scholarly journals Opsin gene repertoires in northern archaic hominids

Genome ◽  
2016 ◽  
Vol 59 (8) ◽  
pp. 541-549 ◽  
Author(s):  
John S. Taylor ◽  
Thomas E. Reimchen
Keyword(s):  
Colour Vision ◽  
Modern Human ◽  
Active Species ◽  
Opsin Gene ◽  
Human Reference Genome ◽  
Northern Latitudes ◽  
Opsin Genes ◽  
Northern Distribution ◽  
Dim Light ◽  
Additional Support

The Neanderthals’ northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. We surveyed visual opsin genes from four Neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. This analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vision in mesopic conditions, and by the observation that dim light active species often have fewer opsin genes than diurnal relatives. We also looked for evidence of convergent amino acid substitutions in Neanderthal opsins and orthologs from crepuscular or nocturnal species. The Altai Neanderthal, the Denisovan, and the Ust’-Ishim early modern human had opsin genes that encoded proteins identical to orthologs in the human reference genome. Opsins from the Vindija Cave Neanderthals (three females) had many nonsynonymous substitutions, including several predicted to influence colour vision (e.g., stop codons). However, the functional implications of these observations were difficult to assess, given that “control” loci, where no substitutions were expected, differed from humans to the same extent. This left unresolved the test for colour vision deficiencies in Vindija Cave Neanderthals.

scholarly journals Functional preservation and variation in the cone opsin genes of nocturnal tarsiers

2017 ◽  
Vol 372 (1717) ◽  
pp. 20160075 ◽  
Author(s):  
Gillian L. Moritz ◽  
Perry S. Ong ◽  
George H. Perry ◽  
Nathaniel J. Dominy
Keyword(s):  
Colour Vision ◽  
Purifying Selection ◽  
Opsin Gene ◽  
Long Wavelength ◽  
Cone Opsin ◽  
Light Levels ◽  
Tarsius Bancanus ◽  
Dim Light ◽  
Two Stages ◽  
Functional Preservation

The short-wavelength sensitive (S-) opsin gene OPN1SW is pseudogenized in some nocturnal primates and retained in others, enabling dichromatic colour vision. Debate on the functional significance of this variation has focused on dark conditions, yet many nocturnal species initiate activity under dim (mesopic) light levels that can support colour vision. Tarsiers are nocturnal, twilight-active primates and exemplary visual predators; they also express different colour vision phenotypes, raising the possibility of discrete adaptations to mesopic conditions. To explore this premise, we conducted a field study in two stages. First, to estimate the level of functional constraint on colour vision, we sequenced OPN1SW in 12 wild-caught Philippine tarsiers ( Tarsius syrichta ). Second, to explore whether the dichromatic visual systems of Philippine and Bornean ( Tarsius bancanus ) tarsiers—which express alternate versions of the medium/long-wavelength sensitive (M/L-) opsin gene OPN1MW / OPN1LW —confer differential advantages specific to their respective habitats, we used twilight and moonlight conditions to model the visual contrasts of invertebrate prey. We detected a signature of purifying selection for OPN1SW , indicating that colour vision confers an adaptive advantage to tarsiers. However, this advantage extends to a relatively small proportion of prey–background contrasts, and mostly brown arthropod prey amid leaf litter. We also found that the colour vision of T. bancanus is advantageous for discriminating prey under twilight that is enriched in shorter (bluer) wavelengths, a plausible idiosyncrasy of understorey habitats in Borneo. This article is part of the themed issue ‘Vision in dim light’.

scholarly journals Evidence for UV-green dichromacy in the basal hymenopteran Sirex noctilio (Siricidae)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Quentin Guignard ◽  
Johannes Spaethe ◽  
Bernard Slippers ◽  
Martin Strube-Bloss ◽  
Jeremy D. Allison
Keyword(s):  
Colour Vision ◽  
Compound Eye ◽  
Phylogenetic Analyses ◽  
Ultra Violet ◽  
Opsin Gene ◽  
Compound Eyes ◽  
Sirex Noctilio ◽  
Long Wavelength ◽  
Opsin Genes ◽  
Related Group

AbstractA precondition for colour vision is the presence of at least two spectral types of photoreceptors in the eye. The order Hymenoptera is traditionally divided into the Apocrita (ants, bees, wasps) and the Symphyta (sawflies, woodwasps, horntails). Most apocritan species possess three different photoreceptor types. In contrast, physiological studies in the Symphyta have reported one to four photoreceptor types. To better understand the evolution of photoreceptor diversity in the Hymenoptera, we studied the Symphyta Sirex noctilio, which belongs to the superfamily Siricoidea, a closely related group of the Apocrita suborder. Our aim was to (i) identify the photoreceptor types of the compound eye by electroretinography (ERG), (ii) characterise the visual opsin genes of S. noctilio by genomic comparisons and phylogenetic analyses and (iii) analyse opsin mRNA expression. ERG measurements revealed two photoreceptor types in the compound eye, maximally sensitive to 527 and 364 nm. In addition, we identified three opsins in the genome, homologous to the hymenopteran green or long-wavelength sensitive (LW) LW1, LW2 and ultra-violet sensitive (UV) opsin genes. The LW1 and UV opsins were found to be expressed in the compound eyes, and LW2 and UV opsins in the ocelli. The lack of a blue or short-wavelength sensitive (SW) homologous opsin gene and a corresponding receptor suggests that S. noctilio is a UV-green dichromate.

scholarly journals UV-green dichromacy in the basal hymenopteran Sirex noctilio (Hymenoptera: Siricidae).

