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D'Anatro A, Calvelo J, Feijóo M, Giorello FM. Differential expression analyses and detection of SNP loci associated with environmental variables: Are salinity and temperature factors involved in population differentiation and speciation in Odontesthes? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101262. [PMID: 38861850 DOI: 10.1016/j.cbd.2024.101262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
Environmental factors play a key role in individual adaptation to different local conditions. Because of this, studies about the physiological and genetic responses of individuals exposed to different natural environments offer clues about mechanisms involved in population differentiation, and as a subsequent result, speciation. Marine environments are especially suited to survey this kind of phenomena because they commonly harbor species adapted to different local conditions along a geographic continuum. Silversides belonging to Odontesthes are commonly distributed in tropical and temperate regions of South America and exhibit noticeable phenotypic plasticity, which allows them to adapt to contrasting environments. In this study, the genetic expression of O. argentinensis sampled along the Uruguayan Atlantic coast and estuarine adjacent areas was investigated. In addition, the correlation between individual genotypes and environmental variables was also analysed in O. argentinensis and O. bonariensis. Results obtained suggest a differential expression pattern of low magnitude among individuals from the different areas sampled and a correlation between several SNP loci and environmental variables. The analyses carried out did not show a clear differentiation among individuals sampled along different salinity regimens, but enriched GOTerms seem to be driven by water oxygen content. On the other hand, a total of 46 SNPs analysed in O. argentinensis and O. bonariensis showed a correlation with salinity and temperature. Although none of the correlated SNPs and corresponding genes from our both analyses were directly associated with hypoxia, genes related to the cardiovascular system and muscle cell differentiation were found. All these genes are interesting candidates for future studies since they are closely related to the differentially expressed genes. Although salinity was also mentioned as an important parameter limiting introgression between O. argentinensis and O. bonariensis, it was found that salinity does not drive differential expression in O. argentinensis, but rather oxygen levels. Moreover, salinity does not directly affect the structure and genetic divergence of the populations, they appear to be structured based on their degree of isolation and geographical distance between them. Further studies, like genome-wide analyses, could help to elucidate additional genes adapted to the different environments in these silverside species.
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Affiliation(s)
- Alejandro D'Anatro
- Laboratorio de Evolución y Sistemática, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Matías Feijóo
- Centro Universitario Regional Este, Sede Treinta y Tres, Universidad de la República, Treinta y Tres, Uruguay
| | - Facundo M Giorello
- Espacio de Biología Vegetal del Noreste, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
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Zafirah Ghazali S, Lavoué S, Sukmono T, Habib A, Min Pau T, Azizah Mohd Nor S. Cenozoic colonisation of the Indian Ocean region by the Australian freshwater originating glassperch family Ambassidae (Teleostei). Mol Phylogenet Evol 2023:107832. [PMID: 37263456 DOI: 10.1016/j.ympev.2023.107832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/29/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
We examined the phylogeny and biogeography of the glassperch family Ambassidae (Teleostei), which is widely distributed in the freshwater, brackish and marine coastal habitats across the Indo-West Pacific region. We first built a comprehensive time-calibrated phylogeny of Ambassidae using five genes. We then used this tree to reconstruct the evolution of the salinity preference and ancestral areas. Our results indicate that the two largest genera of Ambassidae, Ambassis and Parambassis, are each not monophyletic. The most recent common ancestor of Ambassidae was freshwater adapted and lived in Australia about 56 million years ago. Three independent freshwater-to-marine transitions are inferred, but no marine-to-freshwater ones. To explain the distribution of ambassids, we hypothesise two long-distance marine dispersal events from Australia. A first event was towards Southeast Asia during the early Cenozoic, followed by a second one towards Africa during mid-Cenozoic. The phylogenetic signal associated with the salinity adaptation of these events was not detected, possibly because of the selective extinction of intermediate marine lineages. The Ambassidae shares two characteristics with other freshwater fish groups distributed in continental regions surrounding the Indian Ocean: They are too young to support the hypothesis that their distribution is the result of the fragmentation of Gondwana, but they did not retain the phylogenetic signal of their marine dispersal.
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Affiliation(s)
- Siti Zafirah Ghazali
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia.
| | - Tedjo Sukmono
- Department of Biology, Universitas Jambi, Jalan Lintas Jambi - Muara Bulian Km15, 36122 Jambi, Sumatra, Indonesia
| | - Ahasan Habib
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Tan Min Pau
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia
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3
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Pagano AD, Barreto BF, Domingues WB, Silveira TLR, Nunes LS, Blodorn EB, Dellagostin EN, Remião MH, Robaldo RB, Campos VF. Modulation of miR-429 during osmotic stress in the silverside Odontesthes humensis. Front Genet 2022; 13:903201. [PMID: 36159973 PMCID: PMC9490309 DOI: 10.3389/fgene.2022.903201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Silverside fish inhabit marine coastal waters, coastal lagoons, and estuarine regions in southern South America. Although silversides are not fully adapted to freshwater, they can tolerate a wide range of salinity variations. MicroRNAs (miRNAs) are a class of ∼22 nucleotide noncoding RNAs, which are crucial regulators of gene expression at post-transcriptional level. Current data indicate that miRNAs biogenesis is altered by situations of environmental stress, thereby altering the expression of target mRNAs. Foremost, the silversides were acutely exposed to 30 g.L−1 of salt to reveal in which tissue miR-429 could be differentially expressed. Thus, fish were acclimated to freshwater (0 g.L−1) and to brackish water (10 g.L−1), and then exposed to opposite salinity treatment. Here, we reveal that miR-429, a gill-enriched miRNA, emerges as a prime osmoregulator in silversides. Taken together, our findings suggest that miR-429 is an endogenous regulator of osmotic stress, which may be developed as a biomarker to assist silverside aquaculture.
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Affiliation(s)
- Antônio D. Pagano
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Bruna F. Barreto
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - William B. Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tony L. R. Silveira
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Leandro S. Nunes
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Eduardo B. Blodorn
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Eduardo N. Dellagostin
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Mariana H. Remião
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Ricardo B. Robaldo
- Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Vinicius F. Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
- *Correspondence: Vinicius F. Campos,
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de Brito V, Betancur-R R, Burns MD, Buser TJ, Conway KW, Fontenelle JP, Kolmann MA, McCraney WT, Thacker CE, Bloom DD. Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes. Integr Comp Biol 2022; 62:406-423. [PMID: 35675320 DOI: 10.1093/icb/icac085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.
