Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.

Facial and genital color ornamentation, testosterone, and reproductive output in high-ranking male rhesus macaques

Males in many vertebrate species have colorful ornaments that evolved by sexual selection. The role of androgens in the genesis and maintenance of these signals is unclear. We studied 21 adult high-ranking male rhesus macaques from nine social groups in the free-ranging population on Cayo Santiago, Puerto Rico, and analyzed facial and genital skin luminance and redness, fecal androgens, rates of mating behaviors, and offspring sired. Facial and genital coloration varied in relation to age, mating behavior, reproductive success, and testosterone concentration. Our results indicate that skin coloration in high-ranking male rhesus macaques is a sexually-selected trait mediated by androgens. These results add to the growing literature on the proximate and ultimate causes of male sexual signals and highlight the need to examine how these characteristics change with age in other species.

Eyes of love: Java sparrows increase eye ring conspicuousness when pair-bonded

Conspicuous facial features, such as blushing in primates, can communicate social/emotional/physiological states in animals. However, the role of bare facial features is less well studied in birds than in humans or primates. We investigate the Java sparrow, which is characterised by conspicuous rings of swollen and blushed bare skin around the eye. Eye rings show no clear sex difference, although the swelling is associated with breeding. Java sparrows are socially monogamous, with mutual courtships and long-term pair-bonding. Therefore, it is plausible that eye rings function in within-pair communication. Specifically, do eye rings reflect psychophysiological conditions after pair formation? We assessed variations in ring thickness in pair-bonded birds and compared them with single birds and pairs of non-bonded individuals. Over the 12-week experimental period, pair-bonded males and females had an increased ring thickness, unlike the controls. We suggest eye rings convey breeding motivations or serve as fertility signals. This would be of great importance for ensuring reproductive synchrony in tropical birds like the Java sparrow. Our results contribute to understanding the evolution of facial ornamentation in birds, which was often overlooked in the past studies.

Genetic variants in melanogenesis proteins TYRP1 and TYR are associated with the golden rhesus macaque phenotype

Nonhuman primates (NHPs) are vital translational research models due to their high genetic, physiological, and anatomical homology with humans. The "golden" rhesus macaque (Macaca mulatta) phenotype is a naturally occurring, inherited trait with a visually distinct pigmentation pattern resulting in light blonde colored fur. Retinal imaging also reveals consistent hypopigmentation and occasional foveal hypoplasia. Here, we describe the use of genome-wide association in 2 distinct NHP populations to identify candidate variants in genes linked to the golden phenotype. Two missense variants were identified in the Tyrosinase-related protein 1 gene (Asp343Gly and Leu415Pro) that segregate with the phenotype. An additional and distinct association was also found with a Tyrosinase variant (His256Gln), indicating the light-colored fur phenotype can result from multiple genetic mechanisms. The implicated genes are related through their contribution to the melanogenesis pathway. Variants in these 2 genes are known to cause pigmentation phenotypes in other species and to be associated with oculocutaneous albinism in humans. The novel associations presented in this study will permit further investigations into the role these proteins and variants play in the melanogenesis pathway and model the effects of genetic hypopigmentation and altered melanogenesis in a naturally occurring nonhuman primate model.

What Is Written on a Dog's Face? Evaluating the Impact of Facial Phenotypes on Communication between Humans and Canines

Facial phenotypes are significant in communication with conspecifics among social primates. Less is understood about the impact of such markers in heterospecific encounters. Through behavioral and physical phenotype analyses of domesticated dogs living in human households, this study aims to evaluate the potential impact of superficial facial markings on dogs' production of human-directed facial expressions. That is, this study explores how facial markings, such as eyebrows, patches, and widow's peaks, are related to expressivity toward humans. We used the Dog Facial Action Coding System (DogFACS) as an objective measure of expressivity, and we developed an original schematic for a standardized coding of facial patterns and coloration on a sample of more than 100 male and female dogs (N = 103), aged from 6 months to 12 years, representing eight breed groups. The present study found a statistically significant, though weak, correlation between expression rate and facial complexity, with dogs with plainer faces tending to be more expressive (r = -0.326, p ≤ 0.001). Interestingly, for adult dogs, human companions characterized dogs' rates of facial expressivity with more accuracy for dogs with plainer faces. Especially relevant to interspecies communication and cooperation, within-subject analyses revealed that dogs' muscle movements were distributed more evenly across their facial regions in a highly social test condition compared to conditions in which they received ambiguous cues from their owners. On the whole, this study provides an original evaluation of how facial features may impact communication in human-dog interactions.

