The evolution of human skin coloration

MC1R: Front and Center in the Bright Side of Dark Eumelanin and DNA Repair

Melanin, the pigment produced by specialized cells, melanocytes, is responsible for skin and hair color. Skin pigmentation is an important protective mechanism against the DNA damaging and mutagenic effects of solar ultraviolet radiation (UV). It is acknowledged that exposure to UV is the main etiological environmental factor for all forms of skin cancer, including melanoma. DNA repair capacity is another major factor that determines the risk for skin cancer. Human melanocytes synthesize eumelanin, the dark brown form of melanin, as well as pheomelanin, which is reddish-yellow in color. The relative rates of eumelanin and pheomelanin synthesis by melanocytes determine skin color and the sensitivity of skin to the drastic effects of solar UV. Understanding the complex regulation of melanocyte function and how it responds to solar UV has a huge impact on developing novel photoprotective strategies to prevent skin cancer, particularly melanoma, the most fatal form, which originates from melanocytes. This review provides an overview of the known differences in the photoprotective effects of eumelanin versus pheomelanin, how these two forms of melanin are regulated genetically and biochemically, and their impact on the DNA damaging effects of UV exposure. Additionally, this review briefly discusses the role of paracrine factors, focusing on α-melanocortin (α-melanocyte stimulating hormone; α-MSH), in regulating melanogenesis and the response of melanocytes to UV, and describes a chemoprevention strategy based on targeting the melanocortin 1 receptor (MC1R) by analogs of its physiological agonist α-MSH.

Clinical and Biological Characterization of Skin Pigmentation Diversity and Its Consequences on UV Impact

Skin color diversity is the most variable and noticeable phenotypic trait in humans resulting from constitutive pigmentation variability. This paper will review the characterization of skin pigmentation diversity with a focus on the most recent data on the genetic basis of skin pigmentation, and the various methodologies for skin color assessment. Then, melanocyte activity and amount, type and distribution of melanins, which are the main drivers for skin pigmentation, are described. Paracrine regulators of melanocyte microenvironment are also discussed. Skin response to sun exposure is also highly dependent on color diversity. Thus, sensitivity to solar wavelengths is examined in terms of acute effects such as sunburn/erythema or induced-pigmentation but also long-term consequences such as skin cancers, photoageing and pigmentary disorders. More pronounced sun-sensitivity in lighter or darker skin types depending on the detrimental effects and involved wavelengths is reviewed.

The Effects of Active and Passive Leisure on Cognition in Children: Evidence from Exogenous Variation in Weather

Leisure time activity is often positioned as a key factor in child development, yet we know relatively little about the causal significance of various specific activities or the magnitude of their effects. Here, we couple individual fixed effects and instrumental variable approaches in trying to determine whether specific forms of leisure contribute to gains in test performance over time. We merge a restricted access version of the Panel Study of Income Dynamics (PSID) Child Development Supplement (CDS), longitudinally collected from 1997 to 2007, with a database of over three million county-day observations of sunlight. We use this proxy for weather to instrument for the variation in physical, outdoor, sedentary, and screen time behaviors based on CDS time diaries. We find evidence that physical and outdoor activity positively influence math performance, while sedentary behavior and screen time exhibit the opposite effect. Moreover, the effect sizes range from a quarter to three quarters of a standard deviation per additional daily hour of activity, rendering them meaningful in a real world sense. Our stratified results indicate that children from less educated mothers and girls seem to be most sensitive to the effects of active and passive forms of leisure. We conclude with a descriptive examination of the trend lines between our data and the new 2014 CDS cohort, providing relevant contemporary context for our findings.

Acute ultraviolet radiation exposure attenuates nitric oxide-mediated vasodilation in the cutaneous microvasculature of healthy humans

5-methyltetrahydrofolate (5-MTHF) is important for nitric oxide (NO)-mediated cutaneous microvascular vasodilation. Ultraviolet B (UVB) radiation may deplete 5-MTHF, either directly or via production of reactive oxygen species (ROS), decreasing NO-mediated vasodilation. We hypothesized that 1) acute UVB exposure would attenuate NO-dependent cutaneous vasodilation, 2) local perfusion of 5-MTHF or ascorbate (ASC; anti-oxidant) would augment NO-dependent vasodilation after UVB, and 3) darker skin pigmentation would be UVB-protective. Three intradermal microdialysis fibers placed in each forearm of 21 healthy young adults (23±1 yr; 8M/13F) locally delivered lactated Ringer's (control), 5mM 5-MTHF, or 10mM ASC. One arm was UVB-exposed (300mJ/cm²), the other served as non-exposed control (CON). Following UVB exposure, a standardized local heating (42˚C) protocol induced cutaneous vasodilation. After attaining a plateau blood flow, 15mM N^G-nitro-L-arginine methyl ester (L-NAME; nitric oxide synthase inhibiter) was infused at all sites to quantify the NO contribution. Red cell flux was measured at each site by laser-Doppler flowmetry (LDF) and cutaneous vascular conductance (CVC=LDF/MAP) was expressed as a percentage of maximum (%CVC_max; 28mM sodium nitroprusside+43°C). UVB attenuated NO-mediated vasodilation compared to CON (23.1±3.6 vs 33.9±3.4 %; p=0.001). Delivery of 5-MTHF or ASC improved NO-mediated vasodilation versus lactated Ringer's in the UVB-exposed arm (MTHF: 30.1±4.8 vs 23.1±3.8 %; p=0.03; ASC: 30.9±4.3 vs 23.1±3.8 %; p=0.02). Neither treatment affected the response in the non-exposed arm (p≥0.09). Skin pigmentation (M-index) was not predictive of the UVB response (p≥0.34). These data suggest that acute UVB exposure attenuates NO-mediated vasodilation via direct and/or ROS-induced reductions in 5-MTHF, independent of skin pigmentation.

