Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families

Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.

Impact of early visual experience on later usage of color cues

Human visual recognition is remarkably robust to chromatic changes. In this work, we provide a potential account of the roots of this resilience based on observations with 10 congenitally blind children who gained sight late in life. Several months or years following their sight-restoring surgeries, the removal of color cues markedly reduced their recognition performance, whereas age-matched normally sighted children showed no such decrement. This finding may be explained by the greater-than-neonatal maturity of the late-sighted children's color system at sight onset, inducing overly strong reliance on chromatic cues. Simulations with deep neural networks corroborate this hypothesis. These findings highlight the adaptive significance of typical developmental trajectories and provide guidelines for enhancing machine vision systems.

Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments

Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.

Structural Evolution of Primate Glutamate Dehydrogenase 2 as Revealed by In Silico Predictions and Experimentally Determined Structures

Glutamate dehydrogenase (GDH) interconverts glutamate to a-ketoglutarate and ammonia, interconnecting amino acid and carbohydrate metabolism. In humans, two functional GDH genes, GLUD1 and GLUD2, encode for hGDH1 and hGDH2, respectively. GLUD2 evolved from retrotransposition of the GLUD1 gene in the common ancestor of modern apes. These two isoenzymes are involved in the pathophysiology of human metabolic, neoplastic, and neurodegenerative disorders. The 3D structures of hGDH1 and hGDH2 have been experimentally determined; however, no information is available about the path of GDH2 structure changes during primate evolution. Here, we compare the structures predicted by the AlphaFold Colab method for the GDH2 enzyme of modern apes and their extinct primate ancestors. Also, we analyze the individual effect of amino acid substitutions emerging during primate evolution. Our most important finding is that the predicted structure of GDH2 in the common ancestor of apes was the steppingstone for the structural evolution of primate GDH2s. Two changes with a strong functional impact occurring at the first evolutionary step, Arg443Ser and Gly456Ala, had a destabilizing and stabilizing effect, respectively, making this step the most important one. Subsequently, GDH2 underwent additional modifications that fine-tuned its enzymatic properties to adapt to the functional needs of modern-day primate tissues.

Divergences in color perception between deep neural networks and humans

Deep neural networks (DNNs) are increasingly proposed as models of human vision, bolstered by their impressive performance on image classification and object recognition tasks. Yet, the extent to which DNNs capture fundamental aspects of human vision such as color perception remains unclear. Here, we develop novel experiments for evaluating the perceptual coherence of color embeddings in DNNs, and we assess how well these algorithms predict human color similarity judgments collected via an online survey. We find that state-of-the-art DNN architectures - including convolutional neural networks and vision transformers - provide color similarity judgments that strikingly diverge from human color judgments of (i) images with controlled color properties, (ii) images generated from online searches, and (iii) real-world images from the canonical CIFAR-10 dataset. We compare DNN performance against an interpretable and cognitively plausible model of color perception based on wavelet decomposition, inspired by foundational theories in computational neuroscience. While one deep learning model - a convolutional DNN trained on a style transfer task - captures some aspects of human color perception, our wavelet algorithm provides more coherent color embeddings that better predict human color judgments compared to all DNNs we examine. These results hold when altering the high-level visual task used to train similar DNN architectures (e.g., image classification versus image segmentation), as well as when examining the color embeddings of different layers in a given DNN architecture. These findings break new ground in the effort to analyze the perceptual representations of machine learning algorithms and to improve their ability to serve as cognitively plausible models of human vision. Implications for machine learning, human perception, and embodied cognition are discussed.

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.

A treatment within sight: challenges in the development of stem cell-derived photoreceptor therapies for retinal degenerative diseases

Stem cell therapies can potentially treat various retinal degenerative diseases, including age-related macular degeneration (AMD) and inherited retinal diseases like retinitis pigmentosa. For these diseases, transplanted cells may include stem cell-derived retinal pigmented epithelial (RPE) cells, photoreceptors, or a combination of both. Although stem cell-derived RPE cells have progressed to human clinical trials, therapies using photoreceptors and other retinal cell types are lagging. In this review, we discuss the potential use of human pluripotent stem cell (hPSC)-derived photoreceptors for the treatment of retinal degeneration and highlight the progress and challenges for their efficient production and clinical application in regenerative medicine.

