1
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A K BK, George EA, Brockmann A. Tropical and montane Apis cerana show distinct dance-distance calibration curves. J Exp Biol 2024; 227:jeb247510. [PMID: 38853597 DOI: 10.1242/jeb.247510] [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: 02/12/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024]
Abstract
Social bees have evolved sophisticated communication systems to recruit nestmates to newly found food sources. As foraging ranges can vary from a few hundred meters to several kilometers depending on the environment or season, populations of social bee species living in different climate zones likely show specific adaptations in their recruitment communication. Accordingly, studies in the western honey bee, Apis mellifera, demonstrated that temperate populations exhibit shallower dance-calibration curves compared with tropical populations. Here, we report the first comparison of calibration curves for three Indian Apis cerana lineages: the tropical Apis indica, and the two montane Himalayan populations Apis cerana cerana (Himachal Pradesh) and Apis cerana kashmirensis (Jammu and Kashmir). We found that the colonies of the two montane A. cerana populations show dance-distance calibration curves with significantly shallower slopes than those of the tropical A. indica. Next, we transferred A. c. cerana colonies to Bangalore (∼ 2600 km away) to obtain calibration curves in the same location as A. indica. The common garden experiment confirmed this difference in slopes, implying that the lineages exhibit genetically fixed differences in dance-distance coding. However, the slopes of the calibration curves of the transferred A. c. cerana colonies were also significantly higher than those of the colonies tested in their original habitat, indicating an important effect of the environment. The differences in dance-distance coding between temperate and tropical A. cerana lineages resemble those described for Apis mellifera, suggesting that populations of both species independently evolved similar adaptations.
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Affiliation(s)
- Bharath Kumar A K
- National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bengaluru 560065, India
- Department of Apiculture, University of Agricultural Sciences - GKVK, Bengaluru 560065, India
| | - Ebi Antony George
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
| | - Axel Brockmann
- National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bengaluru 560065, India
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2
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Saunders AN, Gallant JR. A review of the reproductive biology of mormyroid fishes: An emerging model for biomedical research. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:144-163. [PMID: 38361399 DOI: 10.1002/jez.b.23242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/13/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
Mormyroidea is a superfamily of weakly electric African fishes with great potential as a model in a variety of biomedical research areas including systems neuroscience, muscle cell and craniofacial development, ion channel biophysics, and flagellar/ciliary biology. However, they are currently difficult to breed in the laboratory setting, which is essential for any tractable model organism. As such, there is a need to better understand the reproductive biology of mormyroids to breed them more reliably in the laboratory to effectively use them as a biomedical research model. This review seeks to (1) briefly highlight the biomedically relevant phenotypes of mormyroids and (2) compile information about mormyroid reproduction including sex differences, breeding season, sexual maturity, gonads, gametes, and courtship/spawning behaviors. We also highlight areas of mormyroid reproductive biology that are currently unexplored and/or have the potential for further investigation that may provide insights into more successful mormyroid laboratory breeding methods.
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Affiliation(s)
- Alyssa N Saunders
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
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3
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Niu YH, Guan LH, Wang C, Jiang HF, Li GG, Yang LD, He SP. Comparative transcriptomic evidence of physiological changes and potential relationships in vertebrates under different dormancy states. Zool Res 2024; 45:341-354. [PMID: 38485504 PMCID: PMC11017076 DOI: 10.24272/j.issn.2095-8137.2023.308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 03/19/2024] Open
Abstract
Dormancy represents a fascinating adaptive strategy for organisms to survive in unforgiving environments. After a period of dormancy, organisms often exhibit exceptional resilience. This period is typically divided into hibernation and aestivation based on seasonal patterns. However, the mechanisms by which organisms adapt to their environments during dormancy, as well as the potential relationships between different states of dormancy, deserve further exploration. Here, we selected Perccottus glenii and Protopterus annectens as the primary subjects to study hibernation and aestivation, respectively. Based on histological and transcriptomic analysis of multiple organs, we discovered that dormancy involved a coordinated functional response across organs. Enrichment analyses revealed noteworthy disparities between the two dormant species in their responses to extreme temperatures. Notably, similarities in gene expression patterns pertaining to energy metabolism, neural activity, and biosynthesis were noted during hibernation, suggesting a potential correlation between hibernation and aestivation. To further explore the relationship between these two phenomena, we analyzed other dormancy-capable species using data from publicly available databases. This comparative analysis revealed that most orthologous genes involved in metabolism, cell proliferation, and neural function exhibited consistent expression patterns during dormancy, indicating that the observed similarity between hibernation and aestivation may be attributable to convergent evolution. In conclusion, this study enhances our comprehension of the dormancy phenomenon and offers new insights into the molecular mechanisms underpinning vertebrate dormancy.
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Affiliation(s)
- Yu-Han Niu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- College of Life Sciences, Qinghai Normal University, Xining, Qinghai 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai 810016, China
| | - Li-Hong Guan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Hai-Feng Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Guo-Gang Li
- College of Life Sciences, Qinghai Normal University, Xining, Qinghai 810008, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai 810016, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, Qinghai 810008, China. E-mail:
| | - Lian-Dong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai 810016, China. E-mail:
| | - Shun-Ping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai 810016, China. E-mail:
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4
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Eastment RV, Wong BBM, McGee MD. Convergent genomic signatures associated with vertebrate viviparity. BMC Biol 2024; 22:34. [PMID: 38331819 PMCID: PMC10854053 DOI: 10.1186/s12915-024-01837-w] [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: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? RESULTS We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages. CONCLUSIONS Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.
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Affiliation(s)
- Rhiannon V Eastment
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia.
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, 3800, Australia
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5
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Hauser FE, Xiao D, Van Nynatten A, Brochu-De Luca KK, Rajakulendran T, Elbassiouny AE, Sivanesan H, Sivananthan P, Crampton WGR, Lovejoy NR. Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes. Biol Lett 2024; 20:20230480. [PMID: 38412964 PMCID: PMC10898970 DOI: 10.1098/rsbl.2023.0480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
Active electroreception-the ability to detect objects and communicate with conspecifics via the detection and generation of electric organ discharges (EODs)-has evolved convergently in several fish lineages. South American electric fishes (Gymnotiformes) are a highly species-rich group, possibly in part due to evolution of an electric organ (EO) that can produce diverse EODs. Neofunctionalization of a voltage-gated sodium channel gene accompanied the evolution of electrogenic tissue from muscle and resulted in a novel gene (scn4aa) uniquely expressed in the EO. Here, we investigate the link between variation in scn4aa and differences in EOD waveform. We combine gymnotiform scn4aa sequences encoding the C-terminus of the Nav1.4a protein, with biogeographic data and EOD recordings to test whether physiological transitions among EOD types accompany differential selection pressures on scn4aa. We found positive selection on scn4aa coincided with shifts in EOD types. Species that evolved in the absence of predators, which likely selected for reduced EOD complexity, exhibited increased scn4aa evolutionary rates. We model mutations in the protein that may underlie changes in protein function and discuss our findings in the context of gymnotiform signalling ecology. Together, this work sheds light on the selective forces underpinning major evolutionary transitions in electric signal production.
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Affiliation(s)
- Frances E. Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Dawn Xiao
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Alexander Van Nynatten
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, Ontario, Canada M5S 3G5
| | - Kristen K. Brochu-De Luca
- Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA
- School of Chemistry, Environmental and Life Sciences, University of The Bahamas, Oakes Field Campus, Nassau, New Providence, The Bahamas
| | - Thanara Rajakulendran
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Ahmed E. Elbassiouny
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, Ontario, Canada M5S 3G5
| | - Harunya Sivanesan
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Pradeega Sivananthan
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - William G. R. Crampton
- Department of Biology, University of Central Florida, 4110 Libra Dr, Orlando, FL 32816, USA
| | - Nathan R. Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, Ontario, Canada M5S 3G5
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, Canada M5S 3B2
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6
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Cheng F, Dennis AB, Baumann O, Kirschbaum F, Abdelilah-Seyfried S, Tiedemann R. Gene and Allele-Specific Expression Underlying the Electric Signal Divergence in African Weakly Electric Fish. Mol Biol Evol 2024; 41:msae021. [PMID: 38410843 PMCID: PMC10897887 DOI: 10.1093/molbev/msae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
In the African weakly electric fish genus Campylomormyrus, electric organ discharge signals are strikingly different in shape and duration among closely related species, contribute to prezygotic isolation, and may have triggered an adaptive radiation. We performed mRNA sequencing on electric organs and skeletal muscles (from which the electric organs derive) from 3 species with short (0.4 ms), medium (5 ms), and long (40 ms) electric organ discharges and 2 different cross-species hybrids. We identified 1,444 upregulated genes in electric organ shared by all 5 species/hybrid cohorts, rendering them candidate genes for electric organ-specific properties in Campylomormyrus. We further identified several candidate genes, including KCNJ2 and KLF5, and their upregulation may contribute to increased electric organ discharge duration. Hybrids between a short (Campylomormyrus compressirostris) and a long (Campylomormyrus rhynchophorus) discharging species exhibit electric organ discharges of intermediate duration and showed imbalanced expression of KCNJ2 alleles, pointing toward a cis-regulatory difference at this locus, relative to electric organ discharge duration. KLF5 is a transcription factor potentially balancing potassium channel gene expression, a crucial process for the formation of an electric organ discharge. Unraveling the genetic basis of the species-specific modulation of the electric organ discharge in Campylomormyrus is crucial for understanding the adaptive radiation of this emerging model taxon of ecological (perhaps even sympatric) speciation.