Tanning Capacity and Nicotine Dependence Among African Americans

PURPOSE

Recent findings suggest a link between facultative melanin and nicotine dependence among African Americans. We hypothesized that tanning capacity is associated with the time to first cigarette (TTFC) of the day.

METHODS

Using a criterion based sample of 150 adult African American current smokers, reflectometer measures of constitutive and facultative melanin, tanning capacity, smoking status and history, saliva cotinine, sociodemographic characteristics, and stress and discrimination scales were recorded. TTFC was categorized as: 1) within the first 5 min versus more than 5 min; and 2) within the first 30 min versus more than 30 min. Descriptive and multivariate analyses were conducted.

RESULTS

Analysis revealed significantly higher tanning capacity among individuals who smoked their first cigarette of the day within the first 5 min of awakening (13.5) than among those who smoked after 5 min (10.3, p = 0.01) and among those who smoked within the first 30 min (12.8 vs. 9.6, p = 0.03) compared to those who initiated after this time point. Multivariate logistic regression indicated that tanning capacity was significantly and positively related (OR = 1.14, 95% CI = 1.05-1.22) to TTFC within the first 5 min and was also significantly related to TTFC within the first 30 min (OR = 1.13, CI = 1.03-1.23).

CONCLUSION

Tanning capacity was positively associated with a behavioral measure of nicotine dependence among African American smokers. This association was consistent whether comparing smokers at higher or lower levels of dependence. Future research should examine tanning capacity and other indicators of melanin content with smoking cessation rates and tobacco-attributable health disparities.

The influences of genes, the environment, and social factors on the evolution of skin color diversity in India

OBJECTIVES

Skin color is a highly visible and variable trait across human populations. It is not yet clear how evolutionary forces interact to generate phenotypic diversity. Here, we sought to unravel through an integrative framework the role played by three factors-demography and migration, sexual selection, and natural selection-in driving skin color diversity in India.

METHODS

Skin reflectance data were collected from 10 diverse socio-cultural populations along the latitudinal expanse of India, including both sexes. We first looked at how skin color varies within and between these populations. Second, we compared patterns of sexual dimorphism in skin color. Third, we studied the influence of ultraviolet radiation on skin color throughout India. Finally, we attempted to disentangle the interactions between these factors in the context of available genetic data.

RESULTS

We found that the relative importance of these forces varied between populations. Social factors and population structure have played a stronger role than natural selection in shaping skin color diversity across India. Phenotypic overprinting resulted from additional genetic mutations overriding the skin lightening effect of variants such as the SLC24A5 rs1426654-A allele in some populations, in the context of the variable influence of sexual selection. Furthermore, specific genotypes are not associated reliably with specific skin color phenotypes. This result has relevance for DNA forensics and ancient DNA research.

CONCLUSIONS

India is a crucible of macro- and micro-evolutionary forces, and the complex interactions of physical and social forces are visible in the patterns of skin color seen today in the country.

Recent evolution of the human skin barrier

The skin is the first line of defense against the environment, with the epidermis as the outermost tissue providing much of the barrier function. Given its direct exposure to and encounters with the environment, the epidermis must evolve to provide an optimal barrier for the survival of an organism. Recent advances in genomics have identified a number of genes for the human skin barrier that have undergone evolutionary changes since humans diverged from chimpanzees. Here, we highlight a selection of key and innovative genetic findings for skin barrier evolution in our divergence from our primate ancestors and among modern human populations.

Constitutive melanin density is associated with higher 25-hydroxyvitamin D and potentially total body BMD in older Caucasian adults via increased sun tolerance and exposure

Greater skin pigmentation reduces dose equivalent cutaneous vitamin D3 production, potentially impacting lifetime vitamin D status and fracture risk. We show that melanin density was positively associated with 25-hydroxyvitamin D and total body bone mineral density. These relationships were partially explained by greater sun exposure due to more permissive skin phenotype.

