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Straube N, Li C, Mertzen M, Yuan H, Moritz T. A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies. BMC Evol Biol 2018; 18:158. [PMID: 30352561 PMCID: PMC6199709 DOI: 10.1186/s12862-018-1267-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 09/26/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene capturing and subsequent next generation sequencing of putative ortholog exons of major clupeocephalan lineages. Sequence information for the RNA bait design was derived from publicly available genomes of bony fishes. Newly acquired sequence data comprising > 800 exon sequences was subsequently used for phylogenetic reconstructions. RESULTS Our results support monophyletic Otomorpha comprising Alepocephaliformes. Within Ostariophysi, Gonorynchiformes are sister to a clade comprising Cypriniformes, Characiformes, Siluriformes and Gymnotiformes, where the interrelationships of Characiformes, Siluriformes and Gymnotiformes remain enigmatic. Euteleosts comprise four major clades: Lepidogalaxiiformes, Protacanthopterygii, Stomiatii, and Galaxiiformes plus Neoteleostei. The monotypic Lepidogalaxiiformes form the sister-group to all remaining euteleosts. Protacanthopterygii, comprising Argentini-, Esoci- and Salmoniformes, is sister to Stomiatii (Osmeriformes and Stomiatiformes) and Galaxiiformes plus Neoteleostei. CONCLUSIONS Several proposed monophyla defined by morphological apomorphies within the Clupeocephalan phylogeny are confirmed by the phylogenetic estimates presented herein. However, other morphologically described groups cannot be reconciled with molecular phylogenies. Thus, numerous morphological apomoprhies of supposed monophyla are called into question. The interpretation of suggested morphological synapomorphies of otomorph fishes is strongly affected by the inclusion of deep-sea inhabiting, and to that effect morphologically adapted Alepocephaliformes. Our revision of these potential synapomorphies, in the context that Alepocephaliformes are otomorph fishes, reveals that only a single character of the total nine characters proposed as synapomorphic for the group is clearly valid for all otomorphs. Three further characters remain possible apomorphies since their status remains unclear in the deep-sea adapted Alepocephaliformes showing developmental lag and lacking a swim bladder. Further, our analysis places Galaxiiformes as sister group to neoteleosts, which contradicts some previous molecular phylogenetic studies. This needs further investigation from a morphological perspective, as suggested synapomophies for several euteleostean lineages are challenged or still lacking. For the verification of results presented herein, a denser phylogenomic-level taxon sampling should be applied.
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Affiliation(s)
- Nicolas Straube
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Zoologische Staatssammlung München, Staatliche Naturwissenschaftliche Sammlungen Bayerns, Münchhausenstraße 21, 81247 Munich, Germany
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic, Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306 China
| | - Matthias Mertzen
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
| | - Hao Yuan
- Key Laboratory of Exploration and Utilization of Aquatic, Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306 China
| | - Timo Moritz
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
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Dagosta FCP, Pinna MCCD. A history of the biogeography of Amazonian fishes. NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT The history of knowledge about Amazonian biogeography is as rich as its fish community, and a fascinating theme of study in itself. Several current paradigms and controversies about Amazonian fish biogeography are rooted in principles dating from the second half of the 18th to the first half of the 19th centuries. The present work establishes a relationship between current biogeographical ideas and their old predecessors, on the basis of a chronologically-oriented historical continuity analysis. The advent of evolutionary theory has not contributed significantly to a transformation of the knowledge on the biogeography of Amazonian fishes. On the other hand, the two main schools of biogeographical thought (dispersalist and vicariant) had major implications on how Amazonian fish distribution is interpreted. The process was gradual and many hypotheses have combined elements from each of the two schools. Chronologically, practically the entire tradition of Amazonian biogeography takes place within the evolutionary paradigm, although its founder Louis Agassiz was himself an anti-evolutionist. The birth of Amazonian biogeography is Agassiz´s travel in Amazon. That document makes it clear that the author did not consider dispersal as a valid explanation for the biogeographical patterns he found. Later, Carl Eigenmann helps to spread the dispersalist tradition as a model for biogeographical explanations in fish distributions, a phase which lasted until the late 20th century. A major shift occurs with the contributions of Marylin Weitzman, Stanley Weitzman and Richard Vari, who associated the temporal framework of phylogenetic hypotheses with distribution patterns, underscoring the predictive power of vicariant biogeography. The present-day paradigm begins with the work of John Lundberg and attempts to incorporate geomorphological and phylogenetic information into integrative biogeographical hypotheses. Some emblematic problems have delayed proposition of general hypotheses on the phylogenetic biogeography of South American fishes, such as the poor state of knowledge of their species-level systematics; an incomplete distributional record for most species and sparse or non-existent data on the phylogenetic history of most supraspecific taxa. Such drawbacks are now being corrected at a fast pace. Recent advances on geographical distribution and an increasing number of phylogenetic hypotheses will allow unprecedented large-scale biogeographic analyses, including those based on event models and Bayesian inference. Thus, the biogeography of South American fishes, especially Amazonian ones, should soon experiment a new age of progress. The success of that new phase will depend on its ability to recognize and segregate multiple overlapping temporal layers of hydrological changes, and to develop analytical tools that can deal with temporal mixing.
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Arratia G. Otomorphs (= otocephalans or ostarioclupeomorphs) revisited. NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT A morphological revision is presented here on the cohort Otomorpha, a clade currently interpreted as the most primitive among the large supercohort Clupeocephala. Otomorpha is a morphologically heterogeneous group represented by clupei forms , alepocephaliforms, and ostariophysans (gonorynchiforms, cypriniforms, characiforms, siluriforms, and gymnoti forms) that inhabit various marine and freshwater environments worldwide. Otomorphs have a long (ca. 145 Ma) and diverse fossil record. They are the largest fish teleostean clade worldwide, as well as the largest of the Neotropical Region. While molecular studies strongly confirm the monophyly of Otomorpha, most potential morphological synapomorphies of the group become homoplastic largely due to the peculiar morphological character states (either losses or transformations) present in alepocephaliforms. The fusion of haemal arches with their respective vertebral centra anterior to preural centrum 2 stands as an unambiguous synapomorphy of the clade. The ankylosis or fusion of the extrascapular and parietal bones, and silvery areas associated with the gas bladder are also interpreted as synapomorphies, although they are homoplastic characters mainly due to secondary losses or further transformations of the morphological features in the alepocephaliforms.
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54
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Zaccone G, Lauriano ER, Capillo G, Kuciel M. Air- breathing in fish: Air- breathing organs and control of respiration: Nerves and neurotransmitters in the air-breathing organs and the skin. Acta Histochem 2018; 120:630-641. [PMID: 30266194 DOI: 10.1016/j.acthis.2018.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In fishes, exploitation of aerial gas exchange has evolved independently many times, involving a variety of air-breathing organs. Indeed, air-breathing occurs in at least 49 known families of fish (Graham, 1997). Many amphibious vertebrates, at some stage of their development are actually trimodal breathers that use various combinations of respiratory surfaces to breath both water (skin and/or gill) and air (skin and/or lung). The present review examines the evolutionary implications of air-breathing organs in fishes and the morphology of the peripheral receptors and the neurotransmitter content of the cells involved in the control of air-breathing. Control of breathing, whether gill ventilation or air-breathing, is influenced by feedback from peripheral and/or central nervous system receptors that respond to changes in PO2, PCO2 and/or pH. Although the specific chemoreceptors mediating the respiratory reflexes have not been conclusively identified, studies in water-breathing teleosts have implicated the neuroepithelial cells (NECs) existing in gill tissues as the O2 sensitive chemoreceptors that initiate the cardiorespiratory reflexes in aquatic vertebrates. Some of the air-breathing fishes, such as Protopterus, Polypterus and Amia have been shown to have NECs in the gills and/or lungs, although the role of these receptors and their innervation in the control of breathing is not known. NECs have been also reported in the specialized respiratory epithelia of accessory respiratory organs (ARO's) of some catfish species and in the gill and skin of the mudskipper Periophthalmodon schlosseri. Unlike teleosts matching an O2-oriented ventilation to ambient O2 levels, lungfishes have central and peripheral H+/CO2 receptors that control the acid-base status of the blood.
