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Deville D, Kawai K, Fujita H, Umino T. Genetic divergences and hybridization within the Sebastes inermis complex. PeerJ 2023; 11:e16391. [PMID: 38025733 PMCID: PMC10656903 DOI: 10.7717/peerj.16391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and "Kumano" (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the "Kumano" morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow.
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Affiliation(s)
- Diego Deville
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japón
| | - Kentaro Kawai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japón
| | - Hiroki Fujita
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Shirahama, Wakayama, Japan
| | - Tetsuya Umino
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japón
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2
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Pampoulie C, Berg PR, Jentoft S. Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters. Evol Appl 2023; 16:223-233. [PMID: 36793686 PMCID: PMC9923494 DOI: 10.1111/eva.13471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/29/2022] [Accepted: 08/18/2022] [Indexed: 11/27/2022] Open
Abstract
Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.
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Affiliation(s)
| | - Paul Ragnar Berg
- Norwegian Institute for Water Research Oslo Norway.,Department of Natural Sciences, Centre for Coastal Research (CCR) University of Agder Kristiansand Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis Oslo Norway
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3
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Ito RK, Harada S, Tabata R, Watanabe K. Molecular evolution and convergence of the rhodopsin gene in Gymnogobius, a goby group having diverged into coastal to freshwater habitats. J Evol Biol 2021; 35:333-346. [PMID: 34689368 DOI: 10.1111/jeb.13955] [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: 09/16/2020] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022]
Abstract
Adaptive evolution of vision-related genes has been frequently observed in the process of invasion of new environments in a wide range of animal taxa. The typical example is that of the molecular evolution of rhodopsin associated with habitat changes in aquatic animals. However, few studies have investigated rhodopsin evolution during adaptive radiation across various habitats. In the present study, we examined the link between molecular evolutionary patterns in the rhodopsin gene and macroscopic habitat changes in Gymnogobius species (Gobiidae), which have adaptively radiated to diverse aquatic habitats including the sea, brackish waters, rivers and lakes. Analysis of amino acid substitutions in rhodopsin in the phylogenetic framework revealed convergent substitutions in 4-5 amino acids in three groups (four species), including two spectral tuning amino acid sites known to change rhodopsin's absorption wavelength. Positive selection was detected in the basal branches of each of these three groups, suggesting adaptive molecular convergence of rhodopsin. However, no significant correlation was observed between amino acid substitutions and the species' habitat changes, suggesting molecular adaptation to some unidentified micro-ecological environments. Taken together, these results emphasize the importance of considering not only macroscopic habitats but also micro-ecological environments when elucidating the driving forces of adaptive evolution of the visual system.
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Affiliation(s)
- Ryosuke K Ito
- Division of Biological Sciences, Department of Zoology, Graduate School of Science, Kyoto University, Kyoto City, Japan
| | - Shigeo Harada
- Resource Management Division, Fisheries Bureau, Agriculture, Forestry and Fisheries Department, Wakayama Prefectural Government, Wakayama City, Japan
| | | | - Katsutoshi Watanabe
- Division of Biological Sciences, Department of Zoology, Graduate School of Science, Kyoto University, Kyoto City, Japan
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4
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Behrens KA, Girasek QL, Sickler A, Hyde J, Buonaccorsi VP. Regions of genetic divergence in depth-separated Sebastes rockfish species pairs: Depth as a potential driver of speciation. Mol Ecol 2021; 30:4259-4275. [PMID: 34181798 DOI: 10.1111/mec.16046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/20/2022]
Abstract
Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation-driving adaptations, particularly along a depth gradient. A reduced-representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black-and-yellow rockfish) and S. carnatus (gopher rockfish) FST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. These corresponded with regions of both elevated DXY values and reduced nucleotide diversity in two cases, suggesting a speciation-with-gene-flow evolutionary model followed by post-speciation selective sweeps within each species. Limited whole-genome resequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated.
