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1.  Is male rhesus macaque red color ornamentation attractive to females? 
Behavioral ecology and sociobiology  2014;68(7):1215-1224.
Male sexually-selected traits can evolve through different mechanisms: conspicuous and colorful ornaments usually evolve through inter-sexual selection, while weapons usually evolve through intra-sexual selection. Male ornaments are rare among mammals in comparison to birds, leading to the notion that female mate choice generally plays little role in trait evolution in this taxon. Supporting this view, when ornaments are present in mammals they typically indicate social status and are products of male-male competition. This general mammalian pattern, however, may not apply to rhesus macaques (Macaca mulatta). Males of this species display conspicuous skin coloration, but this expression is not correlated to dominance rank, and is therefore unlikely to have evolved due to male-male competition. Here, we investigate whether male color expression influences female proceptivity towards males in the Cayo Santiago free-ranging rhesus macaque population. We collected face images of 24 adult males varying in dominance rank and age at the peak of the mating season, and modeled these to rhesus macaque visual perception. We also recorded female socio-sexual behaviors towards these males. Results show that dark red males received more sexual solicitations, by more females, than pale pink ones. Together with previous results, our study suggests that male color ornaments are more likely to be a product of inter- rather than intra-sexual selection. This may especially be the case in rhesus macaques due to the particular characteristics of male-male competition in this species.
doi:10.1007/s00265-014-1732-9
PMCID: PMC4167843  PMID: 25246728
Ornaments; sexual selection; female mate choice; sexual skin; color; anthropoid primates
2.  Signaling in multiple modalities in male rhesus macaques: sex skin coloration and barks in relation to androgen levels, social status, and mating behavior 
Behavioral ecology and sociobiology  2013;67(9):1457-1469.
The past decade has seen an increasing shift in animal communication towards more studies that incorporate aspects of signaling in multiple modalities. Although nonhuman primates are an excellent group for studying the extent to which different aspects of condition may be signaled in different modalities, and how such information may be integrated during mate choice, very few studies of primate species have incorporated such analyses. Here, we present data from free-ranging male rhesus macaques on sex skin coloration (modeled to receiver perception), bark vocal signals, androgen levels, morphometric variables, dominance status, and female mate choice. We show that, consistent with data on females, most intra- and interindividual variation in sex skin appearance occurs in luminance rather than color. Sex skin luminance was significantly correlated across different skin regions. Sex skin luminance did not correlate with the majority of bark parameters, suggesting the potential for the two signals to convey different information. Sex skin appearance was not related to androgen levels although we found some evidence for links between androgen levels and bark parameters, several of which were also related to morphometric variables. We found no evidence that either signal was related to male dominance rank or used in female mate choice, though more direct measures of female proceptive behavior are needed. Overall, the function of male sex skin coloration in this species remains unclear. Our study is among the first nonhuman primate studies to incorporate measurements of multiple signals in multiple modalities, and we encourage other authors to incorporate such analyses into their work.
doi:10.1007/s00265-013-1521-x
PMCID: PMC4084859  PMID: 25013266
Coloration; Luminance; Vocal signals; Multimodal; Primate; Rhesus macaques
3.  Incidence of chromosomal mosaicism in morphologically normal non-human primate preimplantation embryos 
Fertility and sterility  2009;93(8):2545-2550.
Objective
To establish the exact rates of chromosomal mosaicism in morphologically normal rhesus macaque embryos by determining the chromosomal complement of all blastomeres.
Design
Retrospective rhesus monkey IVF study.
Setting
Academic laboratory and Primate Research Center.
Patients
Young fertile rhesus macaque females.
Interventions
Morphologically normal, in vitro produced rhesus macaque embryos were dissociated and cytogenetically assessed using a 5-color fluorescent in situ hybridization assay developed for rhesus macaque chromosomes homologous to human chromosomes 13, 16, 18, X and Y.
Main Outcome Measure(s)
The incidence and extent of chromosomal mosaicism in rhesus macaque preimplantation embryos.
Result(s)
Seventy-seven preimplantation embryos, displaying normal morphology and development, from 17 young rhesus macaque females were analyzed. Overall, 39 embryos (50.6%) were normal, 14 embryos (18.2%) were completely abnormal and 24 embryos were mosaic (31.2%). Of the 226 blastomeres analyzed in the mosaic group, 110 blastomeres (48.7%) were normal.
Conclusion(s)
The observed rate of mosaicism in good quality rhesus embryos resembles previously-documented frequencies in poor-quality human preimplantation embryos. A high incidence of mosaicism may limit the diagnostic accuracy of preimplantation genetic diagnosis.
doi:10.1016/j.fertnstert.2009.06.040
PMCID: PMC3150520  PMID: 19732891
Mosaicism; embryos; monkey; non-human primate; aneuploidy; FISH
4.  Chromosomal instability in rhesus macaque preimplantation embryos 
Fertility and sterility  2008;91(4):1230-1237.
Objective
To establish a relevant animal model to systematically investigate chromosomal instability in human oocytes and preimplantation embryos.
Design
Prospective rhesus monkey IVF study.
Setting
Academic laboratory, Oregon National Primate Research Center and Caribbean Primate Research Center.
Patients
Young Rhesus macaque females.