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Affiliation(s)
- Victor de Brito
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA
| | - Ricardo Betancur-R
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Room 314, Norman, OK 73019, USA
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell Museum of Vertebrates, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850-1923, USA
| | - Thaddaeus J Buser
- Department of BioSciences, Rice University, W100 George R. Brown Hall, 6100 Main Street, Houston, TX 77005, USA
| | - Kevin W Conway
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX 77843, USA
| | - João Pedro Fontenelle
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks St., Toronto, ON M5S 3E8, Canada
| | - Matthew A Kolmann
- Museum of Paleontology, Biological Sciences Building, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109-1085, USA
| | - W Tyler McCraney
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive South, Los Angeles, CA 90095-7246, USA
| | - Christine E Thacker
- Research and Collections, Section of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA 90007, USA.,Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Devin D Bloom
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA.,Institute of the Environment and Sustainability, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5419, USA
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Thieme P, Schnell NK, Parkinson K, Moritz T. Morphological characters in light of new molecular phylogenies: the caudal-fin skeleton of Ovalentaria. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211605. [PMID: 35242353 PMCID: PMC8753169 DOI: 10.1098/rsos.211605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/06/2021] [Indexed: 05/03/2023]
Abstract
The Ovalentaria is a taxon of teleosts that has been proposed based on molecular analyses only. Previously widely separated families are assembled in this taxon. For the first time, the Ovalentaria are analysed using a comparative morphological approach. The caudal-fin skeleton of 355 species covering all 48 ovalentarian families are examined in cleared and stained specimens, µCT datasets and X-ray images as well as from the literature. A total of 38 morphological characters are evaluated and used for ancestral character state reconstructions and phylogenetic analyses. Results provide hypotheses for a scenario of the evolution of the caudal-fin skeleton and its ground plan in Ovalentaria. An evolutionary trend towards the reduction of skeletal elements in the caudal fin is observed. Connections between the evolution of the caudal-fin skeleton and modes of locomotion found in ovalentarian taxa are discussed. Phylogenetic analyses based on the caudal-fin morphology provide topologies for intra-ovalentarian relationships that largely agree with molecular hypotheses.
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Affiliation(s)
- Philipp Thieme
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
- Institute of Zoology and Evolutionary Research, Friedrich-Schiller-University Jena, Ebertstrasse 1, 07743 Jena, Germany
| | - Nalani K. Schnell
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Station Marine de Concarneau, Place de la Croix, 29900 Concarneau, France
| | - Kerryn Parkinson
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia
| | - Timo Moritz
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Strasse 3, 18059 Rostock, Germany
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6
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Strüssmann CA, Yamamoto Y, Hattori RS, Fernandino JI, Somoza GM. Where the Ends Meet: An Overview of Sex Determination in Atheriniform Fishes. Sex Dev 2021; 15:80-92. [PMID: 33951664 DOI: 10.1159/000515191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/22/2021] [Indexed: 11/19/2022] Open
Abstract
Atheriniform fishes have recently emerged as attractive models for evolutionary, ecological, and molecular/physiological studies on sex determination. Many species in this group have marked temperature-dependent sex determination (TSD) and yet many species also have a sex determinant gene that provides a strong drive for male differentiation. Thus, in these species the 2 forms of sex determination that were once considered to be mutually exclusive, environmental (ESD) and genotypic (GSD) sex determination, can coexist at environmentally relevant conditions. Here, we review the current knowledge on sex determination in atheriniform fishes with emphasis on the molecular and physiological mechanisms of ESD and GSD, the coexistence and cross-talk between these 2 mechanisms, the possibility of extragonadal transduction of environmental information and/or extragonadal onset of sex determination, and the results of field studies applying novel tools such as otolith increment analysis and molecular markers of genetic sex developed for selected New World and Old World atheriniform species. We also discuss the existence of molecular and histological mechanisms to prevent the discrepant differentiation in parts of the gonads because of ambiguous or conflicting environmental and genetic signals and particularly the possibility that the female is the default state in these species.
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Affiliation(s)
- Carlos A Strüssmann
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yoji Yamamoto
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ricardo S Hattori
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Juan I Fernandino
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús, Argentina
| | - Gustavo M Somoza
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús, Argentina
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7
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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8
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A fossil-calibrated time-tree of all Australian freshwater fishes. Mol Phylogenet Evol 2021; 161:107180. [PMID: 33887481 DOI: 10.1016/j.ympev.2021.107180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 11/24/2022]
Abstract
Australian freshwater fishes are a relatively species-poor assemblage, mostly comprising groups derived from older repeated freshwater invasions by marine ancestors, plus a small number of Gondwanan lineages. These taxa are both highly endemic and highly threatened, but a comprehensive phylogeny for Australian freshwater fishes is lacking. This has hampered efforts to study their phylogenetic diversity, distribution of extinction risk, speciation rates, and rates of trait evolution. Here, we present a comprehensive dated phylogeny of 412 Australian fishes. We include all formally recognized freshwater species plus a number of genetically distinct subpopulations, species awaiting formal description, and predominantly brackish-water species that sometimes enter fresh water. The phylogeny was inferred using maximum-likelihood analysis of a multilocus data set comprising six mitochondrial and three nuclear genes from 326 taxa. We inferred the evolutionary timescale using penalized likelihood, then used a statistical approach to add 86 taxa for which no molecular data were available. The time-tree inferred in our study will provide a useful resource for macroecological studies of Australian freshwater fishes by enabling corrections for phylogenetic non-independence in evolutionary and ecological comparative analyses.
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Calvelo J, D'Anatro A. Mitochondrial genome architecture and phylogenetic relationships of Odontesthes argentinensis within Atherinomorpha. Genetica 2021; 149:129-141. [PMID: 33817771 DOI: 10.1007/s10709-021-00116-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/15/2021] [Indexed: 12/30/2022]
Abstract
Silversides are a widely distributed group across South America, with several species occupying marine, freshwater and estuarine environments. Several authors suggest main transitions among these environments took place during Pleistocene, and were accompanied with rapid speciation events. This scenario produced very limited genetic and morphological differentiation among the species. However, most of these surveys have an incomplete coverage of the intraspecific genetic diversity of the taxa studied. In this work, we reconstructed six mitochondrial genomes of O. argentinensis using transcriptomic data, and used them-in combination with several nuclear markers retrieved from the same transcriptomes-to explore the effect of additional coverage of intraspecific diversity of this species in phylogenetic reconstructions. Unlike previous works, phylogenetic analyses failed to identify O. argentinensis as a monophyletic group in relation with closely related taxa. Our results suggest that several species of the genus, especially those related to O. argentinensis, need further taxonomic revision.
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Affiliation(s)
- Javier Calvelo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Alejandro D'Anatro
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay.