Little information loss with red-green color deficient vision in natural environments

Inherited color vision deficiency affects red-green discrimination in about one in twelve men from European populations. Its effects have been studied mainly in primitive foraging but also in detecting blushing and breaking camouflage. Yet there is no obvious relationship between these specific tasks and vision in the real world. The aim here was to quantify the impact of color vision deficiency by estimating computationally the information available to observers about colored surfaces in natural scenes. With representative independent sets of 50 and 100 hyperspectral images, estimated information was found to be only a little less in red-green color vision deficiency than in normal trichromacy. Colorimetric analyses revealed the importance of large lightness variations within scenes, small redness-greenness variations, and uneven frequencies of different colored surfaces. While red-green color vision deficiency poses challenges in some tasks, it has much less effect on gaining information from natural environments.

Evolution of cortical geometry and its link to function, behaviour and ecology

Studies in comparative neuroanatomy and of the fossil record demonstrate the influence of socio-ecological niches on the morphology of the cerebral cortex, but have led to oftentimes conflicting theories about its evolution. Here, we study the relationship between the shape of the cerebral cortex and the topography of its function. We establish a joint geometric representation of the cerebral cortices of ninety species of extant Euarchontoglires, including commonly used experimental model organisms. We show that variability in surface geometry relates to species' ecology and behaviour, independent of overall brain size. Notably, ancestral shape reconstruction of the cortical surface and its change during evolution enables us to trace the evolutionary history of localised cortical expansions, modal segregation of brain function, and their association to behaviour and cognition. We find that individual cortical regions follow different sequences of area increase during evolutionary adaptations to dynamic socio-ecological niches. Anatomical correlates of this sequence of events are still observable in extant species, and relate to their current behaviour and ecology. We decompose the deep evolutionary history of the shape of the human cortical surface into spatially and temporally conscribed components with highly interpretable functional associations, highlighting the importance of considering the evolutionary history of cortical regions when studying their anatomy and function.

The evolution of the green-light-sensitive visual opsin genes (RH2) in teleost fishes

Vertebrates have four visual cone opsin classes that mediate sensitivity from ultraviolet to red wavelengths of light. The rhodopsin-like 2 (RH2) opsin is sensitive to the central mostly green part of the spectrum. While lost in some terrestrial vertebrates (mammals), the RH2 opsin gene has proliferated during the evolution of teleost fishes. Here, we investigated the genomes of 132 extant teleosts and found between zero and eight RH2 gene copies per species. The RH2 gene shows a dynamic evolutionary history with repeated gene duplications, gene losses, and gene conversions affecting entire orders, families, and species. At least four ancestral duplications provided the substrate for today's RH2 diversity, with duplications occurring in the common ancestors of Clupeocephala (twice), Neoteleostei, and likely Acanthopterygii as well. Despite these evolutionary dynamics, we identified conserved RH2 synteny in two main gene clusters; the slc6A13/synpr cluster is highly conserved within Percomorpha and also present across most teleosts, including Otomorpha, Euteleostei and in parts in tarpons (Elopomorpha), and the mutSH5 cluster, which is specific for Otomorpha. When comparing the number of visual opsin genes (SWS1, SWS2, RH2, LWS, and total cone opsins) with habitat depth, we found that deeper-dwelling species had less (or none) long-wavelength-sensitive opsins. Using retinal/eye transcriptomes in a phylogenetic representative dataset of 32 species, we show that if present in the genome, RH2 is expressed in most fishes except for some species within the tarpons, characins, and gobies (and Osteoglossomorpha and some other characin species have lost the gene). Those species instead express a green-shifted long-wavelength-sensitive LWS opsin. Our study applies modern genomic and transcriptomic tools within a comparative framework to elucidate the evolutionary history of the visual sensory system in teleost fishes.

