Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD) DOI Creative Commons
Seth A. Frazer, Mahdi Baghbanzadeh, Ali Rahnavard

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 14, 2024

Abstract Background Predicting phenotypes from genetic variation is foundational for fields as diverse bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking changes phenotypic has been a goal decades experimental work, especially some model families including light-sensitive opsin proteins. Opsins can be expressed in vitro measure light absorption parameters, λmax - wavelength maximum absorbance which strongly affects organismal like color vision. Despite extensive research on opsins, data remain dispersed, uncompiled, often challenging access, thereby precluding systematic comprehensive analyses intricate relationships between genotype phenotype. Results Here, we report newly compiled database all heterologously genes with λ max called Visual Physiology Opsin Database ( VPOD ). VPOD_1.0 contains 864 unique genotypes corresponding collected across animals 73 separate publications. We use deepBreaks show regression-based machine learning (ML) models reliably , account non-additive effects mutations function, identify functionally critical amino acid sites. Conclusion The ability functions sequences alone using ML will allow robust exploration molecular-evolutionary patterns governing phenotype, inform functional evolutionary connections an organism’s ecological niche, may used more broadly de-novo protein design. Together, our database, phenotype predictions, comparisons lay groundwork future applicable quantifiable comparable phenotypes. Key Points introduce (VPOD_1.0), includes animal demonstrate that sequence alone, provide approach lays potential broader applications any family

Language: Английский

Diversity and evolution of the vertebrate chemoreceptor gene repertoire DOI Creative Commons
Maxime Policarpo, Maude W. Baldwin, Didier Casañe

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 15, 2024

Abstract Chemoreception – the ability to smell and taste is an essential sensory modality of most animals. The number type chemical stimuli that animals can perceive depends primarily on diversity chemoreceptors they possess express. In vertebrates, six families G protein-coupled receptors form core their chemosensory system, olfactory/pheromone receptor gene OR , TAAR V1R V2R T1R T2R . Here, we study vertebrate chemoreceptor repertoire its evolutionary history. Through examination 1,527 genomes, uncover substantial differences in composition across vertebrates. We show are co-evolving, highly dynamic, characterized by lineage-specific expansions (for example, tetrapods; teleosts; mammals; amphibians) losses. Overall, amphibians, followed mammals, clades with largest repertoires. While marine tetrapods feature a convergent reduction numbers, genes correlates habitat mammals birds migratory behavior birds, diet aquatic environment fish.

Language: Английский

Citations

26
Innovative flavoring behavior in Goffin’s cockatoos DOI Creative Commons
J. S. Zewald, Alice M. I. Auersperg

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Dunking behavior can be a foraging innovation in non-human animals which food is dipped medium prior to consumption.1 Five functions of this have previously been suggested (soaking, cleaning, flavoring, drowning, and transporting liquid).2,3,4,5,6,7,8 Although experimental reports exist,1,5,9,10,11 most dunking observations are anecdotal,12 making it hard infer its function. Previously, we reported innovative group Goffin's cockatoos (Cacatua goffiniana) with the apparent function soaking dry food.13 Here, report soy yogurt likely flavoring their food, something thus far only observationally Japanese macaques.3,14 In an setup two types water, 9 out 18 dragged through yogurt, overall preference for blueberry-flavored over neutral could not explained by color alone. Furthermore, showed combination noodles separate task. This quantitative qualitative results indicates that use flavor preferring rather than Considering all dunk little overlap individuals previous study,13 suggests second preparation species. Our provide evidence outside primate lineage, may supplement our present understanding emergence rare forms behaviors animals. VIDEO ABSTRACT.

Language: Английский

Citations

2
Adaptive evolution and loss of a putative magnetoreceptor in passerines DOI Creative Commons
Corinna Langebrake, Georg Manthey, Anders Frederiksen

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2016)

Published: Feb. 7, 2024

Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, Cry4a from migratory songbird seems show enhanced sensitivity vitro compared resident species. We investigate Cry their potential involvement magnetoreception phylogenetic framework, integrating molecular evolutionary analyses with protein dynamics modelling. Our analysis is based on 363 bird genomes identifies different selection regimes passerines. that characterized by strong positive high variability, typical characteristics of sensor proteins. identify key sites are likely facilitated evolution an optimized sensory for night-time songbirds. Additionally, we Cry4 was lost hummingbirds, parrots Tyranni (Suboscines), thus identified gene deletion, might facilitate testing function birds. In contrast, other avian (Cry1 Cry2) were highly conserved across all species, indicating basal, non-sensory functions. results support specialization or functional differentiation songbirds could magnetosensation.

Language: Английский

Citations

10
Evolution of Temperature Receptors and Their Roles in Sensory Diversification and Adaptation DOI Creative Commons
Shigeru Saito,

Claire T. Saito

ZOOLOGICAL SCIENCE, Journal Year: 2025, Volume and Issue: 42(1)

Published: Jan. 29, 2025

Among various environmental factors, temperature is one of the critical factors for organisms since it can affect most, if not all, biological processes. Therefore, animals precisely sense ambient and body temperatures physiologically behaviorally respond to changes. Taking such nature into consideration, alteration thermal perception should have played a pivotal role in adaptation diverse niches. Temperature as well other physical chemical stimuli are perceived by primary afferent neurons where transient receptor potential (TRP) channels expressed, these serve multimodal receptors somatosensory system. To understand roles TRP evolution sensory perception, comparative analyses been performed using animal species, their functional diversity has documented over past 2 decades. Furthermore, recent years, species differences responses found among closely related inhabiting different niches, which uncovered contributions vertebrate species. The purpose this review summarize studies that addressed associated with diversification adaptation.