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Affiliation(s)
- Feng Cheng
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alice B Dennis
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Laboratory of Adaptive Evolution and Genomics, Research Unit of Environmental and Evolutionary Biology, Institute of Life, Earth & Environment, University of Namur, Namur, Belgium
| | - Otto Baumann
- Department of Animal Physiology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Frank Kirschbaum
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Crop and Animal Science, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Salim Abdelilah-Seyfried
- Department of Animal Physiology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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7
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Liu M, Song Y, Zhang S, Yu L, Yuan Z, Yang H, Zhang M, Zhou Z, Seim I, Liu S, Fan G, Yang H. A chromosome-level genome of electric catfish ( Malapterurus electricus) provided new insights into order Siluriformes evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:1-14. [PMID: 38433969 PMCID: PMC10901758 DOI: 10.1007/s42995-023-00197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 03/05/2024]
Abstract
The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00197-8.
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Affiliation(s)
- Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Lili Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Hengjia Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Zhuocheng Zhou
- Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, 100125 China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023 China
| | - Shanshan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083 China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
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8
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Caputi AA. Living life with an electric touch. J Exp Biol 2023; 226:jeb246060. [PMID: 38009325 DOI: 10.1242/jeb.246060] [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] [Indexed: 11/28/2023]
Abstract
The electric organ discharges (EODs) produced by weakly electric fish have long been a source of scientific intrigue and inspiration. The study of these species has contributed to our understanding of the organization of fixed action patterns, as well as enriching general imaging theory by unveiling the dual impact of an agent's actions on the environment and its own sensory system during the imaging process. This Centenary Review firstly compares how weakly electric fish generate species- and sex-specific stereotyped electric fields by considering: (1) peripheral mechanisms, including the geometry, channel repertoire and innervation of the electrogenic units; (2) the organization of the electric organs (EOs); and (3) neural coordination mechanisms. Secondly, the Review discusses the threefold function of the fish-centered electric fields: (1) to generate electric signals that encode the material, geometry and distance of nearby objects, serving as a short-range sensory modality or 'electric touch'; (2) to mark emitter identity and location; and (3) to convey social messages encoded in stereotypical modulations of the electric field that might be considered as species-specific communication symbols. Finally, this Review considers a range of potential research directions that are likely to be productive in the future.
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Affiliation(s)
- Angel Ariel Caputi
- Sistema Nacional de Investigadores - Uruguay, Av. Wilson Ferreira Aldunate 1219, Pando, PC 15600, Uruguay
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9
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Eshak MIY, Rubbenstroth D, Beer M, Pfaff F. Diving deep into fish bornaviruses: Uncovering hidden diversity and transcriptional strategies through comprehensive data mining. Virus Evol 2023; 9:vead062. [PMID: 38028148 PMCID: PMC10645145 DOI: 10.1093/ve/vead062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Recently, we discovered two novel orthobornaviruses in colubrid and viperid snakes using an in silico data-mining approach. Here, we present the results of a screening of more than 100,000 nucleic acid sequence datasets of fish samples from the Sequence Read Archive (SRA) for potential bornaviral sequences. We discovered the potentially complete genomes of seven bornavirids in datasets from osteichthyans and chondrichthyans. Four of these are likely to represent novel species within the genus Cultervirus, and we propose that one genome represents a novel genus within the family of Bornaviridae. Specifically, we identified sequences of Wǔhàn sharpbelly bornavirus in sequence data from the widely used grass carp liver and kidney cell lines L8824 and CIK, respectively. A complete genome of Murray-Darling carp bornavirus was identified in sequence data from a goldfish (Carassius auratus). The newly discovered little skate bornavirus, identified in the little skate (Leucoraja erinacea) dataset, contained a novel and unusual genomic architecture (N-Vp1-Vp2-X-P-G-M-L), as compared to other bornavirids. Its genome is thought to encode two additional open reading frames (tentatively named Vp1 and Vp2), which appear to represent ancient duplications of the gene encoding the viral glycoprotein (G). The datasets also provided insights into the possible transcriptional gradients of these bornavirids and revealed previously unknown splicing mechanisms.
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Affiliation(s)
- Mirette I Y Eshak
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Dennis Rubbenstroth
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Florian Pfaff
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
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10
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Wu B, Gao X, Hu M, Hu J, Lan T, Xue T, Xu W, Zhu C, Yuan Y, Zheng J, Qin T, Xin P, Li Y, Gong L, Feng C, He S, Liu H, Li H, Wang Q, Ma Z, Qiu Q, Wang K. Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2629-2645. [PMID: 37273070 DOI: 10.1007/s11427-022-2312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 06/06/2023]
Abstract
Although most fishes are ectothermic, some, including tuna and billfish, achieve endothermy through specialized heat producing tissues that are modified muscles. How these heat producing tissues evolved, and whether they share convergent molecular mechanisms, remain unresolved. Here, we generated a high-quality genome from the mackerel tuna (Euthynnus affinis) and investigated the heat producing tissues of this fish by single-nucleus and bulk RNA sequencing. Compared with other teleosts, tuna-specific genetic variation is strongly associated with muscle differentiation. Single-nucleus RNA-seq revealed a high proportion of specific slow skeletal muscle cell subtypes in the heat producing tissues of tuna. Marker genes of this cell subtype are associated with the relative sliding of actin and myosin, suggesting that tuna endothermy is mainly based on shivering thermogenesis. In contrast, cross-species transcriptome analysis indicated that endothermy in billfish relies mainly on non-shivering thermogenesis. Nevertheless, the heat producing tissues of the different species do share some tissue-specific genes, including vascular-related and mitochondrial genes. Overall, although tunas and billfishes differ in their thermogenic strategies, they share similar expression patterns in some respects, highlighting the complexity of convergent evolution.
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Affiliation(s)
- Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xueli Gao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingling Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jing Hu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Tingfeng Xue
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jiangmin Zheng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tao Qin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Peidong Xin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ye Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
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11
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Zhang F, Yu J, Si Y, Ding B. Meta-Aerogel Ion Motor for Nanofluid Osmotic Energy Harvesting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302511. [PMID: 37295070 DOI: 10.1002/adma.202302511] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/08/2023] [Indexed: 06/12/2023]
Abstract
Osmotic power, also known as "blue energy", is a vast, sustainable, and clean energy source that can be directly converted into electricity by nanofluidic membranes. However, the key technological bottleneck for large-scale osmotic electricity is that macroscopic-scale bulky membrane cannot synergistically satisfy the demands of high power density and low resistance without sacrificing scalability and mechanical robustness. Here, inspired by the anatomy and working principle of electric eels, which harness osmotic energy through embedded neuron-mediated fibril nanochannels with nanoconfined transport dynamics. Fibrous nanofluidic meta-aerogel ion motors, 3D-assembled from nanofluidic cable fibers with actuatable stimulation/transport "ion highways" are engineered. The meta-aerogel exhibits the integrated coupling effect of boosted ion propulsion and surface-charge-dominated selective ion transport. Driven by osmosis, the meta-aerogel ion motor can produce an unprecedented output power density of up to 30.7 W m-2 under a 50-fold salinity gradient. Advancing ultra-selective ion transport in nanofluidic meta-aerogels may provide a promising roadmap for blue energy harvesting.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, Shanghai, 201620, China
| | - Jianyong Yu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, Shanghai, 201620, China
- Innovation Center for Textile Science and Technology, Donghua University, Shanghai, 200051, China
| | - Yang Si
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, Shanghai, 201620, China
- Innovation Center for Textile Science and Technology, Donghua University, Shanghai, 200051, China
| | - Bin Ding
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles, Donghua University, Shanghai, 201620, China
- Innovation Center for Textile Science and Technology, Donghua University, Shanghai, 200051, China
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12
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Safian D, Ahmed M, van Kruistum H, Furness AI, Reznick DN, Wiegertjes GF, Pollux BJ. Repeated independent origins of the placenta reveal convergent and divergent organ evolution within a single fish family (Poeciliidae). SCIENCE ADVANCES 2023; 9:eadf3915. [PMID: 37611099 PMCID: PMC10446500 DOI: 10.1126/sciadv.adf3915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
An outstanding question in biology is to what extent convergent evolution produces similar, but not necessarily identical, complex phenotypic solutions. The placenta is a complex organ that repeatedly evolved in the livebearing fish family Poeciliidae. Here, we apply comparative approaches to test whether evolution has produced similar or different placental phenotypes in the Poeciliidae and to what extent these phenotypes correlate with convergence at the molecular level. We show the existence of two placental phenotypes characterized by distinctly different anatomical adaptations (divergent evolution). Furthermore, each placental phenotype independently evolved multiple times across the family, providing evidence for repeated convergence. Moreover, our comparative genomic analysis revealed that the genomes of species with different placentas are evolving at a different pace. Last, we show that the two placental phenotypes correlate with two previously described contrasting life-history optima. Our results argue for high evolvability (both divergent and convergent) of the placenta within a group of closely related species in a single family.