INTRODUCTION

Higher cutaneous melanin reduces vitamin D3 production. This may impact lifetime vitamin D status and increase fracture risk. This study aimed to describe the relationship between spectrophotometrically determined constitutive melanin density, osteoporotic risk factors and potential intermediaries in a cohort of exclusively older Caucasian adults.

METHODS

One thousand seventy-two community-dwelling adults aged 50-80 years had constitutive melanin density quantified using spectrophotometry. Sun exposure, skin phenotype, non-melanoma skin cancer (NMSC) prevalence and smoking status were assessed by questionnaire. Bone mineral density (BMD), falls risk, physical activity and 25-hydroxyvitamin D were measured using DXA, the short form Physiological Profile Assessment, pedometer and radioimmunoassay, respectively.

RESULTS

Higher melanin density was independently associated with greater ability to tan (RR = 1.27, p < 0.001), less propensity to sunburn (RR = 0.92, p < 0.001), fewer lifetime sunburns (RR = 0.94, p = 0.01), current smoking (RR = 1.41, p < 0.001), female sex (RR = 1.24, p < 0.001) and less photodamage (RR = 0.98, p = 0.01). The associations between melanin density and sun exposure (RR = 1.05-1.11, p < 0.001-0.01), sun protection behaviours (RR = 0.89, p < 0.001) and NMSC prevalence (RR = 0.75, p = 0.001) were no longer significant after taking into account skin phenotype and sun exposure, respectively. 25-Hydroxyvitamin D was strongly associated with higher melanin density (β = 1.71-2.05, p = 0.001). The association between melanin density and total body BMD (β = 0.007, p = 0.04) became non-significant after adjustment for 25-hydroxyvitamin D. There was no association between melanin density and physical activity, falls risk or BMD at other sites.

CONCLUSIONS

Our data support a model of higher constitutive melanin density underpinning a less photosensitive skin phenotype, permitting greater sun exposure with fewer sequelae and yielding higher 25-hydroxyvitamin D and, potentially, total body BMD.

Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds

Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. In this study, we systematically investigated the selection signatures in six phenotypically diverse goat breeds using SNPs obtained from pooled whole-genome resequencing data. More than 95.5% of 446–642 million clean reads were mapped to the latest reference goat genome, which generated a sequencing depth ranging from 22.30 to 31.75-fold for each breed. A total of 5,802,307, 6,794,020, 7,562,312, 5,325,119, 8,764,136, and 9,488,057 putative SNPs were detected in Boer, Meigu, Jintang Black, Nanjiang Yellow, Tibetan, and Tibetan cashmere goats, respectively. Based on the genome-wide F_ST and expected heterozygosity scores along 100-kb sliding windows, 68, 89, 44, 44, 19, and 35 outlier windows were deemed as the selection signatures in the six goat breeds. After genome annotation, several genes within the selection signals were found to be possibly associated with important traits in goats, such as coat color (IRF4, EXOC2, RALY, EIF2S2, and KITLG), high-altitude adaptation (EPAS1), growth (LDB2), and reproduction traits (KHDRBS2). In summary, we provide an improved understanding of the genetic diversity and the genomic footprints under positive selection or the adaptations to the local environments in the domestic goat genome.

Toward Understanding the Repeated Occurrence of Associations between Melanin-Based Coloration and Multiple Phenotypes

Melanin is the most widespread pigment in organisms. Melanin-based coloration has been repeatedly observed to be associated with the same traits and in the same direction in different vertebrate and insect species. However, whether any factors that are common to different taxa account for the repeated evolution of melanin-phenotype associations remains unclear. We propose to approach this question from the perspective of convergent and parallel evolution to clarify to what extent different species have evolved the same associations owing to a shared genetic basis and being subjected to similar selective pressures. Our current understanding of the genetic basis of melanin-phenotype associations allows for both convergent and parallel evolution, but this understanding is still limited. Further research is needed to clarify the generality and interdependencies of the different proposed mechanisms (supergenes, pleiotropy based on hormones, or neural crest cells). The general ecological scenarios whereby melanin-based coloration is under selection-protection from ultraviolet radiation, thermoregulation in cold environments, or as a signal of social status-offer a good opportunity to study how melanin-phenotype associations evolve. Reviewing these scenarios shows that some traits associated with melanin-based coloration might be selected together with coloration by also favoring adaptation but that other associated traits might impede adaptation, which may be indicative of genetic constraints. We therefore encourage further research on the relative roles that selection and genetic constraints play in shaping multiple melanin-phenotype associations. Placed into a phylogenetic context, this will help clarify to what extent these associations result from convergent or parallel evolutionary processes and why melanin-phenotype associations are so common across the tree of life.