Language: Английский

Citations

1
Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity DOI Creative Commons
Nathan Harris,

Samuel G. Bates,

Zihao Zhuang

et al.

Current Biology, Journal Year: 2023, Volume and Issue: 33(8), P. 1487 - 1501.e7

Published: March 27, 2023

Language: Английский

Citations

22
Organ Evolution: Emergence of Multicellular Function DOI
Joseph D. Parker

Annual Review of Cell and Developmental Biology, Journal Year: 2024, Volume and Issue: 40(1), P. 51 - 74

Published: July 4, 2024

Instances of multicellularity across the tree life have fostered evolution complex organs composed distinct cell types that cooperate, producing emergent biological functions. How originate is a fundamental evolutionary problem has eluded deep mechanistic and conceptual understanding. Here I propose cell- to organ-level transitions framework, whereby cooperative division labor originates becomes entrenched between through process functional niche creation, cell-type subfunctionalization, irreversible ratcheting interdependencies. Comprehending this transition hinges on explaining how these processes unfold molecularly in evolving populations. Recent single-cell transcriptomic studies analyses terminal fate specification indicate cellular functions are conferred by modular gene expression programs. These discrete components variation may be deployed or combined within cells introduce new properties into multicellular niches, partitioned establish labor. Tracing program at level single populations reveal toward organ complexity.

Language: Английский

Citations

7
Evolution of Sensory Receptors DOI
Wendy A. Valencia‐Montoya, Naomi E. Pierce, Nicholas W. Bellono

et al.

Annual Review of Cell and Developmental Biology, Journal Year: 2024, Volume and Issue: 40(1), P. 353 - 379

Published: July 10, 2024

Sensory receptors are at the interface between an organism and its environment thus represent key sites for biological innovation. Here, we survey major sensory receptor families to uncover emerging evolutionary patterns. Receptors touch, temperature, light constitute part of ancestral toolkit animals, often predating evolution multicellularity nervous system. In contrast, chemoreceptors exhibit a dynamic history lineage-specific expansions contractions correlated with disparate complexity chemical environments. A recurring theme includes independent transitions from neurotransmitter diverse stimuli outside world. We then provide overview mechanisms underlying diversification highlight examples where signatures natural selection used identify novel adaptations. Finally, discuss as hotspots driving reproductive isolation speciation, thereby contributing stunning diversity animals.

Language: Английский

Citations

7
Evolution of sensory systems DOI

Pablo Oteíza,

Maude W. Baldwin

Current Opinion in Neurobiology, Journal Year: 2021, Volume and Issue: 71, P. 52 - 59

Published: Sept. 29, 2021

Language: Английский

Citations

36
Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika DOI Creative Commons
Virginie Ricci, Fabrizia Ronco, Nicolas Boileau

et al.

Science Advances, Journal Year: 2023, Volume and Issue: 9(36)

Published: Sept. 6, 2023

Tuning the visual sensory system to ambient light is essential for survival in many animal species. This often achieved through duplication, functional diversification, and/or differential expression of opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species cichlid fishes Lake Tanganyika unravel adaptive changes gene at macro-evolutionary and ecosystem level one largest vertebrate radiations. We found that, across radiation, all seven cone opsins-but not rhodopsin-rank among most differentially expressed genes retina, together with other vision-, circadian rhythm-, hemoglobin-related propose two palettes characteristic very shallow- deep-water living species, respectively, show that adaptations along major ecological axes, macro-habitat diet, occur primarily via variation a subset

Language: Английский

Citations

11
Evolutionary origins of bitter taste receptors in jawed vertebrates DOI Creative Commons
Akihiro Itoigawa, Yasuka Toda, Shigehiro Kuraku

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(7), P. R271 - R272

Published: April 1, 2024

Taste is a sense that detects information about nutrients and toxins in foods. Of the five basic taste qualities, bitterness associated with detection of potentially harmful substances like plant alkaloids. In bony vertebrates, type 2 receptors (T2Rs), which are G-protein-coupled (GPCRs), act as bitter receptors1Chandrashekar J. Mueller K.L. Hoon M.A. Adler E. Feng L. Guo W. Zuker C.S. Ryba N.J.P. T2Rs function receptors.Cell. 2000; 100: 703-711https://doi.org/10.1016/S0092-8674(00)80706-0Abstract Full Text PDF PubMed Scopus (1135) Google Scholar,2Oike H. Nagai T. Furuyama A. Okada S. Aihara Y. Ishimaru Marui Matsumoto I. Misaka Abe K. Characterization ligands for fish receptors.J. Neurosci. 2007; 27: 5584-5592https://doi.org/10.1523/JNEUROSCI.0651-07.2007Crossref (139) Scholar. six GPCR gene families described chemosensory receptor genes, encoding (T1Rs T2Rs) olfactory (ORs, V1Rs, V2Rs, TAARs). These have been found all major jawed vertebrate lineages, except T2Rs, confined to vertebrates3Baldwin M.W. Ko M.-C. Functional evolution sensory receptors.Horm. Behav. 2020; 124104771https://doi.org/10.1016/j.yhbeh.2020.104771Crossref (19) Therefore, believed emerged later than other genes lineage. So far, only genomes two cartilaginous species mined TAS2R encode T2Rs4Sharma Syed A.S. Ferrando Mazan Korsching S.I. The repertoire true shark dominated by single family.Genome Biol. Evol. 2019; 11: 398-405https://doi.org/10.1093/gbe/evz002Crossref (24) Here, we identified novel elasmobranchs, namely selachimorphs (sharks) batoids (rays, skates, their close relatives) an exhaustive search covering diverse fishes. Using functional mRNA expression analyses, demonstrate expressed oral buds contribute compounds. This finding indicates early origin common ancestor vertebrates.

Language: Английский

Citations

4