Interventions
In vitro produced (IVP) entire rhesus macaque preimplantation embryos were cytogenetically assessed using a 5-color fluorescent in situ hybridization (FISH) assay developed for rhesus macaque chromosomes homologous to human chromosomes 13, 16, 18, X and Y, using human bacterial artificial chromosome (BAC) probes.
Main Outcome Measure(s)
Chromosomal abnormality rates in preimplantation embryos from young rhesus macaque females were established.
Result(s)
Fifty preimplantation embryos, displaying good morphology and normal development, from 11 young rhesus macaque females were analyzed. Overall, 27 embryos (54%) were normal, 11 embryos (22%) mosaic, 3 embryos (6%) chaotic, 2 embryos (4%) aneuploid, 3 embryos (6%) haploid and 4 embryos (8%) triploid.
Conclusion(s)
These data indicate that IVP rhesus macaque and human preimplantation embryos exhibit similar numerical chromosomal aberrations. Rhesus macaques appear to be a suitable animal model for investigating the origin of chromosomal instability observed in human preimplantation embryos.
doi:10.1016/j.fertnstert.2008.01.075
PMCID: PMC3082460  PMID: 18440514
Aneuploidy; ART; Cytogenetics; Embryo; FISH; IVF; Non-human primate; PGD
5.  Estimating rice chlorophyll content and leaf nitrogen concentration with a digital still color camera under natural light 
Plant Methods  2014;10(1):36.
Background
The color of crop leaves is closely correlated with nitrogen (N) status and can be quantified easily with a digital still color camera and image processing software. The establishment of the relationship between image color indices and N status under natural light is important for crop monitoring and N diagnosis in the field. In our study, a digital still color camera was used to take pictures of the canopies of 6 rice (Oryza sativa L.) cultivars with N treatments ranging from 0 to 315 kg N ha-1 in the field under sunny and overcast conditions in 2010 and 2011, respectively.
Results
Significant correlations were observed between SPAD readings, leaf N concentration (LNC) and 13 image color indices calculated from digital camera images using three color models: RGB, widely used additive color model; HSV, a cylindrical-coordinate similar to the human perception of colors; and the L*a*b* system of the International Commission on Illumination. Among these color indices, the index b*, which represents the visual perception of yellow-blue chroma, has the closest linear relationship with SPAD reading and LNC. However, the relationships between LNC and color indices were affected by the developmental phase. Linear regression models were used to predict LNC and SPAD from color indices and phasic development. After that, the models were validated with independent data. Generally, acceptable performance and prediction were found between the color index b*, SPAD reading and LNC with different cultivars and sampling dates under different natural light conditions.
Conclusions
Our study showed that digital color image analysis could be a simple method of assessing rice N status under natural light conditions for different cultivars and different developmental stages.
Electronic supplementary material
The online version of this article (doi:10.1186/1746-4811-10-36) contains supplementary material, which is available to authorized users.
doi:10.1186/1746-4811-10-36
PMCID: PMC4236477  PMID: 25411579
Digital still color camera; Leaf color; Image processing technology; Natural light; Nitrogen; Rice
6.  Facial Musculature in the Rhesus Macaque (Macaca mulatta): Evolutionary and Functional Contexts with Comparisons to Chimpanzees and Humans 
Journal of anatomy  2009;215(3):320-334.
Facial expression is a common mode of visual communication in mammals but especially so in primates. Rhesus macaques (Macaca mulatta) have a well-documented facial expression repertoire that is controlled by the facial/mimetic musculature as in all mammals. However, little is known about the musculature itself and how it compares to those of other primates. Here we present a detailed description of the facial musculature in rhesus macaques in behavioral, evolutionary, and comparative contexts. Foramlin-fixed faces from six adult male specimens were dissected using a novel technique. The morphology, attachments, three-dimensional relationships, and variability of muscles were noted and compared with chimpanzees (Pan troglodytes) and with humans. Results showed that there was a greater number of facial muscles in rhesus macaques than previously described (24) including variably present (and previously unmentioned) zygomaticus minor, levator labii superioris alaeque nasi, depressor septi, anterior auricularis, inferior auricularis, and depressor supercilii muscles. Facial muscles of the rhesus macaque were very similar to those in chimpanzees and in humans but M. mulatta did not possess a risorius muscle. These results support previous studies that describe a highly graded and intricate facial expression repertoire in rhesus macaques. Furthermore, these results indicate that phylogenetic position is not the primary factor governing structure of primate facial musculature and that other factors such as social behavior are probably more important. Results from the present study may provide valuable input to both biomedical studies that use rhesus macaques as a model for human disease and disorder that includes assessment of facial movement and studies into the evolution of primate societies and communication.
doi:10.1111/j.1469-7580.2009.01113.x
PMCID: PMC2750044  PMID: 19563473
macaque; facial muscle; mimetic; chimpanzee; evolution; facial expression; primate
7.  The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human 
BMC Genetics  2012;13:52.
Background
As a model organism in biomedicine, the rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate. Although a draft genome sequence was completed in 2007, there has been no systematic genome-wide comparison of genetic variation of this species to humans. Comparative analysis of functional and nonfunctional diversity in this highly abundant and adaptable non-human primate could inform its use as a model for human biology, and could reveal how variation in population history and size alters patterns and levels of sequence variation in primates.