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Piller KR, Bloom DD, Lyons J, Mercado-Silva N. Systematics and Taxonomy of Chapalichthys (Cyprinodontiformes: Goodeidae), a Small Genus of Live-Bearers from Central Mexico. COPEIA 2020. [DOI: 10.1643/ci2020044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Kyle R. Piller
- Southeastern Louisiana University, Department of Biological Sciences, Hammond, Louisiana 70402; (KRP) . Send reprint requests to KRP
| | - Devin D. Bloom
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008
| | - John Lyons
- University of Wisconsin Zoological Museum, Madison, Wisconsin 53706
| | - Norman Mercado-Silva
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico, C.P. 62209
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11
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García-Martínez RM, de Los Angeles Barriga-Sosa I, López B, Mejía O. "Colonization routes and demographic history of Chirostoma humboldtianum in the central Mexican plateau". JOURNAL OF FISH BIOLOGY 2020; 97:1039-1050. [PMID: 32658333 DOI: 10.1111/jfb.14462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
In the present study we evaluate the population structure and potential colonization routes of the silverside Chirostoma humboldtianum through approximate Bayesian computations. Six microsatellite loci were amplified in a total of 288 individuals from six different locations covering the complete geographic distribution of the species. Additionally, two mitochondrial DNA markers, a D loop control region and cytochrome b were amplified in a subset of 107 individuals. The results found with microsatellites allow recovering well-structured populations that have experienced a drastic reduction in the effective population size. On the other hand, mtDNA sequences showed a moderate phylogeographic structure with shared haplotypes between geographic localities and signalsof a slight increase in the effective population size. Finally, the approximate Bayesian computation analysis performed with both datasets suggested a west-to-east colonization route for the species in Central Mexico.
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Affiliation(s)
- Rosa María García-Martínez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Irene de Los Angeles Barriga-Sosa
- Laboratorio de Genética y Biología Molecular de la Planta Experimental de Producción Acuícola, Departamento de Hidrobiología, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City, Mexico
| | - Benjamín López
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Omar Mejía
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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Majtánová Z, Unmack PJ, Prasongmaneerut T, Shams F, Srikulnath K, Ráb P, Ezaz T. Evidence of Interspecific Chromosomal Diversification in Rainbowfishes (Melanotaeniidae, Teleostei). Genes (Basel) 2020; 11:E818. [PMID: 32708365 PMCID: PMC7397213 DOI: 10.3390/genes11070818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 11/28/2022] Open
Abstract
Rainbowfishes (Melanotaeniidae) are the largest monophyletic group of freshwater fishes occurring in Australia and New Guinea, with 112 species currently recognised. Despite their high taxonomic diversity, rainbowfishes remain poorly studied from a cytogenetic perspective. Using conventional (Giemsa staining, C banding, chromomycin A3 staining) and molecular (fluorescence in situ hybridisation with ribosomal DNA (rDNA) and telomeric probes) cytogenetic protocols, karyotypes and associated chromosomal characteristics of five species were examined. We covered all major lineages of this group, namely, Running River rainbowfish Melanotaenia sp., red rainbowfish Glossolepisincisus, threadfin rainbowfish Iriatherina werneri, ornate rainbowfish Rhadinocentrus ornatus, and Cairns rainbowfish Cairnsichthys rhombosomoides. All species had conserved diploid chromosome numbers 2n = 48, but karyotypes differed among species; while Melanotaenia sp., G. incisus, and I. werneri possessed karyotypes composed of exclusively subtelo/acrocentric chromosomes, the karyotype of R. ornatus displayed six pairs of submetacentric and 18 pairs of subtelo/acrocentric chromosomes, while C. rhombosomoides possessed a karyotype composed of four pairs of submetacentric and 20 pairs of subtelo/acrocentric chromosomes. No heteromorphic sex chromosomes were detected using conventional cytogenetic techniques. Our data indicate a conserved 2n in Melanotaeniidae, but morphologically variable karyotypes, rDNA sites, and heterochromatin distributions. Differences were observed especially in taxonomically divergent species, suggesting interspecies chromosome rearrangements.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic;
| | - Peter J. Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia;
| | - Tulyawat Prasongmaneerut
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.S.)
| | - Foyez Shams
- Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia; (F.S.); (T.E.)
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (T.P.); (K.S.)
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic;
| | - Tariq Ezaz
- Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia; (F.S.); (T.E.)
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13
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Carrillo Muñoz N, Dickson KA, Walter RP. The mitogenome of the California grunion ( Leuresthes tenuis). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1730254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
| | - Kathryn A. Dickson
- Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Ryan P. Walter
- Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
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14
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Turko AJ, Cisternino B, Wright PA. Calcified gill filaments increase respiratory function in fishes. Proc Biol Sci 2020; 287:20192796. [PMID: 32075528 DOI: 10.1098/rspb.2019.2796] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The morphology of fish gills is closely linked to aerobic capacity and tolerance of environmental stressors such as hypoxia. The importance of gill surface area is well studied, but little is known about how the mechanical properties of gill tissues determine function. In some fishes, the bases of the gill filaments are surrounded by a calcified 'sheath' of unknown function. We tested two non-exclusive hypotheses: (i) calcified gill filaments enhance water flow through the gill basket, improving aquatic respiratory function, and (ii) in amphibious fishes, calcification provides support for gills out of water. In a survey of more than 100 species of killifishes and related orders, we found filament calcification was widespread and thus probably arose before the evolution of amphibious lifestyles in killifishes. Calcification also did not differ between amphibious and fully aquatic species, but terrestrial acclimation caused calcium deposition on the filaments of the killifish Kryptolebias marmoratus, suggesting a possible structural role when out of water. We found strong evidence supporting a role for filament calcification in enhancing aquatic respiratory function. First, acclimation to increased respiratory demands (hypoxia, elevated temperatures) induced calcium deposition on the filaments of K. marmoratus. Next, gentle removal of filament calcification decreased branchial resistance to water flow, indicating disruption of gill basket positioning. Thus, the mechanical properties of the gill filaments appear to play an important and previously unappreciated role in determining fish respiratory function.
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Affiliation(s)
- Andy J Turko
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
| | - Bianca Cisternino
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
| | - Patricia A Wright
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
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15
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Hughes LC, Cardoso YP, Sommer JA, Cifuentes R, Cuello M, Somoza GM, González‐Castro M, Malabarba LR, Cussac V, Habit EM, Betancur‐R. R, Ortí G. Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data. Mol Ecol 2020; 29:738-751. [DOI: 10.1111/mec.15350] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/23/2019] [Accepted: 01/03/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Lily C. Hughes
- Department of Biological Sciences George Washington University Washington DC USA
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
| | - Yamila P. Cardoso
- Laboratorio de Sistemática y Biología Evolutiva‐CONICET Facultad de Ciencias Naturales y Museo Universidad Nacional de La Plata La Plata Argentina
| | - Julie A. Sommer
- Vice Chancellor for Research Office University of Nebraska Medical Center Omaha NE USA
| | - Roberto Cifuentes
- Departmento de Sistemas Acuáticos Facultad de Ciencias Ambientales y Centro EULA Universidad de Concepción y Centro de Investigaciones en Ecosistemas Patagónicos Concepción Chile
| | - Mariela Cuello
- Facultad de Ciencias Naturales y Museo Universidad Nacional de La Plata‐CONICET Buenos Aires Argentina
| | - Gustavo M. Somoza
- Instituto Tecnológico de Chascomus (CONICET‐UNSAM) Chascomús, Buenos Aires Argentina
| | - Mariano González‐Castro
- Grupo de Biotaxonomía Morfológica y molecular de peces IIMyC‐CONICET Universidad Nacional de Mar del Plata Mar del Plata Argentina
| | - Luiz R. Malabarba
- Departamento de Zoologia Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Victor Cussac
- Centro Científico Tecnológico CONICET Patagonia Norte – Universidad Nacional del Comahue Bariloche, Rio Negro Argentina
| | - Evelyn M. Habit
- Departmento de Sistemas Acuáticos Facultad de Ciencias Ambientales y Centro EULA Universidad de Concepción y Centro de Investigaciones en Ecosistemas Patagónicos Concepción Chile
| | - Ricardo Betancur‐R.
