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Li W, Song J, Tu H, Jiang S, Pan B, Li J, Zhao Y, Chen L, Xu Q. Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation. Mol Ecol Resour 2024; 24:e13989. [PMID: 38946220 DOI: 10.1111/1755-0998.13989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jie Song
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Huaming Tu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jiazhen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yongpeng Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
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Uebel AS, Pedersen MB, Beedholm K, Stidsholt L, Skalshøi MR, Foskolos I, Madsen PT. Daubenton's bats maintain stereotypical echolocation behaviour and a lombard response during target interception in light. BMC ZOOL 2024; 9:9. [PMID: 38679717 PMCID: PMC11057132 DOI: 10.1186/s40850-024-00200-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024] Open
Abstract
Most bats hunt insects on the wing at night using echolocation as their primary sensory modality, but nevertheless maintain complex eye anatomy and functional vision. This raises the question of how and when insectivorous bats use vision during their largely nocturnal lifestyle. Here, we test the hypothesis that the small insectivorous bat, Myotis daubentonii, relies less on echolocation, or dispenses with it entirely, as visual cues become available during challenging acoustic noise conditions. We trained five wild-caught bats to land on a spherical target in both silence and when exposed to broad-band noise to decrease echo detectability, while light conditions were manipulated in both spectrum and intensity. We show that during noise exposure, the bats were almost three times more likely to use multiple attempts to solve the task compared to in silent controls. Furthermore, the bats exhibited a Lombard response of 0.18 dB/dBnoise and decreased call intervals earlier in their flight during masking noise exposures compared to in silent controls. Importantly, however, these adjustments in movement and echolocation behaviour did not differ between light and dark control treatments showing that small insectivorous bats maintain the same echolocation behaviour when provided with visual cues under challenging conditions for echolocation. We therefore conclude that bat echolocation is a hard-wired sensory system with stereotyped compensation strategies to both target range and masking noise (i.e. Lombard response) irrespective of light conditions. In contrast, the adjustments of call intervals and movement strategies during noise exposure varied substantially between individuals indicating a degree of flexibility that likely requires higher order processing and perhaps vocal learning.
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Affiliation(s)
- Astrid Saermark Uebel
- Section for Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark.
| | | | - Kristian Beedholm
- Section for Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Laura Stidsholt
- Section for Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Ilias Foskolos
- Section for Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Wildlife Ecology, Department of Ecoscience, Aarhus University, Aarhus, Denmark
| | - Peter Teglberg Madsen
- Section for Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
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Zielinska-Dabkowska KM, Szlachetko K, Bobkowska K. An Impact Analysis of Artificial Light at Night (ALAN) on Bats. A Case Study of the Historic Monument and Natura 2000 Wisłoujście Fortress in Gdansk, Poland. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11327. [PMID: 34769843 PMCID: PMC8582723 DOI: 10.3390/ijerph182111327] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022]
Abstract
The artificial light at night (ALAN) present in many cities and towns has a negative impact on numerous organisms that live alongside humans, including bats. Therefore, we investigated if the artificial illumination of the historic Wisłoujście Fortress in Gdańsk, Poland (part of the Natura 2000 network), during nighttime events, which included an outdoor electronic dance music (EDM) festival, might be responsible for increased light pollution and the decline in recent years of the pond bat (Myotis dasycneme). An assessment of light pollution levels was made using the methods of geographical information system (GIS) and free-of-charge satellite remote sensing (SRS) technology. Moreover, this paper reviewed the most important approaches for environmental protection of bats in the context of ecological light pollution, including International, European, and Polish regulatory frameworks. The analysis of this interdisciplinary study confirmed the complexity of the problem and highlighted, too, the need for better control of artificial illumination in such sensitive areas. It also revealed that SRS was not the best light pollution assessment method for this particular case study due to several reasons listed in this paper. As a result, the authors' proposal for improvements also involved practical recommendations for devising suitable strategies for lighting research and practice in the Natura 2000 Wisłoujście Fortress site located adjacent to urban areas to reduce the potential negative impact of ALAN on bats and their natural habitats.