Results
We sequenced the mRNA transcriptome and H3K4me3-marked DNA regions in hippocampus from 14 humans and 14 rhesus macaques. Using equivalent methodology and sampling spaces, we identified 462,802 macaque SNPs, most of which were novel and disproportionately located in the functionally important genomic regions we had targeted in the sequencing. At least one SNP was identified in each of 16,797 annotated macaque genes. Accuracy of macaque SNP identification was conservatively estimated to be >90%. Comparative analyses using SNPs equivalently identified in the two species revealed that rhesus macaque has approximately three times higher SNP density and average nucleotide diversity as compared to the human. Based on this level of diversity, the effective population size of the rhesus macaque is approximately 80,000 which contrasts with an effective population size of less than 10,000 for humans. Across five categories of genomic regions, intergenic regions had the highest SNP density and average nucleotide diversity and CDS (coding sequences) the lowest, in both humans and macaques. Although there are more coding SNPs (cSNPs) per individual in macaques than in humans, the ratio of dN/dS is significantly lower in the macaque. Furthermore, the number of damaging nonsynonymous cSNPs (have damaging effects on protein functions from PolyPhen-2 prediction) in the macaque is more closely equivalent to that of the human.
Conclusions
This large panel of newly identified macaque SNPs enriched for functionally significant regions considerably expands our knowledge of genetic variation in the rhesus macaque. Comparative analysis reveals that this widespread, highly adaptable species is approximately three times as diverse as the human but more closely equivalent in damaging variation.
doi:10.1186/1471-2156-13-52
PMCID: PMC3426462  PMID: 22747632
Rhesus macaque; Human; Single nucleotide polymorphism; Diversity; Comparative genomics
8.  Pathogenicity of Simian-Human Immunodeficiency Virus SHIV-89.6P and SIVmac Is Attenuated in Cynomolgus Macaques and Associated with Early T-Lymphocyte Responses 
Journal of Virology  2005;79(14):8878-8885.
Because most studies of AIDS pathogenesis in nonhuman primates have been performed in Indian-origin rhesus macaques (Macaca mulatta), little is known about lentiviral pathogenicity and control of virus replication following infection of alternative macaque species. Here, we report the consequences of simian-human immunodeficiency virus SHIV-89.6P and SIVmac251 infection in cynomolgus (Macaca fascicularis) and rhesus macaques of Chinese origin. Compared to the pathogenicity of the same viruses in Indian rhesus macaques, both cynomolgus and Chinese rhesus macaques showed lower levels of plasma virus. By 9 to 10 months after infection, both viruses became undetectable in plasma more frequently in cynomolgus than in either Chinese or Indian rhesus macaques. Furthermore, after SHIV-89.6P infection, CD4+ T-cell numbers declined less and survival was longer in cynomolgus and Chinese rhesus macaques than in Indian rhesus macaques. This attenuated pathogenicity was associated with gamma interferon ELISPOT responses to Gag and Env that were generated earlier and of higher frequency in cynomolgus than in Indian rhesus macaques. Cynomolgus macaques also developed higher titer neutralizing antibodies against SHIV-89.6 at 10 and 20 weeks postinoculation than Indian rhesus macaques. These studies demonstrate that the pathogenicity of nonhuman primate lentiviruses varies markedly based on the species or geographic origin of the macaques infected and suggest that the cellular immune responses may contribute to the control of pathogenicity in cynomolgus macaques. While cynomolgus and Chinese rhesus macaques provide alternative animal models of lentiviral infection, the lower levels of viremia in cynomolgus macaques limit the usefulness of infection of this species for vaccine trials that utilize viral load as an experimental endpoint.
doi:10.1128/JVI.79.14.8878-8885.2005
PMCID: PMC1168747  PMID: 15994781
9.  Single nucleotide polymorphisms (SNPs) are highly conserved in rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques 
BMC Genomics  2007;8:480.
Background
Macaca fascicularis (cynomolgus or longtail macaques) is the most commonly used non-human primate in biomedical research. Little is known about the genomic variation in cynomolgus macaques or how the sequence variants compare to those of the well-studied related species, Macaca mulatta (rhesus macaque). Previously we identified single nucleotide polymorphisms (SNPs) in portions of 94 rhesus macaque genes and reported that Indian and Chinese rhesus had largely different SNPs. Here we identify SNPs from some of the same genomic regions of cynomolgus macaques (from Indochina, Indonesia, Mauritius and the Philippines) and compare them to the SNPs found in rhesus.
Results
We sequenced a portion of 10 genes in 20 cynomolgus macaques. We identified 69 SNPs in these regions, compared with 71 SNPs found in the same genomic regions of 20 Indian and Chinese rhesus macaques. Thirty six (52%) of the M. fascicularis SNPs were overlapping in both species. The majority (70%) of the SNPs found in both Chinese and Indian rhesus macaque populations were also present in M. fascicularis. Of the SNPs previously found in a single rhesus population, 38% (Indian) and 44% (Chinese) were also identified in cynomolgus macaques. In an alternative approach, we genotyped 100 cynomolgus DNAs using a rhesus macaque SNP array representing 53 genes and found that 51% (29/57) of the rhesus SNPs were present in M. fascicularis. Comparisons of SNP profiles from cynomolgus macaques imported from breeding centers in China (where M. fascicularis are not native) showed they were similar to those from Indochina.