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Affiliation(s)
- Giacomo Zaccone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168, Messina, Italy.
| | - Eugenia Rita Lauriano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy.
| | - Gioele Capillo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Michał Kuciel
- Poison Information Centre, Department of Toxicology and Environmental Disease, Faculty of Medicine, Jagiellonian University, Kopernika 15, 30-501 Kraków, Poland.
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Vialle RA, de Souza JES, Lopes KDP, Teixeira DG, Alves Sobrinho PDA, Ribeiro-dos-Santos AM, Furtado C, Sakamoto T, Oliveira Silva FA, Herculano Corrêa de Oliveira E, Hamoy IG, Assumpção PP, Ribeiro-dos-Santos Â, Santos Lima JPM, Seuánez HN, de Souza SJ, Santos S. Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades. Genome Biol Evol 2018; 10:2366-2379. [PMID: 29982381 PMCID: PMC6143160 DOI: 10.1093/gbe/evy130] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2018] [Indexed: 01/14/2023] Open
Abstract
The Pirarucu (Arapaima gigas) is one of the world's largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.
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Affiliation(s)
- Ricardo Assunção Vialle
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Katia de Paiva Lopes
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Diego Gomes Teixeira
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | | | - André M Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Carolina Furtado
- Programa de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Tetsu Sakamoto
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | - Igor Guerreiro Hamoy
- Laboratório de Genética Aplicada, Universidade Federal Rural da Amazônia, Belém, PA, Brazil
| | | | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| | - João Paulo Matos Santos Lima
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Héctor N Seuánez
- Programa de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Sandro José de Souza
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
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56
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Anoop VK, Dahanukar N, Philip S, Thomas L, Raghavan R. Phylogeny of the hillstream loach genus Mesonoemacheilus reveals widespread diversification through ancient drainage connections in the Western Ghats Biodiversity Hotspot. Mol Phylogenet Evol 2018; 129:77-84. [PMID: 30153500 DOI: 10.1016/j.ympev.2018.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/09/2018] [Accepted: 08/22/2018] [Indexed: 11/16/2022]
Abstract
Rivers draining the Western Ghats (WG) mountain ranges in peninsular India harbor an exceptionally diverse, unique and evolutionarily distinct assemblage of lower vertebrates with high levels of endemism, attributed to their evolution and potentially long history of isolation during the Late Cretaceous or Early Tertiary. A molecular phylogeny of hillstream loaches of the genus Mesonoemacheilus endemic to the WG revealed the presence of four clades which we designate as 'species groups'. A consensus of various species delimitation methods indicates the likelihood of 'at least' seven more undescribed species within Mesonoemacheilus. Molecular clock analysis dates the basal clade around 38 mya in the Paleogene, and subsequent diversification in the Neogene and Quaternary periods resulting in the current genetic diversity. Biogeographic analysis suggests that vicariance events which separated the rivers on either side of the two geological barriers/gaps, the Palghat and Shencottah, in the Neogene, as well as range contractions and cladogenetic events contributed to the current patterns of diversity and distribution of this genus. Our results also provide preliminary indications on the interconnections and faunal exchange between historical river drainages in the WG region.
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Affiliation(s)
- V K Anoop
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi 682 506, Kerala, India
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research (IISER), G1 Block, Dr. Homi Bhabha Road, Pashan, Pune 411 008, Maharashtra, India
| | - Siby Philip
- Department of Zoology, Nirmalagiri College, Kannur 670 701, Kerala, India
| | - Liju Thomas
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi 682 506, Kerala, India; Department of Zoology, Nirmalagiri College, Kannur 670 701, Kerala, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi 682 506, Kerala, India.
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Rivera-Rivera CJ, Montoya-Burgos JI. Back to the roots: Reducing evolutionary rate heterogeneity among sequences gives support for the early morphological hypothesis of the root of Siluriformes (Teleostei: Ostariophysi). Mol Phylogenet Evol 2018; 127:272-279. [PMID: 29885935 DOI: 10.1016/j.ympev.2018.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 11/15/2022]
Abstract
Catfishes (Teleostei: Siluriformes) are a highly diverse order within Ostariophysi that is distributed worldwide. At the base of this clade emerge three lineages with well-defined monophylies: Diplomystidae, Loricarioidei, and Siluroidei. Morphological phylogeny studies place the Diplomystidae as the earliest branching of these three lineages, but studies based on molecular phylogenetics consistently find the fast-evolving Loricarioidei instead. The high lineage evolutionary rate heterogeneity in this order and the fact that the lineage placed closest to the root in the molecular phylogenies is fast evolving, including many long branches, raises the possibility that the discrepancy between morphological and molecular phylogenies may be the result of a long branch attraction inference artifact. We test this hypothesis by using a 10-gene dataset to evaluate the arrangement of the three main siluriform lineages, and apply the LS3 and LS4 taxon sequence subsampling methods to reduce evolutionary rate heterogeneity among lineages. The initial and complete dataset supports the basal branching of Loricarioidei as in all previous molecular phylogenies, but once lineage rate heterogeneity is reduced with LS3 or LS4 through the removal of sequences disrupting homogeneity, the phylogeny shows Diplomystidae as the earliest branching group, with high supports, as proposed by morphological phylogeny. The result obtained with LS3, however, introduces the misplacement of one of the species with the highest amount of missing data, Scoloplax sp. Because the sequence sub-selection criterion of LS4 has been optimized to reduce data removal, the phylogeny resulting from the LS4-processed data is in agreement with the known intra-lineage relationships in addition to supporting the morphologically-based rooting hypothesis. Our results are the first instance in which a consensus between molecular and morphological phylogeny is reached concerning the root of this order.
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Affiliation(s)
- Carlos J Rivera-Rivera
- Department of Genetics and Evolution, University of Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland.
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58
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Rivera-Rivera CJ, Montoya-Burgos JI. Trunk dental tissue evolved independently from underlying dermal bony plates but is associated with surface bones in living odontode-bearing catfish. Proc Biol Sci 2018; 284:rspb.2017.1831. [PMID: 29046381 PMCID: PMC5666107 DOI: 10.1098/rspb.2017.1831] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/15/2017] [Indexed: 11/30/2022] Open
Abstract
Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge. To address this question, we focus on Loricarioidei: an extant, highly diverse group of catfish whose species all have odontodes. We examined the location and cover of odontodes and trunk dermal bony plates for all six loricarioid families and 17 non-loricarioid catfish families for comparison. We inferred the phylogeny of Loricarioidei using a new 10-gene dataset, eight time-calibration points, and noise-reduction techniques. Based on this phylogeny, we reconstructed the ancestral states of odontode and bony plate cover, and find that trunk odontodes emerged before dermal bony plates in Loricarioidei. Yet we discovered that when bony plates are absent, other surface bones are always associated with odontodes, suggesting a link between osteogenic and odontogenic developmental pathways, and indicating a remarkable trunk odontogenic potential in Loricarioidei.
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Affiliation(s)
- Carlos J Rivera-Rivera
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland .,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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Evolutionary emergence of the rac3b/ rfng/ sgca regulatory cluster refined mechanisms for hindbrain boundaries formation. Proc Natl Acad Sci U S A 2018; 115:E3731-E3740. [PMID: 29610331 DOI: 10.1073/pnas.1719885115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b/rfng/sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis-regulatory interactions. By combining 4C-seq, ATAC-seq, transgenesis, and CRISPR-induced deletions, we characterized this regulatory domain, identifying hindbrain boundary-specific cis-regulatory elements. Our results suggest that the capacity of boundaries to act as an elastic mesh for segregating rhombomeric cells evolved by cooption of critical genes to a novel regulatory block, refining the mechanisms for hindbrain segmentation.