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
- Department of Biology University of Oklahoma Norman OK USA
| | - Guillermo Ortí
- Department of Biological Sciences George Washington University Washington DC USA
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
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16
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Therkildsen NO, Baumann H. A comprehensive non-redundant reference transcriptome for the Atlantic silverside Menidia menidia. Mar Genomics 2020; 53:100738. [PMID: 32883435 DOI: 10.1016/j.margen.2019.100738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/25/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022]
Abstract
The Atlantic silverside (Menidia menidia) has been the focus of extensive research efforts in ecology, evolutionary biology, and physiology over the past three decades, but lack of genomic resources has so far hindered examination of the molecular basis underlying the remarkable patterns of phenotypic variation described in this species. We here present the first reference transcriptome for M. menidia. We sought to capture a single representative sequence from as many genes as possible by first using a combination of Trinity and the CLC Genomics Workbench to de novo assemble contigs based on RNA-seq data from multiple individuals, tissue types, and life stages. To reduce redundancy, we passed the combined raw assemblies through a stringent filtering pipeline based both on sequence similarity to related species and computational predictions of transcript quality, condensing an initial set of >480,000 contigs to a final set of 20,998 representative contigs, amounting to a total length of 53.3 Mb. In this final assembly, 91% of the contigs were functionally annotated with putative gene function and gene ontology (GO) terms and/or InterProScan identifiers. The assembly contains complete or nearly complete copies of >95% of 248 highly conserved core genes present in low copy number across higher eukaryotes, and partial copies of another 3.8%, suggesting that our assembly provides relatively comprehensive coverage of the M. menidia transcriptome. The assembly provided here will be an important resource for future research.
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Affiliation(s)
- Nina Overgaard Therkildsen
- Department of Biology, Hopkins Marine Station, Stanford University, 120 Ocean View Blvd, CA-93950 Pacific Grove, USA.
| | - Hannes Baumann
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, CT-06340 Groton, USA
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17
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Colautti DC, Miranda L, Gonzalez-Castro M, Villanova V, Strüssmann CA, Mancini M, Maiztegui T, Berasain G, Hattori R, Grosman F, Sanzano P, Lozano I, Vegh SL, Salinas V, Del Ponti O, Del Fresno P, Minotti P, Yamamoto Y, Baigún CRM. Evidence of a landlocked reproducing population of the marine pejerrey Odontesthes argentinensis (Actinopterygii; Atherinopsidae). JOURNAL OF FISH BIOLOGY 2020; 96:202-216. [PMID: 31729023 DOI: 10.1111/jfb.14207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In South America, the order Atheriniformes includes the monophyletic genus Odontesthes with 20 species that inhabit freshwater, estuarine and coastal environments. Pejerrey Odontesthes argentinensis is widely distributed in coastal and estuarine areas of the Atlantic Ocean and is known to foray into estuaries of river systems, particularly in conditions of elevated salinity. However, to our knowledge, a landlocked self-sustaining population has never been recorded. In this study, we examined the pejerrey population of Salada de Pedro Luro Lake (south-east of Buenos Aires Province, Argentina) to clarify its taxonomic identity. An integrative taxonomic analysis based on traditional meristic, landmark-based morphometrics and genetic techniques suggests that the Salada de Pedro Luro pejerrey population represents a novel case of physiological and morphological adaptation of a marine pejerrey species to a landlocked environment and emphasises the environmental plasticity of this group of fishes.
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Affiliation(s)
- Darío C Colautti
- Laboratorio de Ecología de Peces Instituto de Limnología 'Dr. Raúl A. Ringuelet' (ILPLA-CONICET), La Plata, Argentina
| | - Leandro Miranda
- Laboratorio de Ictiofisiología y Acuicultura IIB-INTECH (CONICET-UNSAM), Chascomús, Argentina
| | - Mariano Gonzalez-Castro
- Laboratorio de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras (IIMyC-CONICET), Mar del Plata, Argentina
| | - Vanina Villanova
- Laboratorio de Biotecnología Acuática (FCByF-UNR) Centro Científico, Tecnológico y Educativo Acuario del Río Paraná, Rosario, Argentina
- Centro Científico y Tecnológico Conicet Rosario (CCT-Conicet Rosario), Rosario, Argentina
| | - Carlos A Strüssmann
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Miguel Mancini
- Ecología & Acuicultura, Facultad de Agronomía y Veterinaria (UNRC), Río Cuarto, Argentina
| | - Tomas Maiztegui
- Laboratorio de Ecología de Peces Instituto de Limnología 'Dr. Raúl A. Ringuelet' (ILPLA-CONICET), La Plata, Argentina
| | - Gustavo Berasain
- Dirección Provincial de Pesca, Ministerio de agroindustria de la Provincia de Buenos Aires, Lastra y Juarez (7130), Chascomús, Buenos Aires, Argentina
| | - Ricardo Hattori
- São Paulo 31 Fisheries Institute (APTA/SAA), Campos do Jordão, 12460-000, Brazil
| | - Fabian Grosman
- Facultad de Ciencias Veterinarias, Instituto Ecosistemas (UNCPBA-CIC), Tandil, Argentina
| | - Pablo Sanzano
- Facultad de Ciencias Veterinarias, Instituto Ecosistemas (UNCPBA-CIC), Tandil, Argentina
| | - Ismael Lozano
- Laboratorio de Ecotoxicología Acuática, Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA-CONICET), Ciudad Universitaria, Buenos Aires, Argentina
| | - Sabina L Vegh
- Instituto de Investigaciones en Producción Animal (INPA-CONICET), Buenos Aires, Argentina
| | - Victor Salinas
- Ecología & Acuicultura, Facultad de Agronomía y Veterinaria (UNRC), Río Cuarto, Argentina
| | - Omar Del Ponti
- Departamento de Recursos Naturales, Facultad de Ciencias Exactas y Naturales (UNLPam), Santa Rosa, Argentina
| | - Pamela Del Fresno
- Laboratorio de Ictiofisiología y Acuicultura IIB-INTECH (CONICET-UNSAM), Chascomús, Argentina
| | - Priscila Minotti
- Laboratorio de Ecología, Teledetección y Ecoinformática3iA Instituto de Investigación e Ingeniería Ambiental Universidad Nacional de San Martín Campus Miguelete, Martín, Argentina
| | - Yoji Yamamoto
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Claudio R M Baigún
- Laboratorio de Ecología Pesquera Aplicada, Instituto de Investigación e Ingeniería Ambiental (UNSAM-CONICET), Buenos Aires, Argentina
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18
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Phylogeographic patterns and species delimitation in the endangered silverside “humboldtianum” clade (Pisces: Atherinopsidae) in central Mexico: understanding their evolutionary history. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00419-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Abstract
Abstract
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
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Affiliation(s)
- Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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20
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Hattori RS, Somoza GM, Fernandino JI, Colautti DC, Miyoshi K, Gong Z, Yamamoto Y, Strüssmann CA. The Duplicated Y-specific amhy Gene Is Conserved and Linked to Maleness in Silversides of the Genus Odontesthes. Genes (Basel) 2019; 10:genes10090679. [PMID: 31491991 PMCID: PMC6770987 DOI: 10.3390/genes10090679] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 11/16/2022] Open
Abstract
Sex-determining genes have been successively isolated in several teleosts. In Odontesthes hatcheri and O. bonariensis, the amhy gene has been identified as a master sex-determining gene. However, whether this gene is conserved along related species is still unknown. In this study, the presence of amhy and its association with phenotypic sex was analyzed in 10 species of Odontesthes genus. The primer sets from O. hatcheri that amplify both amhs successfully generated fragments that correspond to amha and amhy in all species. The full sequences of amhy and amha isolated for four key species revealed higher identity values among presumptive amhy, including the 0.5 Kbp insertion in the third intron and amhy-specific insertions/deletions. Amha was present in all specimens, regardless of species and sex, whereas amhy was amplified in most but not all phenotypic males. Complete association between amhy-homologue with maleness was found in O. argentinensis, O. incisa, O. mauleanum, O. perugiae, O. piquava, O. regia, and O. smitti, whereas O. humensis, O. mirinensis, and O. nigricans showed varied degrees of phenotypic/genotypic sex mismatch. The conservation of amhy gene in Odontesthes provide an interesting framework to study the evolution and the ecological interactions of genotypic and environmental sex determination in this group.