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Affiliation(s)
- Diego Safian
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Evolutionary Developmental Biology Laboratory, The Francis Crick Institute, London, UK
| | - Marwa Ahmed
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Henri van Kruistum
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
- Animal Breeding and Genomics, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Andrew I. Furness
- U.S. Fish and Wildlife Service, Maryland Fish and Wildlife Conservation Office, Annapolis, MD, USA
| | - David N. Reznick
- Department of Biology, University of California, Riverside, Riverside, CA, USA
| | - Geert F. Wiegertjes
- Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
| | - Bart J.A. Pollux
- Experimental Zoology Group, Department of Animal Sciences, Wageningen University, Wageningen, Netherlands
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13
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Cheng F, Dennis AB, Osuoha JI, Canitz J, Kirschbaum F, Tiedemann R. A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha. BMC Genomics 2023; 24:129. [PMID: 36941548 PMCID: PMC10029256 DOI: 10.1186/s12864-023-09196-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/20/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular. RESULTS A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. CONCLUSIONS We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species.
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Affiliation(s)
- Feng Cheng
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alice B Dennis
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Laboratory of Adaptive Evolution and Genomics, Research Unit of Environmental and Evolutionary Biology, Institute of Life, Earth & Environnment, University of Namur, Namur, Belgium
| | - Josephine Ijeoma Osuoha
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Julia Canitz
- Senckenberg German Entomological Institute, Müncheberg, Germany
| | - Frank Kirschbaum
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Crop and Animal Science, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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14
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Ding L, Zheng M, Xiao D, Zhao Z, Xue J, Zhang S, Caro J, Wang H. Bioinspired Ti
3
C
2
T
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MXene‐Based Ionic Diode Membrane for High‐Efficient Osmotic Energy Conversion. Angew Chem Int Ed Engl 2022; 61:e202206152. [DOI: 10.1002/anie.202206152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Li Ding
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 China
| | - Mengting Zheng
- Centre for Catalysis and Clean Energy School of Environment and Science Gold Coast Campus Griffith University Gold Coast 4222 Australia
| | - Dan Xiao
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 China
| | - Zihao Zhao
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 China
| | - Jian Xue
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 China
| | - Shanqing Zhang
- Centre for Catalysis and Clean Energy School of Environment and Science Gold Coast Campus Griffith University Gold Coast 4222 Australia
| | - Jürgen Caro
- Institute of Physical Chemistry and Electrochemistry Leibniz University Hannover Callinstraße 3A 30167 Hannover Germany
| | - Haihui Wang
- Beijing Key Laboratory for Membrane Materials and Engineering Department of Chemical Engineering Tsinghua University Beijing 100084 China
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15
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Smith CE, Smith ANH, Cooper TF, Moore FBG. Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns. Proc Biol Sci 2022; 289:20221292. [PMID: 36100026 PMCID: PMC9470251 DOI: 10.1098/rspb.2022.1292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Long-term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments and chance events, all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.
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Affiliation(s)
- Chelsea E Smith
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Adam N H Smith
- School of Mathematical and Computational Sciences, Massey University, Auckland 0634, New Zealand
| | - Tim F Cooper
- School of Natural Sciences, Massey University, Auckland 0634, New Zealand
| | - Francisco B-G Moore
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA.,Department of Biology, University of Akron, Akron, OH 44325, USA
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16
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Ford KL, Peterson R, Bernt M, Albert JS. Convergence is Only Skin Deep: Craniofacial Evolution in Electric Fishes from South America and Africa (Apteronotidae and Mormyridae). Integr Org Biol 2022; 4:obac022. [PMID: 35976714 PMCID: PMC9375771 DOI: 10.1093/iob/obac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/31/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022] Open
Abstract
Apteronotidae and Mormyridae are species-rich clades of weakly electric fishes from Neotropical and Afrotropical freshwaters, respectively, known for their high morphological disparity and often regarded as a classic example of convergent evolution. Here, we use CT-imaging and 3D geometric morphometrics to quantify disparity in craniofacial morphologies, and to test the hypothesis of convergent skull-shape evolution in a phylogenetic context. For this study, we examined 391 specimens representing 78 species of Apteronotidae and Mormyridae including 30 of 37 (81%) of all valid genera with the goal to sample most of the craniofacial disparity known in these clades. We found no overlap between Apteronotidae and Mormyridae in the skull-shape morphospace using PCA and a common landmark scheme, and therefore no instances of complete phenotypic convergence. Instead, we found multiple potential instances of incomplete convergence, and at least one parallel shift among electric fish clades. The greatest components of shape variance in both families are the same as observed for most vertebrate clades: heterocephaly (i.e., opposite changes in relative sizes of the snout and braincase regions of the skull), and heterorhynchy (i.e., dorsoventral changes in relative snout flexion and mouth position). Mormyrid species examined here exhibit less craniofacial disparity than do apteronotids, potentially due to constraints associated with a larger brain size, ecological constraints related to food-type availability. Patterns of craniofacial evolution in these two clades depict a complex story of phenotypic divergence and convergence in which certain superficial similarities of external morphology obscure deeper osteological and presumably developmental differences of skull form and function. Among apteronotid and mormyrid electric fishes, craniofacial convergence is only skin deep.
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Affiliation(s)
- Kassandra L Ford
- Institute of Ecology and Evolution, Universität Bern , Switzerland
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology , Switzerland
- Department of Biology, University of Louisiana at Lafayette , USA
| | - Rose Peterson
- Department of Biological Sciences, George Washington University , USA
| | - Maxwell Bernt
- Department of Biology, University of Louisiana at Lafayette , USA
- Department of Ichthyology, American Museum of Natural History , USA
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette , USA
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17
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Ding L, Zheng M, Xiao D, Zhao Z, Xue J, Zhang S, Caro J, Wang H. Bioinspired Ti3C2Tx MXene‐Based Ionic Diode Membrane for High‐Efficient Osmotic Energy Conversion. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Li Ding
- South China University of Technology School of Chemistry and Chemical Engineering CHINA
| | - Mengting Zheng
- Griffith University Centre for Catalysis and Clean Energy, School of Environment and Science AUSTRALIA
| | - Dan Xiao
- South China University of Technology School of Chemistry and Chemical Engineering CHINA
| | - Zihao Zhao
- South China University of Technology School of Chemistry and Chemical Engineering CHINA
| | - Jian Xue
- South China University of Technology School of Chemistry and Chemical Engineering CHINA
| | - Shanqing Zhang
- Griffith University Centre for Catalysis and Clean Energy, School of Environment and Science AUSTRALIA
| | - Jürgen Caro
- Leibniz University Hannover Institute Physical Chemistry and Electrochemistry Callinstr. 3A 30167 Hannover GERMANY
| | - Haihui Wang
- Tsinghua University Department of Chemical Engineering CHINA
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18
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LaPotin S, Swartz ME, Luecke DM, Constantinou SJ, Gallant JR, Eberhart JK, Zakon HH. Divergent cis-regulatory evolution underlies the convergent loss of sodium channel expression in electric fish. SCIENCE ADVANCES 2022; 8:eabm2970. [PMID: 35648851 PMCID: PMC9159570 DOI: 10.1126/sciadv.abm2970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
South American and African weakly electric fish independently evolved electric organs from muscle. In both groups, a voltage-gated sodium channel gene independently lost expression from muscle and gained it in the electric organ, allowing the channel to become specialized for generating electric signals. It is unknown how this voltage-gated sodium channel gene is targeted to muscle in any vertebrate. We describe an enhancer that selectively targets sodium channel expression to muscle. Next, we demonstrate how the loss of this enhancer, but not trans-activating factors, drove the loss of sodium channel gene expression from muscle in South American electric fish. While this enhancer is also altered in African electric fish, key transcription factor binding sites and enhancer activity are retained, suggesting that the convergent loss of sodium channel expression from muscle in these two electric fish lineages occurred via different processes.
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Affiliation(s)
- Sarah LaPotin
- Department of Neuroscience, The University of Texas, Austin, TX 78712, USA
| | - Mary E. Swartz
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
| | - David M. Luecke
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Savvas J. Constantinou
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Jason R. Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Johann K. Eberhart
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
| | - Harold H. Zakon
- Department of Neuroscience, The University of Texas, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA
- Corresponding author.
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19
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Foster CSP, Van Dyke JU, Thompson MB, Smith NMA, Simpfendorfer CA, Murphy CR, Whittington CM. Different genes are recruited during convergent evolution of pregnancy and the placenta. Mol Biol Evol 2022; 39:6564414. [PMID: 35388432 PMCID: PMC9048886 DOI: 10.1093/molbev/msac077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The repeated evolution of the same traits in distantly related groups (convergent evolution) raises a key question in evolutionary biology: do the same genes underpin convergent phenotypes? Here we explore one such trait, viviparity (live birth), which qualitative studies suggest may indeed have evolved via genetic convergence. There are >150 independent origins of live birth in vertebrates, providing a uniquely powerful system to test the mechanisms underpinning convergence in morphology, physiology, and/or gene recruitment during pregnancy. We compared transcriptomic data from eight vertebrates (lizards, mammals, sharks) that gestate embryos within the uterus. Since many previous studies detected qualitative similarities in gene use during independent origins of pregnancy, we expected to find significant overlap in gene use in viviparous taxa. However, we found no more overlap in uterine gene expression associated with viviparity than we would expect by chance alone. Each viviparous lineage exhibits the same core set of uterine physiological functions, yet, contrary to prevailing assumptions about this trait, we find that none of the same genes are differentially expressed in all viviparous lineages, or even in all viviparous amniote lineages. Therefore, across distantly related vertebrates, different genes have been recruited to support the morphological and physiological changes required for successful pregnancy. We conclude that redundancies in gene function have enabled the repeated evolution of viviparity through recruitment of different genes from genomic 'toolboxes', which are uniquely constrained by the ancestries of each lineage.