Why are animals conspicuously colored? Evolution of sexual versus warning signals in land vertebrates

Conspicuous colors (e.g., red, yellow, blue) have evolved numerous times across animals. But the function of this coloration can differ radically among species. Many species use this coloration as a sexual signal to conspecifics, whereas others use it as a warning signal to predators. Why do different species evolve conspicuous coloration in association with one function as opposed to the other? We address this question in terrestrial vertebrates (tetrapods) using phylogenetic approaches, and test whether day-night activities of species help determine these patterns. Using phylogenetic logistic regression, we found that conspicuous, sexually dimorphic coloration is significantly associated with diurnal lineages (e.g., many birds and lizards). By contrast, the evolution of warning signals was significantly associated with large-scale clades that were ancestrally nocturnal (e.g., snakes, amphibians), regardless of the current diel activity of species. Overall, we show that the evolution of conspicuous coloration as warning signals or sexual signals is influenced by the ecology of species, both recently and in the ancient past.

Hair Microbiome Diversity within and across Primate Species

Primate hair and skin are substrates upon which social interactions occur and are host-pathogen interfaces. While human hair and skin microbiomes display body site specificity and immunological significance, little is known about the nonhuman primate (NHP) hair microbiome. Here, we collected hair samples (n = 158) from 8 body sites across 12 NHP species housed at three zoological institutions in the United States to examine the following: (1) the diversity and composition of the primate hair microbiome and (2) the factors predicting primate hair microbiome diversity and composition. If both environmental and evolutionary factors shape the microbiome, then we expect significant differences in microbiome diversity across host body sites, sexes, institutions, and species. We found our samples contained high abundances of gut-, respiratory-, and environment-associated microbiota. In addition, multiple factors predicted microbiome diversity and composition, although host species identity outweighed sex, body site, and institution as the strongest predictor. Our results suggest that hair microbial communities are affected by both evolutionary and environmental factors and are relatively similar across nonhuman primate body sites, which differs from the human condition. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome. IMPORTANCE We created the most comprehensive primate hair and skin data set to date, including data from 12 nonhuman primate species sampled from 8 body regions each. We find that the nonhuman primate hair microbiome is distinct from the human hair and skin microbiomes in that it is relatively uniform-as opposed to distinct-across body regions and is most abundant in gut-, environment-, and respiratory-associated microbiota rather than human skin-associated microbiota. Furthermore, we found that the nonhuman primate hair microbiome varies with host species identity, host sex, host environment, and host body site, with host species identity being the strongest predictor. This result demonstrates that nonhuman primate hair microbiome diversity varies with both evolutionary and environmental factors and within and across primate species. These findings have important implications for understanding the biology and conservation of wild and captive primates and the uniqueness of the human microbiome.

Variation and heritability of retinal cone ratios in a free-ranging population of rhesus macaques

A defining feature of catarrhine primates is uniform trichromacy-the ability to distinguish red (long; L), green (medium; M), and blue (short; S) wavelengths of light. Although the tuning of photoreceptors is conserved, the ratio of L:M cones in the retina is variable within and between species, with human cone ratios differing from other catarrhines. Yet, the sources and structure of variation in cone ratios are poorly understood, precluding a broader understanding of color vision variability. Here, we report a large-scale study of a pedigreed population of rhesus macaques (Macaca mulatta). We collected foveal RNA and analyzed opsin gene expression using cDNA and estimated additive genetic variance of cone ratios. The average L:M ratio and standard error was 1.03:1 ± 0.02. There was no age effect, and genetic contribution to variation was negligible. We found marginal sex effects with females having larger ratios than males. S cone ratios (0.143:1 ± 0.002) had significant genetic variance with a heritability estimate of 43% but did not differ between sexes or age groups. Our results contextualize the derived human condition of L-cone dominance and provide new information about the heritability of cone ratios and variation in primate color vision.

Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats

Cryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.