Contextual Effects in Face Lightness Perception Are Not Expertise-Dependent

Lightness judgments of face stimuli are context-dependent (i.e., judgments of face lightness are influenced by race classification). Here, we tested whether contextual effects in face lightness perception are modulated by expertise, exploiting well-known other race effects in face perception. We used a lightness-matching paradigm where Chinese and White observers were asked to adjust the lightness of a variable face to match that of a standard face. The context (i.e., race category) of the two faces could be the same or different. Our data indicated that both groups had the smallest matching errors in same-context trials, for which errors did not vary across different racial categories. For cross-context trials, observers made the largest (negative) errors when the reference face was Black, as compared to Chinese and White references, for which matching errors were no different from zero or trended positively. Critically, this pattern was similar for both groups. We suggest that contextual influences in lightness perception are unlikely to be guided by classical mechanisms that drive face perception. We instead speculate that such influences manifest in terms of an interaction between race assumptions (e.g., expected surface reflectance patterns) and traditional mechanisms for reflectance computations.

Neutral Theory, Disease Mutations, and Personal Exomes

Genetic differences between species and within populations are two sides of the same coin under the neutral theory of molecular evolution. This theory posits that a vast majority of evolutionary substitutions, which appear as differences between species, are (nearly) neutral, that is, these substitutions are permitted without a significantly adverse impact on a species' survival. We refer to them as evolutionarily permissible (ePerm) variation. Evolutionary permissibility of any possible variant can be inferred from multispecies sequence alignments by applying sophisticated statistical methods to the evolutionary tree of species. Here, we explore the evolutionary permissibility of amino acid variants associated with genetic diseases and those observed in personal exomes. Consistent with the predictions of the neutral theory, disease associated amino acid variants are rarely ePerm, much more biochemically radical, and found predominantly at more conserved positions than their non-disease counterparts. Only 10% of amino acid mutations are ePerm, but these variants rise to become two-thirds of all substitutions in the human lineage (a 6-fold enrichment). In contrast, only a minority of the variants in a personal exome are ePerm, a seemingly counterintuitive pattern that results from a combination of mutational and evolutionary processes that are, in fact, broadly consistent with the neutral theory. Evolutionarily forbidden variants outnumber detrimental variants in individual exomes and may play an underappreciated role in protecting against disease. We discuss these observations and conclude that the long-term evolutionary history of species can illuminate functional biomedical properties of variation present in personal exomes.

Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure

The skin’s tendency to sunburn rather than tan is a major risk factor for skin cancer. Here we report a large genome-wide association study of ease of skin tanning in 176,678 subjects of European ancestry. We identify significant association with tanning ability at 20 loci. We confirm previously identified associations at six of these loci, and report 14 novel loci, of which ten have never been associated with pigmentation-related phenotypes. Our results also suggest that variants at the AHR/AGR3 locus, previously associated with cutaneous malignant melanoma the underlying mechanism of which is poorly understood, might act on disease risk through modulation of tanning ability.

The skin’s tanning response to sun exposure shows great interindividual variability. Here, Visconti et al. perform a genome-wide association study for ease of skin tanning and identify 20 genetic loci, ten of which had not previously been associated with pigmentation-related traits.

Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability

Hair color is one of the most recognizable visual traits in European populations and is under strong genetic control. Here we report the results of a genome-wide association study meta-analysis of almost 300,000 participants of European descent. We identified 123 autosomal and one X-chromosome loci significantly associated with hair color; all but 13 are novel. Collectively, single-nucleotide polymorphisms associated with hair color within these loci explain 34.6% of red hair, 24.8% of blond hair, and 26.1% of black hair heritability in the study populations. These results confirm the polygenic nature of complex phenotypes and improve our understanding of melanin pigment metabolism in humans.

The Vitamin D⁻Folate Hypothesis as an Evolutionary Model for Skin Pigmentation: An Update and Integration of Current Ideas

Vitamin D is unique in being generated in our skin following ultraviolet radiation (UVR) exposure. Ongoing research into vitamin D must therefore always consider the influence of UVR on vitamin D processes. The close relationship between vitamin D and UVR forms the basis of the “vitamin D–folate hypothesis”, a popular theory for why human skin colour has evolved as an apparent adaption to UVR environments. Vitamin D and folate have disparate sensitivities to UVR; whilst vitamin D may be synthesised following UVR exposure, folate may be degraded. The vitamin D–folate hypothesis proposes that skin pigmentation has evolved as a balancing mechanism, maintaining levels of these vitamins. There are several alternative theories that counter the vitamin D–folate hypothesis. However, there is significant overlap between these theories and the now known actions of vitamin D and folate in the skin. The focus of this review is to present an update on the vitamin D–folate hypothesis by integrating these current theories and discussing new evidence that supports associations between vitamin D and folate genetics, UVR, and skin pigmentation. In light of recent human migrations and seasonality in disease, the need for ongoing research into potential UVR-responsive processes within the body is also discussed.

