to a colour-stable and angle-independent green reflection that probably enhances the camouflage of the beetles in their natural habitat.