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Affiliation(s)
| | | | - Katarzyna Bobkowska
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 80-233 Gdansk, Poland;
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4
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Lu B, Jin H, Fu J. Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region. BMC Genomics 2020; 21:839. [PMID: 33246413 PMCID: PMC7694343 DOI: 10.1186/s12864-020-07269-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus, Nanorana parkeri, Rana kukunoris and Scutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. RESULTS Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar's test. Then, the Rconv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3-32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. CONCLUSIONS There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hong Jin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China. .,Department of Integrative Biology, University of Guelph, Guelph, Canada.
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Gutierrez EDA, Castiglione GM, Morrow JM, Schott RK, Loureiro LO, Lim BK, Chang BSW. Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments. Mol Biol Evol 2019; 35:2422-2434. [PMID: 30010964 DOI: 10.1093/molbev/msy140] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.
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Affiliation(s)
- Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James M Morrow
- Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Centre of Forensic Sciences, Toronto, ON, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Livia O Loureiro
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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6
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Simões BF, Foley NM, Hughes GM, Zhao H, Zhang S, Rossiter SJ, Teeling EC. As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats. Mol Biol Evol 2019; 36:54-68. [PMID: 30476197 PMCID: PMC6340466 DOI: 10.1093/molbev/msy192] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufficient sampling of relevant taxa has hindered definitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches (SWS1 n = 115; MWS/LWS n = 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555-560 nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not find support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii. Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.
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Affiliation(s)
- Bruno F Simões
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- School of Earth Science, University of Bristol, Bristol, United Kingdom
- School of Biological Science, The University of Adelaide, South Australia, Australia
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Graham M Hughes
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
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7
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Kries K, Barros MAS, Duytschaever G, Orkin JD, Janiak MC, Pessoa DMA, Melin AD. Colour vision variation in leaf-nosed bats (Phyllostomidae): Links to cave roosting and dietary specialization. Mol Ecol 2018; 27:3627-3640. [PMID: 30059176 DOI: 10.1111/mec.14818] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
Abstract
Bats are a diverse radiation of mammals of enduring interest for understanding the evolution of sensory specialization. Colour vision variation among species has previously been linked to roosting preferences and echolocation form in the suborder Yinpterochiroptera, yet questions remain about the roles of diet and habitat in shaping bat visual ecology. We sequenced OPN1SW and OPN1LW opsin genes for 20 species of leaf-nosed bats (family Phyllostomidae; suborder Yangochiroptera) with diverse roosting and dietary ecologies, along with one vespertilionid species (Myotis lavali). OPN1LW genes appear intact for all species, and predicted spectral tuning of long-wavelength opsins varied among lineages. OPN1SW genes appear intact and under purifying selection for Myotis lavali and most phyllostomid bats, with two exceptions: (a) We found evidence of ancient OPN1SW pseudogenization in the vampire bat lineage, and loss-of-function mutations in all three species of extant vampire bats; (b) we additionally found a recent, independently derived OPN1SW pseudogene in Lonchophylla mordax, a cave-roosting species. These mutations in leaf-nosed bats are independent of the OPN1SW pseudogenization events previously reported in Yinpterochiropterans. Therefore, the evolution of monochromacy (complete colour blindness) has occurred in both suborders of bats and under various evolutionary drivers; we find independent support for the hypothesis that obligate cave roosting drives colour vision loss. We additionally suggest that haematophagous dietary specialization and corresponding selection on nonvisual senses led to loss of colour vision through evolutionary sensory trade-off. Our results underscore the evolutionary plasticity of opsins among nocturnal mammals.
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Affiliation(s)
- Kelly Kries
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri
| | - Marília A S Barros
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Gwen Duytschaever
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Joseph D Orkin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Mareike C Janiak
- Department of Anthropology, Rutgers University, New Brunswick, New Jersey
| | - Daniel M A Pessoa
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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8
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Insights into visual pigment adaptation and diversity from model ecological and evolutionary systems. Curr Opin Genet Dev 2017; 47:110-120. [PMID: 29102895 DOI: 10.1016/j.gde.2017.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/18/2017] [Accepted: 09/29/2017] [Indexed: 01/07/2023]
Abstract
Sensory systems provide valuable insight into the evolution of molecular mechanisms underlying organismal anatomy, physiology, and behaviour. Visual pigments, which mediate the first step in visual transduction, offer a unique window into the relationship between molecular variation and visual performance, and enhance our understanding of how ecology, life history, and physiology may shape genetic variation across a variety of organisms. Here we review recent work investigating vertebrate visual pigments from a number of perspectives. Opsin gene duplication, loss, differential expression, structural variation, and the physiological context in which they operate, have profoundly shaped the visual capabilities of vertebrates adapting to novel environments. We note the importance of conceptual frameworks in investigating visual pigment diversity in vertebrates, highlighting key examples including evolutionary transitions between different photic environments, major shifts in life history evolution and ecology, evolutionary innovations in visual system anatomy and physiology, as well as shifts in visually mediated behaviours and behavioural ecology. We emphasize the utility of studying visual pigment evolution in the context of these different perspectives, and demonstrate how the integrative approaches discussed in this review contribute to a better understanding of the underlying molecular processes mediating adaptation in sensory systems, and the contexts in which they occur.