Molecular cloning and expression analysis of tyr and tyrp1 genes in normal and albino yellow catfish Tachysurus fulvidraco

The full-length complementary DNA of two genes related to vertebrate albinism, the tyrosinase gene tyr and tyrosinase-related protein 1 gene tyrp1, were cloned and analysed from normal and albino yellow catfish Tachysurus fulvidraco. The open reading frames (ORF) of tyr and tyrp1 encode putative peptides of 533 and 526 amino acids (amino-acid), both of which possess two conserved copper binding sites. The homologous identities of deduced amino-acid sequences showed that both Tyr and Tyrp1 of T. fulvidraco share considerable similarity with that of channel catfish Ictalurus punctatus. Both tyr and tyrp1 were expressed in a wide range of adult tissues. Tyr gene had the highest expression level in the brain of both normal and albino T. fulvidraco. Tyrp1 had the highest expression level in the skin of normal groups, and the fin of albino groups. The messenger (m)RNA expressions of tyr and tyrp1 were detectable at different early developmental stages and varied with embryonic and larval growth. Tyr and tyrp1 mRNA have obvious tissue specificity both in normal and albino T. fulvidraco and higher expression levels were detected in the normal group revealing that tyr and tyrp1 may have an important role in pigmentation. These results will provide useful data for understanding the molecular mechanism of melanin formation and the occurrence of albinism in T. fulvidraco.

Estimating Time to the Common Ancestor for a Beneficial Allele

The haplotypes of a beneficial allele carry information about its history that can shed light on its age and the putative cause for its increase in frequency. Specifically, the signature of an allele's age is contained in the pattern of variation that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the surrounding background haplotype diversity. Using simulations, we demonstrate how the inclusion of information from both mutation and recombination events increases accuracy relative to approaches that only consider a single type of event. We also show the behavior of the estimator in cases where data do not conform to model assumptions, and provide some diagnostics for assessing and improving inference. Using the method, we analyze population-specific patterns in the 1000 Genomes Project data to estimate the timing of adaptation for several variants which show evidence of recent selection and functional relevance to diet, skin pigmentation, and morphology in humans.

Human colour in mate choice and competition

The colour of our skin and clothing affects how others perceive us and how we behave. Human skin colour varies conspicuously with genetic ancestry, but even subtle changes in skin colour due to diet, blood oxygenation and hormone levels influence social perceptions. In this review, we describe the theoretical and empirical frameworks in which human colour is researched. We explore how subtle skin colour differences relate to judgements of health and attractiveness. Also, because humans are one of the few organisms able to manipulate their apparent colour, we review how cosmetics and clothing are implicated in courtship and competition, both inside the laboratory and in the real world. Research on human colour is in its infancy compared with human psychophysics and colour research in non-human animals, and hence we present best-practice guidelines for methods and reporting, which we hope will improve the validity and reproducibility of studies on human coloration.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.

The evolution of eccrine sweat glands in human and nonhuman primates

Sweating is an unusual thermoregulatory strategy for most mammals, yet is critical for humans. This trait is commonly hypothesized to result from human ancestors moving from a forest to a warmer and drier open environment. As soft tissue traits do not typically fossilize, this idea has been difficult to test. Therefore, we used a comparative approach to examine 15 eccrine gland traits from 35 primate species. For each trait we measured phylogenetic signal, tested three evolutionary models to explain trait variation, and used phylogenetic models to examine how traits varied in response to climate variables. Phylogenetic signal in traits varied substantially, with the two traits exhibiting the highest values being gland distribution on the body and percent eccrine vs. apocrine glands on the body. Variation in most traits was best explained by an Ornstein-Uhlenbeck model suggesting the importance of natural selection. Two traits were strongly predicted by climate. First, species with high eccrine gland glycogen content were associated with habitats exhibiting warm temperatures and low rainfall. Second, species with increased capillarization were associated with high temperature. Glycogen is a primary energy substrate powering sweat production and sodium reabsorption in the eccrine gland, and increased capillarization permits greater oxygen, glucose and electrolyte delivery. Thus, our results are evidence of natural selection for increased sweating capacity in primate species with body surface eccrine glands living in hot and dry climates. We suggest that selection for increased glycogen content and capillarization may have been part of initial increases in hominin thermoregulatory sweating capacity.

[A question of colour]

GWAS analyses for skin colour performed on a series of diverse African groups reveal new loci involved in this phenotype and, surprisingly, the presence within several African populations of the "light" allele of the SLC24A5 gene at significant frequency. This underlines the complexity of skin colour genetics and the interest of studying a wide range of populations.

The significance of age group, gender and skin complexion in relation to the clinical distribution of developmental oral mucosal alterations in 5-13 year-old children

INTRODUCTION

To describe the relationship and impact of age group, gender and skin complexion on the prevalence and clinical distribution of oral mucosal alterations of developmental origin (OMA-DO) among school children aged 5-13 years.