2021 ◽  
Author(s):  
Quentin Guignard ◽  
Johannes Spaethe ◽  
Bernard Slippers ◽  
Martin Strube-Bloss ◽  
Jeremy D. Allison
Keyword(s):  
Mrna Expression ◽  
Colour Vision ◽  
Compound Eye ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Opsin Gene ◽  
Compound Eyes ◽  
Sirex Noctilio ◽  
Opsin Genes ◽  
Physiological Studies

Abstract A precondition for colour vision is the presence of at least two spectral types of photoreceptors in the eye. The order Hymenoptera is traditionally divided into the Apocrita (ants, bees, wasps) and the Symphyta (sawflies, woodwasps, horntails). Most apocritan species possess three different photoreceptor types. In contrast, physiological studies in the Symphyta have reported one to four photoreceptor types. To better understand the evolution of photoreceptor diversity in the Hymenoptera, we studied Sirex noctilio, which belongs to the superfamily Siricoidea, a sister group of the Apocrita. Our aim was to i) identify the photoreceptor types of the compound eye by electroretinography (ERG), ii) characterise the visual opsins genes of S. noctilio by genomic comparisons and phylogenetic analyses and iii) analyse opsin mRNA expression. ERG measurements revealed two photoreceptor types in the compound eye, maximally sensitive to 527 and 364 nm. In addition, we identified three opsins in the genome, homologous to the hymenopteran LW1, LW2 and UV opsin genes. The LW1 and UV opsins were found to be expressed in the compound eyes, and LW2 and UV opsins in the ocelli. The lack of a SW-homologous opsin gene and a corresponding receptor suggests that S. noctilio is a UV-green dichromate.

scholarly journals Evolutionary analyses of visual opsin genes in anurans reveals diversity and positive selection suggestive of functional adaptation to distinct light environments

2021 ◽  
Author(s):  
Ryan K Schott ◽  
Leah Perez ◽  
Matthew A Kwiatkowski ◽  
Vance Imhoff ◽  
Jennifer M Gumm
Keyword(s):  
Positive Selection ◽  
Spectral Sensitivity ◽  
Life Histories ◽  
Visual Pigments ◽  
Molecular Techniques ◽  
Functional Adaptation ◽  
Opsin Gene ◽  
Visual Systems ◽  
Opsin Genes ◽  
Dim Light

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

scholarly journals Thresholds and noise limitations of colour vision in dim light

2017 ◽  
Vol 372 (1717) ◽  
pp. 20160065 ◽  
Author(s):  
Almut Kelber ◽  
Carola Yovanovich ◽  
Peter Olsson
Keyword(s):  
Shot Noise ◽  
Colour Vision ◽  
Absolute Threshold ◽  
Colour Discrimination ◽  
Dark Noise ◽  
Visual Threshold ◽  
Light Intensities ◽  
Purkinje Shift ◽  
Dim Light ◽  
Receptor Noise

Colour discrimination is based on opponent photoreceptor interactions, and limited by receptor noise. In dim light, photon shot noise impairs colour vision, and in vertebrates, the absolute threshold of colour vision is set by dark noise in cones. Nocturnal insects (e.g. moths and nocturnal bees) and vertebrates lacking rods (geckos) have adaptations to reduce receptor noise and use chromatic vision even in very dim light. In contrast, vertebrates with duplex retinae use colour-blind rod vision when noisy cone signals become unreliable, and their transition from cone- to rod-based vision is marked by the Purkinje shift. Rod–cone interactions have not been shown to improve colour vision in dim light, but may contribute to colour vision in mesopic light intensities. Frogs and toads that have two types of rods use opponent signals from these rods to control phototaxis even at their visual threshold. However, for tasks such as prey or mate choice, their colour discrimination abilities fail at brighter light intensities, similar to other vertebrates, probably limited by the dark noise in cones. This article is part of the themed issue 'Vision in dim light’.