On the manipulation, and meaning(s), of color in food: A historical perspective

While there has long been public concern over the use of artificial/synthetic food colors, it should be remembered that food and drink products (e.g., red wine) have been purposefully colored for millennia. This narrative historical review highlights a number of reasons that food and drink have been colored, including to capture the shopper's visual attention through to signaling the likely taste/flavor. Over the course of the last century, there has, on occasion, also been interest in the playful, or sometimes even deliberately discombobulating, use of food coloring by modernist chefs and others. The coloring (or absence of color) of food and drink can, though, sometimes also take on more of a symbolic meaning, and, in a few cases, specific food colors may acquire a signature, or branded (i.e., semantic) association. That said, with food color being associated with so many different potential "meanings," it is an open question as to which meaning the consumer will associate with any given instance of color in food, and what role context may play in their decision. Laboratory-based sensory science research may not necessarily successfully capture the full range of meanings that may be associated with food color in the mind of the consumer. Nevertheless, it seems likely that food color will continue to play an important role in dictating consumer behavior in the years to come, even though the visual appearance of food is increasingly being mediated via technological means, including virtual and augmented reality.

Evaluating genital skin color as a putative sexual signal in wild saddleback (Leontocebus weddelli) and emperor (Saguinus imperator) tamarins

Coevolution between signalers and receivers has played a significant role in the diversity of animal signals and sensory systems. Platyrrhines (monkeys in the Americas) exhibit a remarkable color vision polymorphism that may have been selected by both natural and sexual selection, but sociosexual color signaling among platyrrhines has received almost no attention. Here, we study the color of reproductive skin among different reproductive classes in free-ranging female saddleback (Leontocebus weddelli) and emperor (Saguinus imperator) tamarins, modeling color spaces, and contrasts for the different visual systems. We find that the chromatic saturation and luminance of genital color vary between reproductive classes in saddleback tamarins. Chromatic contrast between the vulva and belly is lower in the parous females (PFs) relative to adult but not currently breeding females, while achromatic contrast is higher in PFs in saddleback tamarins relative to nonparous females. However, in emperor tamarins, genital color (saturation, hue, and luminance) does not vary between reproductive classes. Overall, genital skin color variation is present in tamarins and may play a role in sexual signaling. Nevertheless, the patterns are inconsistent between species, suggesting interspecific variation. Future studies should integrate the perceiver's behavioral responses and the physical and social signaling environments into comprehensive studies of communication as well as consider the role and interaction between multiple sensory modalities.

Mapping of Orthopaedic Fractures for Optimal Surgical Guidance

Orthopaedic fractures may be difficult to treat surgically if accurate information on the fracture propagation and its exit points are not known. Even with two-dimensional (2D) radiographic images, it is difficult to be completely certain of the exact location of the fracture site, the fracture propagation pattern and the exit points of the fracture. Three-dimensional (3D) computerised tomographic models are better in providing surgeons with the extent of bone fractures, but they may still not be sufficient to allow surgeons to plan open reduction and internal fixation (ORIF) surgery.Fracture patterns and fracture maps are developed to be visual tools in 2D and 3D. These tools can be developed using fractured bones either before or after fracture reduction. Aside from being beneficial to surgeons during pre-surgical planning, these maps aid bioengineers who design fracture fixation plates and implants for these fractures, as well as represent fracture classifications.Fracture maps can be either created ex silico or in silico. Ex silico models are created using 3D printed bone models, onto which fracture patterns are marked. In silico fracture models are created by tracing the fracture lines from a fractured bone to a healthy bone template on a computer. The points of interest in both of these representations are the path of fracture propagation on the bone's surface and exit zones, which eventually determine the surgeon's choice of plate and fracture reduction. Both ex silico and in silico fracture maps are used for pre-surgical planning by the surgeons where they can plan the best way to reduce the fracture as well as template various implants in a low-risk environment before performing the surgery.Recently, fracture maps have been further digitised into heat maps. These heat maps provide visual representations of critical regions of fractures propagating through the bone and identify the weaker zones in the bone structure. These heat maps can allow engineers to develop optimal surgical plates to fix an array of fracture patterns propagating through the bone. Correlation of fractured regions with the mechanisms of injury, age, gender, etc. may improve fracture predictability in the future and optimise the intervention, along with making sure that surgeons do not miss fractures of the bone that may otherwise be hidden from plain sight.

