Special Issue "Genetics of Neotropical fishes: Conservation, Management and Evolution"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 July 2019

Special Issue Editors

Guest Editor
Prof. Manel Vera Rodríguez

Universidad Santiago de Compostela
Website | E-Mail
Interests: Conservation genetics; Population genomics; Phylogeny; Aquatic organisms; Adaptive variation
Guest Editor
Prof. Diogo Teuro Hashimoto

UNESP-Universidade Estadual Paulista, Aquaculture Center
E-Mail

Special Issue Information

Dear colleagues,

Neotropical fishes are one of the most diverse animal groups, representing ~10 % of all living vertebrate species (~ 6000 species). This group inhabits a broad variety of environments, including both freshwater, brackish water and marine ecosystems, which highlights their interest for the study of evolutionary processes. The knowledge of the genetic status of these species (including their diversity, population structure, connectivity and local adaptations) is a key issue for the application of proper management and conservation actions, to ensure their sustainability in the context of the ongoing climate change and the human-mediated disturbances.

In this fish group, several chromosome studies have been performed to understand the evolution of fish genomes, the differentiation between populations, the occurrence of cryptic species and complex of species. Specific mechanisms of sex chromosomes have been detected, revealing multiple systems of sex determination. Moreover, the origin and function of supernumerary chromosomes has been deeply explored in some species.

This Special Issue accepts submissions of research articles, reviews and short communications and it is focused on the genetics of Neotropical fishes including, but not limited to, studies of phylogeography, cytogenetics, population genetics/genomics, conservation, description of endemisms, local adaptations, genetic monitoring and landscape analyses. Moreover, genetic studies of invasive species or hybrids that can compromise the future of native species, and of species with interest for aquaculture in the Neotropical Region with emphasis on their sustainable production will be also welcome.

Prof. Manel Vera Rodríguez
Prof. Diogo Teuro Hashimoto
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genetic diversity
  • Phylogeography
  • Population structure
  • Management of wild resources
  • Endemisms
  • Selection fingerprints
  • Population genomics
  • Landscape analyses
  • Aquaculture
  • Genetic monitoring
  • Sustainability
  • Sex Chromosomes
  • B Chromosomes
  • Cytogenetics

Published Papers (2 papers)

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Research

Open AccessArticle
Molecular Data Reveal Multiple Lineages in Piranhas of the Genus Pygocentrus (Teleostei, Characiformes)
Received: 12 April 2019 / Revised: 9 May 2019 / Accepted: 13 May 2019 / Published: 15 May 2019
PDF Full-text (1820 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Carnivorous piranhas are distributed in four serrasalmid genera including Pygocentrus, which inhabit major river basins of South America. While P. cariba and P. piraya are endemics of the Orinoco and São Francisco basins, respectively, P. nattereri is widely distributed across the Amazonas, Essequibo, [...] Read more.
Carnivorous piranhas are distributed in four serrasalmid genera including Pygocentrus, which inhabit major river basins of South America. While P. cariba and P. piraya are endemics of the Orinoco and São Francisco basins, respectively, P. nattereri is widely distributed across the Amazonas, Essequibo, lower Paraná, Paraguay, and coastal rivers of northeastern Brazil, with recent records of introductions in Asia. Few studies have focused on the genetic diversity and systematics of Pygocentrus and the putative presence of additional species within P. nattereri has never been the subject of a detailed molecular study. Here we aimed to delimit species of Pygocentrus, test the phylogeographic structure of P. nattereri, and access the origin of introduced specimens of P. nattereri in Asia. Phylogenetic analyses based on a mitochondrial dataset involving maximum-likelihood tree reconstruction, genetic distances, Bayesian analysis, three delimitation approaches, and haplotype analysis corroborate the morphological hypothesis of the occurrence of three species of Pygocentrus. However, we provide here strong evidence that P. nattereri contains at least five phylogeographically-structured lineages in the Amazonas, Guaporé (type locality), Itapecuru, Paraná/Paraguay, and Tocantins/Araguaia river basins. We finally found that the introduced specimens in Asia consistently descend from the lineage of P. nattereri from the main Rio Amazonas. These results contribute to future research aimed to detect morphological variation that may occur in those genetic lineages of Pygocentrus. Full article
Figures

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Open AccessArticle
DNA Barcode Reveals the Bycatch of Endangered Batoids Species in the Southwest Atlantic: Implications for Sustainable Fisheries Management and Conservation Efforts
Received: 26 February 2019 / Revised: 1 April 2019 / Accepted: 1 April 2019 / Published: 18 April 2019
PDF Full-text (1375 KB) | HTML Full-text | XML Full-text
Abstract
Today, elasmobranchs are one the most threatened vertebrate groups worldwide. In fact, at least 90% of elasmobranch species are listed in the International Union for Conservation of Nature (IUCN) Red List, while more than 40% are data-deficient. Although these vertebrates are mainly affected [...] Read more.
Today, elasmobranchs are one the most threatened vertebrate groups worldwide. In fact, at least 90% of elasmobranch species are listed in the International Union for Conservation of Nature (IUCN) Red List, while more than 40% are data-deficient. Although these vertebrates are mainly affected by unsustainable fishery activities, bycatch is also one of the major threats to sharks and batoids worldwide, and represents a challenge for both sustainable fishery management and for biodiversity and conservational efforts. Thus, in this study, DNA barcode methodology was used to identify the bycatch composition of batoid species from small-scale industrial fisheries in the southwest Atlantic and artisanal fisheries from southeast Brazil. A total of 228 individuals belonging to four Chondrichthyes orders, seven families, and at least 17 distinct batoid species were sequenced; among these individuals, 131 belonged to species protected in Brazil, 101 to globally threatened species, and some to species with trade restrictions provided by Appendix II of the Convention on International Trade in Endangered Species (CITES). These results highlight the impacts on marine biodiversity of bycatch by small-scale industrial and unmanaged artisanal fisheries from the southwest Atlantic, and support the implementation of DNA-based methodologies for species-specific identification in data-poor fisheries as a powerful tool for improving the quality of fisheries’ catch statistics and for keeping precise bycatch records. Full article
Figures