Anomalous pigmentation in American primates: review and first record of a leucistic black howler monkey in southeast Mexico

Leucism is an aberration of color that occurs in individuals as a consequence of genetic mutations. Along with albinism and piebaldism, leucism is one of the most commonly reported types of chromatic anomalies in mammals, however, detailed descriptions of such conditions are rare. We report the first record of a leucistic black howler monkey (Alouatta pigra) in southern Mexico, an apparently healthy individual who was the male of a typical black howler group. Additionally, we compiled records of anomalous pigmentation in American primates published in peer-reviewed journals between 1960 and 2021, as well as social media posts regarding casual observations of individuals with such conditions. We found 11 scientific articles which described 13 records of anomalous pigmentation in a total of 44 individuals, from five species, three subspecies and one hybrid. Leucism was the most widely reported condition with six records. We discovered 19 online posts of 20 individuals with anomalous pigmentation, which included two species not reported in scientific literature. Our results suggest that anomalous coloration is not a significant threat to survival, but its occurrence raises interesting, and possibly alarming, questions about the causes of such conditions. We encourage researchers and civil society to formally report such observations of animals with color aberrations, to expand upon the understanding of this phenomenon and to get involved in the conservation of tropical forests.

Hormonal correlates of male dominance rank, age, and genital colouration in vervet monkey (Chlorocebus pygerythrus)

Primates are the most colourful members of the Mammalian clade. In vervet monkeys (Chlorocebus pygerythrus), males are characterized by their red penis and blue scrotum. Such colour signals are often used in conspecific communication, and thus could be used to convey signaller condition. We quantified scrotal and penile colour characteristics using digital photographs between May-June 2016 from males in two neighboring groups along the shores of Lake Nabugabo, Uganda. We examined the relationship between fecal hormones, male dominance rank, age (adult vs. immature), and colour. Adult males were higher ranking than immatures, but there were no rank or age differences in fecal hormone levels. Glucocorticoids and androgens were positively correlated in immature, but not adult males. All scrotal characteristics were predicted by age, with adult males having more teal (i.e., less blue, more green) and more luminant scrota. Within adult males, those with higher androgens levels had more saturated blue scrotal colouration and higher-ranking males were more luminant. Penile colouration was also associated with age and rank. High-ranking males had a more saturated red penis, and adult male penile colour was more luminant and bluer than in immature males. Our findings are consistent with previous reports that scrotal colouration advertises sexual or reproductive maturity (i.e., age), but we also find that within adult males, colour also advertises dominance rank and may be mediated by androgen levels. Penile colouration also appears to signal information about male age and dominance rank but does not appear to be mediated by hormones.

Aposematism in mammals

Aposematic coloration is traditionally considered to signal unpalatability or toxicity. In mammals, most research has focused on just one form of defense, namely, noxious anal secretions, and its black-and-white advertisement as exemplified by skunks. The original formulation of aposematism, however, encompassed a broader range of morphological, physiological, and behavioral defenses, and there are many mammal species with black-and-white contrasting patterns that do not have noxious adaptations. Here, using Bayesian phylogenetic models and data from 1726 terrestrial nonvolant mammals we find that two aspects of conspicuous coloration, black-and-white coloration patterns on the head and body, advertise defenses that are morphological (spines, large body size), behavioral (pugnacity), and physiological (anal secretions), as well as being involved with sexual signaling and environmental factors linked to crypsis. Within Carnivora, defensive anal secretions are associated with complex black-and-white head patterns and longitudinal black-and-white body striping; in primates, larger bodied species exhibit irregular patches of black-and-white pelage; and in rodents, pugnacity is linked to sharp countershading and irregular blocks of white and black pelage. We show that black-and-white coloration in mammals is multifunctional, that it serves to warn predators of several defenses other than noxious anal secretions, and that aposematism in mammals is not restricted to carnivores.

The evolution of primate coloration revisited

Primates are noted for their varied and complex pelage and bare skin coloration but the significance of this diverse coloration remains opaque. Using new updated information, novel scoring of coat and skin coloration, and controlling for shared ancestry, we reexamined and extended findings from previous studies across the whole order and the five major clades within it. Across primates, we found (i) direct and indirect evidence for pelage coloration being driven by protective coloration strategies including background matching, countershading, disruptive coloration, and aposematism, (ii) diurnal primates being more colorful, and (iii) the possibility that pelage color diversity is negatively associated with female trichromatic vision; while (iv) reaffirming avoidance of hybridization driving head coloration in males, (v) darker species living in warm, humid conditions (Gloger’s rule), and (vi) advertising to multiple mating partners favoring red genitalia in females. Nonetheless, the importance of these drivers varies greatly across clades. In strepsirrhines and cercopithecoids, countershading is important; greater color diversity may be important for conspecific signaling in more diurnal and social strepsirrhines; lack of female color vision may be associated with colorful strepsirrhines and platyrrhines; whereas cercopithecoids obey Gloger’s rule. Haplorrhines show background matching, aposematism, character displacement, and red female genitalia where several mating partners are available. Our findings emphasize several evolutionary drivers of coloration in this extraordinarily colorful order. Throughout, we used coarse but rigorous measures of coloration, and our ability to replicate findings from earlier studies opens up opportunities for classifying coloration of large numbers of species at a macroevolutionary scale.

Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae)

Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.

Effect of infant pelage colour on infant caring by other group members: a case study of wild Javan lutungs (Trachypithecus auratus)

We observed interactions of group members with seven Javan lutungs (Trachypithecus auratus) infants from January to March 2018. Infants’ pelage colouration changed from bright yellow to black, and it took about 2.9 months (on average) until the yellowness disappeared, and about 6.1 months (on average) until the colouration change was completed. Infants with yellow pelage spent more time being held and screaming, while infants with black pelage spent more time moving and feeding. The number of neighbouring animals decreased as the infants’ pelage became black, which implied that group members are attracted to the yellowness of infants. As the pelage became black and the infant aged, the neighbouring animals exhibited more social behaviour. Our results implied that bright yellow pelage colour triggers their parental instincts. The bright pelage colour would benefit infants because group members protect them from unfamiliar males and predators.

Colour matters more than shape for chimpanzees' recognition of developmental face changes

Social primates must recognise developmental stages of other conspecifics in order to behave appropriately. Infant faces have peculiar morphological characteristics-relatively large eyes, a small nose, and small mouth-known as baby schema. In addition, the infant faces of many primate species have unique skin coloration. However, it is unclear which features serve as critical cues for chimpanzees to recognise developmental changes in their faces. The present study aimed to investigate the relative contributions of facial shape and colour to age categorisation in chimpanzees. We used a symbolic matching-to-sample task in which chimpanzees were trained to discriminate between adult and infant faces. Then, we tested how their age category judgments transferred to a series of morphed faces which systematically differed in facial shape and colour. Statistical image quantification analysis revealed significant differences both in shape and colour between adult and infant faces. However, we found that facial coloration contributed to age categorisation in chimpanzees more than facial shape. Our results showed that chimpanzees use unique infantile facial coloration as a salient cue when discriminating between adult and infant faces. The display of their developmental stages through facial colour may help chimpanzees to induce appropriate behaviour from other individuals.

Does facial hair greying in chimpanzees provide a salient progressive cue of aging?

The greying of human head hair is arguably the most salient marker of human aging. In wild mammal populations, greying can change with life history or environmental factors (e.g., sexual maturity in silverback gorillas). Yet, whether humans are unique in our pattern of age-related hair depigmentation is unclear. We examined the relationship between pigmentation loss in facial hair (greying) to age, population, and sex in wild and captive chimpanzees (Pan troglodytes). Digital facial photographs representing three chimpanzee populations (N = 145; ages 1–60 years) were scored for hair greying on a scale of one [~100% pigmented] to six [~0% pigmented]. Our data suggest that chimpanzee head and facial hair generally greys with age prior to mid-life (~30 years old), but afterwards, greying ceases to increase incrementally. Our results highlight that chimpanzee pigmentation likely exhibits substantial variation between populations, and that both 'grey' and pigmented phenotypes exist across various age classes. Thus, chimpanzee facial hair greying is unlikely a progressive indicator of age beyond mid-life, and thus facial greying in chimpanzees seems different from the pattern observed in humans. Whether this reflects neutral differences in senescence, or potential differences in selection pressures (e.g. related to conspecific communication), is unclear and worthy of more detailed examination across populations and taxa.

Data on First Record of Brown Morph Banded Langur (Presbytis femoralis), Leucistic Dusky Leaf Monkey (Trachypithecus obscurus) in Malaysia and Review of Morph Diversity in Langur (Colobinae)

Morphism refer to polymorphic species, in which multiple colour variants coexist within a population. Morphism in primates is common and langurs also exhibit certain characteristics of morphism, such as conspicuous natal coats. Banded langurs (Presbytis femoralis) and dusky leaf monkey (Trachypithecus obscurus) exhibits the same characteristics of conspicuous natal coats, but these coats are only limited to infants and changed when they reached adulthood. This article reports the first discovery of rare brown morph of two adult male banded langurs and one leucistic adult female dusky leaf monkey in Malaysia. We also conducted a systematic literature search to review the diversity of morphism in leaf monkey globally.