Layered habitats: An evolutionary model for present-day recreational needs

Urbanisation and lifestyle-related illnesses increase globally. This highlights the need to shape modern human habitats to support basic recreational needs, promoting such things as physical activity and restoration of high stress levels and cognitive fatigue. Previous research suggests eight perceived qualities in the outdoor environment, described as eight perceived sensory dimensions, as universally meaningful to people in this regard. However quite extensively studied in relation to various health and wellbeing outcomes, human sensitivity and appreciation for these qualities has not yet been explicitly analysed from an evolutionary perspective. This paper investigates their possible evolutionary roots and suggests an order for their development. This is linked with empirical findings on their relative capacity to support restoration of stress and cognitive fatigue. Qualities of earlier origin are suggested to correspond to older, more fundamental adaptations. Each subsequently developed quality implies an increased complexity of our environmental relations, associated with higher demands on more recently developed capacities. The proposed model thus links the more restorative Serene, Sheltered, Natural, and Cohesive perceived sensory dimensions with earlier stages of our development while the more demanding Diverse, Open, Cultural, and Social qualities are associated with more recent transitions. It might be of relevance when shaping modern human habitats from a health-promoting perspective, and have applications in the planning and design of, e.g., health care settings, rehabilitation gardens, urban green areas, recreational forests or other similar outdoor environments.

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.

Color preference and manual laterality in the emperor tamarin (Saguinus imperator)

The current research focuses on color preference between red and green stimuli and manual laterality in the emperor tamarin (Saguinus imperator). Trichromacy in primates has been related to a foraging advantage allowing frugivore primates to distinguish ripe from unripe fruits as well to socio-sexual communication, as trichromats would be advantaged in recognizing social and sexual signals. As warm colors can affect the emotive state of the subjects, leading to the activation of one hemisphere over the other (e.g., right hemisphere), this could lead to behavioral lateralization. Thus, studying of hand preference may be relevant when testing color preference. Nine adult zoo emperor tamarins were involved and the study aimed to investigate the preference between red, green, and white cones as well as manual laterality. Tamarins were provided with pairs of red-green, red-white, and green-white combinations of cones. Ten 30-min sessions per combination were carried out and data on the interaction with one of the two cones of each apparatus were collected to assess subjects' color preference. We also recorded the hand used by each subject during the interaction with cones of different colors and the position of the apparatus in respect to the tamarin. We found no preferences for colored versus white cones. Similarly, we reported no group-level preferences within different color combinations, whereas individual-level preferences were found when considering all choices. Finally, we found that red cones elicited a left-hand preference, suggesting a right-hemisphere involvement in the presence of red cones. Although we do not have genetic data on trichromat and dichromat females, the tendency to use the left hand when interacting with red stimuli provides further evidence that warm colors can influence the emotive state of the perceiver, affecting their manual lateralization.

Evolutionary analyses of visual opsin genes in frogs and toads: Diversity, duplication, and positive selection

Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found that anurans consistently express four visual opsin genes (RH1, LWS, SWS1, and SWS2, but not RH2) even though reported photoreceptor complements vary widely among species. The proteins encoded by these genes showed considerable sequence variation among species, including at sites known to shift the spectral sensitivity of visual pigments in other vertebrates and had conserved substitutions that may be related to dim-light adaptation. Using molecular evolutionary analyses of selection (dN/dS) we found significant evidence for positive selection at a subset of sites in the dim-light rod opsin gene RH1 and the long wavelength sensitive cone opsin LWS. The function of sites inferred to be under positive selection are largely unknown, but a few are likely to affect spectral sensitivity and other visual pigment functions based on proximity to previously identified sites in other vertebrates. We also found the first evidence of visual opsin duplication in an amphibian with the duplication of the LWS gene in the African bullfrog, which had distinct LWS copies on the sex chromosomes suggesting the possibility of sex-specific visual adaptation. Taken together, our results indicate that ecological factors, such as habitat and life history, as well as behavior, may be driving changes to anuran visual systems.