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9
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Yang W, Lu B, Fu J. Molecular Convergent Evolution of the MYBPC2 Gene Among Three High-Elevation Amphibian Species. J Mol Evol 2017; 84:139-143. [PMID: 28220195 DOI: 10.1007/s00239-017-9782-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 02/03/2017] [Indexed: 11/30/2022]
Abstract
We report a strong pattern of molecular-level convergent/parallel evolution of the MYBPC2 gene. Three high-elevation amphibian species, Bufo gargarizans minshanicus, Nanorana pleskei, Rana kukunoris, revealed remarkable numbers of convergent and parallel amino acid substitutions. On the MYBPC2 gene tree of eleven anurans, the three distantly related species formed a strongly supported clade that was away from their respective relatives. Furthermore, we generated both model-based and empirical data-based null distributions for neutral convergent evolution. All three pairwise comparisons among the three species showed significantly more convergent and parallel substitutions than the null distributions. This study adds to the very small roster of clear cases of non-neutral molecular convergent evolution (e.g. prestin, rhodopsin). Molecular convergent evolution has significant implications in biology and detailed case studies will likely provide more insight into its genetic mechanisms.
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Affiliation(s)
- Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Department of Biology, Lund University, 223 62, Lund, Sweden
| | - Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China. .,Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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10
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Dong D, Lei M, Hua P, Pan YH, Mu S, Zheng G, Pang E, Lin K, Zhang S. The Genomes of Two Bat Species with Long Constant Frequency Echolocation Calls. Mol Biol Evol 2016; 34:20-34. [PMID: 27803123 PMCID: PMC7107545 DOI: 10.1093/molbev/msw231] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats – the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats. Pseudogenization of some vision-related genes in rhinolophoid bats was observed, suggesting that these genes have undergone relaxed natural selection. An extensive contraction of olfactory receptor gene repertoires was observed in the lineage leading to the common ancestor of bats. Further extensive gene contractions can be observed in the branch leading to the rhinolophoid bats. Such concordance suggested that molecular changes at one sensory gene might have direct consequences for genes controlling for other sensory modalities. To characterize the population genetic structure and patterns of evolution, we re-sequenced the genome of 20 great leaf-nosed bats from four different geographical locations of China. The result showed similar sequence diversity values and little differentiation among populations. Moreover, evidence of genetic adaptations to high altitudes in the great leaf-nosed bats was observed. Taken together, our work provided a useful resource for future research on the evolution of bats.
