1
|
Weiß BM, Widdig A. Influence of visual information on sniffing behavior in a routinely trichromatic primate. Behav Ecol 2024; 35:arae055. [PMID: 39034973 PMCID: PMC11258807 DOI: 10.1093/beheco/arae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/05/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Most catarrhine primates are considered to be strongly visually oriented, obtaining information about conspecifics and their environment from a diversity of visual cues. Other sensory modalities may provide information that is redundant and/or complimentary to visual cues. When cues from multiple sensory modalities are available, these may reinforce or suppress each other, as shown in several taxa ranging from insects to humans. Here, we tested how the presence and ambiguity of visual information affect the use of olfactory cues when exploring food and non-food items in semi-free-ranging Barbary macaques at Affenberg Salem, Germany. We presented monkeys with pipes containing food (peanuts, popcorn), non-food (stones, feces), or no items in transparent or opaque containers and assessed whether animals looked, sniffed, and/or grabbed into the pipes depending on the visibility of the contents (experiment 1). Visual information had no robust effect on sniffing probability, but monkeys were more likely to sniff before any other form of inspection if the can was opaque than if it was transparent. Both visual and olfactory information affected, whether or not monkeys attempted to retrieve the items from the pipes, whereby monkeys showed an overall decrease in the propensity to grab after sniffing. Furthermore, we manipulated the visual appearance of familiar food items (popcorn) with food colorant (experiment 2), which resulted in substantially increased olfactory inspections compared to unmanipulated popcorn. Taken together, reliance on the olfactory sense was modulated by the available visual information, emphasizing the interplay between different sensory modalities for obtaining information about the environment.
Collapse
Affiliation(s)
- Brigitte M Weiß
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Behavioural Ecology Group, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
| | - Anja Widdig
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Behavioural Ecology Group, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
| |
Collapse
|
2
|
Vogelsang M, Vogelsang L, Gupta P, Gandhi TK, Shah P, Swami P, Gilad-Gutnick S, Ben-Ami S, Diamond S, Ganesh S, Sinha P. Impact of early visual experience on later usage of color cues. Science 2024; 384:907-912. [PMID: 38781366 DOI: 10.1126/science.adk9587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/29/2024] [Indexed: 05/25/2024]
Abstract
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.
Collapse
Affiliation(s)
- Marin Vogelsang
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute of Cognitive Science, University of Osnabrueck, 49090 Osnabrueck, Germany
| | - Lukas Vogelsang
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Priti Gupta
- Amarnath and Shashi Khosla School of Information Technology, Indian Institute of Technology, New Delhi 110016, India
- Project Prakash, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
- Cognitive Science Programme, Dayalbagh Educational Institute, Agra 282005, India
| | - Tapan K Gandhi
- Department of Electrical Engineering, Indian Institute of Technology, New Delhi 110016, India
| | - Pragya Shah
- Project Prakash, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
| | - Piyush Swami
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, 2650 Hvidovre, Denmark
| | - Sharon Gilad-Gutnick
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shlomit Ben-Ami
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sidney Diamond
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Suma Ganesh
- Department of Pediatric Ophthalmology, Dr. Shroff's Charity Eye Hospital, New Delhi 110002, India
| | - Pawan Sinha
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
3
|
Moreira LAA, Merrigan-Johnson C, Fetherstonhaugh L, Parr NA, Higham JP, Melin AD. Assessing color cues of development, breeding status and reproductive condition in captive golden lion tamarins (Leontopithecus rosalia). Am J Primatol 2023; 85:e23543. [PMID: 37560915 DOI: 10.1002/ajp.23543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/21/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
Color signals play an important role in intraspecific communication and are well studied in catarrhine primates, which exhibit uniform trichromatic vision that is well suited to detecting such signals. Platyrrhine primates exhibit polymorphic color vision with different individuals possessing different color vision types in most species. Intriguingly, some platyrrhine species exhibit bare faces, which are convergent with those of catarrhines. However, putative functions of bare-faced color signals in platyrrhines remain largely unexplored. We measured facial skin color of five captive golden lion tamarins (Leontopithecus rosalia) using color-calibrated digital photography and modeled these colors to the visual systems of the species. Our results show that facial coloration is different between infant and older adults and varies across reproductive condition, but not between breeding and nonbreeding adults. While preliminary, our study suggests that facial coloration may be involved in sociosexual signaling in golden lion tamarins, and provides intriguing evidence that we hope might stimulate more studies of bare-faced signaling in platyrrhines.