Detection of conspicuous and cryptic food by common marmosets (Callithrix jacchus): An evaluation of the importance of color and shape cues

In primates, the advantage of trichromacy (i.e., color vision expressed by most humans) over dichromacy (i.e., color vision expressed by many colorblind humans) has been linked to the detection of yellowish/reddish targets against a background of mature green leaves. Nevertheless, mostly because of studies conducted in humans, we know that achromatic cues might also play an important role in object identification, particularly when camouflage is involved. For instance, dichromacy favors the detection of camouflaged targets by exploitation of shape cues. The present study sought to evaluate the relative importance of color and shape cues on the detection of food targets by female and male marmosets (Callithrix jacchus). Animals were observed with respect to their foraging behavior and the number of food targets captured. We confirmed that females are advantageous in detecting conspicuous food against a green background and revealed that females and males rely on shape cues to segregate cryptic food. Unexpectedly, males outperformed females in cryptic food foraging, while camouflage improved males' (but not females') performance. Here we show that dichromats could potentially benefit from a better segregation of green natural targets (e.g., immature fruits, green insects, and gum trees) when viewed against a green dappled background.

Temporal filtering of luminance and chromaticity in macaque visual cortex

Contrast sensitivity peaks near 10 Hz for luminance modulations and at lower frequencies for modulations between equiluminant lights. This difference is rooted in retinal filtering, but additional filtering occurs in the cerebral cortex. To measure the cortical contributions to luminance and chromatic temporal contrast sensitivity, signals in the lateral geniculate nucleus (LGN) were compared to the behavioral contrast sensitivity of macaque monkeys. Long wavelength-sensitive (L) and medium wavelength-sensitive (M) cones were modulated in phase to produce a luminance modulation (L + M) or in counterphase to produce a chromatic modulation (L - M). The sensitivity of LGN neurons was well matched to behavioral sensitivity at low temporal frequencies but was approximately 7 times greater at high temporal frequencies. Similar results were obtained for L + M and L - M modulations. These results show that differences in the shapes of the luminance and chromatic temporal contrast sensitivity functions are due almost entirely to pre-cortical mechanisms.

Sensory disruption and sensory inequities in the Anthropocene

Anthropogenic disruptions to animal sensory ecology are as old as our species. But what about the effect on human sensory ecology? Human sensory dysfunction is increasing globally at great economic and health costs (mental, physical, and social). Contemporary sensory problems are directly tied to human behavioral changes and activity as well as anthropogenic pollution. The evolutionary sensory ecology and anthropogenic disruptions to three human senses (vision, audition, olfaction) are examined along with the economic and health costs of functionally reduced senses and demographic risk factors contributing to impairment. The primary goals of the paper are (a) to sew an evolutionary and ecological thread through clinical narratives on sensory dysfunction that highlights the impact of the built environment on the senses, and (b) to highlight structural, demographic, and environmental injustices that create sensory inequities in risk and that promote health disparities.

The effect of pelage, background, and distance on predator detection and the evolution of primate color vision

Primates' predators, such as carnivore mammals, usually rely on camouflage to increase proximity to prey and start a predatory attempt. Camouflage depends not only on the color pattern presented by a predator's pelage but also on the background scene in which the hunting takes place. Another factor that influences camouflage effectiveness is prey's color vision since a given camouflage strategy might not work for all visual phenotypes. Still, little research has been made on the effect of primate visual phenotype on predator detection. Here, we investigate the effects of natural pelages, background scenarios, visual phenotypes, and detection distances on predator detection. We used photographs of taxidermized carnivores (ocelots, cougars, and lesser grisons) as detection stimuli, taken in three different natural scenarios (forest, savanna, and grassland), and at two viewing distances (near and far). On a touchscreen monitor, sets of four images (only one containing a hidden animal) were randomly presented to 39 human males (19 dichromats and 20 trichromats). We found that trichromats, when compared to dichromats, present a lower latency and a higher accuracy of carnivore detection for some conditions tested. We also found that pelage color, background scenario, and detection distance interact to influence the effectiveness of camouflage. Our results suggest that trichromacy might be even more advantageous for carnivore detection than thought before, since it facilitates detection of mammals with diverse pelage colorations, in environments with different phytophysiognomies, and at longer distances. We also propose that the higher rates of dichromacy found in modern human societies could have resulted from a relaxation in predation.

