Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review

Genes, Journal Year: 2023, Volume and Issue: 14(2), P. 416 - 416

Published: Feb. 5, 2023

Adaptive evolution is a process in which variation that confers an evolutionary advantage specific environmental context arises and propagated through population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative genotypes. A recent increase molecular data accessibility technological advances has allowed to go beyond description make inferences about the mechanisms underlying adaptive evolution. In systematic review, we discuss articles from 2016 2022 investigated reviewed vertebrates response variation. Regulatory elements within genome regulatory proteins involved either gene expression cellular pathways been shown play key roles most of discussed factors. Gene losses were suggested be associated with some contexts. Future research could benefit more investigations noncoding regions genome, regulation mechanisms, potentially yielding phenotypes. Investigating how novel genotypes are conserved also contribute our knowledge

Language: Английский

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

Vision Research, Journal Year: 2023, Volume and Issue: 206, P. 108204 - 108204

Published: March 1, 2023

Language: Английский

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Damsels in Disguise: Development of Ultraviolet Sensitivity and Colour Patterns in Damselfishes (Pomacentridae)

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

ABSTRACT Damselfishes (Pomacentridae) are widespread and highly abundant on tropical coral reefs. They exhibit diverse body colouration within between the ~250 species across ontogenetic stages. In addition to human‐visible colours (i.e., 400–700 nm), most adult damselfishes reflect ultraviolet (UV, 300–400 nm) colour patches. UV sensitivity signals essential for feeding form basis a secret communication channel invisible many UV‐blind predatory fish reef; however, how these traits develop stages their distribution damselfish family is poorly characterised. Here, we used photography, phylogenetic reconstructions of opsin genes, differential gene expression analysis (DGE) retinal samples investigate development vision patterns in three (pre‐settlement larval, juvenile, adult) 11 species. Using DGE, found similar juveniles adults, which strongly differed from larvae. All all expressed at least one UV‐sensitive sws1 gene. However, only started appear juvenile stage. Moreover, Pomacentrus displayed complex that were correlated with two copies. This could mean some can discriminate change component. We demonstrate dramatic shifts both while highlighting importance considering ontogeny when studying coevolution visual systems signals.

Language: Английский

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Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 8, 2025

ABSTRACT Visual systems are tuned to animals’ ecologies, evolving in response specific light environments and visual needs. Ecological transitions fossorial lifestyles impose strong selective pressures favoring morphological adaptations for underground life, such as increased skull ossification reduced eye protrusion. Fossoriality may simultaneously relax constraints on other aspects of vision leading diminished capabilities. Caecilians (Gymnophiona)— specialized, amphibians—possess eyes covered by skin or bone. For years, these traits, along with the presence a single photoreceptor expressing one functional opsin gene, have been interpreted evidence limited capabilities, including an inability focus perceive color. Our results challenge assumptions: we identified long-wavelength-sensitive ( LWS ) gene 11 species caecilians spanning 8 10 recognized families. Molecular indicates that is intact transcribed at least Caecilia orientalis ). Anatomical observations from five caecilian families indicate highly organized retinae even vestigial eyes. While cone cells our study remains uncertain, putatively suggests capabilities role perception their ecology be underestimated.

Language: Английский

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Dynamic Chromatin Accessibility and Transcriptional Regulation in the Eyes of Red Tilapia (Oreochromis sp.) in Response to Wintering Stress

Marine Biotechnology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Feb. 1, 2025

Language: Английский

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Multiple Pathways of Visual Adaptations for Water Column Usage in an Antarctic Adaptive Radiation

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

ABSTRACT Evolutionary transitions in water column usage have played a major role shaping ray‐finned fish diversity. However, the extent to which vision‐associated trait complexity and is coupled remains unclear. Here we investigated relationship between depth niche, eye size, molecular basis of light detection across Antarctic notothenioid adaptive radiation. Integrating phylogenetic comparative framework with data on size occupancy, provide support for an acceleration rate diversification nearly 20 million years after initial Our results further reveal that levels divergence are often highest closely related taxa. We analyzed opsin tuning site sequences found changes representing repeated instances independent phylogeny generally not associated habitat or species size. Collectively, our strongly multiple evolutionary pathways underlie visual adaptations this iconic