The structure of species discrimination signals across a primate radiation

Discriminating conspecifics from heterospecifics can help avoid costly interactions between closely related sympatric species. The guenons, a recent primate radiation, exhibit high degrees of sympatry and form multi-species groups. Guenons have species-specific colorful face patterns hypothesized to function in species discrimination. Here, we use a machine learning approach to identify face regions most essential for species classification across fifteen guenon species. We validate these computational results using experiments with live guenons, showing that facial traits critical for accurate classification influence selective attention toward con- and heterospecific faces. Our results suggest variability among guenon species in reliance on single-trait-based versus holistic facial characteristics for species discrimination, with behavioral responses and computational results indicating variation from single-trait to whole-face patterns. Our study supports a role for guenon face patterns in species discrimination, and shows how complex signals can be informative about differences between species across a speciose and highly sympatric radiation.

Sexual selection in the Kinda baboon

Due to wide variation in the presence and degree of expression of a diverse suite of sexually-selected traits, the tribe Papionini represents an outstanding model for understanding how variation in sexual selection pressures and mechanisms leads to trait evolution. Here, we discuss the particular value of Papio as a model genus for studies of sexual selection, emphasizing the presence of multiple mating systems, and differences in the expression of sexually-selected traits among closely-related species. We draw particular attention to the Kinda baboon (Papio kindae), a comparatively less-studied baboon species, by providing a primer to Kinda baboon morphology, genetics, physiology, and behavior. Based on observations of large group sizes, combined with low degrees of sexual dimorphism and large relative testis size relative to other baboon species, we test the hypothesis that Kinda baboons have evolved under reduced direct, and increased indirect, male-male competition. We present the first long-term data on wild Kinda baboons in Zambia. Kinda baboon females show seasonal peaks in births and reproductive receptivity, and males exhibit a queing-rather than contest-based dominance acquisition with long alpha-male tenure lengths. We finish by making a number of explicit testable predictions about Kinda baboon sexual signals and behaviors, and suggest that Kinda baboons have potential to offer new insights into the selective environments that may have been experienced during homininization.

Sexual ornaments but not weapons trade off against testes size in primates

Males must partition their limited reproductive investments between traits that promote access to females (sexual ornaments and weapons) and traits that enhance fertilization success, such as testes and ejaculates. Recent studies show that if the most weaponized males can monopolize access to females through contest competition, thereby reducing the risk of sperm competition, they tend to invest less in sperm production. However, how males invest in sexual ornaments relative to sperm production remains less clear. If male ornaments serve as badges of status, with high-ranking males attaining near-exclusive access to females, similar to monopolizing females through combat, their expression should also covary negatively with investment in post-mating traits. In a comparative study across primates, which exhibit considerable diversification in sexual ornamentation, male weaponry and testes size, we found relative testes size to decrease with sexual ornaments but increase with canine size. These contrasting evolutionary trajectories might be driven by differential selection, functional constraints or temporal patterns of metabolic investment between the different types of sexual traits. Importantly, however, our results indicate that the theory of relative investments between weapons and testes in the context of monopolizing females can extend to male ornaments.

Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans

Hair plays an important role in primates and is clearly subject to adaptive selection. While humans have lost most facial hair, eyebrows are a notable exception. Eyebrow thickness is heritable and widely believed to be subject to sexual selection. Nevertheless, few genomic studies have explored its genetic basis. Here, we performed a genome-wide scan for eyebrow thickness in 2961 Han Chinese. We identified two new loci of genome-wide significance, at 3q26.33 near SOX2 (rs1345417: P = 6.51×10(-10)) and at 5q13.2 near FOXD1 (rs12651896: P = 1.73×10(-8)). We further replicated our findings in the Uyghurs, a population from China characterized by East Asian-European admixture (N = 721), the CANDELA cohort from five Latin American countries (N = 2301), and the Rotterdam Study cohort of Dutch Europeans (N = 4411). A meta-analysis combining the full GWAS results from the three cohorts of full or partial Asian descent (Han Chinese, Uyghur and Latin Americans, N = 5983) highlighted a third signal of genome-wide significance at 2q12.3 (rs1866188: P = 5.81×10(-11)) near EDAR. We performed fine-mapping and prioritized four variants for further experimental verification. CRISPR/Cas9-mediated gene editing provided evidence that rs1345417 and rs12651896 affect the transcriptional activity of the nearby SOX2 and FOXD1 genes, which are both involved in hair development. Finally, suitable statistical analyses revealed that none of the associated variants showed clear signals of selection in any of the populations tested. Contrary to popular speculation, we found no evidence that eyebrow thickness is subject to strong selective pressure.

