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Guo J, Chi H, Zhang L, Song S, Rossiter SJ, Liu Y. Convergent evolutionary shifts in rhodopsin retinal release explain shared opsin repertoires in monotremes and crocodilians. Proc Biol Sci 2023; 290:20230530. [PMID: 37040807 PMCID: PMC10089720 DOI: 10.1098/rspb.2023.0530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
The visual ecology of early mammals remains poorly resolved. Studies of ancestral photopigments suggest an ancient transition from nocturnal to more crepuscular conditions. By contrast, the phenotypic shifts following the split of monotremes and therians-which lost their SWS1 and SWS2 opsins, respectively-are less clear. To address this, we obtained new phenotypic data on the photopigments of extant and ancestral monotremes. We then generated functional data for another vertebrate group that shares the same photopigment repertoire as monotremes: the crocodilians. By characterizing resurrected ancient pigments, we show that the ancestral monotreme underwent a dramatic acceleration in its rhodopsin retinal release rate. Moreover, this change was likely mediated by three residue replacements, two of which also arose on the ancestral branch of crocodilians, which exhibit similarly accelerated retinal release. Despite this parallelism in retinal release, we detected minimal to moderate changes in the spectral tuning of cone visual pigments in these groups. Our results imply that ancestral forms of monotremes and crocodilians independently underwent niche expansion to encompass quickly changing light conditions. This scenario-which accords with reported crepuscular activity in extant monotremes-may help account for their loss of the ultraviolet-sensitive SWS1 pigment but retention of the blue-sensitive SWS2.
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Affiliation(s)
- Jinqu Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Linghan Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Shengjing Song
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, People's Republic of China
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2
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Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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3
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Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behavior. Proc Natl Acad Sci U S A 2022; 119:e2118145119. [PMID: 35759662 PMCID: PMC9271160 DOI: 10.1073/pnas.2118145119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cetaceans are fully aquatic mammals that descended from terrestrial ancestors, an iconic evolutionary transition characterized by adaptations for underwater foraging via breath-hold diving. Although the evolutionary history of this specialized behavior is challenging to reconstruct, coevolving sensory systems may offer valuable clues. The dim-light visual pigment, rhodopsin, which initiates phototransduction in the rod photoreceptors of the eye, has provided insight into the visual ecology of depth in several aquatic vertebrate lineages. Here, we use ancestral sequence reconstruction and protein resurrection experiments to quantify light-activation metrics in rhodopsin pigments from ancestors bracketing the cetacean terrestrial-to-aquatic transition. By comparing multiple reconstruction methods on a broadly sampled cetartiodactyl species tree, we generated highly robust ancestral sequence estimates. Our experimental results provide direct support for a blue-shift in spectral sensitivity along the branch separating cetaceans from terrestrial relatives. This blue-shift was 14 nm, resulting in a deep-sea signature (λmax = 486 nm) similar to many mesopelagic-dwelling fish. We also discovered that the decay rates of light-activated rhodopsin increased in ancestral cetaceans, which may indicate an accelerated dark adaptation response typical of deeper-diving mammals. Because slow decay rates are thought to help sequester cytotoxic photoproducts, this surprising result could reflect an ecological trade-off between rod photoprotection and dark adaptation. Taken together, these ancestral shifts in rhodopsin function suggest that some of the first fully aquatic cetaceans could dive into the mesopelagic zone (>200 m). Moreover, our reconstructions indicate that this behavior arose before the divergence of toothed and baleen whales.
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4
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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Rial RV, Canellas F, Akaârir M, Rubiño JA, Barceló P, Martín A, Gamundí A, Nicolau MC. The Birth of the Mammalian Sleep. BIOLOGY 2022; 11:biology11050734. [PMID: 35625462 PMCID: PMC9138988 DOI: 10.3390/biology11050734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Mammals evolved from reptiles as a consequence of an evolutionary bottleneck. Some diurnal reptiles extended their activity, first to twilight and then to the entire dark time. This forced the change of the visual system. Pursuing maximal sensitivity, they abandoned the filters protecting the eyes against the dangerous diurnal light, which, in turn, forced immobility in lightproof burrows during light time. This was the birth of the mammalian sleep. Then, the Cretacic-Paleogene extinction of dinosaurs leaved free the diurnal niche and allowed the expansion of a few early mammals to diurnal life and the high variability of sleep traits. On the other hand, we propose that the idling rest is a state showing homeostatic regulation. Therefore, the difference between behavioral rest and wakeful idling is rather low: both show quiescence, raised sensory thresholds, reversibility, specific sleeping-resting sites and body positions, it is a pleasing state, and both are dependent of circadian and homeostatic regulation. Indeed, the most important difference is the unconsciousness of sleep and the consciousness of wakeful idling. Thus, we propose that sleep is a mere upgrade of the wakeful rest, and both may have the same function: guaranteeing rest during a part of the daily cycle. Abstract Mammals evolved from small-sized reptiles that developed endothermic metabolism. This allowed filling the nocturnal niche. They traded-off visual acuity for sensitivity but became defenseless against the dangerous daylight. To avoid such danger, they rested with closed eyes in lightproof burrows during light-time. This was the birth of the mammalian sleep, the main finding of this report. Improved audition and olfaction counterweighed the visual impairments and facilitated the cortical development. This process is called “The Nocturnal Evolutionary Bottleneck”. Pre-mammals were nocturnal until the Cretacic-Paleogene extinction of dinosaurs. Some early mammals returned to diurnal activity, and this allowed the high variability in sleeping patterns observed today. The traits of Waking Idleness are almost identical to those of behavioral sleep, including homeostatic regulation. This is another important finding of this report. In summary, behavioral sleep seems to be an upgrade of Waking Idleness Indeed, the trait that never fails to show is quiescence. We conclude that the main function of sleep consists in guaranteeing it during a part of the daily cycle.