Genetic variability of the sws1 cone opsin gene among New World monkeys

Vision is a major sense for Primates and the ability to perceive colors has great importance for the species ecology and behavior. Visual processing begins with the activation of the visual opsins in the retina, and the spectral absorption peaks are highly variable among species. In most Primates, LWS/MWS opsins are responsible for sensitivity to long/middle wavelengths within the visible light spectrum, and SWS1 opsins provide sensitivity to short wavelengths, in the violet region of the spectrum. In this study, we aimed to investigate the genetic variation on the sws1 opsin gene of New World monkeys (NWM) and search for amino acid substitutions that might be associated with the different color vision phenotypes described for a few species. We sequenced the exon 1 of the sws1 opsin gene of seven species from the families Callitrichidae, Cebidae, and Atelidae, and searched for variation at the spectral tuning sites 46, 49, 52, 86, 90, 93, 114, 116, and 118. Among the known spectral tuning sites, only residue 114 was variable. To investigate whether other residues have a functional role in the SWS1 absorption peak, we performed computational modeling of wild-type SWS1 and mutants A50I and A50V, found naturally among the species investigated. Although in silico analysis did not show any visible effect caused by these substitutions, it is possible that interactions of residue 50 with other sites might have some effect in the spectral shifts in the order of ~14 nm, found among the NWM. We also performed phylogenetic reconstruction of the sws1 gene, which partially recovered the species phylogeny. Further studies will be important to uncover the mutations responsible for the phenotypic variability of the SWS1 of NWM, and how spectral tuning may be associated with specific ecological features such as preferred food items and habitat use.

Functional evolution of vertebrate sensory receptors

Sensory receptors enable animals to perceive their external world, and functional properties of receptors evolve to detect the specific cues relevant for an organism's survival. Changes in sensory receptor function or tuning can directly impact an organism's behavior. Functional tests of receptors from multiple species and the generation of chimeric receptors between orthologs with different properties allow for the dissection of the molecular basis of receptor function and identification of the key residues that impart functional changes in different species. Knowledge of these functionally important sites facilitates investigation into questions regarding the role of epistasis and the extent of convergence, as well as the timing of sensory shifts relative to other phenotypic changes. However, as receptors can also play roles in non-sensory tissues, and receptor responses can be modulated by numerous other factors including varying expression levels, alternative splicing, and morphological features of the sensory cell, behavioral validation can be instrumental in confirming that responses observed in heterologous systems play a sensory role. Expression profiling of sensory cells and comparative genomics approaches can shed light on cell-type specific modifications and identify other proteins that may affect receptor function and can provide insight into the correlated evolution of complex suites of traits. Here we review the evolutionary history and diversity of functional responses of the major classes of sensory receptors in vertebrates, including opsins, chemosensory receptors, and ion channels involved in temperature-sensing, mechanosensation and electroreception.

Genetic evidence of widespread variation in ethanol metabolism among mammals: revisiting the 'myth' of natural intoxication

Humans have a long evolutionary relationship with ethanol, pre-dating anthropogenic sources, and possess unusually efficient ethanol metabolism, through a mutation that evolved in our last common ancestor with African great apes. Increased exposure to dietary ethanol through fermenting fruits and nectars is hypothesized to have selected for this in our lineage. Yet, other mammals have frugivorous and nectarivorous diets, raising the possibility of natural ethanol exposure and adaptation in other taxa. We conduct a comparative genetic analysis of alcohol dehydrogenase class IV (ADH IV) across mammals to provide insight into their evolutionary history with ethanol. We find genetic variation and multiple pseudogenization events in ADH IV, indicating the ability to metabolize ethanol is variable. We suggest that ADH enzymes are evolutionarily plastic and show promise for revealing dietary adaptation. We further highlight the derived condition of humans and draw attention to problems with modelling the physiological responses of other mammals on them, a practice that has led to potentially erroneous conclusions about the likelihood of natural intoxication in wild animals. It is a fallacy to assume that other animals share our metabolic adaptations, rather than taking into consideration each species' unique physiology.