Collapse
Affiliation(s)
- Lais A A Moreira
- Department of Anthropology & Archaeology, University of Calgary, Calgary, Canada
| | | | | | - Nigel A Parr
- Department of Wildlife Care, Toronto Zoo, Toronto, Canada
| | - James P Higham
- Department of Anthropology, New York University, New York, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology, University of Calgary, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| |
Collapse
|
4
|
Fuzessy L, Silveira FAO, Culot L, Jordano P, Verdú M. Phylogenetic congruence between Neotropical primates and plants is driven by frugivory. Ecol Lett 2021; 25:320-329. [PMID: 34775664 DOI: 10.1111/ele.13918] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/27/2022]
Abstract
Seed dispersal benefits plants and frugivores, and potentially drives co-evolution, with consequences to diversification evidenced for, e.g., primates. Evidence for macro-coevolutionary patterns in multi-specific, plant-animal mutualisms is scarce, and the mechanisms driving them remain unexplored. We tested for phylogenetic congruences in primate-plant interactions and showed strong co-phylogenetic signals across Neotropical forests, suggesting that both primates and plants share evolutionary history. Phylogenetic congruence between Platyrrhini and Angiosperms was driven by the most generalist primates, modulated by their functional traits, interacting with a wide-range of Angiosperms. Consistently similar eco-evolutionary dynamics seem to be operating irrespective of local assemblages, since co-phylogenetic signal emerged independently across three Neotropical regions. Our analysis supports the idea that macroevolutionary, coevolved patterns among interacting mutualistic partners are driven by super-generalist taxa. Trait convergence among multiple partners within multi-specific assemblages appears as a mechanism favouring these likely coevolved outcomes.
Collapse
Affiliation(s)
- Lisieux Fuzessy
- Department of Biodiversity, Universidade Estadual Paulista, UNESP campus Rio Claro, São Paulo, Brazil.,CREAF, Centre de Recerca Ecològica i Aplicacions Foresta, Universitat Autònoma de Barcelona, Catalunya, Spain.,Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Fernando A O Silveira
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Laurence Culot
- Department of Biodiversity, Universidade Estadual Paulista, UNESP campus Rio Claro, São Paulo, Brazil
| | - Pedro Jordano
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain.,Facultad de Biología, Department Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación, CSIC-UV-GV, Moncada, Valencia, Spain
| |
Collapse
|
5
|
Hartje V, Illemann MJ, Schmidtke D. Motion cues increase focused attention towards purely visual stimuli in a nocturnal primate and drive stimulus interaction and approach/avoidance in a context-dependent manner. Am J Primatol 2021; 83:e23286. [PMID: 34169554 DOI: 10.1002/ajp.23286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/06/2021] [Accepted: 05/14/2021] [Indexed: 11/09/2022]
Abstract
Visual information is of pivotal ecological importance to monkeys, apes, and humans, whereas its role in nocturnal primate ecology is less well understood. We explored how purely visual information modulates the behavior of a nocturnal primate. Abstract (shape), photographic (shape + detail), or video (shape + detail + motion) representations of arthropod prey (Zophobas morio; food context) or a male conspecific (social context) were systematically presented to 22 individuals of the gray mouse lemur (Microcebus murinus) using a touchscreen. We assessed stimulus-directed touch interactions, durations of focused visual attention towards the different stimuli, and durations spent in the half of the setup-chamber more distant to the touchscreen (as quantification of approach/avoidance). Focused attention towards the stimulus generally increased from abstract and photographic to videographic stimuli. For the food context, indications for a parallel increase in stimulus-directed touch interactions from abstract stimulus to video were found. Approach/avoidance was independent of the stimulus type within both contexts. A comparison between the contexts under the video condition revealed higher durations of visual attention and lower stimulus avoidance in the food context compared to the social context. The number of touch interactions with the video stimulus was not generally context-dependent, but context-dependency related to sex: In the food context, animals with high and low numbers of touch interactions were equally distributed across sexes. In the social context, females showed the highest numbers of touch interactions. Numbers in males declined compared to the food context. Our results demonstrate for the first time that purely visual information modulates mouse lemur behavior and focused attention in a content- and context-specific manner, suggesting that vision is of high importance for the ecology of these nocturnal primates. The findings emphasize the need for further vision-based experiments to gain deeper insight into the evolution of visual information processing and cognition in nocturnal primates.