Facial display and blushing: Means of visual communication in blue-and-yellow macaws (Ara Ararauna)?

Mainly recognized for their cognitive performance, the visual communication system and, particularly, the potential function of facial displays in parrots remain thus far unexplored. Here, we provide the first descriptive study of facial display use in captive blue-and-yellow macaws. We observed the feather position (sleeked or ruffled) on the crown, nape and cheek at the group level during the macaws' daily routine and individually while interacting with a familiar animal caretaker. In the latter context, blushing was also assessed on the bare skin of the cheek. Group level observations showed that crown, nape and cheek feathers ruffling was more frequent in activities requiring no locomotion than in activities requiring locomotion. With the animal caretaker, crown ruffling was significantly more frequent when the caretaker was actively engaging with the parrot than during a control phase with no mutual interaction. In addition, a significantly higher proportion of naïve observers judged blushing as being present on photographs taken during the mutual interaction phase than during the control phase. We thus showed significant variations in facial displays and bare skin colour based on the birds' social context and activity. Our results broaden the scope for further studies to determine whether parrots' faces provide visual social signals.

Using a multi-gene approach to infer the complicated phylogeny and evolutionary history of lorises (Order Primates: Family Lorisidae)

Extensive phylogenetic studies have found robust phylogenies are modeled by using a multi-gene approach and sampling from the majority of the taxa of interest. Yet, molecular studies focused on the lorises, a cryptic primate family, have often relied on one gene, or just mitochondrial DNA, and many were unable to include all four genera in the analyses, resulting in inconclusive phylogenies. Past phylogenetic loris studies resulted in lorises being monophyletic, paraphyletic, or an unresolvable trichotomy with the closely related galagos. The purpose of our study is to improve our understanding of loris phylogeny and evolutionary history by using a multi-gene approach. We used the mitochondrial genes cytochrome b, and cytochrome c oxidase subunit 1, along with a nuclear intron (recombination activating gene 2) and nuclear exon (the melanocortin 1 receptor). Maximum Likelihood and Bayesian phylogenetic analyses were conducted based on data from each locus, as well as on the concatenated sequences. The robust, concatenated results found lorises to be a monophyletic family (Lorisidae) (PP ≥ 0.99) with two distinct subfamilies: the African Perodictinae (PP ≥ 0.99) and the Asian Lorisinae (PP ≥ 0.99). Additionally, from these analyses all four genera were all recovered as monophyletic (PP ≥ 0.99). Some of our single-gene analyses recovered monophyly, but many had discordances, with some showing paraphyly or a deep-trichotomy. Bayesian partitioned analyses inferred the most recent common ancestors of lorises emerged ∼42 ± 6 million years ago (mya), the Asian Lorisinae separated ∼30 ± 9 mya, and Perodictinae arose ∼26 ± 10 mya. These times fit well with known historical tectonic shifts of the area, as well as with the sparse loris fossil record. Additionally, our results agree with previous multi-gene studies on Lorisidae which found lorises to be monophyletic and arising ∼40 mya (Perelman et al., 2011; Pozzi et al., 2014). By taking a multi-gene approach, we were able to recover a well-supported, monophyletic loris phylogeny and inferred the evolutionary history of this cryptic family.

The role of facial pattern variation for species recognition in red-fronted lemurs (Eulemur rufifrons)

BACKGROUND

Species recognition, i.e., the ability to distinguish conspecifics from heterospecifics, plays an essential role in reproduction. The role of facial cues for species recognition has been investigated in several non-human primate species except for lemurs. We therefore investigated the role of facial cues for species recognition in wild red-fronted lemurs (Eulemur rufifrons) at Kirindy Forest. We presented adult red-fronted lemurs pictures of male faces from five species including red-fronted lemurs, three closely related species, white-fronted lemurs (E. albifrons), brown lemurs (E. fulvus), rufous brown lemurs (E. rufus), and genetically more distant red-bellied lemurs (E. rubriventer), occurring in allopatry with the study population. We predicted that red-fronted lemurs respond stronger to conspecific than to heterospecific pictures and that females show stronger responses than males. In addition, if genetic drift has played a role in the evolution of facial color patterns in the members of this genus, we predicted that responses of red-fronted lemurs correlate negatively with the genetic distance to the different species stimuli.