Conclusion
This study demonstrates a surprisingly high conservation of SNPs between M. fascicularis and M. mulatta, suggesting that the relationship of these two species is closer than that suggested by morphological and mitochondrial DNA analysis alone. These findings indicate that SNP discovery efforts in either species will generate useful resources for both macaque species. Identification of SNPs that are unique to regional populations of cynomolgus macaques indicates that location-specific SNPs could be used to distinguish monkeys of uncertain origin. As an example, cynomolgus macaques obtained from 2 different breeding centers in China were shown to have Indochinese ancestry.
doi:10.1186/1471-2164-8-480
PMCID: PMC2248198  PMID: 18166133
10.  Contrast enhanced ultrasound reveals real-time spatial changes in vascular perfusion during early implantation in the macaque uterus 
Fertility and sterility  2011;95(4):1316-1321.e3.
Objective
To use contrast enhanced ultrasound (CEU) to quantify blood flow in the macaque uterus during early pregnancy.
Design
Prospective nonhuman primate study.
Setting
National Primate Research Center.
Animals
Naturally cycling female rhesus macaques (Macaca mulatta).
Interventions
Female macaques were mated on days 11–14 of the cycle. Females were then imaged by CEU and Doppler ultrasound (DUS) once every 3 days from day 21 through day 39 of the fertile cycle.
Main Outcome Measures
Visualization and quantification of uterine vascular perfusion.
Results
CEU identified the primary placental disc and underlying vessels ~2 days earlier than DUS was able to observe endometrial thickening. CEU revealed spatial differences in vascular perfusion between the endometrium, myometrium, and the endometrial-myometrial (junctional) zone. Myometrium displayed the highest rate of blood flow (>10 mL/min/g tissue). There was less blood flow in the endometrium and junctional zone (<3 mL/min/g). A brief fall in progesterone was observed during early implantation, which was correlated with reduced blood flow to all three uterine compartments, but did not reduce flow to the placenta.
Conclusions
CEU provides a sensitive, non-invasive method to assess vascular perfusion of the uterus during embryo implantation in macaques. We propose CEU as a new diagnostic tool to monitor vascular changes associated with early pregnancy in women.
doi:10.1016/j.fertnstert.2011.01.040
PMCID: PMC3070443  PMID: 21316046
contrast enhanced ultrasound; Doppler ultrasound; endometrium; implantation; macaque; pregnancy; progesterone; uterus; vascular perfusion
11.  Color accuracy of commercial digital cameras for use in dentistry 
Summary
Objectives
The use of calibrated, commercial digital cameras for dental applications is promising. The color accuracy of various calibration models were evaluated as applied to three commercial digital cameras for use in dental color matching.
Methods
CIE LAB values of 264 color patches and 65 shade tabs were measured with a spectroradiometer. Digital images of the samples were taken with the Nikon D100, Canon D60 and Sigma SD9 cameras. Four regression models were formulated from the color patch CIE LAB and the digital image values. Shade tab CIE LAB colors were predicted by applying the digital image values into the calibration models and were compared to the measured CIE LAB values. The Wilcoxon Rank-Sum test determined if the 12 camera/calibration models differed significantly from the color measurement setup.
Results
Every camera/calibration model (ΔE’s ranging from 1.79 to 5.25) showed a statistically significant difference from the color measurement setup.
Significance
Commercial SLR digital cameras when combined with the appropriate calibration protocols showed potential for use in the color replication process of clinical dentistry.
doi:10.1016/j.dental.2005.05.011
PMCID: PMC1808262  PMID: 16198403
Digital cameras; Calibration models; Color measurement; Translucent material
12.  Anomaly in aortic arch alters pathological outcome of transient global ischemia in Rhesus macaques 
Brain research  2009;1286:185-191.
We investigated a non-human primate (NHP) transient global ischemia (TGI) model which was induced by clipping the arteries originating from the aortic arch. Previously we demonstrated that our TGI model in adult Rhesus macaques (Macaca mulatta) results in marked neuronal cell loss in the hippocampal region, specifically the cornu Ammonis (CA1) region. However, we observed varying degrees of hippocampal cell loss among animals. Here, we report for the first time an anomaly of the aortic arch in some Rhesus macaques that appears as a key surgical factor in ensuring the success of the TGI model in this particular NHP. Eleven adult Rhesus macaques underwent the TGI surgery, which involved 10-15-minute clipping of both innominate and subclavian arteries. Animals were allowed to survive between 1 day and 28 days after TGI. Because of our experience and knowledge that Japanese macaques exhibited only innominate and subclavian arteries arising from the aortic arch, macroscopic visualization of these two arteries alone in the Rhesus macaques initially assured us that clipping both arteries was sufficient to produce TGI. During the course of one TGI operation, however, we detected 3 arterial branches arising from the aortic arch, which prompted us to subsequently search for 3 branches in succeeding TGI surgeries. In addition, we performed post-mortem examination of the heart to confirm the number of arterial branches in the aortic arch. Finally, in order to reveal the pathological effect of the aortic arch anomaly, we compared the hippocampal cell loss between animals found to have 3 arterial branches but had all or only two branches clipped during TGI operation. Post-mortem examination revealed eight NHPs had the typical two arterial aortic branches, but three NHPs displayed an extra arterial aortic branch, indicating that about 30% of Rhesus macaques had 3 arterial branches arising from the aorta. Histological analyses using Nissl staining showed that in NHPs with the aortic arch anomaly clipping only two of three arterial branches led to a partial cell loss and minimal alteration in number of cell layers in the hippocampal region when compared with clipping all three branches, with the hippocampal cell death in the latter resembling the pathological outcome achieved by clipping the two arterial branches in NHPs displaying the typical two-artery aortic arch. The finding that 3 of 11 NHPs exhibited an extra arterial aortic branch recognizes this aortic arch anomaly in Rhesus macaques that warrants a critical surgical maneuver in order to successfully produce consistent TGI-induced hippocampal cell loss.