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Affiliation(s)
- Kristen A Behrens
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Quinn L Girasek
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Alex Sickler
- Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John Hyde
- Fisheries Resources Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, California, USA
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5
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Heras J, Aguilar A. Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes). J Hered 2020; 110:340-350. [PMID: 30602025 DOI: 10.1093/jhered/esy070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/31/2018] [Indexed: 01/21/2023] Open
Abstract
The genetic underpinnings that contribute to ecological adaptation and speciation are not completely understood, especially within marine ecosystems. These evolutionary processes can be elucidated by studying adaptive radiations, because they provide replicates of divergence within a given environment or time-frame. Marine rockfishes (genus Sebastes) are an adaptive radiation and unique model system for studying adaptive evolution in the marine realm. We investigated molecular evolution associated with ecological (depth) and life history (lifespan) divergence in 2 closely related clades of Sebastes. Brain transcriptomes were sequenced via RNA-Seq from 3 species within the subgenus Pteropodus and a pair of related congeners from the subgenus Sebastosomus in order to identify patterns of adaptive evolution. De novo assemblies from these transcriptomes were used to identify 3867 orthologous clusters, and genes subject to positive selection were identified based on all 5 species, depth, and lifespan. Within all our analyses, we identified hemoglobin subunit α to be under strong positive selection and is associated with the depth of occurrence. In our lifespan analysis we identified immune function genes under positive selection in association with maximum lifespan. This study provides insight on the molecular evolution of rockfishes and these candidate genes may provide a better understanding of how these subgenera radiated within the Northeast Pacific.
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Affiliation(s)
- Joseph Heras
- School of Natural Sciences and Graduate Group in Quantitative and Systems Biology, University of California, Merced, CA
| | - Andres Aguilar
- School of Natural Sciences and Graduate Group in Quantitative and Systems Biology, University of California, Merced, CA
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6
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Sarasamma S, Lai YH, Liang ST, Liu K, Hsiao CD. The Power of Fish Models to Elucidate Skin Cancer Pathogenesis and Impact the Discovery of New Therapeutic Opportunities. Int J Mol Sci 2018; 19:E3929. [PMID: 30544544 PMCID: PMC6321611 DOI: 10.3390/ijms19123929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/21/2023] Open
Abstract
Animal models play important roles in investigating the pathobiology of cancer, identifying relevant pathways, and developing novel therapeutic tools. Despite rapid progress in the understanding of disease mechanisms and technological advancement in drug discovery, negative trial outcomes are the most frequent incidences during a Phase III trial. Skin cancer is a potential life-threatening disease in humans and might be medically futile when tumors metastasize. This explains the low success rate of melanoma therapy amongst other malignancies. In the past decades, a number of skin cancer models in fish that showed a parallel development to the disease in humans have provided important insights into the fundamental biology of skin cancer and future treatment methods. With the diversity and breadth of advanced molecular genetic tools available in fish biology, fish skin cancer models will continue to be refined and expanded to keep pace with the rapid development of skin cancer research. This review begins with a brief introduction of molecular characteristics of skin cancers, followed by an overview of teleost models that have been used in the last decades in melanoma research. Next, we will detail the importance of the zebrafish (Danio rerio) animal model and other emerging fish models including platyfish (Xiphophorus sp.), and medaka (Oryzias latipes) in future cutaneous malignancy studies. The last part of this review provides the recent development and genome editing applications of skin cancer models in zebrafish and the progress in small molecule screening.
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Affiliation(s)
- Sreeja Sarasamma
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Yu-Heng Lai
- Department of Chemistry, Chinese Culture University, Taipei 11114, Taiwan.
| | - Sung-Tzu Liang
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China.
| | - Chung-Der Hsiao
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Taiwan Center for Biomedical Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
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7
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Hahn C, Genner MJ, Turner GF, Joyce DA. The genomic basis of cichlid fish adaptation within the deepwater "twilight zone" of Lake Malawi. Evol Lett 2017; 1:184-198. [PMID: 30283648 PMCID: PMC6124600 DOI: 10.1002/evl3.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/01/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population‐level RAD‐seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome‐level specialization for life at depth as an important process in cichlid radiation.