Collapse
Affiliation(s)
- Valeria Hartje
- Institute of Zoology, University of Veterinary Medicine, Hannover, Germany
| | - Michele J Illemann
- Institute of Zoology, University of Veterinary Medicine, Hannover, Germany
| | - Daniel Schmidtke
- Institute of Zoology, University of Veterinary Medicine, Hannover, Germany
| |
Collapse
|
6
|
Bell RB, Bradley BJ, Kamilar JM. The Evolutionary Ecology of Primate Hair Coloration: A Phylogenetic Approach. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09547-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
7
|
Liénard MA, Bernard GD, Allen A, Lassance JM, Song S, Childers RR, Yu N, Ye D, Stephenson A, Valencia-Montoya WA, Salzman S, Whitaker MRL, Calonje M, Zhang F, Pierce NE. The evolution of red color vision is linked to coordinated rhodopsin tuning in lycaenid butterflies. Proc Natl Acad Sci U S A 2021; 118:e2008986118. [PMID: 33547236 PMCID: PMC8017955 DOI: 10.1073/pnas.2008986118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Color vision has evolved multiple times in both vertebrates and invertebrates and is largely determined by the number and variation in spectral sensitivities of distinct opsin subclasses. However, because of the difficulty of expressing long-wavelength (LW) invertebrate opsins in vitro, our understanding of the molecular basis of functional shifts in opsin spectral sensitivities has been biased toward research primarily in vertebrates. This has restricted our ability to address whether invertebrate Gq protein-coupled opsins function in a novel or convergent way compared to vertebrate Gt opsins. Here we develop a robust heterologous expression system to purify invertebrate rhodopsins, identify specific amino acid changes responsible for adaptive spectral tuning, and pinpoint how molecular variation in invertebrate opsins underlie wavelength sensitivity shifts that enhance visual perception. By combining functional and optophysiological approaches, we disentangle the relative contributions of lateral filtering pigments from red-shifted LW and blue short-wavelength opsins expressed in distinct photoreceptor cells of individual ommatidia. We use in situ hybridization to visualize six ommatidial classes in the compound eye of a lycaenid butterfly with a four-opsin visual system. We show experimentally that certain key tuning residues underlying green spectral shifts in blue opsin paralogs have evolved repeatedly among short-wavelength opsin lineages. Taken together, our results demonstrate the interplay between regulatory and adaptive evolution at multiple Gq opsin loci, as well as how coordinated spectral shifts in LW and blue opsins can act together to enhance insect spectral sensitivity at blue and red wavelengths for visual performance adaptation.
Collapse
Affiliation(s)
- Marjorie A Liénard
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142;
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Gary D Bernard
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195
| | - Andrew Allen
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142
| | - Jean-Marc Lassance
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Siliang Song
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Richard Rabideau Childers
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Nanfang Yu
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027
| | - Dajia Ye
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Adriana Stephenson
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Wendy A Valencia-Montoya
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Shayla Salzman
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Melissa R L Whitaker
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard University, Cambridge, MA 02142
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Cambridge, MA 02139
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138;
| |
Collapse
|
8
|
de Moraes PZ, Diniz P, Spyrides MHC, Pessoa DMA. The effect of pelage, background, and distance on predator detection and the evolution of primate color vision. Am J Primatol 2021; 83:e23230. [PMID: 33475188 DOI: 10.1002/ajp.23230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 10/23/2020] [Accepted: 11/17/2020] [Indexed: 11/10/2022]
Abstract
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.