doi:10.1016/j.brainres.2009.06.015
PMCID: PMC2744090  PMID: 19524559
non-human primate; cerebral ischemia; aortic arch; anatomy; hippocampal neuronal loss
13.  Functional diversity in the color vision of cichlid fishes 
BMC Biology  2010;8:133.
Background
Color vision plays a critical role in visual behavior. An animal's capacity for color vision rests on the presence of differentially sensitive cone photoreceptors. Spectral sensitivity is a measure of the visual responsiveness of these cones at different light wavelengths. Four classes of cone pigments have been identified in vertebrates, but in teleost fishes, opsin genes have undergone gene duplication events and thus can produce a larger number of spectrally distinct cone pigments. In this study, we examine the question of large-scale variation in color vision with respect to individual, sex and species that may result from differential expression of cone pigments. Cichlid fishes are an excellent model system for examining variation in spectral sensitivity because they have seven distinct cone opsin genes that are differentially expressed.
Results
To examine the variation in the number of cones that participate in cichlid spectral sensitivity, we used whole organism electrophysiology, opsin gene expression and empirical modeling. Examination of over 100 spectral sensitivity curves from 34 individuals of three species revealed that (1) spectral sensitivity of individual cichlids was based on different subsets of four or five cone pigments, (2) spectral sensitivity was shaped by multiple cone interactions and (3) spectral sensitivity differed between species and correlated with foraging mode and the spectral reflectance of conspecifics. Our data also suggest that there may be significant differences in opsin gene expression between the sexes.
Conclusions
Our study describes complex opponent and nonopponent cone interactions that represent the requisite neural processing for color vision. We present the first comprehensive evidence for pentachromatic color vision in vertebrates, which offers the potential for extraordinary spectral discrimination capabilities. We show that opsin gene expression in cichlids, and possibly also spectral sensitivity, may be sex-dependent. We argue that females and males sample their visual environment differently, providing a neural basis for sexually dimorphic visual behaviour. The diversification of spectral sensitivity likely contributes to sensory adaptations that enhance the contrast of transparent prey and the detection of optical signals from conspecifics, suggesting a role for both natural and sexual selection in tuning color vision.
doi:10.1186/1741-7007-8-133
PMCID: PMC2988715  PMID: 21029409
14.  The Heterozygote Superiority Hypothesis for Polymorphic Color Vision Is Not Supported by Long-Term Fitness Data from Wild Neotropical Monkeys 
PLoS ONE  2014;9(1):e84872.
The leading explanatory model for the widespread occurrence of color vision polymorphism in Neotropical primates is the heterozygote superiority hypothesis, which postulates that trichromatic individuals have a fitness advantage over other phenotypes because redgreen chromatic discrimination is useful for foraging, social signaling, or predator detection. Alternative explanatory models predict that dichromatic and trichromatic phenotypes are each suited to distinct tasks. To conclusively evaluate these models, one must determine whether proposed visual advantages translate into differential fitness of trichromatic and dichromatic individuals. We tested whether color vision phenotype is a significant predictor of female fitness in a population of wild capuchins, using longterm 26 years survival and fertility data. We found no advantage to trichromats over dichromats for three fitness measures fertility rates, offspring survival and maternal survival. This finding suggests that a selective mechanism other than heterozygote advantage is operating to maintain the color vision polymorphism. We propose that attention be directed to field testing the alternative mechanisms of balancing selection proposed to explain opsin polymorphism nichedivergence, frequencydependence and mutual benefit of association. This is the first indepth, longterm study examining the effects of color vision variation on survival and reproductive success in a naturallyoccurring population of primates.
doi:10.1371/journal.pone.0084872
PMCID: PMC3880319  PMID: 24404195
15.  Red-green color vision in three catarrhine primates 
The evolution of the red-green visual subsystem in trichromatic primates has been linked to foraging advantages, specifically the detection of either ripe fruits or young leaves amid mature foliage, and to the intraspecific socio-sexual communication, namely the signal of the male rank, the mate choice and the reproductive strategies in females. New data should be added to the debate regarding the evolution of trichromatic color vision. Three catarrhine primates were observed to achieve this goal. The research was performed on captive groups of vervet monkeys (Chlorocebus aethiops), pig-tailed macaques (Macaca nemestrina) and chimpanzees (Pan troglodytes) housed at Parco Natura Viva - Garda Zoological Park (Italy). Using pairs of red-green bags containing the same hidden reward in comparable outdoor enclosures, we recorded the choices by observed individuals (n = 25) to investigate the role of color cues in choosing an object. The results indicate that chimpanzees used red color as cue to choose an object that contains food by showing a preference toward red objects; in contrast, vervet monkeys and pig-tailed macaques do not demonstrate a clear choice based on the color of the object. Our findings highlight the importance of the foraging hypothesis but not rule out the potential role of the intraspecific socio-sexual communication and may serve to add useful information to the debate regarding the adaptive value of the evolution of color vision in order to fill a phylogenetic gap from Old World monkeys to humans. Future studies should address the role of socio-sexual communication, such as the selection of the reproductive partner of both high genetic quality and with compatible genes, to determine how this influenced the evolution of color vision in non-human primates.