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Affiliation(s)
- Ricardo S Hattori
- Unidade de Pesquisa e Desenvolvimento de Campos do Jordão, Sao Paulo Fisheries Institue, APTA/SAA, Campos do Jordão 12460-000, Brazil.
| | - Gustavo M Somoza
- Instituto Tecnológico de Chascomús (Consejo Nacional de Investigaciones Científicasy Técnicas-Universidad Nacional de San Martin), Chascomús 7130, Argentina.
| | - Juan I Fernandino
- Instituto Tecnológico de Chascomús (Consejo Nacional de Investigaciones Científicasy Técnicas-Universidad Nacional de San Martin), Chascomús 7130, Argentina.
| | - Dario C Colautti
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) (Consejo Nacional de Investigaciones Científicasy Técnicas-Universidad Nacional de La Plata), La Plata 1900, Argentina.
| | - Kaho Miyoshi
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
| | - Zhuang Gong
- School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316002, China.
| | - Yoji Yamamoto
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
| | - Carlos A Strüssmann
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
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21
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Therkildsen NO, Wilder AP, Conover DO, Munch SB, Baumann H, Palumbi SR. Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing. Science 2019; 365:487-490. [DOI: 10.1126/science.aaw7271] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
Humans cause widespread evolutionary change in nature, but we still know little about the genomic basis of rapid adaptation in the Anthropocene. We tracked genomic changes across all protein-coding genes in experimental fish populations that evolved pronounced shifts in growth rates due to size-selective harvest over only four generations. Comparisons of replicate lines show parallel allele frequency shifts that recapitulate responses to size-selection gradients in the wild across hundreds of unlinked variants concentrated in growth-related genes. However, a supercluster of genes also rose rapidly in frequency and dominated the evolutionary dynamic in one replicate line but not in others. Parallel phenotypic changes thus masked highly divergent genomic responses to selection, illustrating how contingent rapid adaptation can be in the face of strong human-induced selection.
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22
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Majtánová Z, Moy KG, Unmack PJ, Ráb P, Ezaz T. Characterization of the karyotype and accumulation of repetitive sequences in Australian Darling hardyhead Craterocephalus amniculus (Atheriniformes, Teleostei). PeerJ 2019; 7:e7347. [PMID: 31392095 PMCID: PMC6677120 DOI: 10.7717/peerj.7347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/25/2019] [Indexed: 11/20/2022] Open
Abstract
Belonging to the order Atheriniformes, Craterocephalus is one of the most widespread genera of freshwater fishes in Australia, spanning along the northern coast from central Western Australia to central New South Wales and across the Murray-Darling and Lake Eyre basins. In this study, both conventional cytogenetic techniques (Giemsa, C-banding, CMA3/DAPI staining), and fluorescence in situ hybridization (FISH) with telomeric DNA and rDNA probes were used to examine the karyotypes and other chromosomal characteristics of Darling hardyhead (Craterocephalus amniculus) from New South Wales, Australia. We identified a diploid chromosome number 2n = 48 (NF = 58) in all studied individuals. FISH with rDNA probes showed a nonsyntenic pattern, with signals on one pair of subtelocentric chromosomes for 5S rDNA and one pair of submetacentric chromosomes for 28S rDNA. C-banding displayed the accumulation of constitutive heterochromatin in the centromeric regions of approximately 40 chromosomes. CMA3/DAPI fluorescence staining revealed extremely GC-rich signals in the pericentromeric region of one submetacentric chromosomal pair with size polymorphism. We detected telomeric signals at the end of all chromosomes and no interstitial signals.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | - Karl G Moy
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
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23
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González-Castro M, Rosso JJ, Delpiani SM, Mabragaña E, Díaz de Astarloa JM. Inferring boundaries among fish species of the new world silversides (Atherinopsidae; genus Odontesthes): new evidences of incipient speciation between marine and brackish populations of Odontesthes argentinensis. Genetica 2019; 147:217-229. [PMID: 31069611 DOI: 10.1007/s10709-019-00066-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/02/2019] [Indexed: 11/24/2022]
Abstract
Species of new world silversides (Actinopterygii; Atherinopsidae; genus Odontesthes) possess economic relevance, biological interest and ecological importance. In the present paper we: (A) investigate the molecular diversity in marine species of Odontesthes from the South West Atlantic Ocean (SWAO), and analyse their interspecific relationships and divergence by means of DNA Barcoding, including its freshwater congeners, as well. (B) Explore the suitability of DNA Barcoding to analyse the diversity and distribution of haplotypes in Odontesthes argentinensis, the only well documented marine species from the SWAO that exhibit putative estuarine and marine populations. Molecular analysis revealed 100% of agreement between morphological identification and molecular identity. Odontesthes argentinensis, Odontesthes platensis, Odontesthes smitti, Odontesthes nigricans and Odontesthes incisa were assigned to five different barcode index numbers (BINs). Maximum-likelihood analysis showed that all marine species of Odontesthes clustered separately in a unique monophyletic phylogroup, comprising five well defined haplogroups, with genetic divergence between groups ranging from 2.75 to 7.11%. The genetic analysis including freshwater congeners showed that O. incisa clustered alone occupying a basal position. The Fst pairwise comparisons within O. argentinensis support the existence of three population groups: one conformed by Mar Chiquita Lagoon (MCh) specimens, and the others by Mar del Plata/Mar Chiquita coast and San Blas Bay coastal specimens, respectively. The AMOVA showed significant overall differentiation (Fst = 0.238; p = 0.00001) for the entire data set. The previous/present evidence is discussed, and strongly suggests that incipient speciation is occurring in O. argentinensis argentinean populations, and specimens from MCh would be considered at present as the leading candidate of a marine to freshwater incipient speciation event.