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Affiliation(s)
- Christoph Hahn
- Evolutionary and Environmental Genomics Group (@EvoHull), School of Environmental Sciences University of Hull Hull HU5 7RX United Kingdom.,Institute of Zoology University of Graz A-8010 Graz Austria
| | - Martin J Genner
- School of Biological Sciences University of Bristol Bristol Life Sciences Building, 24 Tyndall Avenue Bristol BS8 1TQ United Kingdom
| | - George F Turner
- School of Biological Sciences Bangor University Bangor Gwynedd LL57 2UW Wales United Kingdom
| | - Domino A Joyce
- Evolutionary and Environmental Genomics Group (@EvoHull), School of Environmental Sciences University of Hull Hull HU5 7RX United Kingdom
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8
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Tuset VM, Otero-Ferrer JL, Gómez-Zurita J, Venerus LA, Stransky C, Imondi R, Orlov AM, Ye Z, Santschi L, Afanasiev PK, Zhuang L, Farré M, Love M, Lombarte A. Otolith shape lends support to the sensory drive hypothesis in rockfishes. J Evol Biol 2016; 29:2083-2097. [DOI: 10.1111/jeb.12932] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/28/2016] [Accepted: 06/27/2016] [Indexed: 12/26/2022]
Affiliation(s)
- V. M. Tuset
- Instituto de Ciencias del Mar (CSIC); Barcelona Spain
| | - J. L. Otero-Ferrer
- Departamento de Ecoloxía e Bioloxía Animal; Universidad de Vigo; 36310 Vigo (Pontevedra) Spain
| | - J. Gómez-Zurita
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona Spain
| | - L. A. Venerus
- Centro para el Estudio de Sistemas Marinos (CESIMAR); Centro Nacional Patagónico (CENPAT-CONICET); Puerto Madryn, Chubut Argentina
| | - C. Stransky
- Thünen Institute of Sea Fisheries; Hamburg Germany
| | - R. Imondi
- Coastal Marine Biolabs; Integrative Biosciences Program; Ventura CA USA
| | - A. M. Orlov
- Russian Federal Research Institute of Fisheries and Oceanography; Moscow Russia
- A.N. Severtsov Institute of Ecology and Evolution; Moscow Russia
- Department of Ichthyology; Faculty of Biology; Dagestan State University; Makhachkala Russia
| | - Z. Ye
- Fisheries College; Ocean University of China; Qingdao China
| | - L. Santschi
- Coastal Marine Biolabs; Integrative Biosciences Program; Ventura CA USA
| | - P. K. Afanasiev
- Russian Federal Research Institute of Fisheries and Oceanography; Moscow Russia
| | - L. Zhuang
- Fisheries College; Ocean University of China; Qingdao China
| | - M. Farré
- Instituto de Ciencias del Mar (CSIC); Barcelona Spain
| | - M.S. Love
- Marine Science Institute; University of California; Santa Barbara CA USA
| | - A. Lombarte
- Instituto de Ciencias del Mar (CSIC); Barcelona Spain
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9
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Kelley JL, Brown AP, Therkildsen NO, Foote AD. The life aquatic: advances in marine vertebrate genomics. Nat Rev Genet 2016; 17:523-34. [DOI: 10.1038/nrg.2016.66] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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10
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Fernández-Sampedro MA, Invergo BM, Ramon E, Bertranpetit J, Garriga P. Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution. Sci Rep 2016; 6:21570. [PMID: 26865329 PMCID: PMC4749998 DOI: 10.1038/srep21570] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/27/2016] [Indexed: 12/22/2022] Open
Abstract
Visual rhodopsins are membrane proteins that function as light photoreceptors in the vertebrate retina. Specific amino acids have been positively selected in visual pigments during mammal evolution, which, as products of adaptive selection, would be at the base of important functional innovations. We have analyzed the top candidates for positive selection at the specific amino acids and the corresponding reverse changes (F13M, Q225R and A346S) in order to unravel the structural and functional consequences of these important sites in rhodopsin evolution. We have constructed, expressed and immunopurified the corresponding mutated pigments and analyzed their molecular phenotypes. We find that position 13 is very important for the folding of the receptor and also for proper protein glycosylation. Position 225 appears to be important for the function of the protein affecting the G-protein activation process, and position 346 would also regulate functionality of the receptor by enhancing G-protein activation and presumably affecting protein phosphorylation by rhodopsin kinase. Our results represent a link between the evolutionary analysis, which pinpoints the specific amino acid positions in the adaptive process, and the structural and functional analysis, closer to the phenotype, making biochemical sense of specific selected genetic sequences in rhodopsin evolution.