doi:10.4161/cib.21414
PMCID: PMC3541326  PMID: 23336029
trichromacy; red-green color preference; vervet monkey; pig-tailed macaque; chimpanzee
16.  The Verriest Lecture: Color lessons from space, time, and motion 
The appearance of a chromatic stimulus depends on more than the wavelengths composing it. The scientific literature has countless examples showing that spatial and temporal features of light influence the colors we see. Studying chromatic stimuli that vary over space, time or direction of motion has a further benefit beyond predicting color appearance: the unveiling of otherwise concealed neural processes of color vision. Spatial or temporal stimulus variation uncovers multiple mechanisms of brightness and color perception at distinct levels of the visual pathway. Spatial variation in chromaticity and luminance can change perceived three-dimensional shape, an example of chromatic signals that affect a percept other than color. Chromatic objects in motion expose the surprisingly weak link between the chromaticity of objects and their physical direction of motion, and the role of color in inducing an illusory motion direction. Space, time and motion – color’s colleagues – reveal the richness of chromatic neural processing.
PMCID: PMC3492961  PMID: 22330398
17.  Core knowledge and its limits: The domain of food 
Cognition  2009;112(1):120-140.
Adults, preschool children, and nonhuman primates detect and categorize food objects according to substance information, conveyed primarily by color and texture. In contrast, they perceive and categorize artifacts primarily by shape and rigidity. The present experiments investigated the origins of this distinction. Using a looking time procedure, Experiment 1 extended previous findings that rhesus macaques (Macaca mulatta) generalize learning about novel food objects by color over changes in shape. Six additional experiments then investigated whether human infants show the same signature patterns of perception and generalization. Nine-month-old infants failed to detect food objects in accord with their intrinsic properties, in contrast to rhesus monkeys tested in previous research with identical displays. Eight-month-old infants did not privilege substance information over other features when categorizing foods, even though they detected and remembered this information. Moreover, infants showed the same property generalization patterns when presented with foods and tools. The category-specific patterns of perception and categorization shown by human adults, children, and adult monkeys therefore were not found in human infants, providing evidence for limits to infants’ domains of knowledge.
doi:10.1016/j.cognition.2009.03.005
PMCID: PMC2760822  PMID: 19409538
18.  Traceable Calibration, Performance Metrics, and Uncertainty Estimates of Minirhizotron Digital Imagery for Fine-Root Measurements 
PLoS ONE  2014;9(11):e112362.
Even though fine-root turnover is a highly studied topic, it is often poorly understood as a result of uncertainties inherent in its sampling, e.g., quantifying spatial and temporal variability. While many methods exist to quantify fine-root turnover, use of minirhizotrons has increased over the last two decades, making sensor errors another source of uncertainty. Currently, no standardized methodology exists to test and compare minirhizotron camera capability, imagery, and performance. This paper presents a reproducible, laboratory-based method by which minirhizotron cameras can be tested and validated in a traceable manner. The performance of camera characteristics was identified and test criteria were developed: we quantified the precision of camera location for successive images, estimated the trueness and precision of each camera's ability to quantify root diameter and root color, and also assessed the influence of heat dissipation introduced by the minirhizotron cameras and electrical components. We report detailed and defensible metrology analyses that examine the performance of two commercially available minirhizotron cameras. These cameras performed differently with regard to the various test criteria and uncertainty analyses. We recommend a defensible metrology approach to quantify the performance of minirhizotron camera characteristics and determine sensor-related measurement uncertainties prior to field use. This approach is also extensible to other digital imagery technologies. In turn, these approaches facilitate a greater understanding of measurement uncertainties (signal-to-noise ratio) inherent in the camera performance and allow such uncertainties to be quantified and mitigated so that estimates of fine-root turnover can be more confidently quantified.
doi:10.1371/journal.pone.0112362
PMCID: PMC4229195  PMID: 25391023
19.  The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype 
Immunogenetics  2010;62(7):451-464.
Of the two rhesus macaque subspecies used for AIDS studies, the Simian immunodeficiency virus-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection, providing both insight into pathogenesis and a system for testing novel vaccines. Despite the Chinese rhesus macaque potentially being a more relevant model for AIDS outcomes than the Indian rhesus macaque, the Chinese-origin rhesus macaques have not been well-characterized for their major histocompatibility complex (MHC) composition and function, reducing their greater utilization. In this study, we characterized a total of 50 unique Chinese rhesus macaques from several varying origins for their entire MHC class I allele composition and identified a total of 58 unique complete MHC class I sequences. Only nine of the sequences had been associated with Indian rhesus macaques, and 28/58 (48.3%) of the sequences identified were novel. From all MHC alleles detected, we prioritized Mamu-A1*02201 for functional characterization based on its higher frequency of expression. Upon the development of MHC/peptide binding assays and definition of its associated motif, we revealed that this allele shares peptide binding characteristics with the HLA-B7 supertype, the most frequent supertype in human populations. These studies provide the first functional characterization of an MHC class I molecule in the context of Chinese rhesus macaques and the first instance of HLA-B7 analogy for rhesus macaques.