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Affiliation(s)
- Charles S P Foster
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - James U Van Dyke
- School of Molecular Sciences, La Trobe University, Albury-Wodonga campus, VIC, Australia
| | - Michael B Thompson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Nicholas M A Smith
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Colin A Simpfendorfer
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Christopher R Murphy
- School of Medical Sciences and The Bosch Institute, University of Sydney, Sydney, NSW, Australia
| | - Camilla M Whittington
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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20
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Bray IE, Alshami IJJ, Kudoh T. The diversity and evolution of electric organs in Neotropical knifefishes. EvoDevo 2022; 13:9. [PMID: 35365204 PMCID: PMC8973549 DOI: 10.1186/s13227-022-00194-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 02/28/2022] [Indexed: 12/03/2022] Open
Abstract
The Gymnotiformes, also known as the South American or Neotropical knifefishes, include the strongly electric Electrophorus electricus and many other weakly electric species. These fish possess specialised electric organs that are able to release electric discharges into the water, for electrolocation and communication, and sometimes for predation and defence. All Gymnotiform species possess a myogenic electric organ (mEO) derived from the muscle tissue, and members of the Apteronotidae family uniquely possess a neurogenic electric organ (nEOs) derived from the nervous tissue. A mEO may consist of ‘Type A’ electrocytes that develop within the tail muscle (for example, in Apteronotus leptorhynchus), or ‘Type B’ electrocytes that develop below the tail muscle (for example, in Brachyhypopomus gauderio). In this review, we discuss the diversity in the anatomy, electric discharge and development of electric organs found in different Gymnotiform species, as well as the ecological and environmental factors that have likely contributed to this diversity. We then describe various hypotheses regarding the evolution of electric organs, and discuss the potential evolutionary origin of the nEO: a pair of nerve cords that are located on either side of the aorta in B. gauderio, and which may have expanded and developed into a nEO in the Apteronotidae family during its evolution from a common ancestral species. Finally, we compare potential Gymnotiform phylogenies and their supporting evidence.
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Affiliation(s)
- Isabelle E Bray
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Ilham J J Alshami
- Department of Fisheries and Marine Resources, College of Agriculture, University of Basrah, Basrah, Iraq
| | - Tetsuhiro Kudoh
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
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21
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Ford KL, Albert JS. Is the medium the message? Functional diversity across abiotic gradients in freshwater electric fishes. Integr Comp Biol 2022; 62:945-957. [DOI: 10.1093/icb/icac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Evolutionary transitions across abiotic gradients can occur among habitats at multiple spatial scales, and among taxa and biotas through a range of ecological and evolutionary time frames. Two diverse groups of electric fishes, Neotropical Gymnotiformes and Afrotropical Mormyroidea, offer interesting examples of potentially convergent evolution in aspects of morphological, physiological, and life history traits. We examined biogeographical, morphological, and functional patterns across these two groups to assess the degree of convergence in association with abiotic environmental variables. While there are superficial similarities across the groups and continents, we found substantially more differences in terms of habitat occupancy, electric signal diversity, and morphological disparity. These differences likely correlate to differences in biogeographical histories across the Neotropics and Afrotropics, biotic factors associated with aquatic life and electric signals, and sampling issues plaguing both groups. Additional research and sampling are required to make further inferences about how electric fishes transition throughout diverse freshwater habitats across both microevolutionary and macroevolutionary scales. We find little evidence that abiotic gradients in the freshwater habitat medium have driven convergent evolution of functional traits in these two continental radiations of electric fishes.
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Affiliation(s)
- Kassandra L Ford
- Institute of Ecology and Evolution, Universität Bern, Switzerland
- Department of Biology, University of Louisiana at Lafayette, USA
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, USA
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22
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Distinguishing Evolutionary Conservation from Derivedness. Life (Basel) 2022; 12:life12030440. [PMID: 35330191 PMCID: PMC8954198 DOI: 10.3390/life12030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, “transcriptomic derivedness index”, for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.
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23
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Peterson RD, Sullivan JP, Hopkins CD, Santaquiteria A, Dillman CB, Pirro S, Betancur-R R, Arcila D, Hughes LC, Ortí G. Phylogenomics of bonytongue fishes (Osteoglossomorpha) shed light on the craniofacial evolution and biogeography of the weakly electric clade Mormyridae. Syst Biol 2022; 71:1032-1044. [PMID: 35041001 DOI: 10.1093/sysbio/syac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 11/14/2022] Open
Abstract
Bonytongues (Osteoglossomorpha) constitute an ancient clade of teleost fishes distributed in freshwater habitats throughout the world. The group includes well-known species such as arowanas, featherbacks, pirarucus, and the weakly electric fishes in the family Mormyridae. Their disjunct distribution, extreme morphologies, and electrolocating capabilities (Gymnarchidae and Mormyridae) have attracted much scientific interest, but a comprehensive phylogenetic framework for comparative analysis is missing, especially for the species-rich family Mormyridae. Of particular interest are disparate craniofacial morphologies among mormyrids which might constitute an exceptional model system to study convergent evolution. We present a phylogenomic analysis based on 546 exons of 179 species (out of 260), 28 out of 29 genera, and all six families of extant bonytongues. Based on a recent reassessment of the fossil record of osteoglossomorphs, we inferred dates of divergence among trans-continental clades and the major groups. The estimated ages of divergence among extant taxa (e.g., Osteoglossomorpha, Osteoglossiformes, Mormyroidea) are older than previous reports, but most of the divergence dates obtained for clades on separate continents are too young to be explained by simple vicariance hypotheses. Biogeographic analysis of mormyrids indicates that their high species diversity in the Congo Basin is a consequence of range reductions of previously widespread ancestors and that the highest diversity of craniofacial morphologies among mormyrids originated in this basin. Special emphasis on a taxon-rich representation for mormyrids revealed pervasive misalignment between our phylogenomic results and mormyrid taxonomy due to repeated instances of convergence for extreme craniofacial morphologies. Estimation of ancestral phenotypes revealed contingent evolution of snout elongation and unique projections from the lower jaw to form the distinctive Schnauzenorgan. Synthesis of comparative analyses suggests that the remarkable craniofacial morphologies of mormyrids evolved convergently due to niche partitioning, likely enabled by interactions between their exclusive morphological and electrosensory adaptations.
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Affiliation(s)
- Rose D Peterson
- Department of Biological Sciences, The George Washington University, Washington, DC USA
| | - John P Sullivan
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology Ithaca, NY USA
| | - Carl D Hopkins
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology Ithaca, NY USA
| | | | - Casey B Dillman
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology Ithaca, NY USA
| | | | | | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, OK USA.,Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA
| | - Lily C Hughes
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL USA
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, Washington, DC USA.,National Museum of Natural History, Smithsonian Institution, Washington, DC USA
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24
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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25
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Wang Z, Lv TY, Shi ZB, Yang SS, Gu ZY. Two-dimensional materials as solid-state nanopores for chemical sensing. Dalton Trans 2021; 50:13608-13619. [PMID: 34518861 DOI: 10.1039/d1dt02206g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.
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Affiliation(s)
- Zhan Wang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Tian-Yi Lv
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zi-Bo Shi
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China. .,Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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26
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Arias CF, Dikow RB, McMillan WO, De León LF. De Novo Genome Assembly of the Electric Fish Brachyhypopomus occidentalis (Hypopomidae, Gymnotiformes). Genome Biol Evol 2021; 13:6377337. [PMID: 34581791 PMCID: PMC8536545 DOI: 10.1093/gbe/evab223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
The bluntnose knifefish Brachyhypopomus occidentalis is a primary freshwater fish from north-western South America and Lower Central America. Like other Gymnotiformes, it has an electric organ that generates electric discharges used for both communication and electrolocation. We assembled a high-quality reference genome sequence of B. occidentalis by combining Oxford Nanopore and 10X Genomics linked-reads technologies. We also describe its demographic history in the context of the rise of the Isthmus of Panama. The size of the assembled genome is 540.3 Mb with an N50 scaffold length of 5.4 Mb, which includes 93.8% complete, 0.7% fragmented, and 5.5% of missing vertebrate/Actinoterigie Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 11.04% of the genome, and 34,347 protein-coding genes were predicted, of which 23,935 have been functionally annotated. Demographic analysis suggests a rapid effective population expansion between 3 and 5 Myr, corresponding to the final closure of the Isthmus of Panama (2.8–3.5 Myr). This event was followed by a sudden and constant population decline during the last 1 Myr, likely associated with strong shifts in both precipitation and sea level during the Pleistocene glacial-interglacial cycles. The de novo genome assembly of B. occidentalis will provide novel insights into the molecular basis of both electric signal productions and detection and will be fundamental for understanding the processes that have shaped the diversity of Neotropical freshwater environments.