RESULTS

Red-fronted lemurs looked significantly longer at pictures of their own species than at those of heterospecifics. Females spent less time looking at pictures of white-fronted, brown and red-bellied lemurs than males did, but not to pictures of red-bellied lemurs and a control stimulus. Individuals also exhibited sniffing behavior while looking at visual stimuli, and the time spent sniffing was significantly longer for pictures of conspecifics compared to those of heterospecifics. Moreover, the time spent looking and sniffing towards the pictures correlated negatively with the genetic distance between their own species and the species presented as stimulus.

CONCLUSIONS

We conclude that red-fronted lemurs have the ability for species recognition using visual facial cues, which may allow them to avoid costly interbreeding. If so, sexual selection might have influenced the evolution of facial patterns in eulemurs. Since responses also correlated with genetic distance, our findings suggest a potential role of genetic drift as well as sexual selection in influencing the evolution of facial variation in eulemurs. Because study subjects looked and sniffed towards the presented pictures, red-fronted lemurs might have the ability for multi-modal species recognition.

Potential Causative Mutation for Melanism in Rats Identified in the Agouti Signaling Protein Gene (Asip) of the Rattus rattus Species Complex on Okinawa Island, Japan

The occurrence of black fur, or melanism, in many mammalian species is known to be linked to DNA sequence variation in the agouti signaling protein (Asip) gene, which is a major determinant of eumelanin and pheomelanin pigments in coat color. We investigated 38 agouti (i.e., banded wildtype) and four melanistic Rattus rattus species complex (RrC) lineage II specimens from Okinawa Island, Ryukyu Islands, Japan, for genetic variation in three exons and associated flanking regions in the Asip gene. On Okinawa, a predicted loss-of-function mutation caused by a cysteine to serine amino acid change at p.124C>S (c.370T>A) in the highly conserved functional domain of Asip was found in melanistic rats, but was absent in agouti specimens, suggesting that the p.124C>S mutation is responsible for the observed melanism. Phylogeographic analysis found that Asip sequences from Okinawan RrC lineage II, including both agouti and melanistic specimens, differed from: 1) both agouti and melanistic RrC lineage I from Otaru, Hokkaido, Japan, and 2) agouti RrC lineages I and II from South Australia. This suggests the possibility of in-situ mutation of the Asip gene, either within the RrC lineage II population on Okinawa or in an unsampled RrC lineage II population with biogeographic links to Okinawa, although incomplete lineage sorting could not be ruled out.

Evolution of facial color pattern complexity in lemurs

Interspecific variation in facial color patterns across New and Old World primates has been linked to species recognition and group size. Because group size has opposite effects on interspecific variation in facial color patterns in these two radiations, a study of the third large primate radiation may shed light on convergences and divergences in this context. We therefore compiled published social and ecological data and analyzed facial photographs of 65 lemur species to categorize variation in hair length, hair and skin coloration as well as color brightness. Phylogenetically controlled analyses revealed that group size and the number of sympatric species did not influence the evolution of facial color complexity in lemurs. Climatic factors, however, influenced facial color complexity, pigmentation and hair length in a few facial regions. Hair length in two facial regions was also correlated with group size and may facilitate individual recognition. Since phylogenetic signals were moderate to high for most models, genetic drift may have also played a role in the evolution of facial color patterns of lemurs. In conclusion, social factors seem to have played only a subordinate role in the evolution of facial color complexity in lemurs, and, more generally, group size appears to have no systematic functional effect on facial color complexity across all primates.

Is male rhesus macaque facial coloration under intrasexual selection?

Exaggerated male traits can evolve under intra- or intersexual selection, but it remains less clear how often both mechanisms act together on trait evolution. While the males of many anthropoid primate species exhibit colorful signals that appear to be badges of status under intrasexual selection, the red facial coloration of male rhesus macaques (Macaca mulatta) appears to have evolved primarily under intersexual selection and female mate choice. Nonetheless, experiments show that red color is salient to males, raising the question of whether the signal may also be under intrasexual selection. Here, we examine whether males express this signal more strongly in competitive contexts. Facial images were collected on all 15 adult males of a free-ranging social group during the peak of the mating season, and coloration was quantified using visual models. Results show that males more similar in facial redness were more likely to interact aggressively than more dissimilar ones, suggesting that color may be involved in the assessment of rivals. Furthermore, males exhibited darker coloration on days they were observed copulating, and dominance rank predicted facial redness only on copulating days, suggesting that coloration may also advertise motivation to defend a mate. Male rhesus macaque facial coloration may thus mediate agonistic interactions with rivals during competition over reproductive opportunities, such that it is under both inter- and intrasexual selection. However, color differences were small, raising perceptibility questions. It remains possible that color variation reflects differences in male condition, which in turn alter investment towards male-male competition and mating effort.