METHODS

A randomized representative national survey of Jordanian school children including all Country geographic areas was performed. Cut-off age that significantly correlated with presence and distribution of OMA-DO was identified (ROC curve). Skin complexion was classified into light/fair, intermediate/tan, dark/brown based on skin complexion index. Chi square test with P value≤0.05 was used for significance of correlations.

RESULTS

Two thousand two hundred and fifty one children were clinically examined. The average age that significantly correlated with prevalence and distribution of OMA-DO was 9.9 years. Female gender was significantly correlated with four OMA-DO: leukoedema (L), linea Alba (LA), Fordyce's granules (FG), commissural lip pits (CLP) and wider distribution of racial pigmentations (RP) (P<0.05, χ² test). Older age group (9.9-13 years) was significantly correlated with 7 OMA-DO: L, LA, FG, frenal tag, CLP, mandibular and maxillary tori (MT) as well as wider clinical distribution of RP, FG, L (P<0.05 χ² test). Dark skin complexion significantly correlated with 5 OMA-DO: L, LA, FG, RP, MT and wider clinical distribution of RP (P<0.02, χ² test).

CONCLUSIONS

Increased prevalence and wider clinical distribution of OMA-DO are significantly associated with older age group of 9.9-13 years, female gender, and dark skin complexion. Oral health care provides are encouraged to be familiar with these correlations. This knowledge is expected to improve OMA-DO diagnosis and clinical management. Continuous education programs in this field are recommended.

Loci associated with skin pigmentation identified in African populations

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.

Environment-Related Variation in the Human Mid-Face

Previous studies that have examined mid-facial morphology in geographically dispersed and genetically diverse groups of humans have shown a strong adaptation of the nasal part to extreme cold environments, which was not observed in non-Arctic regions. However, it remains unclear whether different parts of the mid-face area show independent adaptation to nonpolar climates, and if so, how this adaptation impacted the morphology. To address this question, we investigated potential associations between climatic variables and the mid-facial shape in 14 populations, focusing on four aspects of the morphology: total shape, zygomatic, nasal and alveolar. The results show that when the genetic distance between populations is not considered, all aspects of the morphology are strongly correlated with all climatic variables. When the genetic distance is considered, significant correlations remain only for the zygomatic, and nasal parts with temperature, and for the nasal part and alveolar with sunshine exposure. A strong but probably artificial correlation of the alveolar with atmospheric pressure is also observed. Additionally, partial least square analyses indicate that tropical and subtropical environments are associated with smaller zygomatic and more triangular nose aperture compared to more temperate environments. These findings suggest that temperate and tropical climates have induced adaptation of zygomatic and nasal parts of the mid-face in humans, and that this adaptation was probably driven by temperature and sunlight exposure conditions. Anat Rec, 300:238-250, 2017. © 2016 Wiley Periodicals, Inc.

Onset and duration of cycloplegic action of 1% cyclopentolate - 1% tropicamide combination

PURPOSE

To study the time course (onset, time and duration of maximal cycloplegia, and the full duration) of cycloplegic action of 1% Cyclopentolate - 1% Tropicamide.

METHODS

Seventy-seven students, aged 15-24 years were purposively sampled from the University of Cape Coast and Cape Coast Technical Institute. Subjective near addition (ADD) determination and pupil diameter measurement before and after a drop of the test agent (1% Cyclopentolate - 1% Tropicamide combination in the right eye) and the control (1% Cyclopentolate in the left eye) were performed. Measurements of subjective near ADD and pupil diameter were made after the initial reading at 5 minutes interval for the first hour and every 30 minutes for the next 7 hours for each participant. Time of onset, time of peak cycloplegia, duration of peak cycloplegia and duration of total cycloplegic effect was indirectly determined.

RESULTS

1% Cyclopentolate - 1% Tropicamide combination had rapid onset of cycloplegia (5-10 minutes), shorter time of maximal cycloplegia (55 versus 90 minutes), and recovery (7 versus ≥ 8hours) in the majority (79.2%) of subjects.

CONCLUSION

Cyclopentolate -Tropicamide combination was comparable to Cyclopentolate in depth of cycloplegia produced, and clinically superior to 1% Cyclopentolate in rapidity of cycloplegic onset, time of maximal cycloplegia and recovery from cycloplegia.