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60
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Carriero MM, Henrique-Silva F, Caetano AR, Lobo FP, Alves AL, Varela ES, Del Collado M, Moreira GSA, Maia AAM. Characterization and gene expression analysis of pacu (Piaractus mesopotamicus) inducible nitric oxide synthase (iNOS) following Aeromonas dhakensis infection. FISH & SHELLFISH IMMUNOLOGY 2018; 74:94-100. [PMID: 29277697 DOI: 10.1016/j.fsi.2017.12.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/01/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
Nitric oxide (NO) is an important effector molecule which is involved in a myriad of biological processes, including immune responses against pathogens such as parasites, virus and bacteria. During the inflammatory processes in vertebrates, NO is produced by the inducible nitric oxide synthase (iNOS) enzyme in practically all nucleated cells to suppress or kill intracellular pathogens. The aim of the present study was to characterize the full coding region of the iNOS gene of pacu (Piaractus mesopotamicus), an economically and ecologically important South American fish species, and to analyze mRNA expression levels following intraperitoneal infection with the pathogenic bacterium Aeromonas dhakensis by means of quantitative real time PCR (qPCR). The results showed that the pacu iNOS transcript is 3237 bp in length, encoding a putative protein composed of 1078 amino acid residues. The amino acid sequence showed similarities ranging from 69.03% to 94.34% with other teleost fish and 57.70% with the human iNOS, with all characteristic domains and cofactor binding sites of the enzyme detected. Phylogenetic analysis showed that the iNOS from the red-bellied piranha, another South American characiform, was the closest related sequence to the pacu iNOS. iNOS transcripts were constitutively detected in the liver, spleen and head kidney, and there was a significant upregulation in the liver and spleen at 12, 24 and 48 h after infection with A. dhakensis. No significant variations were observed in the head kidney during the periods analyzed. These results show that iNOS expression was induced by A. dhakensis infection and suggest that this enzyme may be involved in the response to this bacterium in pacu.
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Affiliation(s)
- Mateus M Carriero
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil; Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
| | - Flávio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | | | | | | | - Maite Del Collado
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Gabriel S A Moreira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Antonio A M Maia
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
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Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME. Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes. Syst Biol 2018; 66:881-895. [PMID: 28334176 DOI: 10.1093/sysbio/syx038] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/24/2016] [Indexed: 12/30/2022] Open
Abstract
Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes-one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation sequencing; UCEs.].
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Affiliation(s)
- Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Fernando Alda
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - William B Ludt
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Caleb D Mcmahan
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,The Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - James S Albert
- Department of Biology, University of Louisiana, Lafayette, LA 70504, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Laurie Sorenson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
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62
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Xu GH, Ma XY. Redescription and phylogenetic reassessment of Asialepidotus shingyiensis (Holostei: Halecomorphi) from the Middle Triassic (Ladinian) of China. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Guang-Hui Xu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Xin-Ying Ma
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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63
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Dai W, Zou M, Yang L, Du K, Chen W, Shen Y, Mayden RL, He S. Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages. Sci Rep 2018; 8:205. [PMID: 29317769 PMCID: PMC5760653 DOI: 10.1038/s41598-017-18432-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes. Based on a selection of 125 nuclear genes screened from single-gene maximum likelihood (ML) analyses and sequence bias testing, well-established relationships among Otocephala were reconstructed. We suggested that Gymnotiformes are more closely related to Characiformes than to Siluriformes and Characiformes are possibly paraphyletic. We also estimated that Otocephala originated in the Early-Late Jurassic, which postdates most previous estimations, and hypothesized scenarios of the early historical biogeographies of major otocephalan lineages.
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Affiliation(s)
- Wei Dai
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Ming Zou
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Beijing, 430070, People's Republic of China
| | - Liandong Yang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Kang Du
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Weitao Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Yanjun Shen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Richard L Mayden
- Department of Biology, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
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64
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Nakamura G, Vicentin W, Súarez YR. Functional and phylogenetic dimensions are more important than the taxonomic dimension for capturing variation in stream fish communities. AUSTRAL ECOL 2017. [DOI: 10.1111/aec.12529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel Nakamura
- Programa de Pós-graduação em Ecologia; Universidade Federal do Rio Grande do Sul; A. Bento Gonçalves 9500 CP 15007 Porto Alegre Brazil
| | - Wagner Vicentin
- Programa de Pós-graduação em Ecologia e Conservação; Universidade Federal de Mato Grosso do Sul; Campo Grande Brazil
| | - Yzel Rondon Súarez
- Centro Integrado de Análise e Monitoramento Ambiental (CInAM); Universidade Estadual de Mato Grosso do Sul; Dourados Brazil
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65
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66
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de Pinna M, Zuanon J, Rapp Py-Daniel L, Petry P. A new family of neotropical freshwater fishes from deep fossorial Amazonian habitat, with a reappraisal of morphological characiform phylogeny (Teleostei: Ostariophysi). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Jansen Zuanon
- Instituto Nacional de Pesquisas da Amazônia– COBIO, Coleção de Peixes, Brazil
| | | | - Paulo Petry
- The Nature Conservancy, Latin American Conservation Region, USA
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67
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Gross JB, Weagley J, Stahl BA, Ma L, Espinasa L, McGaugh SE. A local duplication of the Melanocortin receptor 1 locus in Astyanax. Genome 2017; 61:254-265. [PMID: 28738163 DOI: 10.1139/gen-2017-0049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a ∼820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share ∼89% sequence similarity and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus and if this novel copy number variant may have adaptive significance for the Astyanax lineage.
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Affiliation(s)
- Joshua B Gross
- a Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - James Weagley
- b Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Bethany A Stahl
- a Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Li Ma
- a Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Luis Espinasa
- c School of Science, Marist College, Poughkeepsie, NY 12601, USA
| | - Suzanne E McGaugh
- b Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
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68
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Betancur-R R, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, Lecointre G, Ortí G. Phylogenetic classification of bony fishes. BMC Evol Biol 2017; 17:162. [PMID: 28683774 PMCID: PMC5501477 DOI: 10.1186/s12862-017-0958-3] [Citation(s) in RCA: 420] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/26/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. RESULTS The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. CONCLUSIONS This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras, P.O. Box 23360, San Juan, PR 00931 USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Edward O. Wiley
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS USA
- Sam Houston State Natural History Collections, Sam Houston State University, Huntsville, Texas USA
| | - Gloria Arratia
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS USA
| | - Arturo Acero
- Universidad Nacional de Colombia sede Caribe, Cecimar, El Rodadero, Santa Marta, Magdalena Colombia
| | - Nicolas Bailly
- FishBase Information and Research Group, Los Baños, Philippines
| | - Masaki Miya
- Department Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Guillaume Lecointre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Department of Biology, The George Washington University, Washington, DC USA
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69
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Moreira DA, Buckup PA, Furtado C, Val AL, Schama R, Parente TE. Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics. BMC Genomics 2017; 18:345. [PMID: 28472937 PMCID: PMC5418769 DOI: 10.1186/s12864-017-3709-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/19/2017] [Indexed: 01/11/2023] Open
Abstract
Background The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses. Results Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3′ end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group. Conclusions Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3709-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Andrade Moreira
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil.,Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Paulo Andreas Buckup
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro (UFRJ), Quinta da Boa Vista, Rio de Janeiro, RJ, Brasil
| | - Carolina Furtado
- Unidade de Genômica, Instituto Nacional do Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, Brasil
| | - Adalberto Luis Val
- Laboratório de Ecofisiologia e Evolução Molecular, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Manaus, Brasil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Thiago Estevam Parente
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil. .,Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil.