Platyrrhine color signals: New horizons to pursue

Like catarrhines, some platyrrhines show exposed and reddish skin, raising the possibility that reddish signals have evolved convergently. This variation in skin exposure and color combined with sex-linked polymorphic color vision in platyrrhines presents a unique, and yet underexplored, opportunity to investigate the relative importance of chromatic versus achromatic signals, the influence of color perception on signal evolution, and to understand primate communication broadly. By coding the facial skin exposure and color of 96 platyrrhines, 28 catarrhines, 7 strepsirrhines, 1 tarsiiform, and 13 nonprimates, and by simulating the ancestral character states for these traits, we provide the first analysis of the distribution and evolution of facial skin exposure and color in platyrrhini. We highlight ways in which studying the presence and use of color signals by platyrrhines and other primates will enhance our understanding of the evolution of color signals, and the forces shaping color vision.

Paradoxical impact of memory on color appearance of faces

What is color vision for? Here we compared the extent to which memory modulates color appearance of objects and faces. Participants matched the colors of stimuli illuminated by low-pressure sodium light, which renders scenes monochromatic. Matches for fruit were not predicted by stimulus identity. In contrast, matches for faces were predictable, but surprising: faces appeared green and looked sick. The paradoxical face-color percept could be explained by a Bayesian observer model constrained by efficient coding. The color-matching data suggest that the face-color prior is established by visual signals arising from the recently evolved L-M cone system, not the older S-cone channel. Taken together, the results show that when retinal mechanisms of color vision are impaired, the impact of memory on color perception is greatest for face color, supporting the idea that trichromatic color plays an important role in social communication.

What is the function of color vision? Here, the authors show that when retinal mechanisms of color are impaired, memory has a paradoxical impact on color appearance that is selective for faces, providing evidence that color contributes to face encoding and social communication.

How conspicuous are peacock eyespots and other colorful feathers in the eyes of mammalian predators?

Colorful feathers have long been assumed to be conspicuous to predators, and hence likely to incur costs due to enhanced predation risk. However, many mammals that prey on birds have dichromatic visual systems with only two types of color-sensitive visual receptors, rather than the three and four photoreceptors characteristic of humans and most birds, respectively. Here, we use a combination of multispectral imaging, reflectance spectroscopy, color vision modelling and visual texture analysis to compare the visual signals available to conspecifics and to mammalian predators from multicolored feathers from the Indian peacock (Pavo cristatus), as well as red and yellow parrot feathers. We also model the effects of distance-dependent blurring due to visual acuity. When viewed by birds against green vegetation, most of the feathers studied are estimated to have color and brightness contrasts similar to values previously found for ripe fruit. On the other hand, for dichromat mammalian predators, visual contrasts for these feathers were only weakly detectable and often below detection thresholds for typical viewing distances. We also show that for dichromat mammal vision models, the peacock's train has below-detection threshold color and brightness contrasts and visual textures that match various foliage backgrounds. These findings are consistent with many feathers of similar hue to those studied here being inconspicuous, and in some cases potentially cryptic, in the eyes of common mammalian predators of adult birds. Given that birds perform many conspicuous motions and behaviors, this study suggests that mammalian predators are more likely to use other sensory modalities (e.g., motion detection, hearing, and olfaction), rather than color vision, to detect avian prey. This suggests new directions for future behavioral studies and emphasizes the importance of understanding the influence of the sensory ecology of predators in the evolution of animal coloration.

Detection of insect prey by wild common marmosets: The effect of color vision

Most species of New World primates have an unusual color vision pattern that can affect an individual's ability to detect food. Whereas males can only be dichromatic, females can be either dichromatic or trichromatic. Trichromats are expected to have an advantage in detecting conspicuous food whereas dichromats should be better at locating cryptic resources. Here we aimed to understand how color vision phenotype influences insect foraging by five groups of common marmosets living in a semiarid environment. We recorded insect predation events, noting morphotype and color of the captured insect, and the substrate from which it was captured. Color modeling suggested that, for all values of chromatic contrast resulting from comparing the measured insect-substrate pairs, trichromats outperformed dichromats. Females showed an overall higher insect capture rate than males. Females also showed a higher capture rate of conspicuous insects but there was no sex difference for the capture of cryptic insects. When we compared only dichromatic individuals there was no difference between sexes. These findings suggest that differences found in capture rate related not only to sex but also to visual polymorphism and that the latter is a crucial factor determining insect capture rate in common marmosets. Nevertheless, these results should be interpreted with caution because of the small number (three) of dichromat females and the unknown phenotype of the remaining females. Our results support the balancing selection hypothesis, suggesting that the advantage of one phenotype over the other may depend on environmental circumstances. This hypothesis has recently been considered as the most plausible for the maintenance of visual polymorphism in New World primates.