Electronic supplementary material
The online version of this article (doi:10.1007/s00251-010-0450-3) contains supplementary material, which is available to authorized users.
doi:10.1007/s00251-010-0450-3
PMCID: PMC2890073  PMID: 20480161
Rhesus macaque; MHC; HLA; CTL
20.  Do common mechanisms of adaptation mediate color discrimination and appearance? Uniform backgrounds 
Color vision is useful for detecting surface boundaries and identifying objects. Are the signals used to perform these two functions processed by common mechanisms, or has the visual system optimized its processing separately for each task? We measured the effect of mean chromaticity and luminance on color discriminability and on color appearance under well-matched stimulus conditions. In the discrimination experiments, a pedestal spot was presented in one interval and a pedestal + test in a second. Observers indicated which interval contained the test. In the appearance experiments, observers matched the appearance of test spots across a change in background. We analyzed the data using a variant of Fechner's proposal, that the rate of apparent stimulus change is proportional to visual sensitivity. We found that saturating visual response functions together with a model of adaptation that included multiplicative gain control and a subtractive term accounted for data from both tasks. This result suggests that effects of the contexts we studied on color appearance and discriminability are controlled by the same underlying mechanism.
PMCID: PMC1815483  PMID: 16277280
21.  Large-scale polymorphism discovery in macaque G-protein coupled receptors 
BMC Genomics  2013;14:703.
Background
G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disease. GPCRs also represent the single largest class of drug targets and associated pharmacogenetic effects are modulated, in part, by polymorphisms. Recently, non-human primate models have been developed focusing on naturally-occurring, functionally-parallel polymorphisms in candidate genes. This work aims to extend those studies broadly across the roughly 377 non-olfactory GPCRs. Initial efforts include resequencing 44 Indian-origin rhesus macaques (Macaca mulatta), 20 Chinese-origin rhesus macaques, and 32 cynomolgus macaques (M. fascicularis).
Results
Using the Agilent target enrichment system, capture baits were designed for GPCRs off the human and rhesus exonic sequence. Using next generation sequencing technologies, nearly 25,000 SNPs were identified in coding sequences including over 14,000 non-synonymous and more than 9,500 synonymous protein-coding SNPs. As expected, regions showing the least evolutionary constraint show greater rates of polymorphism and greater numbers of higher frequency polymorphisms. While the vast majority of these SNPs are singletons, roughly 1,750 non-synonymous and 2,900 synonymous SNPs were found in multiple individuals.
Conclusions
In all three populations, polymorphism and divergence is highly concentrated in N-terminal and C-terminal domains and the third intracellular loop region of GPCRs, regions critical to ligand-binding and signaling. SNP frequencies in macaques follow a similar pattern of divergence from humans and new polymorphisms in primates have been identified that may parallel those seen in humans, helping to establish better non-human primate models of disease.
doi:10.1186/1471-2164-14-703
PMCID: PMC3907043  PMID: 24119066
Resequencing; Single-nucleotide polymorphism; Indian-origin rhesus macaques; Chinese-origin rhesus macaques; Cynomolgus macaques
22.  Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity 
Although many computational models have been proposed to explain orientation maps in primary visual cortex (V1), it is not yet known how similar clusters of color-selective neurons in macaque V1/V2 are connected and develop. In this work, we address the problem of understanding the cortical processing of color information with a possible mechanism of the development of the patchy distribution of color selectivity via computational modeling. Each color input is decomposed into a red, green, and blue representation and transmitted to the visual cortex via a simulated optic nerve in a luminance channel and red–green and blue–yellow opponent color channels. Our model of the early visual system consists of multiple topographically-arranged layers of excitatory and inhibitory neurons, with sparse intra-layer connectivity and feed-forward connectivity between layers. Layers are arranged based on anatomy of early visual pathways, and include a retina, lateral geniculate nucleus, and layered neocortex. Each neuron in the V1 output layer makes synaptic connections to neighboring neurons and receives the three types of signals in the different channels from the corresponding photoreceptor position. Synaptic weights are randomized and learned using spike-timing-dependent plasticity (STDP). After training with natural images, the neurons display heightened sensitivity to specific colors. Information-theoretic analysis reveals mutual information between particular stimuli and responses, and that the information reaches a maximum with fewer neurons in the higher layers, indicating that estimations of the input colors can be done using the output of fewer cells in the later stages of cortical processing. In addition, cells with similar color receptive fields form clusters. Analysis of spiking activity reveals increased firing synchrony between neurons when particular color inputs are presented or removed (ON-cell/OFF-cell).
doi:10.3389/fncir.2014.00016
PMCID: PMC3950416  PMID: 24659956
brain modeling; visual cortex; neocortex; color; color selectivity; self-organizing color maps; self-organizing feature maps; STDP
23.  Sex and vision II: color appearance of monochromatic lights 
Background
Because cerebral cortex has a very large number of testosterone receptors, we examined the possible sex differences in color appearance of monochromatic lights across the visible spectrum. There is a history of men and women perceiving color differently. However, all of these studies deal with higher cognitive functions which may be culture-biased. We study basic visual functions, such as color appearance, without reference to any objects. We present here a detailed analysis of sex differences in primary chromatic sensations.