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70
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Testing for the Occurrence of Selective Episodes During the Divergence of Otophysan Fishes: Insights from Mitogenomics. J Mol Evol 2017; 84:162-173. [PMID: 28378191 DOI: 10.1007/s00239-017-9790-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/05/2016] [Indexed: 10/19/2022]
Abstract
How natural selection shapes biodiversity constitutes a topic of renewed interest during the last few decades. The division Otophysi comprises approximately two-thirds of freshwater fish diversity and probably underwent an extensive adaptive radiation derived from a single invasion of the supercontinent Pangaea, giving place to the evolution of the main five Otophysan lineages during a short period of time. Little is known about the factors involved in the processes that lead to lineage diversification among this group of fishes and identifying directional selection acting over protein-coding genes could offer clues about the processes acting on species diversification. The main objective of this study was to explore the otophysan mitochondrial genome evolution, in order to account for the possible signatures of selective events in this lineage, and to explore for the functional connotations of these molecular substitutions. Mainly, three different approaches were used: the "ω-based" BS-REL and MEME methods, implemented in the DATAMONKEY web server, and analysis of selection on amino acid properties, implemented in the software TreeSAAP. We found evidence of selective episodes along several branches of the evolutionary history of othophysan fishes. Analyses carried out using the BS-REL algorithm suggest episodic diversifying selection at basal branches of the otophysan lineage, which was also supported by analyses implemented in MEME and TreeSAAP. These results suggest that throughout the Siluriformes radiation, an important number of adaptive changes occurred in their mitochondrial genome. The metabolic consequences and ecological correlates of these molecular substitutions should be addressed in future studies.
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71
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Hirt MV, Arratia G, Chen WJ, Mayden RL, Tang KL, Wood RM, Simons AM. Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- M. Vincent Hirt
- University of Minnesota, Ecology, Evolution, and Behavior Graduate Program, St. Paul, MN 55108, USA
- University of Minnesota, Bell Museum of Natural History, Minneapolis, MN 55455, USA
| | - Gloria Arratia
- Biodiversity Research Center, University of Kansas, Lawrence, KS 66045, USA
| | - Wei-Jen Chen
- National Taiwan University, Institute of Oceanography, Taipei 10617, Taiwan
| | - Richard L. Mayden
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Kevin L. Tang
- Department of Biology, University of Michigan-Flint, Flint, MI 48502, USA
| | - Robert M. Wood
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Andrew M. Simons
- University of Minnesota, Bell Museum of Natural History, Minneapolis, MN 55455, USA
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN 55108, USA
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72
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Parente TE, Moreira DA, Magalhães MGP, de Andrade PCC, Furtado C, Haas BJ, Stegeman JJ, Hahn ME. The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families. MARINE POLLUTION BULLETIN 2017; 115:352-361. [PMID: 28062095 PMCID: PMC5310677 DOI: 10.1016/j.marpolbul.2016.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 06/02/2023]
Abstract
Pterygoplichthys is a genus of related suckermouth armoured catfishes native to South America, which have invaded tropical and subtropical regions worldwide. Physiological features, including an augmented resistance to organic xenobiotics, may have aided their settlement in foreign habitats. The liver transcriptome of Pterygoplichthys anisitsi was sequenced and used to characterize the diversity of mRNAs potentially involved in the responses to natural and anthropogenic chemicals. In total, 66,642 transcripts were assembled. Among the identified defensome genes, cytochromes P450 (CYP) were the most abundant, followed by sulfotransferases (SULT), nuclear receptors (NR) and ATP binding cassette transporters (ABC). A novel expansion in the CYP2Y subfamily was identified, as well as an independent expansion of the CYP2AAs. Two expansions were also observed among SULT1. Thirty-two transcripts were classified into twelve subfamilies of NR, while 21 encoded ABC transporters. The diversity of defensome transcripts sequenced herein could contribute to this species' resistance to organic xenobiotics.
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Affiliation(s)
- Thiago E Parente
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil; Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil; Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA.
| | - Daniel A Moreira
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil
| | - Maithê G P Magalhães
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil
| | - Paula C C de Andrade
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil
| | - Carolina Furtado
- Unidade de Genômica, Instituto Nacional do Cancer (INCA), Rio de Janeiro 20230-130, Brasil
| | - Brian J Haas
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John J Stegeman
- Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA
| | - Mark E Hahn
- Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA
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Villela LCV, Alves AL, Varela ES, Yamagishi MEB, Giachetto PF, da Silva NMA, Ponzetto JM, Paiva SR, Caetano AR. Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree. Genetica 2017; 145:51-66. [DOI: 10.1007/s10709-016-9945-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 12/22/2016] [Indexed: 01/08/2023]
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74
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Arcila D, Ortí G, Vari R, Armbruster JW, Stiassny MLJ, Ko KD, Sabaj MH, Lundberg J, Revell LJ, Betancur-R R. Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life. Nat Ecol Evol 2017; 1:20. [PMID: 28812610 DOI: 10.1038/s41559-016-0020] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/25/2016] [Indexed: 12/21/2022]
Abstract
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary histories among early otophysan lineages. By contrast, GGI revealed that the vast majority of gene genealogies supports a single tree topology grounded on morphology that was not obtained by previous molecular studies. We also reanalysed published data sets for exemplary groups with recalcitrant resolution to assess the power of this approach. GGI supports the notion that ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance.
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Affiliation(s)
- Dahiana Arcila
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington DC 20052, USA.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 159, Washington DC 20013, USA
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington DC 20052, USA
| | - Richard Vari
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 159, Washington DC 20013, USA
| | | | - Melanie L J Stiassny
- Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024, USA
| | - Kyung D Ko
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington DC 20052, USA
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103, USA
| | - John Lundberg
- Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103, USA
| | - Liam J Revell
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts 02125, USA
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 159, Washington DC 20013, USA.,Department of Biology, University of Puerto Rico - Río Piedras, PO Box 23360, San Juan, Puerto Rico
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75
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Sales CF, Silva RF, Amaral MGC, Domingos FFT, Ribeiro RIMA, Thomé RG, Santos HB. Comparative histology in the liver and spleen of three species of freshwater teleost. NEOTROPICAL ICHTHYOLOGY 2017. [DOI: 10.1590/1982-0224-20160041] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT We describe and compare the histology of liver and spleen ofGeophagus brasiliensis (Perciformes), Hypostomus francisci (Siluriformes) and Hoplias aff. malabaricus (Characiformes), tropical freshwater fishes. InG. brasiliensisandH. aff. malabaricusthe hepatocytes were arranged in tubular form whereas in H. franciscithey cord-like. In all species, hepatocytes presented glycogen, but in G. brasiliensis and H. aff. malabaricus they showed strong stained for hemossiderin in the cytoplasm. InG. brasiliensis and H. aff. malabaricus, melanomacrophage centres (MMCs) were associated to hepatic structures and only in G. brasiliensis was observed intrahepatic exocrine pancreas. The spleen, in all species, was characterized by red and white pulp without boundary between the two regions, but only in H. francisci was recorded nodular organization in splenic parenchyma. The G. brasiliensisandH. aff. malabaricuspresented in the white pulp MMCs linked mainly to ellipsoids. Besides, we observed large MMCs in the spleen in relation to liver of G. brasiliensis and H. aff. malabaricus. In liver, highest values of reticular fibers and collagen were observed inG. brasiliensis. In spleen, highest values of reticular fibers and collagen were recorded inH. aff. malabaricusandH. francisci, respectively. Histological differences confirm the hypothesis that the phylogenetic distance is reflected in liver and spleen.
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76
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Behera BK, Baisvar VS, Kumari K, Rout AK, Pakrashi S, Paria P, Das A, Rao AR, Rai A. The complete mitochondrial genome of the Asian stinging catfish , Heteropneustes fossilis (Siluriformes, Heteropneustidae) and its comparison with other related fish species. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:804-805. [PMID: 33473634 PMCID: PMC7799967 DOI: 10.1080/23802359.2016.1219628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The complete mitogenome of Heteropneustes fossilis is described using Ion Torrent (PGM sequencer), which showed it was 16,489 bp in size comprising 13 mRNAs, 22 tRNAs, 2 rRNA genes, and 858 bp as D-Loop control region, along with gene order and organization, being similar to most of the other related Siluriformes fish mitogenome of NCBI databases. The 20 RNAs were packed into a typical cloverleaf structure. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of H. fossilis mitogenome reported earlier and also would be helpful in understanding the population genetics, phylogenetics, and evolution of catfishes.