Duetting Patterns of Titi Monkeys (Primates, Pitheciidae: Callicebinae) and Relationships with Phylogeny

Long-range vocal communication in socially monogamous titi monkeys is mediated by the production of loud, advertising calls in the form of solos, duets, and choruses. We conducted a power spectral analysis of duets and choruses (simply "duets" hereafter) followed by linear discriminant analysis using three acoustic parameters-dominant frequency of the combined signal, duet sequence duration, and pant call rate-comparing the coordinated vocalizations recorded from 36 family groups at 18 sites in Bolivia, Peru and Ecuador. Our analysis identified four distinct duetting patterns: (1) a donacophilus pattern, sensu largo, characteristic of P. donacophilus, P. pallescens, P. olallae, and P. modestus; (2) a moloch pattern comprising P. discolor, P. toppini, P. aureipalatii, and P. urubambensis; (3) a torquatus pattern exemplified by the duet of Cheracebus lucifer; and (4) the distinctive duet of P. oenanthe, a putative member of the donacophilus group, which is characterized by a mix of broadband and narrowband syllables, many of which are unique to this species. We also document a sex-related difference in the bellow-pant phrase combination among the three taxa sampled from the moloch lineage. Our data reveal a presumptive taxonomic incoherence illustrated by the distinctive loud calls of both P. urubambensis and P. oenanthe within the donacophilus lineage, sensu largo. The results are discussed in light of recent reassessments of the callicebine phylogeny, based on a suite of genetic studies, and the potential contribution of environmental influences, including habitat acoustics and social learning. A better knowledge of callicebine loud calls may also impact the conservation of critically endangered populations, such as the vocally distinctive Peruvian endemic, the San Martin titi, P. oenanthe.

Experimental evidence that primate trichromacy is well suited for detecting primate social colour signals

Primate trichromatic colour vision has been hypothesized to be well tuned for detecting variation in facial coloration, which could be due to selection on either signal wavelengths or the sensitivities of the photoreceptors themselves. We provide one of the first empirical tests of this idea by asking whether, when compared with other visual systems, the information obtained through primate trichromatic vision confers an improved ability to detect the changes in facial colour that female macaque monkeys exhibit when they are proceptive. We presented pairs of digital images of faces of the same monkey to human observers and asked them to select the proceptive face. We tested images that simulated what would be seen by common catarrhine trichromatic vision, two additional trichromatic conditions and three dichromatic conditions. Performance under conditions of common catarrhine trichromacy, and trichromacy with narrowly separated LM cone pigments (common in female platyrrhines), was better than for evenly spaced trichromacy or for any of the dichromatic conditions. These results suggest that primate trichromatic colour vision confers excellent ability to detect meaningful variation in primate face colour. This is consistent with the hypothesis that social information detection has acted on either primate signal spectral reflectance or photoreceptor spectral tuning, or both.

Insights into visual pigment adaptation and diversity from model ecological and evolutionary systems

Sensory systems provide valuable insight into the evolution of molecular mechanisms underlying organismal anatomy, physiology, and behaviour. Visual pigments, which mediate the first step in visual transduction, offer a unique window into the relationship between molecular variation and visual performance, and enhance our understanding of how ecology, life history, and physiology may shape genetic variation across a variety of organisms. Here we review recent work investigating vertebrate visual pigments from a number of perspectives. Opsin gene duplication, loss, differential expression, structural variation, and the physiological context in which they operate, have profoundly shaped the visual capabilities of vertebrates adapting to novel environments. We note the importance of conceptual frameworks in investigating visual pigment diversity in vertebrates, highlighting key examples including evolutionary transitions between different photic environments, major shifts in life history evolution and ecology, evolutionary innovations in visual system anatomy and physiology, as well as shifts in visually mediated behaviours and behavioural ecology. We emphasize the utility of studying visual pigment evolution in the context of these different perspectives, and demonstrate how the integrative approaches discussed in this review contribute to a better understanding of the underlying molecular processes mediating adaptation in sensory systems, and the contexts in which they occur.