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Affiliation(s)
- Rubén V. Rial
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- Correspondence: ; Tel.: +34-971-173-147; Fax: +34-971-173-184
| | - Francesca Canellas
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Mourad Akaârir
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - José A. Rubiño
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Pere Barceló
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Aida Martín
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - Antoni Gamundí
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
| | - M. Cristina Nicolau
- Laboratori de Neurofisiologia del Son i dels Ritmes Biològics, Grup de Recerca Neurofisiologia del Son i Ritmes Biològics, Department of Biologia, Universitat de les Illes Balears, Ctra Valldemossa, km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain; (F.C.); (M.A.); (J.A.R.); (P.B.); (A.M.); (A.G.); (M.C.N.)
- IdISBa, Institut d’Investigació Sanitària de les Illes Balears, Hospital Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
- IUNICS, Institut Universitari d’Investigació en Ciències de la Salut, Hospital Universitary Son Espases, 07120 Palma de Mallorca, Illes Balears, Spain
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6
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Xia Y, Cui Y, Wang A, Liu F, Chi H, Potter JHT, Williamson J, Chen X, Rossiter SJ, Liu Y. Convergent Phenotypic Evolution of Rhodopsin for Dim-Light Sensing across Deep-Diving Vertebrates. Mol Biol Evol 2021; 38:5726-5734. [PMID: 34463769 PMCID: PMC8662592 DOI: 10.1093/molbev/msab262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rhodopsin comprises an opsin attached to a retinal chromophore and is the only visual pigment conferring dim-light vision in vertebrates. On activation by photons, the retinal group becomes detached from the opsin, which is then inactive until it is recharged. Of all vertebrate species, those that dive face unique visual challenges, experiencing rapid decreases in light level and hunting in near darkness. Here, we combine sequence analyses with functional assays to show that the rhodopsin pigments of four divergent lineages of deep-diving vertebrates have undergone convergent increases in their retinal release rate. We compare gene sequences and detect parallel amino acids between penguins and diving mammals and perform mutagenesis to show that a single critical residue fully explains the observed increases in retinal release rate in both the emperor penguin and beaked whale. At the same time, we find that other shared sites have no significant effect on retinal release, implying that convergence does not always signify adaptive significance. We propose that accelerated retinal release confers rapid rhodopsin recharging, enabling the visual systems of diving species to adjust quickly to changing light levels as they descend through the water column. This contrasts with nocturnal species, where adaptation to darkness has been attributed to slower retinal release rates.
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Affiliation(s)
- Yu Xia
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yimeng Cui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | | | - Fangnan Liu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | | | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Zoonosis of Liaoning Province, Shenyang Agricultural University, Shenyang, China
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7
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Van Nynatten A, Castiglione GM, de A Gutierrez E, Lovejoy NR, Chang BSW. Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation. Mol Biol Evol 2021; 38:2076-2087. [PMID: 33481002 PMCID: PMC8097279 DOI: 10.1093/molbev/msab008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.
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Affiliation(s)
- Alexander Van Nynatten
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nathan R Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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8
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Convergent spectral shifts to blue-green vision in mammals extends the known sensitivity of vertebrate M/LWS pigments. Proc Natl Acad Sci U S A 2020; 117:8303-8305. [PMID: 32241894 PMCID: PMC7165416 DOI: 10.1073/pnas.2002235117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Daylight vision in most mammals is mediated predominantly by a middle/long wavelength-sensitive (M/LWS) pigment. Although spectral sensitivity and associated shifts in M/LWS are mainly determined by five critical sites, predicted phenotypic variation is rarely validated, and its ecological significance is unclear. We experimentally determine spectral tuning of M/LWS pigments and show that two highly divergent taxa, the gerbil and the elephant-shrew, have undergone independent dramatic blue-green shifts to 490 nm. By generating mutant proteins, we identify additional critical sites contributing to these shifts. Our results, which extend the known range of spectral tuning of vertebrate M/LWS, provide a compelling case of functional convergence, likely related to parallel adaptive shifts from nocturnal to brighter light conditions in similar habitats.
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9
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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol 2020; 88:211-226. [PMID: 32060574 PMCID: PMC7386396 DOI: 10.1007/s00239-020-09932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.
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Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Belinda Chang
- Department of Ecology and Evolutionary Biology and Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Aaron Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Jody Hey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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