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Affiliation(s)
- Dong Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai , China
| | - Ming Lei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai , China
| | - Panyu Hua
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai , China
| | - Yi-Hsuan Pan
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai , China
| | - Shuo Mu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai , China
| | - Guantao Zheng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai , China
| | - Erli Pang
- School of Life Sciences, Beijing Normal University, Beijing, China
| | - Kui Lin
- School of Life Sciences, Beijing Normal University, Beijing, China
| | - Shuyi Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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11
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Dungan SZ, Kosyakov A, Chang BS. Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment. Mol Biol Evol 2015; 33:323-36. [DOI: 10.1093/molbev/msv217] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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12
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Sander SE, Hall DW. Variation in opsin genes correlates with signalling ecology in North American fireflies. Mol Ecol 2015; 24:4679-96. [PMID: 26289828 PMCID: PMC4599352 DOI: 10.1111/mec.13346] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/30/2015] [Accepted: 08/16/2015] [Indexed: 12/27/2022]
Abstract
Genes underlying signal reception should evolve to maximize signal detection in a particular environment. In animals, opsins, the protein component of visual pigments, are predicted to evolve according to this expectation. Fireflies are known for their bioluminescent mating signals. The eyes of nocturnal species are expected to maximize the detection of conspecific signal colours emitted in the typical low-light environment. This is not expected for species that have transitioned to diurnal activity in bright daytime environments. Here, we test the hypothesis that opsin gene sequence plays a role in modifying firefly eye spectral sensitivity. We use genome and transcriptome sequencing in four firefly species, transcriptome sequencing in six additional species and targeted gene sequencing in 28 other species to identify all opsin genes present in North American fireflies and to elucidate amino acid sites under positive selection. We also determine whether amino acid substitutions in opsins are linked to evolutionary changes in signal mode, signal colour and light environment. We find only two opsins, one long wavelength and one ultraviolet, in all firefly species and identify 25 candidate sites that may be involved in determining spectral sensitivity. In addition, we find elevated rates of evolution at transitions to diurnal activity, and changes in selective constraint on long wavelength opsin associated with changes in light environment. Our results suggest that changes in eye spectral sensitivity are at least partially due to opsin sequence. Fireflies continue to be a promising system in which to investigate the evolution of signals, receptors and signalling environments.
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Affiliation(s)
- S E Sander
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - D W Hall
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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Liu HQ, Wei JK, Li B, Wang MS, Wu RQ, Rizak JD, Zhong L, Wang L, Xu FQ, Shen YY, Hu XT, Zhang YP. Divergence of dim-light vision among bats (order: Chiroptera) as estimated by molecular and electrophysiological methods. Sci Rep 2015; 5:11531. [PMID: 26100095 PMCID: PMC5155579 DOI: 10.1038/srep11531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 05/13/2015] [Indexed: 02/05/2023] Open
Abstract
Dim-light vision is present in all bats, but is divergent among species. Old-World fruit bats (Pteropodidae) have fully developed eyes; the eyes of insectivorous bats are generally degraded, and these bats rely on well-developed echolocation. An exception is the Emballonuridae, which are capable of laryngeal echolocation but prefer to use vision for navigation and have normal eyes. In this study, integrated methods, comprising manganese-enhanced magnetic resonance imaging (MEMRI), f-VEP and RNA-seq, were utilized to verify the divergence. The results of MEMRI showed that Pteropodidae bats have a much larger superior colliculus (SC)/ inferior colliculus (IC) volume ratio (3:1) than insectivorous bats (1:7). Furthermore, the absolute visual thresholds (log cd/m(2)•s) of Pteropodidae (-6.30 and -6.37) and Emballonuridae (-3.71) bats were lower than those of other insectivorous bats (-1.90). Finally, genes related to the visual pathway showed signs of positive selection, convergent evolution, upregulation and similar gene expression patterns in Pteropodidae and Emballonuridae bats. Different results imply that Pteropodidae and Emballonuridae bats have more developed vision than the insectivorous bats and suggest that further research on bat behavior is warranted.
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Affiliation(s)
- He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jing-Kuan Wei
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Bo Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, and Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Wu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, and Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Joshua D. Rizak
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Li Zhong
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, 650091, China
| | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, 650091, China
| | - Fu-Qiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, and Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yong-Yi Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, 515041, China
| | - Xin-Tian Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, 650091, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
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14
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Zhu L, Yin Q, Irwin DM, Zhang S. Phosphoenolpyruvate carboxykinase 1 gene (Pck1) displays parallel evolution between Old World and New World fruit bats. PLoS One 2015; 10:e0118666. [PMID: 25807515 PMCID: PMC4373879 DOI: 10.1371/journal.pone.0118666] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 12/15/2014] [Indexed: 11/19/2022] Open
Abstract
Bats are an ideal mammalian group for exploring adaptations to fasting due to their large variety of diets and because fasting is a regular part of their life cycle. Mammals fed on a carbohydrate-rich diet experience a rapid decrease in blood glucose levels during a fast, thus, the development of mechanisms to resist the consequences of regular fasts, experienced on a daily basis, must have been crucial in the evolution of frugivorous bats. Phosphoenolpyruvate carboxykinase 1 (PEPCK1, encoded by the Pck1 gene) is the rate-limiting enzyme in gluconeogenesis and is largely responsible for the maintenance of glucose homeostasis during fasting in fruit-eating bats. To test whether Pck1 has experienced adaptive evolution in frugivorous bats, we obtained Pck1 coding sequence from 20 species of bats, including five Old World fruit bats (OWFBs) (Pteropodidae) and two New World fruit bats (NWFBs) (Phyllostomidae). Our molecular evolutionary analyses of these sequences revealed that Pck1 was under purifying selection in both Old World and New World fruit bats with no evidence of positive selection detected in either ancestral branch leading to fruit bats. Interestingly, however, six specific amino acid substitutions were detected on the ancestral lineage of OWFBs. In addition, we found considerable evidence for parallel evolution, at the amino acid level, between the PEPCK1 sequences of Old World fruit bats and New World fruit bats. Test for parallel evolution showed that four parallel substitutions (Q276R, R503H, I558V and Q593R) were driven by natural selection. Our study provides evidence that Pck1 underwent parallel evolution between Old World and New World fruit bats, two lineages of mammals that feed on a carbohydrate-rich diet and experience regular periods of fasting as part of their life cycle.