Collapse
Affiliation(s)
- Pedro Z de Moraes
- Laboratory of Sensory Ecology, Department of Physiology and Behavior, Federal University of Rio Grande do Norte, Natal, 59078-970, Brazil
| | - Pedro Diniz
- Ecology Graduation Program, University of Brasilia, Brasilia, 70910-900, Brazil.,Laboratory of Animal Behavior, Department of Zoology, University of Brasilia, Brasilia, 70910-900, Brazil
| | - Maria Helena C Spyrides
- Department of Statistics, Federal University of Rio Grande do Norte, Natal, 59078-970, Brazil
| | - Daniel M A Pessoa
- Laboratory of Sensory Ecology, Department of Physiology and Behavior, Federal University of Rio Grande do Norte, Natal, 59078-970, Brazil.,Primate Center, Department of Physiology and Behavior, Federal University of Rio Grande do Norte, Natal, 59078-970, Brazil
| |
Collapse
|
9
|
Grogan KE, Perry GH. Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools. Evol Anthropol 2020; 29:143-158. [PMID: 32142200 PMCID: PMC10574139 DOI: 10.1002/evan.21825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.
Collapse
Affiliation(s)
- Kathleen E. Grogan
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| |
Collapse
|
10
|
Abstract
Nervous systems allow animals to acutely respond and behaviorally adapt to changes and recurring patterns in their environment at multiple timescales-from milliseconds to years. Behavior is further shaped at intergenerational timescales by genetic variation, drift, and selection. This sophistication and flexibility of behavior makes it challenging to measure behavior consistently in individual subjects and to compare it across individuals. In spite of these challenges, careful behavioral observations in nature and controlled measurements in the laboratory, combined with modern technologies and powerful genetic approaches, have led to important discoveries about the way genetic variation shapes behavior. A critical mass of genes whose variation is known to modulate behavior in nature is finally accumulating, allowing us to recognize emerging patterns. In this review, we first discuss genetic mapping approaches useful for studying behavior. We then survey how variation acts at different levels-in environmental sensation, in internal neuronal circuits, and outside the nervous system altogether-and then discuss the sources and types of molecular variation linked to behavior and the mechanisms that shape such variation. We end by discussing remaining questions in the field.
Collapse
Affiliation(s)
- Natalie Niepoth
- Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; ,
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; ,
| |
Collapse
|
11
|
Atilano SR, Kenney MC, Briscoe AD, Jameson KA. A two-step method for identifying photopigment opsin and rhodopsin gene sequences underlying human color vision phenotypes. Mol Vis 2020; 26:158-172. [PMID: 32180681 PMCID: PMC7058431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/03/2020] [Indexed: 11/02/2022] Open
Abstract
Purpose To present a detailed, reliable long range-PCR and sequencing (LR-PCR-Seq) procedure to identify human opsin gene sequences for variations in the long wavelength-sensitive (OPN1LW), medium wavelength-sensitive (OPN1MW), short wavelength-sensitive (OPN1SW), and rhodopsin (RHO) genes. Methods Color vision was assessed for nine subjects using the Farnsworth-Munsell 100 hue test, Ishihara pseudoisochromatic plates, and the Rabin cone-contrast threshold procedure (ColorDX, Konan Medical). The color vision phenotypes were normal trichromacy (n = 3), potential tetrachromacy (n = 3), dichromacy (n = 2), and unexplained low color vision (n = 1). DNA was isolated from blood or saliva and LR-PCR amplified into individual products: OPN1LW (4,045 bp), OPN1MW (4,045 bp), OPN1SW (3,326 bp), and RHO (6,715 bp). Each product was sequenced using specific internal primer sets. Analysis was performed with Mutation Surveyor software. Results The LR-PCR-Seq technique identified known single nucleotide polymorphisms (SNPs) in OPN1LW and OPN1MW gene codons (180, 230, 233, 277, and 285), as well as those for lesser studied codons (174, 178, 236, 274, 279, 298 and 309) in the OPN1LW and OPN1MW genes. Additionally, six SNP variants in the OPN1MW and OPN1LW genes not previously reported in the NCBI dbSNP database were identified. An unreported poly-T region within intron 5(c.36+126) of the rhodopsin gene was also found, and analysis showed it to be highly conserved in mammalian species. Conclusions This LR-PCR-Seq procedure (single PCR reaction per gene followed by sequencing) can identify exonic and intronic SNP variants in OPN1LW, OPN1MW, OPN1SW, and rhodopsin genes. There is no need for restriction enzyme digestion or multiple PCR steps that can introduce errors. Future studies will combine the LR-PCR-Seq with perceptual behavior measures, allowing for accurate correlations between opsin genotypes, retinal photopigment phenotypes, and color perception behaviors.