Alteration of sheep coat color pattern by disruption of ASIP gene via CRISPR Cas9

Coat color is an important characteristic and economic trait in domestic sheep. Aiming at alteration of Chinese merino sheep coat color by genome manipulation, we disrupted sheep agouti signaling protein gene by CRISPR/Cas9. A total of seven indels were identified in 5 of 6 born lambs. Each targeted lamb happened at least two kinds of modifications, and targeted lambs with multiple modifications displayed variety of coat color patterns. Three lambs with 4 bp deletion showed badgerface with black body coat color in two lambs, and brown coat color with light ventral pigmentation in another one. The black-white spotted color was observed in two lambs with 2 bp deletion. Further analysis unraveled that modifications happened in one or more than two copies of ASIP gene, and moreover, the additional spontaneous mutations of D9 and/or D5 preceding the targeting modification could also involve the formation of coat color patterns. Taken together, the entanglement of ASIP modifications by CRISPR/Cas9, spontaneous D9/D5 mutations, and ASIP gene duplications contributed to the variety of coat color patterns in targeted lambs.

Facial Contrast Is a Cross-Cultural Cue for Perceiving Age

Age is a fundamental social dimension and a youthful appearance is of importance for many individuals, perhaps because it is a relevant predictor of aspects of health, facial attractiveness and general well-being. We recently showed that facial contrast-the color and luminance difference between facial features and the surrounding skin-is age-related and a cue to age perception of Caucasian women. Specifically, aspects of facial contrast decrease with age in Caucasian women, and Caucasian female faces with higher contrast look younger (Porcheron et al., 2013). Here we investigated faces of other ethnic groups and raters of other cultures to see whether facial contrast is a cross-cultural youth-related attribute. Using large sets of full face color photographs of Chinese, Latin American and black South African women aged 20-80, we measured the luminance and color contrast between the facial features (the eyes, the lips, and the brows) and the surrounding skin. Most aspects of facial contrast that were previously found to decrease with age in Caucasian women were also found to decrease with age in the other ethnic groups. Though the overall pattern of changes with age was common to all women, there were also some differences between the groups. In a separate study, individual faces of the 4 ethnic groups were perceived younger by French and Chinese participants when the aspects of facial contrast that vary with age in the majority of faces were artificially increased, but older when they were artificially decreased. Altogether these findings indicate that facial contrast is a cross-cultural cue to youthfulness. Because cosmetics were shown to enhance facial contrast, this work provides some support for the notion that a universal function of cosmetics is to make female faces look younger.

Quantifying phenotype-environment matching in the protected Kerry spotted slug (Mollusca: Gastropoda) using digital photography: exposure to UV radiation determines cryptic colour morphs

BACKGROUND

Animal colours and patterns commonly play a role in reducing detection by predators, social signalling or increasing survival in response to some other environmental pressure. Different colour morphs can evolve within populations exposed to different levels of predation or environmental stress and in some cases can arise within the lifetime of an individual as the result of phenotypic plasticity. Skin pigmentation is variable for many terrestrial slugs (Mollusca: Gastropoda), both between and within species. The Kerry spotted slug Geomalacus maculosus Allman, an EU protected species, exhibits two distinct phenotypes: brown individuals occur in forested habitats whereas black animals live in open habitats such as blanket bog. Both colour forms are spotted and each type strongly resembles the substrate of their habitat, suggesting that G. maculosus possesses camouflage.

RESULTS

Analysis of digital images of wild slugs demonstrated that each colour morph is strongly and positively correlated with the colour properties of the background in each habitat but not with the substrate of the alternative habitats, suggesting habitat-specific crypsis. Experiments were undertaken on laboratory-reared juvenile slugs to investigate whether ultraviolet (UV) radiation or diet could induce colour change. Exposure to UV radiation induced the black (bog) phenotype whereas slugs reared in darkness did not change colour. Diet had no effect on juvenile colouration. Examination of skin tissue from specimens exposed to either UV or dark treatments demonstrated that UV-exposed slugs had significantly higher concentrations of black pigment in their epithelium.

CONCLUSIONS

These results suggest that colour dimorphism in G. maculosus is an example of phenotypic plasticity which is explained by differential exposure to UV radiation. Each resulting colour morph provides incidental camouflage against the different coloured substrate of each habitat. This, to our knowledge, is the first documented example of colour change in response to UV radiation in a terrestrial mollusc. Pigmentation appears to be correlated with a number of behavioural traits in G. maculosus, and we suggest that understanding melanisation in other terrestrial molluscs may be useful in the study of pestiferous and invasive species. The implications of colour change for G. maculosus conservation are also discussed.

The colours of humanity: the evolution of pigmentation in the human lineage

Humans are a colourful species of primate, with human skin, hair and eye coloration having been influenced by a great variety of evolutionary forces throughout prehistory. Functionally naked skin has been the physical interface between the physical environment and the human body for most of the history of the genus Homo, and hence skin coloration has been under intense natural selection. From an original condition of protective, dark, eumelanin-enriched coloration in early tropical-dwelling Homo and Homo sapiens, loss of melanin pigmentation occurred under natural selection as Homo sapiens dispersed into non-tropical latitudes of Africa and Eurasia. Genes responsible for skin, hair and eye coloration appear to have been affected significantly by population bottlenecks in the course of Homo sapiens dispersals. Because specific skin colour phenotypes can be created by different combinations of skin colour-associated genetic markers, loss of genetic variability due to genetic drift appears to have had negligible effects on the highly redundant genetic 'palette' for the skin colour. This does not appear to have been the case for hair and eye coloration, however, and these traits appear to have been more strongly influenced by genetic drift and, possibly, sexual selection.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.