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Affiliation(s)
- Carlos F Arias
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA.,Smithsonian Tropical Research Institute, Panamá, Panamá
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| | | | - Luis F De León
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA.,Smithsonian Tropical Research Institute, Panamá, Panamá.,Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Panamá, Panamá
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27
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Comparative genomics provides insights into the aquatic adaptations of mammals. Proc Natl Acad Sci U S A 2021; 118:2106080118. [PMID: 34503999 PMCID: PMC8449357 DOI: 10.1073/pnas.2106080118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/30/2022] Open
Abstract
Divergent lineages can respond to common environmental factors through convergent processes involving shared genomic components or pathways, but the molecular mechanisms are poorly understood. Here, we provide genomic resources and insights into the evolution of mammalian lineages adapting to aquatic life. Our data suggest convergent evolution, for example, in association with thermoregulation through genes associated with a surface heat barrier (NFIA) and internal heat exchange (SEMA3E). Combined with the support of previous reports showing that the UCP1 locus has been lost in many marine mammals independently, our results suggest that the thermostatic strategy of marine mammals shifted from enhancing heat production to limiting heat loss. The ancestors of marine mammals once roamed the land and independently committed to an aquatic lifestyle. These macroevolutionary transitions have intrigued scientists for centuries. Here, we generated high-quality genome assemblies of 17 marine mammals (11 cetaceans and six pinnipeds), including eight assemblies at the chromosome level. Incorporating previously published data, we reconstructed the marine mammal phylogeny and population histories and identified numerous idiosyncratic and convergent genomic variations that possibly contributed to the transition from land to water in marine mammal lineages. Genes associated with the formation of blubber (NFIA), vascular development (SEMA3E), and heat production by brown adipose tissue (UCP1) had unique changes that may contribute to marine mammal thermoregulation. We also observed many lineage-specific changes in the marine mammals, including genes associated with deep diving and navigation. Our study advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.
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28
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Dunlap KD, Koukos HM, Chagnaud BP, Zakon HH, Bass AH. Vocal and Electric Fish: Revisiting a Comparison of Two Teleost Models in the Neuroethology of Social Behavior. Front Neural Circuits 2021; 15:713105. [PMID: 34489647 PMCID: PMC8418312 DOI: 10.3389/fncir.2021.713105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/12/2021] [Indexed: 11/30/2022] Open
Abstract
The communication behaviors of vocal fish and electric fish are among the vertebrate social behaviors best understood at the level of neural circuits. Both forms of signaling rely on midbrain inputs to hindbrain pattern generators that activate peripheral effectors (sonic muscles and electrocytes) to produce pulsatile signals that are modulated by frequency/repetition rate, amplitude and call duration. To generate signals that vary by sex, male phenotype, and social context, these circuits are responsive to a wide range of hormones and neuromodulators acting on different timescales at multiple loci. Bass and Zakon (2005) reviewed the behavioral neuroendocrinology of these two teleost groups, comparing how the regulation of their communication systems have both converged and diverged during their parallel evolution. Here, we revisit this comparison and review the complementary developments over the past 16 years. We (a) summarize recent work that expands our knowledge of the neural circuits underlying these two communication systems, (b) review parallel studies on the action of neuromodulators (e.g., serotonin, AVT, melatonin), brain steroidogenesis (via aromatase), and social stimuli on the output of these circuits, (c) highlight recent transcriptomic studies that illustrate how contemporary molecular methods have elucidated the genetic regulation of social behavior in these fish, and (d) describe recent studies of mochokid catfish, which use both vocal and electric communication, and that use both vocal and electric communication and consider how these two systems are spliced together in the same species. Finally, we offer avenues for future research to further probe how similarities and differences between these two communication systems emerge over ontogeny and evolution.
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Affiliation(s)
- Kent D Dunlap
- Department of Biology, Trinity College, Hartford, CT, United States
| | - Haley M Koukos
- Department of Biology, Trinity College, Hartford, CT, United States
| | - Boris P Chagnaud
- Institute of Biology, Karl-Franzens-University Graz, Graz, Austria
| | - Harold H Zakon
- Department of Neuroscience, University of Texas at Austin, Austin, TX, United States.,Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Andrew H Bass
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, United States
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29
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Buckner JC, Sanders RC, Faircloth BC, Chakrabarty P. The critical importance of vouchers in genomics. eLife 2021; 10:68264. [PMID: 34061026 PMCID: PMC8186901 DOI: 10.7554/elife.68264] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
A voucher is a permanently preserved specimen that is maintained in an accessible collection. In genomics, vouchers serve as the physical evidence for the taxonomic identification of genome assemblies. Unfortunately, the vast majority of vertebrate genomes stored in the GenBank database do not refer to voucher specimens. Here, we urge researchers generating new genome assemblies to deposit voucher specimens in accessible, permanent research collections, and to link these vouchers to publications, public databases, and repositories. We also encourage scientists to deposit voucher specimens in order to recognize the work of local field biologists and promote a diverse and inclusive knowledge base, and we recommend best practices for voucher deposition to prevent taxonomic errors and ensure reproducibility and legality in genetic studies.
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Affiliation(s)
- Janet C Buckner
- Museum of Natural Science, Louisiana State University, Baton Rouge, United States
| | - Robert C Sanders
- Museum of Natural Science, Louisiana State University, Baton Rouge, United States
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, United States
| | - Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, United States.,Carleton University, Ottawa, Canada.,American Museum of Natural History, New York, United States
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30
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Beery AK, Shambaugh KL. Comparative Assessment of Familiarity/Novelty Preferences in Rodents. Front Behav Neurosci 2021; 15:648830. [PMID: 33927601 PMCID: PMC8076734 DOI: 10.3389/fnbeh.2021.648830] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022] Open
Abstract
Sociality-i.e., life in social groups-has evolved many times in rodents, and there is considerable variation in the nature of these groups. While many species-typical behaviors have been described in field settings, the use of consistent behavioral assays in the laboratory provides key data for comparisons across species. The preference for interaction with familiar or novel individuals is an important dimension of social behavior. Familiarity preference, in particular, may be associated with more closed, less flexible social groups. The dimension from selectivity to gregariousness has been used as a factor in classification of social group types. Laboratory tests of social choice range from brief (10 minutes) to extended (e.g., 3 hours). As familiarity preferences typically need long testing intervals to manifest, we used 3-hour peer partner preference tests to test for the presence of familiarity preferences in same-sex cage-mates and strangers in rats. We then conducted an aggregated analysis of familiarity preferences across multiple rodent species (adult male and female rats, mice, prairie voles, meadow voles, and female degus) tested with the same protocol. We found a high degree of consistency within species across data sets, supporting the existence of strong, species-typical familiarity preferences in prairie voles and meadow voles, and a lack of familiarity preferences in other species tested. Sociability, or total time spent near conspecifics, was unrelated to selectivity in social preference. These findings provide important background for interpreting the neurobiological mechanisms involved in social behavior in these species.
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Affiliation(s)
- Annaliese K Beery
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States.,Neuroscience Program, Departments of Psychology and Biology, Smith College, Northampton, MA, United States
| | - Katharine L Shambaugh
- Neuroscience Program, Departments of Psychology and Biology, Smith College, Northampton, MA, United States
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31
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Lin Z, Meng Z, Miao H, Wu R, Qiu W, Lin N, Liu XY. Biomimetic Salinity Power Generation Based on Silk Fibroin Ion-Exchange Membranes. ACS NANO 2021; 15:5649-5660. [PMID: 33660992 DOI: 10.1021/acsnano.1c00820] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Powering implanted medical devices (IMDs) is a long-term challenge since their use in biological environments requires a long-term and stable supply of power and a biocompatible and biodegradable battery system. Here, silk fibroin-based ion-exchange membranes are developed using bionics principles for reverse electrodialysis devices (REDs). Silk fibroin nanofibril (SNF) membranes are negatively and positively modified, resulting in strong cation and anion selectivity that regulates ion diffusion to generate electric power. These oppositely charged SNF membranes are assembled with Ag/AgCl electrodes into a multicompartment RED. By filling them with 10 and 0.001 mM NaCl solutions, a maximum output power density of 0.59 mW/m2 at an external loading resistance of 66 kΩ is obtained. In addition, 10 pairs of SNF membranes produce a considerable voltage of 1.58 V. This work is a proof of concept that key components of battery systems can be fabricated with protein materials. Combined with the emergence of water-based battery technologies, the findings in this study provide insights for the construction of tissue-integrated batteries for the next generation of IMDs.
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Affiliation(s)
- Zaifu Lin
- Research Institution for Biomimetics and Soft Matter, Fujian Key Provincial Laboratory for Soft Functional Materials Research, College of Materials, Xiamen University, 422 Siming South Road, Xiamen, 361005, People's Republic of China
| | - Zhaohui Meng
- Research Institution for Biomimetics and Soft Matter, Fujian Key Provincial Laboratory for Soft Functional Materials Research, College of Materials, Xiamen University, 422 Siming South Road, Xiamen, 361005, People's Republic of China
| | - Hao Miao
- Research Institution for Biomimetics and Soft Matter, Fujian Key Provincial Laboratory for Soft Functional Materials Research, College of Materials, Xiamen University, 422 Siming South Road, Xiamen, 361005, People's Republic of China
| | - Ronghui Wu
- Research Institution for Biomimetics and Soft Matter, Fujian Key Provincial Laboratory for Soft Functional Materials Research, College of Materials, Xiamen University, 422 Siming South Road, Xiamen, 361005, People's Republic of China
| | - Wu Qiu
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117542, Republic of Singapore
| | - Naibo Lin
- Research Institution for Biomimetics and Soft Matter, Fujian Key Provincial Laboratory for Soft Functional Materials Research, College of Materials, Xiamen University, 422 Siming South Road, Xiamen, 361005, People's Republic of China
| | - Xiang Yang Liu
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore, 117542, Republic of Singapore
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32
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Flanagan SP, Rose E, Jones AG. The population genomics of repeated freshwater colonizations by Gulf pipefish. Mol Ecol 2021; 30:1672-1687. [PMID: 33580570 DOI: 10.1111/mec.15841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/30/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022]
Abstract
How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome-level changes underlying local adaptation. Here, we present a genomic analysis of colonization of freshwater habitats by a primarily marine fish, the Gulf pipefish (Syngnathus scovelli). We sample pipefish from four geographically distinct freshwater locations and use double-digest restriction site associated DNA sequencing to compare them to 12 previously studied saltwater populations. The two most geographically distant and isolated freshwater populations are the most genetically distinct, although demographic analysis suggests that these populations are experiencing ongoing migration with their saltwater neighbours. Additionally, outlier regions were found genome-wide, showing parallelism across ecotype pairs. We conclude that these multiple freshwater colonizations involve similar genomic regions, despite the large geographical distances and different underlying mechanisms. These similar patterns are probably facilitated by the interacting effects of intrinsic barriers, gene flow among populations and ecological selection in the Gulf pipefish.