Methods
We tested large groups of young adults with normal vision, including spatial and temporal resolution, and stereopsis. Based on standard color-screening and anomaloscope data, we excluded all color-deficient observers. Stimuli were equi-luminant monochromatic lights across the spectrum. They were foveally-viewed flashes presented against a dark background. The elicited sensations were measured using magnitude estimation of hue and saturation. When the only permitted hue terms are red (R) yellow (Y), green (G), blue (B), alone or in combination, such hue descriptions are language-independent and the hue and saturation values can be used to derive a wide range of color-discrimination functions.
Results
There were relatively small but clear and significant, differences between males and females in the hue sensations elicited by almost the entire spectrum. Generally, males required a slightly longer wavelength to experience the same hue as did females. The spectral loci of the unique hues are not correlated with anomaloscope matches; these matches are directly determined by the spectral sensitivities of L- and M-cones (genes for these cones are on the X-chromosomes). Nor are there correlations between loci of pairs of unique hues (R, Y, G, B). Wavelength-discrimination functions derived from the scaling data show that males have a broader range of poorer discrimination in the middle of the spectrum. The precise values for all the data depend on whether Newtonian or Maxwellian optics were used, but the sex differences were the same for both optical systems.
Conclusion
As with our associated paper on spatio-temporal vision, there are marked sex differences in color vision. The color-appearances we measured are determined by inputs from thalamic neurons (LGN) to individual neurons in primary visual cortex. This convergence from LGN to cortex is guided by the cortex during embryogenesis. We hypothesize that testosterone plays a major role, somehow leading to different connectivities for males and females: color appearance requires a re-combination and re-weighting of neuronal inputs from the LGN to the cortex, which, as we show, depends on the sex of the participant.
doi:10.1186/2042-6410-3-21
PMCID: PMC3483194  PMID: 22943488
24.  Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta) 
BMC Genomics  2008;9:256.
Background
Rhesus macaques (Macaca mulatta) are the primate most used for biomedical research, but phenotypic differences between Indian-origin and Chinese rhesus macaques have encouraged genetic methods for identifying genetic differences between these two populations. The completion of the rhesus genome has led to the identification of many single nucleotide polymorphisms (SNPs) in this species. These single nucleotide polymorphisms have many advantages over the short tandem repeat (STR) loci currently used to assay genetic variation. However, the number of currently identified polymorphisms is too small for whole genome analysis or studies of quantitative trait loci. To that end, we tested a combination of methods to identify large numbers of high-confidence SNPs, and screen those with high minor allele frequencies (MAF).
Results
By testing our previously reported single nucleotide polymorphisms, we identified a subset of high-confidence, high-MAF polymorphisms. Resequencing revealed a large number of regionally specific SNPs not identified through a single pyrosequencing run. By resequencing a pooled sample of four individuals, we reliably identified loci with a MAF of at least 12.5%. Finally, we found that when applied to a larger, geographically variable sample of rhesus, a large proportion of our loci were variable in both populations, and very few loci were ancestry informative. Despite this fact, the SNP loci were more effective at discriminating Indian and Chinese rhesus than STR loci.
Conclusion
Pyrosequencing and pooled resequencing are viable methods for the identification of high-MAF SNP loci in rhesus macaques. These SNP loci are appropriate for screening both the inter- and intra-population genetic variation.
doi:10.1186/1471-2164-9-256
PMCID: PMC2443142  PMID: 18510772
25.  Variation in the Visual Habitat May Mediate the Maintenance of Color Polymorphism in a Poeciliid Fish 
PLoS ONE  2014;9(7):e101497.
The conspicuousness of animal signals is influenced by their contrast against the background. As such, signal conspicuousness will tend to vary in nature because habitats are composed of a mosaic of backgrounds. Variation in attractiveness could result in variation in conspecific mate choice and risk of predation, which, in turn, may create opportunities for balancing selection to maintain distinct polymorphisms. We quantified male coloration, the absorbance spectrum of visual pigments and the photic environment of Poecilia parae, a fish species with five distinct male color morphs: a drab (i.e., grey), a striped, and three colorful (i.e., blue, red and yellow) morphs. Then, using physiological models, we assessed how male color patterns can be perceived in their natural visual habitats by conspecific females and a common cichlid predator, Aequidens tetramerus. Our estimates of chromatic and luminance contrasts suggest that the three most colorful morphs were consistently the most conspicuous across all habitats. However, variation in the visual background resulted in variation in which morph was the most conspicuous to females at each locality. Likewise, the most colorful morphs were the most conspicuous morphs to cichlid predators. If females are able to discriminate between conspicuous prospective mates and those preferred males are also more vulnerable to predation, variable visual habitats could influence the direction and strength of natural and sexual selection, thereby allowing for the persistence of color polymorphisms in natural environments.
doi:10.1371/journal.pone.0101497
PMCID: PMC4079317  PMID: 24987856

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