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Affiliation(s)
- Mariano González-Castro
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Juan José Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sergio Matías Delpiani
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan Martín Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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24
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Yamamoto Y, Hattori RS, Patiño R, Strüssmann CA. Environmental regulation of sex determination in fishes: Insights from Atheriniformes. Curr Top Dev Biol 2019; 134:49-69. [DOI: 10.1016/bs.ctdb.2019.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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25
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Silveira T, Varela Junior AS, Corcini CD, Domingues WB, Remião M, Santos L, Barreto B, Lessa I, Martins D, Boyle RT, Costa PG, Bianchini A, Robaldo RB, Campos VF. Roundup® Herbicide Decreases Quality Parameters of Spermatozoa of Silversides Odontesthes Humensis. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 102:1-6. [PMID: 30511085 DOI: 10.1007/s00128-018-2508-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
The silverside (Odontesthes humensis) is a very interesting model for toxicological studies due its high sensitivity and need for good water quality. The aim of this study was to evaluate the effects of Roundup on spermatozoa of O. humensis, after acute exposure. The fish were exposed to 0 and 7.8 mg L-1 (a.e.) of glyphosate, respectively. Through computer-assisted sperm analysis, a significant decrease in concentration, total and progressive motility, average path distance, straight line distance, path average velocity, curved line velocity, straight line velocity linearity, wobble, amplitude of lateral head displacement, cross beat frequency, and motility period of silverside spermatozoa exposed to Roundup was observed. Also, increase in membrane fluidity, ROS production and lipid peroxidation and a decrease in the mitochondrial functionality was observed in spermatozoa of Roundup exposed silversides. It was demonstrated that Roundup exposure in a concentration that can be achieve in natural water bodies soon after its application in fields is able to cause losses in several sperm quality parameters, consequently decreasing the fertilization potential of O. humensis spermatozoa.
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Affiliation(s)
- Tony Silveira
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Antonio Sergio Varela Junior
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
- Laboratório de Reprodução Animal Comparada, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Carine Dahl Corcini
- Laboratório de Reprodução Animal Comparada, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Mariana Remião
- Laboratório de Biotecnologia do Câncer, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Lucas Santos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Bruna Barreto
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Ingrid Lessa
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Diego Martins
- Laboratório de Reprodução Animal Comparada, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Robert T Boyle
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Patrícia Gomes Costa
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Ricardo B Robaldo
- Laboratório de Fisiologia, Programa de Pós-Graduação em Biologia Animal, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius Farias Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
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Capobianco A, Friedman M. Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective. Biol Rev Camb Philos Soc 2018; 94:662-699. [DOI: 10.1111/brv.12473] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Alessio Capobianco
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
| | - Matt Friedman
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
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De-novo assembly and transcriptome analysis of Odontesthes argentinensis gill tissue, with development of single sequence repeat markers. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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28
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Betancourt-Resendes I, Pérez-Rodríguez R, Domínguez-Domínguez O. Speciation of silverside Chirostoma attenuatum
(Pisces: Atheriniformes) in Central Mexico. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Isaí Betancourt-Resendes
- Programa Institucional de Doctorado en Ciencias Biológicas; Facultad de Biología; Universidad Michoacana de San Nicolás de Hidalgo; Morelia Michoacán México
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática; Facultad de Biología; Universidad Michoacana de San Nicolás de Hidalgo; Morelia Michoacán México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática; Facultad de Biología; Universidad Michoacana de San Nicolás de Hidalgo; Morelia Michoacán México
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29
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Silveira TLR, Martins GB, Domingues WB, Remião MH, Barreto BF, Lessa IM, Santos L, Pinhal D, Dellagostin OA, Seixas FK, Collares T, Robaldo RB, Campos VF. Gene and Blood Analysis Reveal That Transfer from Brackish Water to Freshwater Is More Stressful to the Silverside Odontesthes humensis. Front Genet 2018; 9:28. [PMID: 29541090 PMCID: PMC5836595 DOI: 10.3389/fgene.2018.00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/22/2018] [Indexed: 11/13/2022] Open
Abstract
Silversides are fish that inhabit marine coastal waters, coastal lagoons, and estuarine regions in southern South America. The freshwater (FW) silversides have the ability to tolerate salinity variations. Odontesthes humensis have similar habitats and biological characteristics of congeneric O. bonariensis, the most studied silverside species and with great economic importance. Studies revealed that O. bonariensis is not fully adapted to FW, despite inhabiting hyposmotic environments in nature. However, there is little information about stressful environments for cultivation of silverside O. humensis. Thus, the aim of this study was to evaluate the stress and osmoregulation responses triggered by the osmotic transfers on silverside O. humensis. Silversides were acclimated to FW (0 ppt) and to brackish water (BW, 10 ppt) and then they were exposed to opposite salinity treatment. Silverside gills and blood were sampled on pre-transfer (D0) and 1, 7, and 15 days (D1, D7, and D15) after changes in environmental salinity, the expression levels of genes atp1a3a, slc12a2b, kcnh1, and hspa1a were determined by quantitative reverse transcription-PCR for evaluation of osmoregulatory and stress responses. Furthermore, glycemia, hematocrit, and osmolality were also evaluated. The expression of atp1a3a was up- and down-regulated at D1 after the FW-BW and BW-FW transfers, respectively. Slc12a2b was up-regulated after FW-BW transfer. Similarly, kcnh1 and hspa1a were up-regulated at D1 after the BW-FW transfer. O. humensis blood osmolality decreased after the exposure to FW. It remained stable after exposure to BW, indicating an efficient hyposmoregulation. The glycemia had a peak at D1 after BW-FW transfer. No changes were observed in hematocrit. The return to the pre-transfer levels at D7 after the significant increases in responses of almost all evaluated molecular and blood parameters indicated that this period is enough for acclimation to the experimental conditions. In conclusion, our results suggest that BW-FW transfer is more stressful to O. humensis than FW-BW transfer and the physiology of O. humensis is only partially adapted to FW.