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Affiliation(s)
- Lei Zhu
- Institute of Molecular Ecology and Evolution, SKLEC & IECR & IAIR, East China Normal University, Shanghai, China
| | - Qiuyuan Yin
- Institute of Molecular Ecology and Evolution, SKLEC & IECR & IAIR, East China Normal University, Shanghai, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Shuyi Zhang
- Institute of Molecular Ecology and Evolution, SKLEC & IECR & IAIR, East China Normal University, Shanghai, China
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15
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Parallel Evolution of the Glycogen Synthase 1 (Muscle) Gene Gys1 Between Old World and New World Fruit Bats (Order: Chiroptera). Biochem Genet 2014; 52:443-58. [DOI: 10.1007/s10528-014-9659-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/06/2014] [Indexed: 01/09/2023]
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16
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Schott RK, Refvik SP, Hauser FE, López-Fernández H, Chang BSW. Divergent positive selection in rhodopsin from lake and riverine cichlid fishes. Mol Biol Evol 2014; 31:1149-65. [PMID: 24509690 DOI: 10.1093/molbev/msu064] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly different spectral properties from the African rift lakes. These ecological and/or biogeographic differences may have imposed divergent selective pressures on the evolution of the cichlid visual system. To test these hypotheses, we investigated the molecular evolution of the dim-light visual pigment, rhodopsin. We sequenced rhodopsin from Neotropical and African riverine cichlids and combined these data with published sequences from African cichlids. We found significant evidence for positive selection using random sites codon models in all cichlid groups, with the highest levels in African lake cichlids. Tests using branch-site and clade models that partitioned the data along ecological (lake, river) and/or biogeographic (African, Neotropical) boundaries found significant evidence of divergent selective pressures among cichlid groups. However, statistical comparisons among these models suggest that ecological, rather than biogeographic, factors may be responsible for divergent selective pressures that have shaped the evolution of the visual system in cichlids. We found that branch-site models did not perform as well as clade models for our data set, in which there was evidence for positive selection in the background. One of our most intriguing results is that the amino acid sites found to be under positive selection in Neotropical and African lake cichlids were largely nonoverlapping, despite falling into the same three functional categories: spectral tuning, retinal uptake/release, and rhodopsin dimerization. Taken together, these results would imply divergent selection across cichlid clades, but targeting similar functions. This study highlights the importance of molecular investigations of ecologically important groups and the flexibility of clade models in explicitly testing ecological hypotheses.
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Affiliation(s)
- Ryan K Schott
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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17
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Ai WM, Chen SB, Chen X, Shen XJ, Shen YY. Parallel evolution of IDH2 gene in cetaceans, primates and bats. FEBS Lett 2014; 588:450-4. [PMID: 24374336 DOI: 10.1016/j.febslet.2013.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 12/03/2013] [Accepted: 12/13/2013] [Indexed: 02/05/2023]
Abstract
Cetaceans and primates both have large brains that require large amounts of aerobic energy metabolism. In bats, the cost of flight makes locomotion energetically demanding. These mammalian groups may represent three independent evolutionary origins of an energy-demanding lifestyle in mammals. IDH2 encodes an enzyme in the tricarboxylic acid cycle in the mitochondrion, which plays a key role in aerobic energy metabolism. In this study, we cloned and sequenced this gene in two cetaceans, and 19 bat species, and compared the data with available primate sequences to test its evolution. We found significant signals of parallel evolution in this gene among these three groups. Parallel evolution of this gene may reflect their parallel evolution towards a higher demand for energy.