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'.

Sensory Drive, Color, and Color Vision

Colors often appear to differ in arbitrary ways among related species. However, a fraction of color diversity may be explained because some signals are more easily perceived in one environment rather than another. Models show that not only signals but also the perception of signals should regularly evolve in response to different environments, whether these primarily involve detection of conspecifics or detection of predators and prey. Thus, a deeper understanding of how perception of color correlates with environmental attributes should help generate more predictive models of color divergence. Here, I briefly review our understanding of color vision in vertebrates. Then I focus on opsin spectral tuning and opsin expression, two traits involved in color perception that have become amenable to study. I ask how opsin tuning is correlated with ecological differences, notably the light environment, and how this potentially affects perception of conspecific colors. Although opsin tuning appears to evolve slowly, opsin expression levels are more evolutionarily labile but have been difficult to connect to color perception. The challenge going forward will be to identify how physiological differences involved in color vision, such as opsin expression levels, translate into perceptual differences, the selection pressures that have driven those differences, and ultimately how this may drive evolution of conspecific colors.

Tropical bat as mammalian model for skin carotenoid metabolism

Animals cannot synthesize carotenoid pigments de novo, and must consume them in their diet. Most mammals, including humans, are indiscriminate accumulators of carotenoids but inefficiently distribute them to some tissues and organs, such as skin. This limits the potential capacity of these organisms to benefit from the antioxidant and immunostimulatory functions that carotenoids fulfill. Indeed, to date, no mammal has been known to have evolved physiological mechanisms to incorporate and deposit carotenoids in the skin or hair, and mammals have therefore been assumed to rely entirely on other pigments such as melanins to color their integument. Here we use high-performance liquid chromatography (HPLC) in combination with time-of-flight mass spectrometry (HPLC-TOF/MS) to show that the frugivorous Honduran white bat Ectophylla alba colors its skin bright yellow with the deposition of the xanthophyll lutein. The Honduran white bat is thus a mammalian model that may help developing strategies to improve the assimilation of lutein in humans to avoid macular degeneration. This represents a change of paradigm in animal physiology showing that some mammals actually have the capacity to accumulate dietary carotenoids in the integument. In addition, we have also discovered that the majority of the lutein in the skin of Honduran white bats is present in esterified form with fatty acids, thereby permitting longer-lasting coloration and suggesting bright color traits may have an overlooked role in the visual communication of bats.

Phylogenetic relationships within the Callicebus cupreus species group (Pitheciidae: Primates): Biogeographic and taxonomic implications

The genus Callicebus (Thomas, 1903) is one of the most diverse of Neotropical primate genera and the only extant member of the Callicebinae subfamily. It has a widespread distribution from Colombia to Brazil, Bolivia, Peru and northern Paraguay. Coat colouring and colour pattern vary substantially within the genus, and this has led to the description of numerous species and subspecies, as well as numerous species groups. However, a lack of molecular phylogenetic analyses on the genus means that phylogenetic relationships and biogeographic history of species are poorly understood. Here, we examined phylogenetic relationships and patterns of diversification within the Callicebus cupreus species Group (sensu Kobayashi, 1995) using complete mitochondrial DNA cytochrome b gene sequence. Analyses indicate that the Callicebus cupreus Group underwent recent and extensive diversification. The common ancestor appears to have emerged some 2.3 million years ago (Ma) from a centre of origin in the western Amazon region, followed by diversification of the group between about 1.5 and 1.2Ma. Phylogenetic analyses were able to recover most previously described species (including the recently described Colombian endemic Callicebus caquetensis). However, there are some notable inconsistences between the obtained phylogeny and current taxonomy. Some previously recognized taxa were not separated by our data (e.g., Callicebus caligatus and Callicebus dubius), while currently unrecognized species diversity was uncovered within C. cupreus in the form of two divergent lineages: one of which exhibited greater phylogenetic similarity to species from the C. moloch Group. Based on the present study, we challenge current taxonomic arrangements for the C. cupreus species Group and call for a thorough taxonomic revision within the genus Callicebus.