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Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emily Rose
- Department of Biology, Valdosta State University, Valdosta, GA, USA
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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33
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Wang Y, Yang L. Genomic Evidence for Convergent Molecular Adaptation in Electric Fishes. Genome Biol Evol 2021; 13:6151746. [PMID: 33638979 PMCID: PMC7952227 DOI: 10.1093/gbe/evab038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Fishes have independently evolved electric organs (EOs) at least six times, and the electric fields are used for communication, defense, and predation. However, the genetic basis of convergent evolution of EOs remains unclear. In this study, we conducted comparative genomic analyses to detect genes showing signatures of positive selection and convergent substitutions in electric fishes from three independent lineages (Mormyroidea, Siluriformes, and Gymnotiformes). Analysis of 4,657 orthologs between electric fishes and their corresponding control groups identified consistent evidence for accelerated evolution in electric fish lineages. A total of 702 positively selected genes (PSGs) were identified in electric fishes, and many of these genes corresponded to cell membrane structure, ion channels, and transmembrane transporter activity. Comparative genomic analyses revealed that widespread convergent amino acid substitutions occurred along the electric fish lineages. The overlap of convergent genes and PSGs was identified as adaptive convergence, and a subset of genes was putatively associated with electrical and muscular activities, especially scn4aa (a voltage-gated sodium channel gene). Our results provide hints to the genetic basis for the independent evolution of EOs during millions of years of evolution.
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Affiliation(s)
- Ying Wang
- College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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34
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Modes of genetic adaptations underlying functional innovations in the rumen. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1-21. [PMID: 33165812 DOI: 10.1007/s11427-020-1828-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We analyzed 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations. We identified genes with relatively high expression in the rumen, of which many appeared to be recruited from other tissues. These genes show functional enrichment in ketone body metabolism, regulation of microbial community, and epithelium absorption, which are the most prominent biological processes involved in rumen innovations. Several modes of genetic change underlying rumen functional innovations were uncovered, including coding mutations, genes newly evolved, and changes of regulatory elements. We validated that the key ketogenesis rate-limiting gene (HMGCS2) with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals. Two newly evolved genes (LYZ1 and DEFB1) are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium. Furthermore, we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment. These results greatly improve our understanding of rumen evolution and organ evo-devo in general.
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35
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Albert JS, Tagliacollo VA, Dagosta F. Diversification of Neotropical Freshwater Fishes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011620-031032] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.
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Affiliation(s)
- James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Louisiana 70504, USA
| | | | - Fernando Dagosta
- Faculty of Biological and Environmental Sciences, Universidade Federal da Grande Dourados, Brazil 79825-070
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36
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Alshami IJJ, Ono Y, Correia A, Hacker C, Lange A, Scholpp S, Kawasaki M, Ingham PW, Kudoh T. Development of the electric organ in embryos and larvae of the knifefish, Brachyhypopomus gauderio. Dev Biol 2020; 466:99-108. [PMID: 32687892 PMCID: PMC7507958 DOI: 10.1016/j.ydbio.2020.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/04/2020] [Accepted: 06/23/2020] [Indexed: 11/05/2022]
Abstract
South American Gymnotiform knifefish possess electric organs that generate electric fields for electro-location and electro-communication. Electric organs in fish can be derived from either myogenic cells (myogenic electric organ/mEO) or neurogenic cells (neurogenic electric organ/nEO). To date, the embryonic development of EOs has remained obscure. Here we characterize the development of the mEO in the Gymnotiform bluntnose knifefish, Brachyhypopomus gauderio. We find that EO primordial cells arise during embryonic stages in the ventral edge of the tail myotome, translocate into the ventral fin and develop into syncytial electrocytes at early larval stages. We also describe a pair of thick nerve cords that flank the dorsal aorta, the location and characteristic morphology of which are reminiscent of the nEO in Apteronotid species, suggesting a common evolutionary origin of these tissues. Taken together, our findings reveal the embryonic origins of the mEO and provide a basis for elucidating the mechanisms of evolutionary diversification of electric charge generation by myogenic and neurogenic EOs. Developmental staging of the electric bluntnose knifefish, Brachyhypopomus gauderio embryos and larvae. The primordia of the myogenic electric organ originate in the ventral somite, migrate in the ventral fin and develop to the electric organ. Evolutionary conservation between the nerve codes in the B. gauderio and the neurogenic electric organs in the Apteronotidae.
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Affiliation(s)
- Ilham J J Alshami
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Yosuke Ono
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK; Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
| | - Ana Correia
- Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EG, UK
| | - Christian Hacker
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Anke Lange
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Steffen Scholpp
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK
| | - Masashi Kawasaki
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Philip W Ingham
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tetsuhiro Kudoh
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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Nolte MJ, Jing P, Dewey CN, Payseur BA. Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs. Genome Biol Evol 2020; 12:1277-1301. [PMID: 32531054 PMCID: PMC7487164 DOI: 10.1093/gbe/evaa118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2020] [Indexed: 12/02/2022] Open
Abstract
Island populations repeatedly evolve extreme body sizes, but the genomic basis of this pattern remains largely unknown. To understand how organisms on islands evolve gigantism, we compared genome-wide patterns of gene expression in Gough Island mice, the largest wild house mice in the world, and mainland mice from the WSB/EiJ wild-derived inbred strain. We used RNA-seq to quantify differential gene expression in three key metabolic organs: gonadal adipose depot, hypothalamus, and liver. Between 4,000 and 8,800 genes were significantly differentially expressed across the evaluated organs, representing between 20% and 50% of detected transcripts, with 20% or more of differentially expressed transcripts in each organ exhibiting expression fold changes of at least 2×. A minimum of 73 candidate genes for extreme size evolution, including Irs1 and Lrp1, were identified by considering differential expression jointly with other data sets: 1) genomic positions of published quantitative trait loci for body weight and growth rate, 2) whole-genome sequencing of 16 wild-caught Gough Island mice that revealed fixed single-nucleotide differences between the strains, and 3) publicly available tissue-specific regulatory elements. Additionally, patterns of differential expression across three time points in the liver revealed that Arid5b potentially regulates hundreds of genes. Functional enrichment analyses pointed to cell cycling, mitochondrial function, signaling pathways, inflammatory response, and nutrient metabolism as potential causes of weight accumulation in Gough Island mice. Collectively, our results indicate that extensive gene regulatory evolution in metabolic organs accompanied the rapid evolution of gigantism during the short time house mice have inhabited Gough Island.
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Affiliation(s)
- Mark J Nolte
- Laboratory of Genetics, University of Wisconsin - Madison
| | - Peicheng Jing
- Laboratory of Genetics, University of Wisconsin - Madison
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin - Madison
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38
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Fukutomi M, Carlson BA. A History of Corollary Discharge: Contributions of Mormyrid Weakly Electric Fish. Front Integr Neurosci 2020; 14:42. [PMID: 32848649 PMCID: PMC7403230 DOI: 10.3389/fnint.2020.00042] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/08/2020] [Indexed: 12/05/2022] Open
Abstract
Corollary discharge is an important brain function that allows animals to distinguish external from self-generated signals, which is critical to sensorimotor coordination. Since discovery of the concept of corollary discharge in 1950, neuroscientists have sought to elucidate underlying neural circuits and mechanisms. Here, we review a history of neurophysiological studies on corollary discharge and highlight significant contributions from studies using African mormyrid weakly electric fish. Mormyrid fish generate brief electric pulses to communicate with other fish and to sense their surroundings. In addition, mormyrids can passively locate weak, external electric signals. These three behaviors are mediated by different corollary discharge functions including inhibition, enhancement, and predictive “negative image” generation. Owing to several experimental advantages of mormyrids, investigations of these mechanisms have led to important general principles that have proven applicable to a wide diversity of animal species.
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Affiliation(s)
- Matasaburo Fukutomi
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Bruce A Carlson
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
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Zhang J, Qi J, Shi F, Pan H, Liu M, Tian R, Geng Y, Li H, Qu Y, Chen J, Seim I, Li M. Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensis. iScience 2020; 23:101267. [PMID: 32593955 PMCID: PMC7327861 DOI: 10.1016/j.isci.2020.101267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/28/2020] [Accepted: 06/08/2020] [Indexed: 12/23/2022] Open
Abstract
Salangids, known as Asian icefishes, represent a peculiar radiation within the bony fish order Protacanthopterygii where adult fish retain larval characteristics such as transparent and miniaturized bodies and a cartilaginous endoskeleton into adulthood. Here, we report a de novo genome of Protosalanx chinensis, the most widely distributed salangid lineage. The P. chinensis genome assembly is more contiguous and complete than a previous assembly. We estimate that P. chinensis, salmons, trouts, and pikes diverged from a common ancestor 185 million years ago. A juxtaposition with other fish genomes revealed loss of the genes encoding ectodysplasin-A receptor (EDAR), SCPP1, and four Hox proteins and likely lack of canonical fibroblast growth factor 5 (FGF5) function. We also report genomic variations of P. chinensis possibly reflecting the immune system repertoire of a species with a larval phenotype in sexually mature individuals. The new Asian icefish reference genome provides a solid foundation for future studies.