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Affiliation(s)
- Wei-Ming Ai
- Department of Marine Science, School of Life Science, Wenzhou Medical College, Wenzhou 325035, China
| | - Shao-Bo Chen
- Department of Marine Science, School of Life Science, Wenzhou Medical College, Wenzhou 325035, China
| | - Xiao Chen
- Department of Marine Science, School of Life Science, Wenzhou Medical College, Wenzhou 325035, China; Guangxi Key Lab for Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai 536000, China
| | - Xue-Juan Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China
| | - Yong-Yi Shen
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou 515041, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.
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18
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The Glycogen Synthase 2 Gene (Gys2) Displays Parallel Evolution Between Old World and New World Fruit Bats. J Mol Evol 2013; 78:66-74. [DOI: 10.1007/s00239-013-9600-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 11/12/2013] [Indexed: 01/02/2023]
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19
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Cellular location and major terminal networks of the orexinergic system in the brain of two megachiropterans. J Chem Neuroanat 2013; 53:64-71. [DOI: 10.1016/j.jchemneu.2013.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 11/19/2022]
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20
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Jones G, Teeling EC, Rossiter SJ. From the ultrasonic to the infrared: molecular evolution and the sensory biology of bats. Front Physiol 2013; 4:117. [PMID: 23755015 PMCID: PMC3667242 DOI: 10.3389/fphys.2013.00117] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/07/2013] [Indexed: 01/06/2023] Open
Abstract
Great advances have been made recently in understanding the genetic basis of the sensory biology of bats. Research has focused on the molecular evolution of candidate sensory genes, genes with known functions [e.g., olfactory receptor (OR) genes] and genes identified from mutations associated with sensory deficits (e.g., blindness and deafness). For example, the FoxP2 gene, underpinning vocal behavior and sensorimotor coordination, has undergone diversification in bats, while several genes associated with audition show parallel amino acid substitutions in unrelated lineages of echolocating bats and, in some cases, in echolocating dolphins, representing a classic case of convergent molecular evolution. Vision genes encoding the photopigments rhodopsin and the long-wave sensitive opsin are functional in bats, while that encoding the short-wave sensitive opsin has lost functionality in rhinolophoid bats using high-duty cycle laryngeal echolocation, suggesting a sensory trade-off between investment in vision and echolocation. In terms of olfaction, bats appear to have a distinctive OR repertoire compared with other mammals, and a gene involved in signal transduction in the vomeronasal system has become non-functional in most bat species. Bitter taste receptors appear to have undergone a "birth-and death" evolution involving extensive gene duplication and loss, unlike genes coding for sweet and umami tastes that show conservation across most lineages but loss in vampire bats. Common vampire bats have also undergone adaptations for thermoperception, via alternative splicing resulting in the evolution of a novel heat-sensitive channel. The future for understanding the molecular basis of sensory biology is promising, with great potential for comparative genomic analyses, studies on gene regulation and expression, exploration of the role of alternative splicing in the generation of proteomic diversity, and linking genetic mechanisms to behavioral consequences.