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Affiliation(s)
- Tony L. R. Silveira
- Laboratory of Structural Genomics, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Gabriel B. Martins
- Laboratory of Physiology, Institute of Biology, Federal University of Pelotas, Pelotas, Brazil
| | - William B. Domingues
- Laboratory of Structural Genomics, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Mariana H. Remião
- Laboratory of Cancer Biotechnology, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Bruna F. Barreto
- Laboratory of Structural Genomics, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Ingrid M. Lessa
- Laboratory of Structural Genomics, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Lucas Santos
- Laboratory of Structural Genomics, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Danillo Pinhal
- Genomics and Molecular Evolution Laboratory, Department of Genetics, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, Brazil
| | - Odir A. Dellagostin
- Laboratory of Vaccinology, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Fabiana K. Seixas
- Laboratory of Cancer Biotechnology, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Tiago Collares
- Laboratory of Cancer Biotechnology, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Ricardo B. Robaldo
- Laboratory of Physiology, Institute of Biology, Federal University of Pelotas, Pelotas, Brazil
| | - Vinicius F. Campos
- Laboratory of Structural Genomics, Technological Development Center, Federal University of Pelotas, Pelotas, Brazil
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30
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Nash CM, Kraczkowski ML, Chernoff B. Insight into the population structure of hardhead silverside, Atherinomorus stipes (Teleostei: Atherinidae), in Belize and the Florida Keys using nd2. Ecol Evol 2017; 7:9503-9517. [PMID: 29187985 PMCID: PMC5696406 DOI: 10.1002/ece3.3457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/07/2017] [Accepted: 08/11/2017] [Indexed: 11/18/2022] Open
Abstract
Little is known about the natural history, biology, and population genetic structure of the Hardhead Silverside, Atherinomorus stipes, a small schooling fish found around islands throughout the Caribbean. Our field observations of A. stipes in the cays of Belize and the Florida Keys found that populations tend to be in close association with the shoreline in mangrove habitats. Due to this potential island‐based population structuring, A. stipes represents an ideal system to examine questions about gene flow and isolation by distance at different geographic scales. For this study, the mitochondrial gene nd2 was amplified from 394 individuals collected from seven different Belizean Cays (N = 175) and eight different Floridian Keys (N = 219). Results show surprisingly high haplotype diversity both within and between island‐groups, as well as a high prevalence of unique haplotypes within each island population. The results are consistent with models that require gene flow among populations as well as in situ evolution of rare haplotypes. There was no evidence for an isolation by distance model. The nd2 gene tree consists of two well‐supported monophyletic groups: a Belizean‐type clade and a Floridian‐type clade, indicating potential species‐level differentiation.
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Affiliation(s)
- Chloe M Nash
- Biology Department Wesleyan University Middletown CT USA.,College of the Environment Wesleyan University Middletown CT USA
| | - Michelle L Kraczkowski
- College of the Environment Wesleyan University Middletown CT USA.,Biology Department University of Saint Joseph West Hartford CT USA
| | - Barry Chernoff
- Biology Department Wesleyan University Middletown CT USA.,College of the Environment Wesleyan University Middletown CT USA.,Department of Earth & Environmental Sciences Wesleyan University Middletown CT USA
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31
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Abstract
The diversity of forms found among animals on Earth is striking. Despite decades of study, it has been difficult to reconcile the patterns of diversity seen between closely related species with those observed when studying single species on ecological timescales. We propose a set of models, called Lévy processes, to attempt to reconcile rapid evolution between species with the relatively stable distributions of phenotypes seen within species. These models, which have been successfully used to model stock market data, allow for long periods of stasis followed by bursts of rapid change. We find that many vertebrate groups are well fitted by Lévy models compared with models for which traits evolve toward a stationary optimum or evolve in an incremental and wandering manner. The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest some lineages experience very fast rates of evolution. One way to reconcile these observations is to imagine that evolution proceeds in pulses, rather than in increments, on geological timescales. To test this hypothesis, we developed a maximum-likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both an incremental and a pulsed component. We found that a plurality of modern vertebrate clades examined are best fitted by pulsed processes over models of incremental change, stationarity, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and observations from the fossil record.
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32
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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: 418] [Impact Index Per Article: 59.7] [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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33
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Conway KW, Kim D, Rüber L, Espinosa Pérez HS, Hastings PA. Molecular systematics of the New World clingfish genus Gobiesox (Teleostei: Gobiesocidae) and the origin of a freshwater clade. Mol Phylogenet Evol 2017; 112:138-147. [DOI: 10.1016/j.ympev.2017.04.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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34
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Hughes LC, Somoza GM, Nguyen BN, Bernot JP, González-Castro M, Díaz de Astarloa JM, Ortí G. Transcriptomic differentiation underlying marine-to-freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes). Ecol Evol 2017; 7:5258-5268. [PMID: 28770064 PMCID: PMC5528240 DOI: 10.1002/ece3.3133] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/22/2022] Open
Abstract
Salinity gradients are critical habitat determinants for freshwater organisms. Silverside fishes in the genus Odontesthes have recently and repeatedly transitioned from marine to freshwater habitats, overcoming a strong ecological barrier. Genomic and transcriptomic changes involved in this kind of transition are only known for a few model species. We present new data and analyses of gene expression and microbiome composition in the gills of two closely related silverside species, marine O. argentinensis and freshwater O. bonariensis and find more than three thousand transcripts differentially expressed, with osmoregulatory/ion transport genes and immune genes showing very different expression patterns across species. Interspecific differences also involve more than one thousand transcripts with nonsynonymous SNPs in the coding sequences, most of which were not differentially expressed. In addition to characterizing gill transcriptomes from wild‐caught marine and freshwater fishes, we test experimentally the response to salinity increases by O. bonariensis collected from freshwater habitats. Patterns of expression in gill transcriptomes of O. bonariensis exposed to high salinity do not resemble O. argentinensis mRNA expression, suggesting lack of plasticity for adaptation to marine conditions in this species. The diversity of functions associated with both the differentially expressed set of transcripts and those with sequence divergence plus marked microbiome differences suggest that multiple abiotic and biotic factors in marine and freshwater habitats are driving transcriptomic differences between these species.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences The George Washington University Washington DC USA
| | - Gustavo M Somoza
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (CONICET-UNSAM) Chascomús Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina
| | - Bryan N Nguyen
- Department of Biological Sciences The George Washington University Washington DC USA.,Computational Biology Institute The George Washington University Washington DC USA
| | - James P Bernot
- Computational Biology Institute The George Washington University Washington DC USA.,Institute for Biomedical Sciences The George Washington University Washington DC USA
| | - Mariano González-Castro
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina.,Grupo de Biotaxonomía Morfológica y molecular de peces IIMyC-CONICET Universidad Nacional de Mar del PlataMar del Plata Argentina
| | - Juan Martín Díaz de Astarloa
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina.,Grupo de Biotaxonomía Morfológica y molecular de peces IIMyC-CONICET Universidad Nacional de Mar del PlataMar del Plata Argentina
| | - Guillermo Ortí
- Department of Biological Sciences The George Washington University Washington DC USA
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Pinpointing cryptic borders: Fine-scale phylogeography and genetic landscape analysis of the Hormogaster elisae complex (Oligochaeta, Hormogastridae). Mol Phylogenet Evol 2017; 112:185-193. [PMID: 28487260 DOI: 10.1016/j.ympev.2017.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/24/2017] [Accepted: 05/05/2017] [Indexed: 11/20/2022]
Abstract
Spatial and temporal aspects of the evolution of cryptic species complexes have received less attention than species delimitation within them. The phylogeography of the cryptic complex Hormogaster elisae (Oligochaeta, Hormogastridae) lacks knowledge on several aspects, including the small-scale distribution of its lineages or the palaeogeographic context of their diversification. To shed light on these topics, a dense specimen collection was performed in the center of the Iberian Peninsula - resulting in 28 new H. elisae collecting points, some of them as close as 760m from each other- for a higher resolution of the distribution of the cryptic lineages and the relationships between the populations. Seven molecular regions were amplified: mitochondrial subunit 1 of cytochrome c oxidase (COI), 16S rRNA and tRNA Leu, Ala, and Ser (16S t-RNAs), one nuclear ribosomal gene (a fragment of 28S rRNA) and one nuclear protein-encoding gene (histone H3) in order to infer their phylogenetic relationships. Different representation methods of the pairwise divergence in the cytochrome oxidase I sequence (heatmap and genetic landscape graphs) were used to visualize the genetic structure of H. elisae. A nested approach sensu Mairal et al. (2015) (connecting the evolutionary rates of two datasets of different taxonomic coverage) was used to obtain one approximation to a time-calibrated phylogenetic tree based on external Clitellata fossils and a wide molecular dataset. Our results indicate that limited active dispersal ability and ecological or biotic barriers could explain the isolation of the different cryptic lineages, which never co-occur. Rare events of long distance dispersal through hydrochory appear as one of the possible causes of range expansion.