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Affiliation(s)
- Jie Zhang
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China.
| | - Jiwei Qi
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
| | - Fanglei Shi
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huijuan Pan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Huaying Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Yujie Qu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource, Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China.
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD 4102, Australia.
| | - Ming Li
- Chinese Academy of Sciences Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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40
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Signal Diversification Is Associated with Corollary Discharge Evolution in Weakly Electric Fish. J Neurosci 2020; 40:6345-6356. [PMID: 32661026 DOI: 10.1523/jneurosci.0875-20.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/11/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Communication signal diversification is a driving force in the evolution of sensory and motor systems. However, little is known about the evolution of sensorimotor integration. Mormyrid fishes generate stereotyped electric pulses (electric organ discharge [EOD]) for communication and active sensing. The EOD has diversified extensively, especially in duration, which varies across species from 0.1 to >10 ms. In the electrosensory hindbrain, a corollary discharge that signals the timing of EOD production provides brief, precisely timed inhibition that effectively blocks responses to self-generated EODs. However, corollary discharge inhibition has only been studied in a few species, all with short-duration EODs. Here, we asked how corollary discharge inhibition has coevolved with the diversification of EOD duration. We addressed this question by comparing 7 mormyrid species (both sexes) having varied EOD duration. For each individual fish, we measured EOD duration and then measured corollary discharge inhibition by recording evoked potentials from midbrain electrosensory nuclei. We found that delays in corollary discharge inhibition onset were strongly correlated with EOD duration as well as delay to the first peak of the EOD. In addition, we showed that electrosensory receptors respond to self-generated EODs with spikes occurring in a narrow time window immediately following the first peak of the EOD. Direct comparison of time courses between the EOD and corollary discharge inhibition revealed that the inhibition overlaps the first peak of the EOD. Our results suggest that internal delays have shifted the timing of corollary discharge inhibition to optimally block responses to self-generated signals.SIGNIFICANCE STATEMENT Corollary discharges are internal copies of motor commands that are essential for brain function. For example, corollary discharge allows an animal to distinguish self-generated from external stimuli. Despite widespread diversity in behavior and its motor control, we know little about the evolution of corollary discharges. Mormyrid fishes generate stereotyped electric pulses used for communication and active sensing. In the electrosensory pathway that processes communication signals, a corollary discharge inhibits sensory responses to self-generated signals. We found that fish with long-duration pulses have delayed corollary discharge inhibition, and that this time-shifted corollary discharge optimally blocks electrosensory responses to the fish's own signal. Our study provides the first evidence for evolutionary change in sensorimotor integration related to diversification of communication signals.
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Li L, Liu D, Liu A, Li J, Wang H, Zhou J. Genomic Survey of Tyrosine Kinases Repertoire in Electrophorus electricus With an Emphasis on Evolutionary Conservation and Diversification. Evol Bioinform Online 2020; 16:1176934320922519. [PMID: 32546936 PMCID: PMC7249569 DOI: 10.1177/1176934320922519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/07/2020] [Indexed: 12/05/2022] Open
Abstract
Tyrosine kinases (TKs) play key roles in the regulation of multicellularity in
organisms and involved primarily in cell growth, differentiation, and
cell-to-cell communication. Genome-wide characterization of TKs has been
conducted in many metazoans; however, systematic information regarding this
superfamily in Electrophorus electricus (electric eel) is still
lacking. In this study, we identified 114 TK genes in the E
electricus genome and investigated their evolution, molecular
features, and domain architecture using phylogenetic profiling to gain a better
understanding of their similarities and specificity. Our results suggested that
the electric eel TK (EeTK) repertoire was shaped by whole-genome duplications
(WGDs) and tandem duplication events. Compared with other vertebrate TKs, gene
members in Jak, Src, and EGFR subfamily duplicated specifically, but with
members lost in Eph, Axl, and Ack subfamily in electric eel. We also conducted
an exhaustive survey of TK genes in genomic databases, identifying 1674 TK
proteins in 31 representative species covering all the main metazoan lineages.
Extensive evolutionary analysis indicated that TK repertoire in vertebrates
tended to be remarkably conserved, but the gene members in each subfamily were
very variable. Comparative expression profile analysis showed that electric
organ tissues and muscle shared a similar pattern with specific highly expressed
TKs (ie, epha7, musk, jak1, and pdgfra), suggesting that regulation of TKs might
play an important role in specifying an electric organ identity from its muscle
precursor. We further identified TK genes exhibiting tissue-specific expression
patterns, indicating that members in TKs participated in subfunctionalization
representing an evolutionary divergence required for the performance of
different tissues. This work generates valuable information for further gene
function analysis and identifying candidate TK genes reflecting their unique
tissue-function specializations in electric eel.
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Affiliation(s)
- Ling Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Dangyun Liu
- Department of Central Laboratory, The Affiliated Huaian No.1 People's Hospital, Nanjing Medical University, Huai'an, P.R. China
| | - Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, P.R. China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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42
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Brain transcriptomics of agonistic behaviour in the weakly electric fish Gymnotus omarorum, a wild teleost model of non-breeding aggression. Sci Rep 2020; 10:9496. [PMID: 32528029 PMCID: PMC7289790 DOI: 10.1038/s41598-020-66494-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/22/2020] [Indexed: 11/28/2022] Open
Abstract
Differences in social status are often mediated by agonistic encounters between competitors. Robust literature has examined social status-dependent brain gene expression profiles across vertebrates, yet social status and reproductive state are often confounded. It has therefore been challenging to identify the neuromolecular mechanisms underlying social status independent of reproductive state. Weakly electric fish, Gymnotus omarorum, display territorial aggression and social dominance independent of reproductive state. We use wild-derived G. omarorum males to conduct a transcriptomic analysis of non-breeding social dominance relationships. After allowing paired rivals to establish a dominance hierarchy, we profiled the transcriptomes of brain sections containing the preoptic area (region involved in regulating aggressive behaviour) in dominant and subordinate individuals. We identified 16 differentially expressed genes (FDR < 0.05) and numerous genes that co-varied with behavioural traits. We also compared our results with previous reports of differential gene expression in other teleost species. Overall, our study establishes G. omarorum as a powerful model system for understanding the neuromolecular bases of social status independent of reproductive state.
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43
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Wang Y, Zhao Y, Wang Y, Li Z, Guo B, Merilä J. Population transcriptomics reveals weak parallel genetic basis in repeated marine and freshwater divergence in nine‐spined sticklebacks. Mol Ecol 2020; 29:1642-1656. [DOI: 10.1111/mec.15435] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yongxin Zhao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Yu Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
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44
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Card DC, Adams RH, Schield DR, Perry BW, Corbin AB, Pasquesi GIM, Row K, Van Kleeck MJ, Daza JM, Booth W, Montgomery CE, Boback SM, Castoe TA. Genomic Basis of Convergent Island Phenotypes in Boa Constrictors. Genome Biol Evol 2020; 11:3123-3143. [PMID: 31642474 PMCID: PMC6836717 DOI: 10.1093/gbe/evz226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Convergent evolution is often documented in organisms inhabiting isolated environments with distinct ecological conditions and similar selective regimes. Several Central America islands harbor dwarf Boa populations that are characterized by distinct differences in growth, mass, and craniofacial morphology, which are linked to the shared arboreal and feast-famine ecology of these island populations. Using high-density RADseq data, we inferred three dwarf island populations with independent origins and demonstrate that selection, along with genetic drift, has produced both divergent and convergent molecular evolution across island populations. Leveraging whole-genome resequencing data for 20 individuals and a newly annotated Boa genome, we identify four genes with evidence of phenotypically relevant protein-coding variation that differentiate island and mainland populations. The known roles of these genes involved in body growth (PTPRS, DMGDH, and ARSB), circulating fat and cholesterol levels (MYLIP), and craniofacial development (DMGDH and ARSB) in mammals link patterns of molecular evolution with the unique phenotypes of these island forms. Our results provide an important genome-wide example for quantifying expectations of selection and convergence in closely related populations. We also find evidence at several genomic loci that selection may be a prominent force of evolutionary change—even for small island populations for which drift is predicted to dominate. Overall, while phenotypically convergent island populations show relatively few loci under strong selection, infrequent patterns of molecular convergence are still apparent and implicate genes with strong connections to convergent phenotypes.
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Affiliation(s)
- Daren C Card
- Department of Biology, University of Texas Arlington.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts.,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | | | | | - Blair W Perry
- Department of Biology, University of Texas Arlington
| | | | | | | | | | - Juan M Daza
- Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Warren Booth
- Department of Biological Science, University of Tulsa, Oklahoma
| | | | - Scott M Boback
- Department of Biology, Dickinson College, Carlisle, Pennsylvania
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington
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45
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Ayan B, Heo DN, Zhang Z, Dey M, Povilianskas A, Drapaca C, Ozbolat IT. Aspiration-assisted bioprinting for precise positioning of biologics. SCIENCE ADVANCES 2020; 6:eaaw5111. [PMID: 32181332 PMCID: PMC7060055 DOI: 10.1126/sciadv.aaw5111] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/13/2019] [Indexed: 05/13/2023]
Abstract
Three-dimensional (3D) bioprinting is an appealing approach for building tissues; however, bioprinting of mini-tissue blocks (i.e., spheroids) with precise control on their positioning in 3D space has been a major obstacle. Here, we unveil "aspiration-assisted bioprinting (AAB)," which enables picking and bioprinting biologics in 3D through harnessing the power of aspiration forces, and when coupled with microvalve bioprinting, it facilitated different biofabrication schemes including scaffold-based or scaffold-free bioprinting at an unprecedented placement precision, ~11% with respect to the spheroid size. We studied the underlying physical mechanism of AAB to understand interactions between aspirated viscoelastic spheroids and physical governing forces during aspiration and bioprinting. We bioprinted a wide range of biologics with dimensions in an order-of-magnitude range including tissue spheroids (80 to 600 μm), tissue strands (~800 μm), or single cells (electrocytes, ~400 μm), and as applications, we illustrated the patterning of angiogenic sprouting spheroids and self-assembly of osteogenic spheroids.