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Affiliation(s)
- Gareth Jones
- School of Biological Sciences, University of Bristol Bristol, UK
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21
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Opsin Evolution in Damselfish: Convergence, Reversal, and Parallel Evolution Across Tuning Sites. J Mol Evol 2012; 75:79-91. [DOI: 10.1007/s00239-012-9525-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 10/03/2012] [Indexed: 11/27/2022]
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22
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Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal. Vis Neurosci 2012; 29:211-7. [PMID: 22874131 DOI: 10.1017/s0952523812000223] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Monotremes are the most basal egg-laying mammals comprised of two extant genera, which are largely nocturnal. Visual pigments, the first step in the sensory transduction cascade in photoreceptors of the eye, have been examined in a variety of vertebrates, but little work has been done to study the rhodopsin of monotremes. We isolated the rhodopsin gene of the nocturnal short-beaked echidna (Tachyglossus aculeatus) and expressed and functionally characterized the protein in vitro. Three mutants were also expressed and characterized: N83D, an important site for spectral tuning and metarhodopsin kinetics, and two sites with amino acids unique to the echidna (T158A and F169A). The λ(max) of echidna rhodopsin (497.9 ± 1.1 nm) did not vary significantly in either T158A (498.0 ± 1.3 nm) or F169A (499.4 ± 0.1 nm) but was redshifted in N83D (503.8 ± 1.5 nm). Unlike other mammalian rhodopsins, echidna rhodopsin did react when exposed to hydroxylamine, although not as fast as cone opsins. The retinal release rate of light-activated echidna rhodopsin, as measured by fluorescence spectroscopy, had a half-life of 9.5 ± 2.6 min-1, which is significantly shorter than that of bovine rhodopsin. The half-life of the N83D mutant was 5.1 ± 0.1 min-1, even shorter than wild type. Our results show that with respect to hydroxylamine sensitivity and retinal release, the wild-type echidna rhodopsin displays major differences to all previously characterized mammalian rhodopsins and appears more similar to other nonmammalian vertebrate rhodopsins such as chicken and anole. However, our N83D mutagenesis results suggest that this site may mediate adaptation in the echidna to dim light environments, possibly via increased stability of light-activated intermediates. This study is the first characterization of a rhodopsin from a most basal mammal and indicates that there might be more functional variation in mammalian rhodopsins than previously assumed.
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23
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Shen YY, Lim BK, Liu HQ, Liu J, Irwin DM, Zhang YP. Multiple episodes of convergence in genes of the dim light vision pathway in bats. PLoS One 2012; 7:e34564. [PMID: 22509324 PMCID: PMC3324491 DOI: 10.1371/journal.pone.0034564] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 03/02/2012] [Indexed: 01/10/2023] Open
Abstract
The molecular basis of the evolution of phenotypic characters is very complex and is poorly understood with few examples documenting the roles of multiple genes. Considering that a single gene cannot fully explain the convergence of phenotypic characters, we choose to study the convergent evolution of rod vision in two divergent bats from a network perspective. The Old World fruit bats (Pteropodidae) are non-echolocating and have binocular vision, whereas the sheath-tailed bats (Emballonuridae) are echolocating and have monocular vision; however, they both have relatively large eyes and rely more on rod vision to find food and navigate in the night. We found that the genes CRX, which plays an essential role in the differentiation of photoreceptor cells, SAG, which is involved in the desensitization of the photoactivated transduction cascade, and the photoreceptor gene RH, which is directly responsible for the perception of dim light, have undergone parallel sequence evolution in two divergent lineages of bats with larger eyes (Pteropodidae and Emballonuroidea). The multiple convergent events in the network of genes essential for rod vision is a rare phenomenon that illustrates the importance of investigating pathways and networks in the evolution of the molecular basis of phenotypic convergence.
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Affiliation(s)
- Yong-Yi Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Burton K. Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Canada
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - David M. Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
- * E-mail:
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Li Y, Robins JH, Ye J, Huang Z, Wen Q, Zhang G. Adaptive diversity of innate immune receptor family short pentraxins in Murinae. FEBS Lett 2012; 586:798-803. [PMID: 22306119 DOI: 10.1016/j.febslet.2012.01.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/20/2012] [Accepted: 01/23/2012] [Indexed: 10/14/2022]
Abstract
The short pentraxins C-reactive protein (CRP) and serum amyloid P component (SAP) constitute a group of innate immune receptors that trigger immune activation by detecting molecules of the microbial cell wall. Here, we examined the evolution of short pentraxins in Murinae lineages. By molecular evolutionary analysis, CRP and SAP have been experiencing rapid diversification, driven by adaptive selection. Further, our protein modeling demonstrates that adaptively selected amino acids lie in the ligand-binding region and contact region between subunits. Our findings suggest that rapid diversification of these regions could contribute to the determinants of recognizing specificity and the interaction between subunits.
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Affiliation(s)
- Yan Li
- College of Animal Science and Technology, Sichuan Agriculture University, Yaan, Sichuan, PR China.