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36
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Richter P, Moritz T. Lessons from the first dorsal fin in atheriniforms-A new mode of dorsal fin development and its phylogenetic implications. J Morphol 2017; 278:848-864. [PMID: 28370120 PMCID: PMC5434871 DOI: 10.1002/jmor.20679] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/10/2017] [Accepted: 03/17/2017] [Indexed: 11/16/2022]
Abstract
The median fins in extant actinopterygians are the product of millions of years of evolution. During this time, different developmental patterns for the dorsal and anal fins emerged leading to a high variation in median fin morphology and ontogeny. In this study, the development of anal and dorsal fins in atheriniforms is described and its consequences for the current phylogenetic hypothesis are discussed. Developmental series of five atheriniform species were investigated using clearing and staining as well as antibody staining. The skeletal elements of the second dorsal fin and the anal fin emerge in a bidirectional pattern. The first dorsal fin, however, arises separately in front of the second dorsal fin after this one is almost completely formed. The pterygiophores of the first dorsal fin, including the interdorsal pterygiophores, develop from caudal to rostral, but the fin‐spines of the first dorsal fin form in the opposite direction. This new mode of fin development has been found in all examined atheriniform species with two dorsal fins. Several morphological characters of atheriniforms, including interdorsal pterygiophores, are also found in one other taxon: the Mugiliformes. Thus, several dorsal fin characteristics may provide evidence for a closer relationship of these two taxa.
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Affiliation(s)
- Philipp Richter
- Institut für Spezielle Zoologie & Evolutionsbiologie mit Phyletischem Museum, Friedrich Schiller Universität Jena, Erbertstraße 1, Jena, 07743, Germany.,Deutsches Meeresmuseum Stralsund, Katharinenberg 14-20, Stralsund, 18439, Germany
| | - Timo Moritz
- Institut für Spezielle Zoologie & Evolutionsbiologie mit Phyletischem Museum, Friedrich Schiller Universität Jena, Erbertstraße 1, Jena, 07743, Germany.,Deutsches Meeresmuseum Stralsund, Katharinenberg 14-20, Stralsund, 18439, Germany
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37
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Martínez-Aquino A, Vigliano-relva J, Brusa F, Damborenea C. Historical biogeography of Temnocephalida (Platyhelminthes, Rhabdocoela): testing the Gondwanan hypothesis. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1252441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Andres Martínez-Aquino
- Laboratorio de Patología Acuática, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Km 6 Carretera Antigua a Progreso, Cordemex, Mérida, Yucatán 97310, México
| | - Julieta Vigliano-relva
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
| | - Francisco Brusa
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Cristina Damborenea
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
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38
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Rueda EC, Mullaney KA, Conte-Grand C, Habit EM, Cussac V, Ortí G. Displacement of native Patagonian freshwater silverside populations (Odontesthes hatcheri, Atherinopsidae) by introgressive hybridization with introduced O. bonariensis. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1295-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Díaz J, Villanova GV, Brancolini F, del Pazo F, Posner VM, Grimberg A, Arranz SE. First DNA Barcode Reference Library for the Identification of South American Freshwater Fish from the Lower Paraná River. PLoS One 2016; 11:e0157419. [PMID: 27442116 PMCID: PMC4956254 DOI: 10.1371/journal.pone.0157419] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/31/2016] [Indexed: 11/22/2022] Open
Abstract
Valid fish species identification is essential for biodiversity conservation and fisheries management. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I for a valid identification of 79 freshwater fish species from the Lower Paraná River. Neighbour-joining analysis based on K2P genetic distances formed non-overlapping clusters for almost all species with a ≥99% bootstrap support each. Identification was successful for 97.8% of species as the minimum genetic distance to the nearest neighbour exceeded the maximum intraspecific distance in all these cases. A barcoding gap of 2.5% was apparent for the whole data set with the exception of four cases. Within-species distances ranged from 0.00% to 7.59%, while interspecific distances varied between 4.06% and 19.98%, without considering Odontesthes species with a minimum genetic distance of 0%. Sequence library validation was performed by applying BOLDs BIN analysis tool, Poisson Tree Processes model and Automatic Barcode Gap Discovery, along with a reliable taxonomic assignment by experts. Exhaustive revision of vouchers was performed when a conflicting assignment was detected after sequence analysis and BIN discordance evaluation. Thus, the sequence library presented here can be confidently used as a benchmark for identification of half of the fish species recorded for the Lower Paraná River.
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Affiliation(s)
- Juan Díaz
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Santa Fe, Argentina
| | - Gabriela Vanina Villanova
- Area Biología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- Laboratorio de Biotecnología Acuática (FCByF-UNR/SeCTEI-Santa Fe), Acuario del río Paraná, Rosario, Santa Fe, Argentina
| | - Florencia Brancolini
- Instituto de Limnología “Dr. Raúl A. Ringuelet” (ILPLA, CONICET-UNLP), La Plata, Buenos Aires, Argentina
| | - Felipe del Pazo
- Area Biología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Victoria Maria Posner
- Area Biología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Alexis Grimberg
- Laboratorio de Biotecnología Acuática (FCByF-UNR/SeCTEI-Santa Fe), Acuario del río Paraná, Rosario, Santa Fe, Argentina
| | - Silvia Eda Arranz
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Santa Fe, Argentina
- Area Biología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- Laboratorio de Biotecnología Acuática (FCByF-UNR/SeCTEI-Santa Fe), Acuario del río Paraná, Rosario, Santa Fe, Argentina
- * E-mail:
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