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Affiliation(s)
- Bijay Kumar Behera
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Vishwamitra Singh Baisvar
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Kavita Kumari
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Ajaya Kumar Rout
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Sudip Pakrashi
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Prasenjet Paria
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Abhishek Das
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - A R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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77
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Kappas I, Vittas S, Pantzartzi CN, Drosopoulou E, Scouras ZG. A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes). PLoS One 2016; 11:e0166988. [PMID: 27907107 PMCID: PMC5132296 DOI: 10.1371/journal.pone.0166988] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.
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Affiliation(s)
- Ilias Kappas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Spiros Vittas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysoula N. Pantzartzi
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elena Drosopoulou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Zacharias G. Scouras
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
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78
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Morrow JM, Lazic S, Dixon Fox M, Kuo C, Schott RK, de A Gutierrez E, Santini F, Tropepe V, Chang BSW. A second visual rhodopsin gene, rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes. ACTA ACUST UNITED AC 2016; 220:294-303. [PMID: 27811293 DOI: 10.1242/jeb.145953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022]
Abstract
Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene; however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localized expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1 We also expressed, purified and characterized Rh1-2, including investigation of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we found the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to that of the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressure to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1 These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.
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Affiliation(s)
- James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Savo Lazic
- Department of Molecular Genetics, University of Toronto, Toronto, Canada, M5S 1A8
| | - Monica Dixon Fox
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Claire Kuo
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Francesco Santini
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada, M5T 3A9.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5 .,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
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79
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Carvalho DC, Perini VDR, Bastos AS, Costa IRD, Luz RK, Furtado C, Prosdocimi F. The complete mitochondrial genome of the threatened Neotropical catfish Lophiosilurus alexandri (Silurifomes: Pseudopimelodidae) and phylogenomic analysis indicate monophyly of Pimelodoidea. Genet Mol Biol 2016; 39:674-677. [PMID: 27648766 PMCID: PMC5127154 DOI: 10.1590/1678-4685-gmb-2016-0007] [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: 01/19/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
Lophiosilurus alexandri is an endemic catfish from the São Francisco River Basin (Brazil) popularly known as pacamã, which has economic potential for aquaculture farming. The mitochondrial genome was sequenced for the threatened Neotropical catfish L. alexandri. Assembly into scaffolds using MIRA and MITObim software produced the whole, circularized mitochondrial genome, which comprises 16,445 bp and presents the typical gene arrangement of Teleostei mitochondria. A phylogenomic analysis was performed after the concatenation of all proteins obtained from whole mitogenomes of 20 Siluriformes and two outgroups. The results confirmed the monophyly of nine families of catfishes and also clustered L. alexandri as a sister group to the family Pimelodidae, thus confirming the monophyly of the superfamily Pimelodoidea. This is the first mitochondrial phylogenomics study for Pimelodoidea and the first mitogenome described for the Pseudopimelodidae family, representing an important resource for phylogeography, evolutionary biology, and conservation genetics studies in Neotropical fishes.
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Affiliation(s)
- Daniel Cardoso Carvalho
- Laboratório de Genética da Conservação, Programa de Pós-Graduação em Biologia dos Vertebrados, Pontifícia Universidade Católica de Minas Gerais (PUC Minas), Belo Horizonte, MG, Brazil
| | - Violeta da Rocha Perini
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Alex Schomaker Bastos
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Igor Rodrigues da Costa
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ronald Kennedy Luz
- Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais (UFMG, Belo Horizonte, MG, Brazil
| | | | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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80
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Mirande JM. Combined phylogeny of ray-finned fishes (Actinopterygii) and the use of morphological characters in large-scale analyses. Cladistics 2016; 33:333-350. [DOI: 10.1111/cla.12171] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 01/27/2023] Open
Affiliation(s)
- Juan Marcos Mirande
- Unidad Ejecutora Lillo (UEL, Fundación Miguel Lillo-CONICET); San Miguel de Tucumán 4000 Argentina
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81
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Stange M, Aguirre-Fernández G, Cooke RG, Barros T, Salzburger W, Sánchez-Villagra MR. Evolution of opercle bone shape along a macrohabitat gradient: species identification using mtDNA and geometric morphometric analyses in neotropical sea catfishes (Ariidae). Ecol Evol 2016; 6:5817-30. [PMID: 27547357 PMCID: PMC4983594 DOI: 10.1002/ece3.2334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/29/2016] [Indexed: 12/19/2022] Open
Abstract
Transitions between the marine and freshwater macrohabitat have occurred repeatedly in the evolution of teleost fishes. For example, ariid catfishes have moved from freshwater to marine environments, and vice versa. Opercles, a skeletal feature that has been shown to change during such transitions, were subjected to 2D geometric morphometric analyses in order to investigate evolutionary shape changes during habitat transition in ariid catfishes and to test the influence of habitat on shape changes. A mtDNA marker, which proved useful in previous studies, was used to verify species identities. It greatly improved the assignment of specimens to a species, which are difficult to assign by morphology alone. The application of a mtDNA marker confirmed the occurrence of Notarius biffi in Central America, South of El Salvador. Molecular identification together with principal component analysis (PCA) and further morphological inspection of neurocrania indicated the existence of a cryptic species within Bagre pinnimaculatus. Principal component (PC) scores of individual specimens clustered in morphospace by genus rather than by habitat. Strong phylogenetic structure was detected using a permutation test of PC scores of species means on a phylogenetic tree. Calculation of Pagel's λ suggested that opercle shape evolved according to a Brownian model of evolution. Yet canonical variate analysis (CVA) conducted on the habitat groups showed significant differences in opercle shapes among freshwater and marine species. Overall, opercle shape in tropical American Ariidae appears to be phylogenetically constrained. This verifies the application of opercle shape as a taxonomic tool for species identification in fossil ariid catfishes. At the same time, adaptation to freshwater habitats shows characteristic opercle shape trajectories in ariid catfishes, which might be used to detect habitat preferences in fossils.
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Affiliation(s)
- Madlen Stange
- Palaeontological Institute and Museum University of Zurich Karl-Schmid-Strasse 48006 Zurich Switzerland; Zoological Institute University of Basel Vesalgasse 14051 Basel Switzerland
| | - Gabriel Aguirre-Fernández
- Palaeontological Institute and Museum University of Zurich Karl-Schmid-Strasse 4 8006 Zurich Switzerland
| | - Richard G Cooke
- Smithsonian Tropical Research Institute MRC 0580-08 Apartado 0843-03092 Panama Republic of Panama
| | - Tito Barros
- Museo de Biología Facultad Experimental de Ciencias La Universidad del Zulia Apartado Postal 526 Maracaibo 4011 Estado Zulia Venezuela
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Marcelo R Sánchez-Villagra
- Palaeontological Institute and Museum University of Zurich Karl-Schmid-Strasse 4 8006 Zurich Switzerland
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82
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Wang Y, Shen Y, Feng C, Zhao K, Song Z, Zhang Y, Yang L, He S. Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude. Sci Rep 2016; 6:29690. [PMID: 27417983 PMCID: PMC4945904 DOI: 10.1038/srep29690] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/23/2016] [Indexed: 01/11/2023] Open
Abstract
Tibetan loaches are the largest group of Tibetan fishes and are well adapted to the Tibetan Plateau. To investigate the origin of Tibetan loaches and their adaptations to the Tibetan Plateau, we determined 32 complete mitochondrial genomes that included 29 Tibetan loach species, two Barbatula species and Schistura longus. By combining these newly determined sequences with other previously published mitochondrial genomes, we assembled a large mitogenomic data set (11,433 bp) of 96 species in the superfamily Cobitoidea, to investigate the phylogenetic status of the genus Triplophysa. The resulting phylogeny strongly supported that the genus Triplophysa forms a monophyletic group within Nemacheilidae. Our molecular dating time suggests that the lineage leading to the Tibetan loaches and other loaches diverged approximately 23.5 Ma, which falls within the period of recent major uplifts of the Tibetan Plateau in the Early Miocene. Selection analyses revealed that the mitochondrial protein-coding genes of Tibetan loaches have larger ratios of nonsynonymous to synonymous substitutions than do those of non-Tibetan loaches, indicating that Tibetan loaches accumulated more nonsynonymous mutations than non-Tibetan loaches and exhibited rapid evolution. Two positively selected sites were identified in the ATP8 and ND1 genes.