Adaptation of human skin color in various populations

BACKGROUND

Skin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine.

DISCUSSION

Impressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies.

CONCLUSION

Previous studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.

Inference on the Genetic Basis of Eye and Skin Color in an Admixed Population via Bayesian Linear Mixed Models

Genetic association studies in admixed populations are underrepresented in the genomics literature, with a key concern for researchers being the adequate control of spurious associations due to population structure. Linear mixed models (LMMs) are well suited for genome-wide association studies (GWAS) because they account for both population stratification and cryptic relatedness and achieve increased statistical power by jointly modeling all genotyped markers. Additionally, Bayesian LMMs allow for more flexible assumptions about the underlying distribution of genetic effects, and can concurrently estimate the proportion of phenotypic variance explained by genetic markers. Using three recently published Bayesian LMMs, Bayes R, BSLMM, and BOLT-LMM, we investigate an existing data set on eye (n = 625) and skin (n = 684) color from Cape Verde, an island nation off West Africa that is home to individuals with a broad range of phenotypic values for eye and skin color due to the mix of West African and European ancestry. We use simulations to demonstrate the utility of Bayesian LMMs for mapping loci and studying the genetic architecture of quantitative traits in admixed populations. The Bayesian LMMs provide evidence for two new pigmentation loci: one for eye color (AHRR) and one for skin color (DDB1).

Global skin colour prediction from DNA

Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.

Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project

The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology. Melanocortin-1 receptor (MC1R) is one of the most studied genes involved in pigmentation variation. As MC1R has already been suggested to affect melanogenesis and increase risk of developing melanoma, it constitutes one of the best models to understand how natural selection acts on pigmentation. Here we employed a locally developed pipeline to obtain genotype and haplotype data for MC1R from the raw sequencing data provided by the 1000 Genomes FTP site. We also compared such genotype data to Phase 3 VCF to evaluate its quality and discover any polymorphic sites that may have been overlooked. In conclusion, either the VCF file or one of the presently described pipelines could be used to obtain reliable and accurate genotype calling from the 1000 Genomes Phase 3 data.

Identifying signatures of positive selection in pigmentation genes in two South Asian populations

OBJECTIVES

Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations.

METHODS

Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL).

RESULTS

Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population.

CONCLUSIONS

These results suggest that selection may have affected these loci broadly across the region.

Prevalence and Determinants of Suboptimal Vitamin D Levels in a Multiethnic Asian Population

This population-based cross-sectional study examined the prevalence and risk factors of suboptimal vitamin D levels (assessed using circulating 25-hydroxycholecalciferol (25(OH)D)) in a multi-ethnic sample of Asian adults. Plasma 25(OH)D concentration of 1139 Chinese, Malay and Indians (40–80 years) were stratified into normal (≥30 ng/mL), and suboptimal (including insufficiency and deficiency, <30 ng/mL) based on the 2011 Endocrine Society Clinical Practice Guidelines. Logistic regression models were used to assess the associations of demographic, lifestyle and clinical risk factors with the outcome. Of the 1139 participants, 25(OH)D concentration was suboptimal in 76.1%. In multivariable models, age ≤65 years (compared to age >65 years), Malay and Indian ethnicities (compared to Chinese ethnicity), and higher body mass index, HbA1c, education and income levels were associated with suboptimal 25(OH)D concentration (p < 0.05). In a population-based sample of Asian adults, approximately 75% had suboptimal 25(OH)D concentration. Targeted interventions and stricter reinforcements of existing guidelines for vitamin D supplementation are needed for groups at risk of vitamin D insufficiency/deficiency.

Investigating the case of human nose shape and climate adaptation

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.

The study of human adaptation is essential to our understanding of disease etiology. Evolutionary investigations into why certain disease phenotypes such as sickle-cell anemia and lactose intolerance occur at different rates in different populations have led to a better understanding of the genetic and environmental risk factors involved. Similarly, research into the geographical distribution of skin pigmentation continues to yield important clues regarding risk of vitamin D deficiency and skin cancer. Here, we investigate whether variation in the shape of the external nose across populations has been driven by regional differences in climate. We find that variation in both nares width and alar base width appear to have experienced accelerated divergence across human populations. We also find that the geospatial distribution of nares width is correlated with temperature, and absolute humidity, but not with relative humidity. Our results support the claim that local adaptation to climate may have had a role in the evolution of nose shape differences across human populations.