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Affiliation(s)
- Miguel A Fernández-Sampedro
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Brandon M Invergo
- IBE - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Eva Ramon
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Jaume Bertranpetit
- IBE - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
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11
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Borges R, Khan I, Johnson WE, Gilbert MTP, Zhang G, Jarvis ED, O'Brien SJ, Antunes A. Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. BMC Genomics 2015; 16:751. [PMID: 26438339 PMCID: PMC4595237 DOI: 10.1186/s12864-015-1924-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 09/11/2015] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. RESULTS We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. CONCLUSIONS We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.
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Affiliation(s)
- Rui Borges
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| | - Imran Khan
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350, Copenhagen, Denmark.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzen, 518083, China.
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark.
| | - Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center Durham, Box 3209, North Carolina, 27710, USA.
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA.
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia.
- Oceanographic Center, Nova Southeastern University, 8000 N. Ocean Drive, Ft Lauderdale, Florida, 33004, USA.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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12
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Heras J, McClintock K, Sunagawa S, Aguilar A. Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes). BMC Genomics 2015; 16:656. [PMID: 26329285 PMCID: PMC4557894 DOI: 10.1186/s12864-015-1870-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 08/20/2015] [Indexed: 12/12/2022] Open
Abstract
Background The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates. Results We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3’ and 5’ UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions. Conclusions We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1870-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph Heras
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA.
| | - Kelly McClintock
- School of Natural Sciences and Graduate Group in Quantitative and Systems Biology, University of California Merced, 5200 N Lake Rd, Merced, CA, 95344, USA.
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Meyerhofstr 1, 69117, Heidelberg, Germany.
| | - Andres Aguilar
- Department of Biological Sciences, California State University Los Angeles, 5151 State University Dr, Los Angeles, CA, 90032, USA.
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13
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Sander SE, Hall DW. Variation in opsin genes correlates with signalling ecology in North American fireflies. Mol Ecol 2015; 24:4679-96. [PMID: 26289828 PMCID: PMC4599352 DOI: 10.1111/mec.13346] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/30/2015] [Accepted: 08/16/2015] [Indexed: 12/27/2022]
Abstract
Genes underlying signal reception should evolve to maximize signal detection in a particular environment. In animals, opsins, the protein component of visual pigments, are predicted to evolve according to this expectation. Fireflies are known for their bioluminescent mating signals. The eyes of nocturnal species are expected to maximize the detection of conspecific signal colours emitted in the typical low-light environment. This is not expected for species that have transitioned to diurnal activity in bright daytime environments. Here, we test the hypothesis that opsin gene sequence plays a role in modifying firefly eye spectral sensitivity. We use genome and transcriptome sequencing in four firefly species, transcriptome sequencing in six additional species and targeted gene sequencing in 28 other species to identify all opsin genes present in North American fireflies and to elucidate amino acid sites under positive selection. We also determine whether amino acid substitutions in opsins are linked to evolutionary changes in signal mode, signal colour and light environment. We find only two opsins, one long wavelength and one ultraviolet, in all firefly species and identify 25 candidate sites that may be involved in determining spectral sensitivity. In addition, we find elevated rates of evolution at transitions to diurnal activity, and changes in selective constraint on long wavelength opsin associated with changes in light environment. Our results suggest that changes in eye spectral sensitivity are at least partially due to opsin sequence. Fireflies continue to be a promising system in which to investigate the evolution of signals, receptors and signalling environments.