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Affiliation(s)
- Ying Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenguang Feng
- University of the Chinese Academy of Sciences, Beijing 100049, PR China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yanping Zhang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou 730030, PR China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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83
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Elbassiouny AA, Schott RK, Waddell JC, Kolmann MA, Lehmberg ES, Van Nynatten A, Crampton WGR, Chang BSW, Lovejoy NR. Mitochondrial genomes of the South American electric knifefishes (Order Gymnotiformes). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:401-403. [PMID: 33473497 PMCID: PMC7799549 DOI: 10.1080/23802359.2016.1174090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Three complete mitochondrial genomes of South American electric fishes (Gymnotiformes), derived from high-throughput RNA sequencing (RNA-Seq), are reported herein. We report the complete mitochondrial genome of the bluntnose knifefish Brachyhypopomus n.sp. VERD, determined from newly sequenced data. We also provide the complete mitochondrial genomes for Sternopygus arenatus and the electric eel Electrophorus electricus, assembled from previously published transcriptome data. The mitochondrial genomes of Brachyhypopomus n.sp. VERD, Sternopygus arenatus and Electrophorus electricus have 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs and 22 transfer RNAs, and are 16,547, 16,667 and 16,906 bp in length, respectively. Phylogenetic analysis of the eight available mitochondrial genomes of gymnotiform fishes shows Apteronotus to be the sister lineage of other gymnotiformes, contradicting the “Sinusoidea” hypothesis that Apteronotidae and Sternopygidae are sister taxa.
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Affiliation(s)
- Ahmed A Elbassiouny
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Joseph C Waddell
- Department of Biology, University of Central Florida, Orlando, FL, USA
| | - Matthew A Kolmann
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Emma S Lehmberg
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Alexander Van Nynatten
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nathan R Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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84
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Mei Q, Sadovy Y, Dvornyk V. Molecular evolution of cryptochromes in fishes. Gene 2015; 574:112-20. [PMID: 26238701 DOI: 10.1016/j.gene.2015.07.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 07/03/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022]
Abstract
Circadian rhythmicity is an endogenous biological cycle of about 24h, which exists in cyanobacteria and fungi, plants and animals. Circadian rhythms improve the adaptability of organisms in both constant and changing environments. The cryptochrome (CRY) is a key element of the circadian system in various animal groups including fishes. We studied evolution of cryptochromes in the phylogenetically and ecologically diverse fish taxa. The phylogenetic tree of fish Cry features two major clades: Cry1 and Cry2. Teleosts possess extra copies of Cry1 due to the genome duplication, which resulted in 3 main paralogous subfamilies (1A, 1B and 1C). Cry1 experienced further diversification through additional duplications in some taxa. 1A of Cry1 is more conserved than the other paralogs (dN=0.010 ± 0.003, π=0.119 ± 0.058). The analysis of selection indicated that, while the Cry homologs in fish evolved under the different levels of selection pressure, strong purifying selection (average ω=0.017) dominated in their evolution.
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Affiliation(s)
- Qiming Mei
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Yvonne Sadovy
- School of Biological Sciences, University of Hong Kong, Pokfulam Rd., Hong Kong, SAR, People's Republic of China
| | - Volodymyr Dvornyk
- School of Biological Sciences, University of Hong Kong, Pokfulam Rd., Hong Kong, SAR, People's Republic of China; Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia.
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85
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Moreira DA, Furtado C, Parente TE. Mitochondrial transcripts and associated heteroplasmies of Ancistrus spp. (Siluriformes: Loricariidae). Data Brief 2015; 5:513-5. [PMID: 26629496 PMCID: PMC4631843 DOI: 10.1016/j.dib.2015.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 10/28/2022] Open
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86
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Moreira DA, Furtado C, Parente TE. The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae). Gene 2015; 573:171-5. [DOI: 10.1016/j.gene.2015.08.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/20/2015] [Accepted: 08/28/2015] [Indexed: 11/27/2022]
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87
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Myllykoski M, Seidel L, Muruganandam G, Raasakka A, Torda AE, Kursula P. Structural and functional evolution of 2',3'-cyclic nucleotide 3'-phosphodiesterase. Brain Res 2015; 1641:64-78. [PMID: 26367445 DOI: 10.1016/j.brainres.2015.09.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 02/06/2023]
Abstract
2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an abundant membrane-associated enzyme within the vertebrate myelin sheath. While the physiological function of CNPase still remains to be characterized in detail, it is known - in addition to its in vitro enzymatic activity - to interact with other proteins, small molecules, and membrane surfaces. From an evolutionary point of view, it can be deduced that CNPase is not restricted to myelin-forming cells or vertebrate tissues. Its evolution has involved gene fusion, addition of other small segments with distinct functions, such as membrane attachment, and possibly loss of function at the polynucleotide kinase-like domain. Currently, it is unclear whether the enzymatic function of the conserved phosphodiesterase domain in vertebrate myelin has a physiological role, or if CNPase could actually function - like many other classical myelin proteins - in a more structural role. This article is part of a Special Issue entitled SI: Myelin Evolution.
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Affiliation(s)
- Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Leonie Seidel
- Centre for Bioinformatics, University of Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | | | - Arne Raasakka
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Aapistie 7, 90220 Oulu, Finland; Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Andrew E Torda
- Centre for Bioinformatics, University of Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Aapistie 7, 90220 Oulu, Finland; German Electron Synchrotron, Notkestraße 85, 22607 Hamburg, Germany; Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.
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88
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A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco). PLoS One 2015; 10:e0131504. [PMID: 26114548 PMCID: PMC4482592 DOI: 10.1371/journal.pone.0131504] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 06/03/2015] [Indexed: 11/25/2022] Open
Abstract
Body colours are important and striking features for individual survival and reproductive success, in particular in vertebrates where mating behaviour and mate preference may be strongly influenced by non-normal phenotypes. Pigmentation disorders may be generated by disruption of one or many independent genes as well as by environmental factors. The first discovery of albino yellow catfish (Pelteobagrus fulvidraco Richardson) with golden skin colour from fish farms in China provides us valuable material to study the molecular mechanism underlying the abnormalities of pigmentation. In this study, transcriptome sequencing of fin tissues corresponding to the distinct body colours, wild type and mutant albino yellow catfish, were performed using Illumina sequencing technology. Based on next-generation sequencing technology and de novo assembly, we generated a transcriptome of P. fulvidraco. A number of genes differentially expressed between the wild types and albinos were identified, suggesting their contribution to the different phenotypes and fitness. However, non-synonymous mutations result from single nucleotide substitutions residing in coding regions may not contribute to such differences. Based on the high-throughput expression data generated for the two different types of P. fulvidraco, we found that alterations of expression pattern may be more common than non-synonymous mutations. The transcriptome of P. fulvidraco will be an invaluable resource for subsequent comparative genomics and evolutionary analyses of this economically important fish.