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Affiliation(s)
- Bugra Ayan
- Engineering Science and Mechanics Department, Penn State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
| | - Dong Nyoung Heo
- Engineering Science and Mechanics Department, Penn State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
- Department of Dental Materials, School of Dentistry, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Zhifeng Zhang
- Engineering Science and Mechanics Department, Penn State University, University Park, PA 16802, USA
| | - Madhuri Dey
- The Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
| | - Adomas Povilianskas
- Engineering Science and Mechanics Department, Penn State University, University Park, PA 16802, USA
| | - Corina Drapaca
- Engineering Science and Mechanics Department, Penn State University, University Park, PA 16802, USA
| | - Ibrahim T. Ozbolat
- Engineering Science and Mechanics Department, Penn State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA
- Biomedical Engineering Department, Penn State University, University Park, PA 16802, USA
- Materials Research Institute, Penn State University, University Park, PA 16802, USA
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Abstract
Neuroscience has a long, rich history in embracing unusual animals for research. Over the past several decades, there has been a technology-driven bottleneck in the species used for neuroscience research. However, an oncoming wave of technologies applicable to many animals hold promise for enabling researchers to address challenging scientific questions that cannot be solved using traditional laboratory animals. Here, we discuss how leveraging the convergent evolution of physiological or behavioral phenotypes can empower research mapping genotype to phenotype interactions. We present two case studies using electric fish and poison frogs and discuss how comparative work can teach us about evolutionary constraint and flexibility at various levels of biological organization. We also offer advice on the potential and pitfalls of establishing novel model systems in neuroscience research. Finally, we end with a discussion on the use of charismatic animals in neuroscience research and their utility in public outreach. Overall, we argue that convergent evolution frameworks can help identify generalizable principles of neuroscience.
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Affiliation(s)
- Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
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47
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Losilla M, Luecke DM, Gallant JR. The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish. BMC Evol Biol 2020; 20:6. [PMID: 31918666 PMCID: PMC6953315 DOI: 10.1186/s12862-019-1572-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/24/2019] [Indexed: 01/10/2023] Open
Abstract
Background Understanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits. In this study, we focus on a rapidly diverged species group of mormyrid electric fish in the genus Paramormyrops, which are characterized by extensive phenotypic variation in electric organ discharges (EODs). The main components of EOD diversity are waveform duration, complexity and polarity. Using an RNA-sequencing based approach, we sought to identify gene expression correlates for each of these EOD waveform features by comparing 11 specimens of Paramormyrops that exhibit variation in these features. Results Patterns of gene expression among Paramormyrops are highly correlated, and 3274 genes (16%) were differentially expressed. Using our most restrictive criteria, we detected 145–183 differentially expressed genes correlated with each EOD feature, with little overlap between them. The predicted functions of several of these genes are related to extracellular matrix, cation homeostasis, lipid metabolism, and cytoskeletal and sarcomeric proteins. These genes are of significant interest given the known morphological differences between electric organs that underlie differences in the EOD waveform features studied. Conclusions In this study, we identified plausible candidate genes that may contribute to phenotypic differences in EOD waveforms among a rapidly diverged group of mormyrid electric fish. These genes may be important targets of selection in the evolution of species-specific differences in mate-recognition signals.
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Affiliation(s)
- Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - David Michael Luecke
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA.
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48
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Souza-Shibatta L, Ferreira DG, Santos KF, Galindo BA, Shibatta OA, Sofia SH, Giacomin RM, Bastos DA, Mendes-Júnior RNG, Santana CDD. Electric eels galore: microsatellite markers for population studies. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2020-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Fourteen novel microsatellite loci are described and characterized in two species of electric eels, Electrophorus variiand E. voltaifrom floodplains and rivers of the Amazon rainforest. These loci are polymorphic, highly informative, and have the capacity to detect reliable levels of genetic diversity. Likewise, the high combined probability of paternity exclusion value and low combined probability of genetic identity value obtained demonstrate that the new set of loci displays suitability for paternity studies on electric eels. In addition, the cross-amplification of electric eel species implies that it may also be useful in the study of the closely related E. electricus, and to other Neotropical electric fishes (Gymnotiformes) species as tested herein.
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Aguilar C, Miller MJ, Loaiza JR, González R, Krahe R, De León LF. Tempo and mode of allopatric divergence in the weakly electric fish Sternopygus dariensis in the Isthmus of Panama. Sci Rep 2019; 9:18828. [PMID: 31827183 PMCID: PMC6906317 DOI: 10.1038/s41598-019-55336-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/27/2019] [Indexed: 01/12/2023] Open
Abstract
Spatial isolation is one of the main drivers of allopatric speciation, but the extent to which spatially-segregated populations accumulate genetic differences relevant to speciation is not always clear. We used data from ultraconserved elements (UCEs) and whole mitochondrial genomes (i.e., mitogenomes) to explore genetic variation among allopatric populations of the weakly electric fish Sternopygus dariensis across the Isthmus of Panama. We found strong genetic divergence between eastern and western populations of S. dariensis. Over 77% of the UCE loci examined were differentially fixed between populations, and these loci appear to be distributed across the species' genome. Population divergence occurred within the last 1.1 million years, perhaps due to global glaciation oscillations during the Pleistocene. Our results are consistent with a pattern of genetic differentiation under strict geographic isolation, and suggest the presence of incipient allopatric species within S. dariensis. Genetic divergence in S. dariensis likely occurred in situ, long after the closure of the Isthmus of Panama. Our study highlights the contribution of spatial isolation and vicariance to promoting rapid diversification in Neotropical freshwater fishes. The study of spatially-segregated populations within the Isthmus of Panama could reveal how genetic differences accumulate as allopatric speciation proceeds.
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Affiliation(s)
- Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Matthew J Miller
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Jose R Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Panamá, República de Panamá
| | - Rigoberto González
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá
| | - Rüdiger Krahe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, República de Panamá.
- Smithsonian Tropical Research Institute, Balboa Ancón, P.O. Box 0843-03092, Panamá, República de Panamá.
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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Tran MP, Tsutsumi R, Erberich JM, Chen KD, Flores MD, Cooper KL. Evolutionary loss of foot muscle during development with characteristics of atrophy and no evidence of cell death. eLife 2019; 8:50645. [PMID: 31612857 PMCID: PMC6855805 DOI: 10.7554/elife.50645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022] Open
Abstract
Many species that run or leap across sparsely vegetated habitats, including horses and deer, evolved the severe reduction or complete loss of foot muscles as skeletal elements elongated and digits were lost, and yet the developmental mechanisms remain unknown. Here, we report the natural loss of foot muscles in the bipedal jerboa, Jaculus jaculus. Although adults have no muscles in their feet, newborn animals have muscles that rapidly disappear soon after birth. We were surprised to find no evidence of apoptotic or necrotic cell death during stages of peak myofiber loss, countering well-supported assumptions of developmental tissue remodeling. We instead see hallmarks of muscle atrophy, including an ordered disassembly of the sarcomere associated with upregulation of the E3 ubiquitin ligases, MuRF1 and Atrogin-1. We propose that the natural loss of muscle, which remodeled foot anatomy during evolution and development, involves cellular mechanisms that are typically associated with disease or injury. Intrinsic muscles are a group of muscles deep inside the hands and feet. They help to control the precise movements required, for example, for a pianist to play their instrument or for certain animals to climb with remarkable agility. Some animals, such as horses and deer, have evolved in such a way that they no longer grasp objects with hands and feet. Where intrinsic muscles were once present in the hands and feet of their ancestors, these animals now have strong ligaments that prevent over-extension of the wrist and ankle joints during hard landings. Given their size, it is difficult to study horses and deer in the laboratory and understand how they lost their intrinsic muscles during evolution. Tran et al. therefore focused on a small rodent called the lesser Egyptian jerboa, which also displays long legs with strong ligaments and no intrinsic muscles. Newborn jerboas have foot muscles that look very much like the intrinsic muscles found in mice, but these muscles disappear within 4 days of birth. A mechanism called programmed cell death is often responsible for specific tissues disappearing during development, but the experiments of Tran et al. revealed that this was not the case in jerboas. Instead, their intrinsic muscles were degraded by processes triggered by genes that disassemble underused muscles. In mice and humans, fasting, nerve injuries, or immobility trigger this type of muscle degradation, but in jerboas these processes appear to be a normal part of development. This unexpected discovery shows that development and disease-like processes are linked, and that more studies of nontraditional research animals may help scientists better understand these connections.
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Affiliation(s)
- Mai P Tran
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Rio Tsutsumi
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Joel M Erberich
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Kevin D Chen
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Michelle D Flores
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, United States
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