Collapse
Affiliation(s)
- Shari R. Atilano
- Gavin Herbert Eye Institute, School of Medicine, University of California, Irvine, CA
| | - M. Cristina Kenney
- Gavin Herbert Eye Institute, School of Medicine, University of California, Irvine, CA,Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA
| | - Adriana D. Briscoe
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Kimberly A. Jameson
- Institute for Mathematical Behavioral Sciences, University of California Irvine, Irvine, CA
| |
Collapse
|
12
|
Nikitin D, Kolosov N, Murzina A, Pats K, Zamyatin A, Tkachev V, Sorokin M, Kopylov P, Buzdin A. Retroelement-Linked H3K4me1 Histone Tags Uncover Regulatory Evolution Trends of Gene Enhancers and Feature Quickly Evolving Molecular Processes in Human Physiology. Cells 2019; 8:cells8101219. [PMID: 31597351 PMCID: PMC6830109 DOI: 10.3390/cells8101219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Retroelements (REs) are mobile genetic elements comprising ~40% of human DNA. They can reshape expression patterns of nearby genes by providing various regulatory sequences. The proportion of regulatory sequences held by REs can serve a measure of regulatory evolution rate of the respective genes and molecular pathways. Methods: We calculated RE-linked enrichment scores for individual genes and molecular pathways based on ENCODE project epigenome data for enhancer-specific histone modification H3K4me1 in five human cell lines. We identified consensus groups of molecular processes that are enriched and deficient in RE-linked H3K4me1 regulation. Results: We calculated H3K4me1 RE-linked enrichment scores for 24,070 human genes and 3095 molecular pathways. We ranked genes and pathways and identified those statistically significantly enriched and deficient in H3K4me1 RE-linked regulation. Conclusion: Non-coding RNA genes were statistically significantly enriched by RE-linked H3K4me1 regulatory modules, thus suggesting their high regulatory evolution rate. The processes of gene silencing by small RNAs, DNA metabolism/chromatin structure, sensory perception/neurotransmission and lipids metabolism showed signs of the fastest regulatory evolution, while the slowest processes were connected with immunity, protein ubiquitination/degradation, cell adhesion, migration and interaction, metals metabolism/ion transport, cell death, intracellular signaling pathways.
Collapse
Affiliation(s)
- Daniil Nikitin
- Group for genomic analysis of cell signaling systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia.
- Omicsway Corp., Walnut, CA 91789, USA.
| | | | | | - Karina Pats
- ITMO University, 195251 Saint-Petersburg, Russia.
| | | | | | - Maxim Sorokin
- Omicsway Corp., Walnut, CA 91789, USA.
- Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
| | - Philippe Kopylov
- Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
| | - Anton Buzdin
- Group for genomic analysis of cell signaling systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia.
- Omicsway Corp., Walnut, CA 91789, USA.