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89
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Guinot G, Cavin L. 'Fish' (Actinopterygii and Elasmobranchii) diversification patterns through deep time. Biol Rev Camb Philos Soc 2015; 91:950-981. [PMID: 26105527 DOI: 10.1111/brv.12203] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
Actinopterygii (ray-finned fishes) and Elasmobranchii (sharks, skates and rays) represent more than half of today's vertebrate taxic diversity (approximately 33000 species) and form the largest component of vertebrate diversity in extant aquatic ecosystems. Yet, patterns of 'fish' evolutionary history remain insufficiently understood and previous studies generally treated each group independently mainly because of their contrasting fossil record composition and corresponding sampling strategies. Because direct reading of palaeodiversity curves is affected by several biases affecting the fossil record, analytical approaches are needed to correct for these biases. In this review, we propose a comprehensive analysis based on comparison of large data sets related to competing phylogenies (including all Recent and fossil taxa) and the fossil record for both groups during the Mesozoic-Cainozoic interval. This approach provides information on the 'fish' fossil record quality and on the corrected 'fish' deep-time phylogenetic palaeodiversity signals, with special emphasis on diversification events. Because taxonomic information is preserved after analytical treatment, identified palaeodiversity events are considered both quantitatively and qualitatively and put within corresponding palaeoenvironmental and biological settings. Results indicate a better fossil record quality for elasmobranchs due to their microfossil-like fossil distribution and their very low diversity in freshwater systems, whereas freshwater actinopterygians are diverse in this realm with lower preservation potential. Several important diversification events are identified at familial and generic levels for elasmobranchs, and marine and freshwater actinopterygians, namely in the Early-Middle Jurassic (elasmobranchs), Late Jurassic (actinopterygians), Early Cretaceous (elasmobranchs, freshwater actinopterygians), Cenomanian (all groups) and the Paleocene-Eocene interval (all groups), the latter two representing the two most exceptional radiations among vertebrates. For each of these events along with the Cretaceous-Paleogene extinction, we provide an in-depth review of the taxa involved and factors that may have influenced the diversity patterns observed. Among these, palaeotemperatures, sea-levels, ocean circulation and productivity as well as continent fragmentation and environment heterogeneity (reef environments) are parameters that largely impacted on 'fish' evolutionary history, along with other biotic constraints.
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Affiliation(s)
- Guillaume Guinot
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland.
| | - Lionel Cavin
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland
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90
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Xu J, Han C, Huang JR. The complete mitogenome of the Sheatfish Pterocryptis cochinchinensis (Siluriformes: Siluridae) and phylogenetic implications. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2785-6. [PMID: 26094986 DOI: 10.3109/19401736.2015.1053066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To better understand the phylogenetic status of the Sheatfish, Pterocryptis cochinchinensis, we determined its complete mitogenome sequence using polymerase chain reaction and the direct sequencing method. The complete mitogenome sequence was 16,501bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (D-loop), the gene was identical to typical vertebrate. This was the first report of the complete mitogenome sequence in genus Pterocryptis. Phylogenetic based on mitogenome sequences and cytb gene suggested that the Sheatfish formed the most basal branch having sister relationship with the clade containing all other analyzed genus Silurus fishes.
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Affiliation(s)
- JunQiu Xu
- a School of Life Sciences, Sun Yat-Sen University , Guangzhou , China
| | - Chong Han
- a School of Life Sciences, Sun Yat-Sen University , Guangzhou , China
| | - Jian Rong Huang
- a School of Life Sciences, Sun Yat-Sen University , Guangzhou , China
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91
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Sahoo L, Kumar S, Das SP, Patnaik S, Bit A, Sundaray JK, Jayasankar P, Das P. Complete mitochondrial genome sequence of Heteropneustes fossilis obtained by paired end next generation sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2485-6. [PMID: 26016883 DOI: 10.3109/19401736.2015.1033710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, the complete mitochondrial genome sequence of Heteropneustes fossilis is reported using massive parallel sequence technology. The complete mitogenome of H. fossilis is obtained by de novo assembly of paired end Illumina sequences using CLC Genomics Workbench version 7.0.4, which is 16,489 bp in length. It comprised of 13 protein- coding genes, 22 tRNAs, 2 rRNA genes and a putative control region along with the gene order and organization, being similar to most of vertebrates. The mitogenome in the present study has 99% similarity to the complete mitogneome sequence of H. Fossilis, as reported earlier. Phylogenetic analysis of Siluriformes depicted that Heteropneustids were closer to Clariids. The mitogenome sequence of H. fossilis contributes better understanding of population genetics, phylogenetics and evolution of Indian catfish species.
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Affiliation(s)
- Lakshman Sahoo
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Santosh Kumar
- b Fish Conservation Division, ICAR-National Bureau of Fish Genetics Resources , Lucknow , Uttar Pradesh , India
| | - Sofia P Das
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Siddhi Patnaik
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Amrita Bit
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Jitendra Kumar Sundaray
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - P Jayasankar
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
| | - Paramananda Das
- a Fish Genetics and Biotechnology Division , ICAR-Central Institute of Freshwater Aquaculture , Bhubaneswar , Odisha , India and
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92
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Rangel-Medrano JD, Alzate JF, Márquez EJ. Complete mitochondrial genome of the Neotropical catfish Pseudoplatystoma magdaleniatum (Siluriformes, Pimelodidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4033-4034. [PMID: 25629466 DOI: 10.3109/19401736.2014.1003830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Neotropical freshwater fish Pseudoplatystoma magdaleniatum is a trans-Andean species that belongs to the family of long-whiskered catfishes (family Pimelodidae). In this study, the complete mitochondrial genome of P. magdaleniatum was sequenced using the MiSeq Illumina platform. The complete circular mitogenome is 16,568 bp in length, exhibiting an average GC content of 44.19% and codes for 13 proteins, 2 ribosomal RNA genes and 22 transfer RNA genes. Additionally, it exhibits perfect synteny and similar length with the mitogenome of Pimelodus pictus.
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Affiliation(s)
- Jose D Rangel-Medrano
- a Facultad de Ciencias , Universidad Nacional de Colombia-Sede Medellín , Medellín , Colombia and
| | - Juan F Alzate
- b Facultad de Medicina , Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia , Medellín , Colombia
| | - Edna J Márquez
- a Facultad de Ciencias , Universidad Nacional de Colombia-Sede Medellín , Medellín , Colombia and
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93
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Carvalho M, Vari RP. Development of the splanchnocranium in Prochilodus argenteus (Teleostei: Characiformes) with a discussion of the basal developmental patterns in the Otophysi. ZOOLOGY 2015; 118:34-50. [PMID: 25595854 DOI: 10.1016/j.zool.2014.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/23/2014] [Accepted: 10/11/2014] [Indexed: 11/18/2022]
Abstract
Development of the mandibular, hyoid and gill arches, which constitute the splanchnocranium, are described for Prochilodus argenteus, order Characiformes, one of the basal lineages of the Otophysi. Development was examined from just hatched larvae through juveniles using whole specimens cleared and counterstained for cartilage and bone as well as histological preparations. Observations are compared with the developmental trends reported for Cypriniformes, the basalmost clade of the Otophysi. Shortened developmental sequences for Prochilodus compared to the cypriniform Catostomus were discovered in the ontogeny of the ceratohyals, ceratobranchials 1-5, epibranchials 1-4 and the symplectic portion of the hyosymplectic. Prochilodus also differs from Catostomus in having the basihyal plus the anterior copula appearing at different stages of ontogeny rather than simultaneously. Contrary to previous assumptions, developmental information indicates that hypobranchial 4 as well as likely basibranchial 5 are present in Prochilodus. Various developmental patterns in Prochilodus considered basal for the Otophysi, the predominant component of the Ostariophysi, are likely conserved from patterns prevalent in basal groups in the Actinopterygii.