The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Zuzana Musilova ◽  
Walter Salzburger ◽  
Fabio Cortesi
Keyword(s):  
Sensory System ◽  
Photoreceptor Cells ◽  
Opsin Gene ◽  
Annual Review ◽  
Specific Gene ◽  
Publication Date ◽  
Teleost Fishes ◽  
Opsin Genes ◽  
The Rich ◽  
Species Specific

Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The visual ecology of Holocentridae, a nocturnal coral reef fish family with a deep-sea-like multibank retina

2020 ◽  
pp. jeb.233098
Author(s):  
Fanny de Busserolles ◽  
Fabio Cortesi ◽  
Lily Fogg ◽  
Sara M. Stieb ◽  
Martin Luehrmann ◽  
...  
Keyword(s):  
Visual System ◽  
Reef Fish ◽  
Deep Sea ◽  
Colour Vision ◽  
Ganglion Cells ◽  
Light Sensitivity ◽  
Fish Family ◽  
Visual Systems ◽  
Retinal Topography ◽  
Dim Light

The visual systems of teleost fishes usually match their habitats and lifestyles. Since coral reefs are bright and colourful environments, the visual systems of their diurnal inhabitants have been more extensively studied than those of nocturnal species. In order to fill this knowledge gap, we conducted a detailed investigation of the visual system of the nocturnal reef fish family Holocentridae. Results showed that the visual system of holocentrids is well adapted to their nocturnal lifestyle with a rod-dominated retina. Surprisingly, rods in all species were arranged into 6-17 well-defined banks, a feature most commonly found in deep-sea fishes, that may increase the light sensitivity of the eye and/or allow colour discrimination in dim-light. Holocentrids also have the potential for dichromatic colour vision during the day with the presence of at least two spectrally different cone types: single cones expressing the blue-sensitive SWS2A gene, and double cones expressing one or two green-sensitive RH2 genes. Some differences were observed between the two subfamilies, with Holocentrinae (squirrelfish) having a slightly more developed photopic visual system than Myripristinae (soldierfish). Moreover, retinal topography of both ganglion cells and cone photoreceptors showed specific patterns for each cell type, likely highlighting different visual demands at different times of the day, such as feeding. Overall, their well-developed scotopic visual systems and the ease of catching and maintaining holocentrids in aquaria, make them ideal models to investigate teleost dim-light vision and more particularly shed light on the function of the multibank retina and its potential for dim-light colour vision.

scholarly journals Testing the sensory trade-off hypothesis in New World bats

2018 ◽  
Vol 285 (1885) ◽  
pp. 20181523 ◽  
Author(s):  
Jinwei Wu ◽  
Hengwu Jiao ◽  
Nancy B. Simmons ◽  
Qin Lu ◽  
Huabin Zhao
Keyword(s):  
Colour Vision ◽  
New World ◽  
Sensory System ◽  
The Other ◽  
Opsin Gene ◽  
Molecular Approach ◽  
Trade Off ◽  
Old World ◽  
High Duty Cycle ◽  
Vampire Bats

Detection of evolutionary shifts in sensory systems is challenging. By adopting a molecular approach, our earlier study proposed a sensory trade-off hypothesis between a loss of colour vision and an origin of high-duty-cycle (HDC) echolocation in Old World bats. Here, we test the hypothesis in New World bats, which include HDC echolocators that are distantly related to Old World HDC echolocators, as well as vampire bats, which have an infrared sensory system apparently unique among bats. Through sequencing the short-wavelength opsin gene ( SWS1 ) in 16 species (29 individuals) of New World bats, we identified a novel SWS1 polymorphism in an HDC echolocator: one allele is pseudogenized but the other is intact, while both alleles are either intact or pseudogenized in other individuals. Strikingly, both alleles were found to be pseudogenized in all three vampire bats. Since pseudogenization, transcriptional or translational changes could separately result in functional loss of a gene, a pseudogenized SWS1 indicates a loss of dichromatic colour vision in bats. Thus, the same sensory trade-off appears to have repeatedly occurred in the two divergent lineages of HDC echolocators, and colour vision may have also been traded off against the infrared sense in vampire bats.

scholarly journals Genome Graphs and the Evolution of Genome Inference

2017 ◽  
Author(s):  
Benedict Paten ◽  
Adam M. Novak ◽  
Jordan M. Eizenga ◽  
Garrison Erik
Keyword(s):  
Reference Genome ◽  
Variant Calling ◽  
Modern Human ◽  
Human Biology ◽  
Scientific Achievement ◽  
Read Mapping ◽  
Human Genomics ◽  
Human Reference Genome ◽  
Human Genomes ◽  
Reference Bias

AbstractThe human reference genome is part of the foundation of modern human biology, and a monumental scientific achievement. However, because it excludes a great deal of common human variation, it introduces a pervasive reference bias into the field of human genomics. To reduce this bias, it makes sense to draw on representative collections of human genomes, brought together into reference cohorts. There are a number of techniques to represent and organize data gleaned from these cohorts, many using ideas implicitly or explicitly borrowed from graph based models. Here, we survey various projects underway to build and apply these graph based structures—which we collectively refer to as genome graphs—and discuss the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce.

scholarly journals Molecular evolution and expression of opsin genes in Hydra vulgaris

2019 ◽  
Author(s):  
Aide Macias Munoz ◽  
Rabi Murad ◽  
Ali Mortazavi
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Tree ◽  
Opsin Gene ◽  
Expression Data ◽  
Rna Seq ◽  
Light Detection ◽  
Hydra Vulgaris ◽  
Visual Diversity ◽  
Opsin Genes ◽  
Insight Into

Abstract Background: The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions. Results: We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades. Conclusions: This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgarisopsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.

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