- Institute of Personalized Medicine, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
| |
Collapse
|
13
|
Fennell JG, Talas L, Baddeley RJ, Cuthill IC, Scott-Samuel NE. Optimizing colour for camouflage and visibility using deep learning: the effects of the environment and the observer's visual system. J R Soc Interface 2019; 16:20190183. [PMID: 31138092 PMCID: PMC6544896 DOI: 10.1098/rsif.2019.0183] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/01/2019] [Indexed: 11/22/2022] Open
Abstract
Avoiding detection can provide significant survival advantages for prey, predators, or the military; conversely, maximizing visibility would be useful for signalling. One simple determinant of detectability is an animal's colour relative to its environment. But identifying the optimal colour to minimize (or maximize) detectability in a given natural environment is complex, partly because of the nature of the perceptual space. Here for the first time, using image processing techniques to embed targets into realistic environments together with psychophysics to estimate detectability and deep neural networks to interpolate between sampled colours, we propose a method to identify the optimal colour that either minimizes or maximizes visibility. We apply our approach in two natural environments (temperate forest and semi-arid desert) and show how a comparatively small number of samples can be used to predict robustly the most and least effective colours for camouflage. To illustrate how our approach can be generalized to other non-human visual systems, we also identify the optimum colours for concealment and visibility when viewed by simulated red-green colour-blind dichromats, typical for non-human mammals. Contrasting the results from these visual systems sheds light on why some predators seem, at least to humans, to have colouring that would appear detrimental to ambush hunting. We found that for simulated dichromatic observers, colour strongly affected detection time for both environments. In contrast, trichromatic observers were more effective at breaking camouflage.
Collapse
Affiliation(s)
- J. G. Fennell
- School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK
| | - L. Talas
- School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK
| | - R. J. Baddeley
- School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK
| | - I. C. Cuthill
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - N. E. Scott-Samuel
- School of Psychological Science, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK
| |
Collapse
|
14
|
Duytschaever G, Janiak MC, Ong PS, Wells K, Dominy NJ, Melin AD. Opsin genes of select treeshrews resolve ancestral character states within Scandentia. ROYAL SOCIETY OPEN SCIENCE 2019; 6:182037. [PMID: 31183134 PMCID: PMC6502361 DOI: 10.1098/rsos.182037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Treeshrews are small, squirrel-like mammals in the order Scandentia, which is nested together with Primates and Dermoptera in the superordinal group Euarchonta. They are often described as living fossils, and researchers have long turned to treeshrews as a model or ecological analogue for ancestral primates. A comparative study of colour vision-encoding genes within Scandentia found a derived amino acid substitution in the long-wavelength sensitive opsin gene (OPN1LW) of the Bornean smooth-tailed treeshrew (Dendrogale melanura). The opsin, by inference, is red-shifted by ca 6 nm with an inferred peak sensitivity of 561 nm. It is tempting to view this trait as a novel visual adaptation; however, the genetic and functional diversity of visual pigments in treeshrews is unresolved outside of Borneo. Here, we report gene sequences from the northern smooth-tailed treeshrew (Dendrogale murina) and the Mindanao treeshrew (Tupaia everetti, the senior synonym of Urogale everetti). We found that the opsin genes are under purifying selection and that D. murina shares the same substitution as its congener, a result that distinguishes Dendrogale from other treeshrews, including T. everetti. We discuss the implications of opsin functional variation in light of limited knowledge about the visual ecology of smooth-tailed treeshrews.