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25
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Aitken-Palmer C, Isaza R, Pope B, Reese D. Delayed growth in a young fruit bat (Pteropus pumilis) due to nutritional hypovitaminosis C. Vet Rec 2012; 170:22. [PMID: 22027185 DOI: 10.1136/vr.100214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- C Aitken-Palmer
- Department of Small Animal Clinical Sciences, University of Florida, 2015 SW, 16th Ave, Gainesville, Florida 32610, USA
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Tierney SM, Sanjur O, Grajales GG, Santos LM, Bermingham E, Wcislo WT. Photic niche invasions: phylogenetic history of the dim-light foraging augochlorine bees (Halictidae). Proc Biol Sci 2011; 279:794-803. [PMID: 21795273 DOI: 10.1098/rspb.2011.1355] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most bees rely on flowering plants and hence are diurnal foragers. From this ancestral state, dim-light foraging in bees requires significant adaptations to a new photic environment. We used DNA sequences to evaluate the phylogenetic history of the most diverse clade of Apoidea that is adapted to dim-light environments (Augochlorini: Megalopta, Megaloptidia and Megommation). The most speciose lineage, Megalopta, is distal to the remaining dim-light genera, and its closest diurnal relative (Xenochlora) is recovered as a lineage that has secondarily reverted to diurnal foraging. Tests for adaptive protein evolution indicate that long-wavelength opsin shows strong evidence of stabilizing selection, with no more than five codons (2%) under positive selection, depending on analytical procedure. In the branch leading to Megalopta, the amino acid of the single positively selected codon is conserved among ancestral Halictidae examined, and is homologous to codons known to influence molecular structure at the chromophore-binding pocket. Theoretically, such mutations can shift photopigment λ(max) sensitivity and enable visual transduction in alternate photic environments. Results are discussed in light of the available evidence on photopigment structure, morphological specialization and biogeographic distributions over geological time.
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Affiliation(s)
- Simon M Tierney
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Ancón, República de Panamá.
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27
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Dell LA, Kruger JL, Bhagwandin A, Jillani NE, Pettigrew JD, Manger PR. Nuclear organization of cholinergic, putative catecholaminergic and serotonergic systems in the brains of two megachiropteran species. J Chem Neuroanat 2010; 40:177-95. [DOI: 10.1016/j.jchemneu.2010.05.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/28/2010] [Accepted: 05/28/2010] [Indexed: 10/19/2022]
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28
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Cassey P, Portugal SJ, Maurer G, Ewen JG, Boulton RL, Hauber ME, Blackburn TM. Variability in avian eggshell colour: a comparative study of museum eggshells. PLoS One 2010; 5:e12054. [PMID: 20711258 PMCID: PMC2918502 DOI: 10.1371/journal.pone.0012054] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 07/06/2010] [Indexed: 11/24/2022] Open
Abstract
Background The exceptional diversity of coloration found in avian eggshells has long fascinated biologists and inspired a broad range of adaptive hypotheses to explain its evolution. Three main impediments to understanding the variability of eggshell appearance are: (1) the reliable quantification of the variation in eggshell colours; (2) its perception by birds themselves, and (3) its relation to avian phylogeny. Here we use an extensive museum collection to address these problems directly, and to test how diversity in eggshell coloration is distributed among different phylogenetic levels of the class Aves. Methodology and Results Spectrophotometric data on eggshell coloration were collected from a taxonomically representative sample of 251 bird species to determine the change in reflectance across different wavelengths and the taxonomic level where the variation resides. As many hypotheses for the evolution of eggshell coloration assume that egg colours provide a communication signal for an avian receiver, we also modelled reflectance spectra of shell coloration for the avian visual system. We found that a majority of species have eggs with similar background colour (long wavelengths) but that striking differences are just as likely to occur between congeners as between members of different families. The region of greatest variability in eggshell colour among closely related species coincided with the medium-wavelength sensitive region around 500 nm. Conclusions The majority of bird species share similar background eggshell colours, while the greatest variability among species aligns with differences along a red-brown to blue axis that most likely corresponds with variation in the presence and concentration of two tetrapyrrole pigments responsible for eggshell coloration. Additionally, our results confirm previous findings of temporal changes in museum collections, and this will be of particular concern for studies testing intraspecific hypotheses relating temporal patterns to adaptation of eggshell colour. We suggest that future studies investigating the phylogenetic association between the composition and concentration of eggshell pigments, and between the evolutionary drivers and functional impacts of eggshell colour variability will be most rewarding.
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Affiliation(s)
- Phillip Cassey
- Centre for Ornithology, School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
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