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Affiliation(s)
- Murilo Carvalho
- Laboratório de Ictiologia de Ribeirão Preto (LIRP), Departamento de Biologia, Universidade de São Paulo, PPG Biologia Comparada, Av. Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
| | - Richard P Vari
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 159, Washington, DC 20013-7012, USA
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94
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Restrepo-Escobar N, Alzate JF, Márquez EJ. Mitochondrial genome of the Trans-Andean shovelnose catfish Sorubim cuspicaudus (Siluriformes, Pimelodidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3964-3965. [PMID: 25541312 DOI: 10.3109/19401736.2014.989506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Trans-Andean shovelnose catfish Sorubim cuspicaudus is the largest species within the genus Sorubim. In this work, the pyrosequencing technology was used to obtain the complete mitochondrial genome sequence of S. cuspicaudus. The 16,544 bp molecule contains 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs and exhibit perfect synteny with other South-American catfishes.
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Affiliation(s)
| | - Juan F Alzate
- b Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia
| | - Edna J Márquez
- a Facultad de Ciencias , Universidad Nacional de Colombia , Medellín , Colombia and
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95
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Conway KW, Britz R, Shrestha J, Manimekalan A, Rüber L. Molecular systematics of the Asian torrent minnows (Ostariophysi: Psilorhynchidae) inferred from nuclear and mitochondrial DNA sequence data. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections; Texas A&M University; College Station TX USA
| | - Ralf Britz
- Department of Zoology; The Natural History Museum; London UK
| | - Jiwan Shrestha
- Nepal Academy for Science and Technology (NAST); Khumaltar; Lalitpur Kathmandu Nepal
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern; Bern Switzerland
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96
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Yazbeck GDM, Oliveira RS, Ribeiro JM, Carmo FMDS, Carvalho MB. First complete mitochondrial genome for any anostomid fish: Leporinus piavussu, a recently described piracema species. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2293-4. [PMID: 25469815 DOI: 10.3109/19401736.2014.987239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The first complete mitochondrial genome for the Anostomidae fish family has been announced. Piracema fishes are the potamodromous migratory species from South America, which undergo lengthy and dramatic yearly reproductive upstream runs. The piracema species Leporinus piavussu has recently been described after a long misidentification history. Its mitogenome, assembled using NGS data and Sanger sequencing, consists in a 16,682 bp circular molecule (GenBank accession number KM886569). The exact sequence and position of 37 mitochondrial genes and the control region is established. A possible case of heteroplasmy was found with NGS and corroborated by Sanger sequencing. These results will positively contribute to the debate about this group's taxonomy, evolution and conservation.
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Affiliation(s)
- Gabriel de Menezes Yazbeck
- a Laboratório de Recursos Genéticos , DEZOO, Universidade Federal de São João del-Rei, Praça Frei Orlando, São João del-Rei , Minas Gerais , Brazil and
| | - Rafael Sachetto Oliveira
- b DCOMP - CTAN - Universidade Federal de São João del-Rei, Praça Frei Orlando, São João del-Rei , Minas Gerais , Brazil
| | - José Mauro Ribeiro
- a Laboratório de Recursos Genéticos , DEZOO, Universidade Federal de São João del-Rei, Praça Frei Orlando, São João del-Rei , Minas Gerais , Brazil and
| | - Fausto Moreira da Silva Carmo
- a Laboratório de Recursos Genéticos , DEZOO, Universidade Federal de São João del-Rei, Praça Frei Orlando, São João del-Rei , Minas Gerais , Brazil and
| | - Milene Barbosa Carvalho
- b DCOMP - CTAN - Universidade Federal de São João del-Rei, Praça Frei Orlando, São João del-Rei , Minas Gerais , Brazil
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97
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Landínez-García RM, Alzate JF, Márquez EJ. Complete mitogenome of the Neotropical fish Brycon henni, Eigenmann 1913 (Characiformes, Bryconidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2259-60. [PMID: 25423503 DOI: 10.3109/19401736.2014.984170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Brycon henni (Characiformes, Bryconidae) is a trans-Andean omnivorous fish considered as promising species in aquaculture of temperate zones. In this work we report for first time the complete mitochondrial genome of B. henni. This mitogenome spans 16,885 bp and encodes 13 proteins, 22 tRNAs and 2 ribosomal RNAs. Additionally, the synteny is conserved with others species of the order Characiformes.
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Affiliation(s)
| | - Juan F Alzate
- b Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia
| | - Edna J Márquez
- a Facultad de Ciencias , Universidad Nacional de Colombia , Medellín , Colombia and
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98
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Landínez-García RM, Alzate JF, Márquez EJ. Mitochondrial genome of the Neotropical detritivore fish Curimata mivartii Steindachner 1878 (Characiformes, Curimatidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2196-7. [PMID: 25423519 DOI: 10.3109/19401736.2014.982623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Curimata mivartii is a detritivorous species Neotropical, which is of great importance to local fisheries and riverine ecosystems. In this work, the mitochondrial genome of C. mivartii was completely sequenced using a combination of 454 FLX(+) platform and Sanger/capillary sequencing. The mitogenome is 16,705 bp in length, encodes 13 proteins, 22 tRNAs, 2 ribosomal RNAs and exhibit perfect synteny with others Characiformes.
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Affiliation(s)
| | - Juan F Alzate
- b Facultad de Medicina , Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia , Medellín , Colombia
| | - Edna J Márquez
- a Facultad de Ciencias , Universidad Nacional de Colombia , Medellín , Colombia and
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99
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Restrepo-Escobar N, Alzate JF, Márquez EJ. Mitochondrial genome of the Neotropical catfishAgeneiosus pardalis,Lütken 1874 (Siluriformes, Auchenipteridae). ACTA ACUST UNITED AC 2014; 27:2176-7. [DOI: 10.3109/19401736.2014.982613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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100
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Braga MP, Razzolini E, Boeger WA. Drivers of parasite sharing among Neotropical freshwater fishes. J Anim Ecol 2014; 84:487-97. [PMID: 25283218 DOI: 10.1111/1365-2656.12298] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 09/26/2014] [Indexed: 12/28/2022]
Abstract
Because host-parasite interactions are so ubiquitous, it is of primary interest for ecologists to understand the factors that generate, maintain and constrain these associations. Phylogenetic comparative studies have found abundant evidence for host-switching to relatively unrelated hosts, sometimes related to diversification events, in a variety of host-parasite systems. For Monogenoidea (Platyhelminthes) parasites, it has been suggested that the co-speciation model alone cannot explain host occurrences, hence host-switching and/or non-vicariant modes of speciation should be associated with the origins and diversification of several monogenoid taxa. The factors that shape broad patterns of parasite sharing were investigated using path analysis as a way to generate hypotheses about the origins of host-parasite interactions between monogenoid gill parasites and Neotropical freshwater fishes. Parasite sharing was assessed from an interaction matrix, and explanatory variables included phylogenetic relationships, environmental preferences, biological traits and geographic distribution for each host species. Although geographic distribution of hosts and host ecology are important factors to understand host-parasite interactions, especially within host lineages that share a relatively recent evolutionary history, phylogeny had the strongest overall direct effect on parasite sharing. Phylogenetic contiguity of host communities may allow a 'stepping-stone' mode of host-switching, which increases parasite sharing. Our results reinforce the importance of including evolutionary history in the study of ecological associations, including emerging infectious diseases risk assessment.
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Affiliation(s)
- Mariana P Braga
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva, Departamento de Zoologia, Universidade Federal do Paraná, Setor de Ciências Biológicas, Caixa Postal 19073, CEP 81531-980, Curitiba, PR, Brazil
| | - Emanuel Razzolini
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva, Departamento de Zoologia, Universidade Federal do Paraná, Setor de Ciências Biológicas, Caixa Postal 19073, CEP 81531-980, Curitiba, PR, Brazil
| | - Walter A Boeger
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva, Departamento de Zoologia, Universidade Federal do Paraná, Setor de Ciências Biológicas, Caixa Postal 19073, CEP 81531-980, Curitiba, PR, Brazil
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