Language: Английский

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The visual system of the longest-living vertebrate, the Greenland shark

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

Abstract The Greenland shark ( Somniosus microcephalus ) is the longest-living vertebrate and inhabits extremely dim cold waters of Arctic deep sea. This has led to speculations that it may have lost functional vision. Here, we present genomic, transcriptomic, histological evidence retains an intact visual system well-adapted for life in light. Histology vitro opsin expression revealed adaptations typical deep-sea species, including densely packed, elongated rods a short-wavelength shift rod pigment sensitivity. RNAscope confirmed presence essential cell types, such as rods, Müller glia, bipolar, amacrine, ganglion cells. Moreover, despite being centuries old, examined specimens showed no signs retinal degeneration. Using whole genome RNA-sequencing, further show dim-light (rod-based) vision genes are robustly expressed, while many bright-light (cone-based) become pseudogenized and/or longer expressed. Finally, our data suggest efficient DNA repair mechanisms contribute long-term preservation function over shark.

Language: Английский

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Dietary carotenoids enhance SWS1 expression in female western mosquitofish (Gambusia affinis) but do not impair their likelihood of pregnancy in the presence of male guppy

Journal of Comparative Physiology A, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

Language: Английский

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From Genes to Pathways: A Curated Gene Approach to Accurate Pathway Reconstruction in Teleost Fish Transcriptomics

Journal of Experimental Zoology Part B Molecular and Developmental Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

ABSTRACT Interpreting the vast amounts of data generated by high‐throughput sequencing technologies can often present a significant challenge, particularly for non‐model organisms. While automated approaches like GO (Gene Ontology) and KEGG (Kyoto Encyclopedia Genes Genomes) enrichment analyses are widely used, they lack specificity To bridge this gap, we manually curated gene list tailored teleost fish transcriptomics. This resource focuses on key biological processes crucial understanding physiology, development, adaptation, including hormone signaling, various metabolic pathways, appetite regulation, digestion, gastrointestinal function, vision, ossification, osmoregulation, pigmentation. Developed through collaborative efforts specialists in diverse fields, prioritizes genes with established roles experimental evidence, conservation across species. aims to provide researchers reliable starting point transcriptomic analyses, offering carefully evaluated set relevant current research priorities. By streamlining process selection interpretation, supports broader community designing analyzing studies that investigate molecular responses developmental environmental changes. We encourage scientific collaboratively expand refine list, ensuring its continued relevance utility research.

Language: Английский

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Molecular Evolution of Ultraviolet Visual Opsins and Spectral Tuning of Photoreceptors in Anemonefishes (Amphiprioninae)

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 13(10)

Published: Aug. 9, 2021

Many animals including birds, reptiles, insects, and teleost fishes can see ultraviolet (UV) light (shorter than 400 nm), which has functional importance for foraging communication. For coral reef fishes, shallow environments transmit a broad spectrum of light, rich in UV, driving the evolution diverse spectral sensitivities. However, identities sites specific visual genes that underly vision remain elusive are useful determining how tuned to suit life on reef. We investigated systems 11 anemonefish (Amphiprioninae) species, specifically probing molecular pathways facilitate UV-sensitivity. Searching genomes anemonefishes, we identified total eight opsin from all five vertebrate subfamilies. found rare instances UV-sensitive SWS1 gene duplications produced two functionally coding paralogs (SWS1α SWS1β) pseudogene. also separate green sensitive RH2A duplicates not yet reported family Pomacentridae. Transcriptome analysis revealed false clown (Amphiprion ocellaris) expressed one rod (RH1) six cone opsins (SWS1β, SWS2B, RH2B, RH2A-1, RH2A-2, LWS) retina. Fluorescent situ hybridization highlighted (co-)expression SWS1β with SWS2B single cones, either RH2A, or together LWS different members double photoreceptors (two cones fused together). Our study provides first in-depth characterization anemonefishes basis further UV-vision fishes.

Language: Английский

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