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Affiliation(s)
- S E Sander
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - D W Hall
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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Andersen Ø, Johnsen H, De Rosa MC, Præbel K, Stjelja S, Kirubakaran TG, Pirolli D, Jentoft S, Fevolden SE. Evolutionary history and adaptive significance of the polymorphic Pan I in migratory and stationary populations of Atlantic cod (Gadus morhua). Mar Genomics 2015; 22:45-54. [DOI: 10.1016/j.margen.2015.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/19/2015] [Accepted: 03/19/2015] [Indexed: 11/27/2022]
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Shum P, Pampoulie C, Kristinsson K, Mariani S. Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish. Mol Ecol 2015; 24:3652-67. [PMID: 26073046 PMCID: PMC4744735 DOI: 10.1111/mec.13262] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 01/27/2023]
Abstract
Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of ‘redfish’ occurring in the North Atlantic – which is known for a widely distributed ‘shallow‐pelagic’ oceanic type inhabiting waters between 250 and 550 m, and a more localized ‘deep‐pelagic’ population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an ‘hourglass’ to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.
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Affiliation(s)
- Peter Shum
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
| | | | | | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
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Pampoulie C, Skirnisdottir S, Star B, Jentoft S, Jónsdóttir IG, Hjörleifsson E, Thorsteinsson V, Pálsson ÓK, Berg PR, Andersen Ø, Magnusdottir S, Helyar SJ, Daníelsdóttir AK. Rhodopsin Gene Polymorphism Associated with Divergent Light Environments in Atlantic Cod. Behav Genet 2015; 45:236-44. [DOI: 10.1007/s10519-014-9701-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/15/2014] [Indexed: 11/24/2022]
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17
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Tuset VM, Imondi R, Aguado G, Otero-Ferrer JL, Santschi L, Lombarte A, Love M. Otolith patterns of rockfishes from the northeastern pacific. J Morphol 2014; 276:458-69. [DOI: 10.1002/jmor.20353] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 11/17/2014] [Accepted: 11/23/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Victor M. Tuset
- Institute of Marine Sciences (ICM-CSIC); Passeig Marítim 37-49 08003 Barcelona Catalonia Spain
| | - Ralph Imondi
- Coastal Marine Biolabs, Integrative Biosciences Program; 1559 Spinnaker Drive, Suite 101 Ventura California
| | - Guillermo Aguado
- Institute of Marine Sciences (ICM-CSIC); Passeig Marítim 37-49 08003 Barcelona Catalonia Spain
| | - José L. Otero-Ferrer
- Departamento de Ecoloxía e Bioloxía Animal-Facultade de Ciencias; Universidade de Vigo; 36310 Vigo Spain
| | - Linda Santschi
- Coastal Marine Biolabs, Integrative Biosciences Program; 1559 Spinnaker Drive, Suite 101 Ventura California
| | - Antoni Lombarte
- Institute of Marine Sciences (ICM-CSIC); Passeig Marítim 37-49 08003 Barcelona Catalonia Spain
| | - Milton Love
- Marine Science Institute, University of California; Santa Barbara California
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Shum P, Pampoulie C, Sacchi C, Mariani S. Divergence by depth in an oceanic fish. PeerJ 2014; 2:e525. [PMID: 25165634 PMCID: PMC4137662 DOI: 10.7717/peerj.525] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/25/2014] [Indexed: 11/20/2022] Open
Abstract
Despite the striking physical and environmental gradients associated with depth variation in the oceans, relatively little is known about their impact on population diversification, adaptation and speciation. Changes in light associated with increasing depth are likely to alter the visual environment of organisms, and adaptive changes in visual systems may be expected. The pelagic beaked redfish, Sebastes mentella, exhibits depth-associated patterns of substructure in the central North Atlantic, with a widely distributed shallow-pelagic population inhabiting waters between 250 and 550 m depth and a deep-pelagic population dwelling between 550 and 800 m. Here we performed a molecular genetic investigation of samples from fish collected from ‘shallow’ and ‘deep’ populations, using the mitochondrial control region and the gene coding for the visual-pigment rhodopsin. We identify patterns suggestive of potential adaptation to different depths, by detecting a specific amino acid replacement at the rhodopsin gene. Mitochondrial DNA results reflect a scenario of long-term demographic independence between the two S. mentella groups, and raise the possibility that these ‘stocks’ may in fact be two incipient species.