Collapse
Affiliation(s)
- Gwen Duytschaever
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Mareike C. Janiak
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Perry S. Ong
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines
| | - Konstans Wells
- Department of Biosciences, Swansea University, Wales, UK
| | - Nathaniel J. Dominy
- Department of Anthropology, Dartmouth College, Hanover, NH, USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Amanda D. Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
15
|
Widayati KA. Color Perception in Protanomalous Female Macaca fascicularis. Iperception 2019; 10:2041669519846136. [PMID: 31066374 PMCID: PMC6488792 DOI: 10.1177/2041669519846136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 04/02/2019] [Indexed: 11/17/2022] Open
Abstract
Protanomalous females with X chromosome-linked color vision deficiency exhibit mild abnormalities, whereas dichromats show a distinct deficiency in discriminating certain color pairs. Dichromats have an advantage in detecting a textured target when it is camouflaged by red-green colors, owing to their insensitivity to these colors. However, it is not certain whether protanomalous females possess a similar advantage in breaking camouflage. Here, we introduce an animal model of dichromatic macaque monkeys and protanomalous females. We examined whether protanomalous females have the same advantage in breaking color camouflage as shown by dichromatic macaques. We also tested whether they could discriminate a certain color pair that trichromats could, where the dichromats are confused. Our experiments show that protanomalous macaques can break color camouflage, similar to dichromats, and can discriminate colors similarly to trichromats. Protanomalous females are thus thought to have the combined ecological advantages of being both trichromats and dichromats.
Collapse
|
16
|
Evolutionary history of the medaka long-wavelength sensitive genes and effects of artificial regression by gene loss on behavioural photosensitivity. Sci Rep 2019; 9:2726. [PMID: 30804415 PMCID: PMC6389941 DOI: 10.1038/s41598-019-39978-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/28/2018] [Indexed: 01/28/2023] Open
Abstract
Tandem gene duplication has led to an expansion of cone-opsin repertoires in many fish, but the resulting functional advantages have only been conjectured without empirical demonstration. Medaka (Oryzias latipes and O. sakaizumii) have eight (two red, three green, two blue, and one violet) cone opsin genes. Absorbance maxima (λmax) of the proteins vary from 356 nm to 562 nm, but those of the red opsins (long-wavelength sensitive; LWS) are nearly identical, obscuring the necessity of their coexistence. Here, we compared the LWSa and LWSb loci of these sister species and found that the gene duplication occurred long before the latipes–sakaizumii speciation (4–18 million years ago), and the high sequence similarity between the paralogues is the result of at least two events of gene conversion. These repetitive gene conversions would indicate the importance for medaka of retaining two identical LWSs in the genome. However, a newly established medaka mutant with a single LWS showed no defect in LWS expression or behavioural red-light sensitivity, demonstrating functional redundancy of the paralogs. Thus, as with many other genes after whole-genome duplication, the redundant LWS might be on the way to being lost from the current cone opsin repertoire. Thus, non-allelic gene conversion may temporarily provide an easier and more frequent solution than gene loss for reducing genetic diversity, which should be considered when assessing history of gene evolution by phylogenetic analyses.
Collapse
|
17
|
Snodderly DM, Ellis KM, Lieberman SR, Link A, Fernandez-Duque E, Di Fiore A. Initiation of feeding by four sympatric Neotropical primates (Ateles belzebuth, Lagothrix lagotricha poeppigii, Plecturocebus (Callicebus) discolor, and Pithecia aequatorialis) in Amazonian Ecuador: Relationships to photic and ecological factors. PLoS One 2019; 14:e0210494. [PMID: 30673746 PMCID: PMC6344106 DOI: 10.1371/journal.pone.0210494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/22/2018] [Indexed: 12/11/2022] Open
Abstract
We examined photic and ecological factors related to initiation of feeding by four sympatric primates in the rain forest of Amazonian Ecuador. With rare exceptions, morning activities of all taxa began only after the onset of nautical twilight, which occurred 47-48 min before sunrise. The larger spider and woolly monkeys, Ateles belzebuth and Lagothrix lagotricha poeppigii, left their sleeping trees before sunrise about half the time, while the smaller sakis and titi monkeys, Pithecia aequatorialis and Plecturocebus (formerly Callicebus) discolor, did not emerge until sunrise or later. None of the four taxa routinely began feeding before sunrise. Pithecia began feeding a median 2.17 h after sunrise, at least 0.8 h later than the median feeding times of the other three taxa. The early movement of Ateles and Lagothrix, and late initiation of feeding by Pithecia are consistent with temporal niche partitioning. Among most New World primate species, all males and many females, have dichromatic color vision, with only two cone photopigments, while some females are trichromats with three cone photopigments. Current evidence indicates that the dichromats have a foraging advantage in dim light, which could facilitate utilization of twilight periods and contribute to temporal niche partitioning. However, in our study, dichromatic males did not differentially exploit the dim light of twilight, and times of first feeding bouts of female Ateles and Lagothrix were similar to those of males. First feeding bouts followed a seasonal pattern, occurring latest in May-August, when ripe fruit abundance and ambient temperature were both relatively low. The most frugivorous taxon, Ateles, exhibited the greatest seasonality, initiating feeding 1.4 h later in May-August than in January-April. This pattern may imply a strategy of conserving energy when ripe fruit is scarcer, but starting earlier to compete successfully when fruit is more abundant. Lower temperatures were associated with later feeding of Ateles (by 26 min / °C) and perhaps Pithecia, but not Lagothrix or Plecturocebus. The potential for modification of temporal activity patterns and temporal niche partitioning by relatively small changes in temperature should be considered when predicting the effects of climate change.
Collapse
Affiliation(s)
- D. Max Snodderly
- Department of Neuroscience, University of Texas at Austin, Austin, TX, United States of America
| | - Kelsey M. Ellis
- Department of Anthropology, University of Texas at Austin, Austin, TX, United States of America
| | - Sarina R. Lieberman
- Department of Neuroscience, University of Texas at Austin, Austin, TX, United States of America
| | - Andrés Link
- Department of Biological Sciences and School of Management, Universidad de Los Andes, Bogota, Colombia
| | | | - Anthony Di Fiore
- Department of Anthropology, University of Texas at Austin, Austin, TX, United States of America
| |
Collapse
|
18
|
May CA. Intrinsic Neurons and Nonvascular Smooth Muscle Cells in the Choroid of a Chimpanzee (Pan troglodytes). INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0028-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
19
|
Hiramatsu C, Melin AD, Allen WL, Dubuc C, Higham JP. Experimental evidence that primate trichromacy is well suited for detecting primate social colour signals. Proc Biol Sci 2018; 284:rspb.2016.2458. [PMID: 28615496 PMCID: PMC5474062 DOI: 10.1098/rspb.2016.2458] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/17/2017] [Indexed: 12/14/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Chihiro Hiramatsu
- Department of Human Science, Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minamiku, Fukuoka 815-8540, Japan .,Physiological Anthropology Research Center, Kyushu University, 4-9-1 Shiobaru, Minamiku, Fukuoka 815-8540, Japan
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - William L Allen
- Department of Anthropology, New York University, New York, NY, USA.,Department of Biosciences, Swansea University, Swansea, UK
| | - Constance Dubuc
- Department of Anthropology, New York University, New York, NY, USA.,Department of Zoology, University of Cambridge, Cambridge, UK
| | - James P Higham
- Department of Anthropology, New York University, New York, NY, USA
| |
Collapse
|
20
|
Ishengoma E, Agaba M, Cavener DR. Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi. PeerJ 2017; 5:e3145. [PMID: 28396824 PMCID: PMC5385128 DOI: 10.7717/peerj.3145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/04/2017] [Indexed: 12/20/2022] Open
Abstract
Background The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe’s unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood. Methods The recent availability of giraffe and okapi genomes provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals. Results Signatures of selection were identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW. Significant selection divergence was identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. Discussion By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptations. At least some of the genes that exhibit signature of selection may reflect adaptive response to differences in giraffe and okapi habitat. We hypothesize that requirement for long distance vision associated with predation and communication with conspecifics likely played an important role in the adaptive pressure on giraffe vision genes.
Collapse
Affiliation(s)
- Edson Ishengoma
- The School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; Mkwawa University of College of Education, University of Dar-es-Salaam, Iringa, Tanzania
| | - Morris Agaba
- The School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology , Arusha , Tanzania
| | - Douglas R Cavener
- Department of Biology and the Huck Institute of Life Sciences, Pennsylvania State University , University Park , PA , United States
| |
Collapse
|