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Affiliation(s)
- Peter Shum
- School of Environment & Life Sciences, University of Salford , Manchester , UK
| | | | - Carlotta Sacchi
- School of Biology & Environmental Science, University College Dublin , Dublin , Ireland
| | - Stefano Mariani
- School of Environment & Life Sciences, University of Salford , Manchester , UK
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20
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Schott RK, Refvik SP, Hauser FE, López-Fernández H, Chang BSW. Divergent positive selection in rhodopsin from lake and riverine cichlid fishes. Mol Biol Evol 2014; 31:1149-65. [PMID: 24509690 DOI: 10.1093/molbev/msu064] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly different spectral properties from the African rift lakes. These ecological and/or biogeographic differences may have imposed divergent selective pressures on the evolution of the cichlid visual system. To test these hypotheses, we investigated the molecular evolution of the dim-light visual pigment, rhodopsin. We sequenced rhodopsin from Neotropical and African riverine cichlids and combined these data with published sequences from African cichlids. We found significant evidence for positive selection using random sites codon models in all cichlid groups, with the highest levels in African lake cichlids. Tests using branch-site and clade models that partitioned the data along ecological (lake, river) and/or biogeographic (African, Neotropical) boundaries found significant evidence of divergent selective pressures among cichlid groups. However, statistical comparisons among these models suggest that ecological, rather than biogeographic, factors may be responsible for divergent selective pressures that have shaped the evolution of the visual system in cichlids. We found that branch-site models did not perform as well as clade models for our data set, in which there was evidence for positive selection in the background. One of our most intriguing results is that the amino acid sites found to be under positive selection in Neotropical and African lake cichlids were largely nonoverlapping, despite falling into the same three functional categories: spectral tuning, retinal uptake/release, and rhodopsin dimerization. Taken together, these results would imply divergent selection across cichlid clades, but targeting similar functions. This study highlights the importance of molecular investigations of ecologically important groups and the flexibility of clade models in explicitly testing ecological hypotheses.
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Affiliation(s)
- Ryan K Schott
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Niemiller ML, Fitzpatrick BM, Shah P, Schmitz L, Near TJ. Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae). Evolution 2012; 67:732-48. [PMID: 23461324 DOI: 10.1111/j.1558-5646.2012.01822.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The genetic mechanisms underlying regressive evolution-the degeneration or loss of a derived trait--are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appears to have retained functional amino acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional constraint of rhodopsin in amblyopsid cavefishes, as at least three cave lineages have independently accumulated unique loss-of-function mutations over the last 10.3 Mya. Although several cave lineages still possess functional rhodopsin, they exhibit increased rates of nonsynonymous mutations that have greater effect on the structure and function of rhodopsin compared to those in surface lineages. These results indicate that functionality of rhodopsin has been repeatedly lost in amblyopsid cavefishes. The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization.
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Affiliation(s)
- Matthew L Niemiller
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.
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LARMUSEAU MHD, VANHOVE MPM, HUYSE T, VOLCKAERT FAM, DECORTE R. Signature of selection on the rhodopsin gene in the marine radiation of American seven-spined gobies (Gobiidae, Gobiosomatini). J Evol Biol 2011; 24:1618-25. [DOI: 10.1111/j.1420-9101.2011.02290.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Oceans are home to much of the world's biodiversity, but we know little about the processes driving speciation in marine ecosystems with few geographical barriers to gene flow. Ecological speciation resulting from divergent natural selection between ecological niches can occur in the face of gene flow. Sister species in the young and ecologically diverse rockfish genus Sebastes coexist in the northeast Pacific, implying that speciation may not require geographical isolation. Here, I use a novel phylogenetic comparative analysis to show that rockfish speciation is instead associated with divergence in habitat depth and depth-associated morphology, consistent with models of parapatric speciation. Using the same analysis, I find no support for alternative hypotheses that speciation involves divergence in diet or life history, or that speciation involves geographic isolation by latitude. These findings support the hypothesis that rockfishes undergo ecological speciation on an environmental gradient.
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Affiliation(s)
- Travis Ingram
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, , 2370-6270 University Boulevard, Vancouver, BC, Canada , V6T 1Z4.
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