Figure 1

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Identification of Y-linked amhy gene in New World Silversides and field survey of sex-reversed individuals

Ricardo Shohei Hattori, Gustavo Manuel Somoza, Juan Ignacio Fernandino, Dario Cesar Colautti, Sonia Crichigno Alejandra, Cecilia Conte-Grand, Víctor Cussac, Brian Dyer, Lurdes Foresti de Almeida-Toledo, Yoji Yamamoto, Carlos Augusto Strüssmann

Sex-determining genes have been successively identified in several groups of teleosts. In Odontesthes hatcheri and O. bonariensis the duplicated Y-specific amh gene, amhy, has been identified as the candidate of master sex-determining gene in these species. However, whether this gene in conserved along other related species is still unknown. In this study, the amhy gene was detected in 10 out of 16 species described so far and used for screening of sex reversal in natural populations. amhy was successfully amplified in all Odontesthes species analyzed and its expression confirmed in testis of O. incisa, O. piquava, and O. smitti. The partial ORF sequences showed higher identity values with amhy in relation to amha and amhy-specific insertion and deletion were also detected, supporting that the isolated fragment comprises the amhy of these species. Field surveys in 12 Odontesthes species also evidenced the occurrence of sex reversal in O. bonariensis, O. hatcheri, O. cf. humensis, O. mirinensis and O. nigricans whereas in other 7, no sex reversal was observed. By making an association between the environments these species inhabit and the frequency of sex reversal, we observed that species inhabiting inland waters (rivers and lakes) show higher rates of sex reversal than those inhabiting marine or estuarine environments. These patterns can be related to higher susceptibility to thermal fluctuations or vulnerability to endocrine disruptors in inland waters, which could induce the appearance of sex-reversed animals. The conservation of amhy gene in Odontesthes genus increase the usefulness of this group of fish in ecological and evolutionary studies.

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DNA barcode reveals the bycatch of endangered batoids species in the Southwest Atlantic: implications for sustainable fisheries management and conservation efforts

Fernando F. Mendoça

Nowadays, elasmobranchs are one the most threatened vertebrate groups worldwide. In fact, at least 90% of elasmobranch species are listed in the IUCN Red List while more than 40% are data-deficient. Although, these vertebrates are mainly affected by unsustainable fishery activities, bycatch is also one of the major threats to sharks and batoids worldwide and represents a challenge for both sustainable fishery management and for biodiversity and conservational efforts. Thus, in this study the DNA barcode methodology was used to identify the bycatch composition of batoids species from small-scale industrial fisheries in the Southwest Atlantic and artisanal fisheries from southeast Brazil. A total of 228 individuals belonging to four Chondrichthyes orders, seven families, and at least 17 distinct batoid species were sequenced; among these individuals, 131 belong to species protected in Brazil, 101 threatened globally and some have trade restrictions provided by Appendix II of CITES. These results highlight the impacts of bycatch on marine biodiversity by small-scale industrial and unmanaged artisanal fisheries from Southwest Atlantic and support the implementation of DNA-based methodologies for species-specific identification in data-poor fisheries as a powerful tool for improving the quality of fisheries catch-statistics and keep precise bycatch records.

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Low indices of genetic diversity in threatened species of guitarfish (Elasmobranchii, Rhinobatidae) in the Brazilian and Argentinian coast: an alert for conservation

Vanessa P. Cruz, Aisni M.C. L. Adachi, Pablo H. Oliveira, Giovana S. Ribeiro, Fabilene G. Paim, Bruno C. Souza, Alexandre S.F. Rodrigues, Natália J.Mendes, Marcelo Vianna, Sergio M. Delpiani, Fernando F. Mendonça, Claudio Oliveira, Rosangela P. Lessa, Fausto Foresti

Pseudobatos horkelii (critically endangered) and Pseudobatos percellens (near threatened), all commonly known as guitarfish, are found in coastal regions of the west Atlantic and are commonly caught as bycatches of small local inshore fisheries and can be captured in a variety of gear. In the last decades, these species have all suffered significant declines in population size. The capture of P. horkelii by the fishing industry is prohibited under national legislation in the states of the regions on the southern coast, however, this species is illegally marketed. Owing to the absence of information on the genetic structure of these populations, the present study aimed to identify the genetic variability and population structure of guitarfish P. horkelii and P. percellens, from the Southeastern and Southern regions of Brazil and northern coast of Argentina using mitochondrial DNA of the control region. The total of 82 individuals of P. horkelii were analyzed, distributed in six localities (North of Argentina, in Brazil on states Rio Grande do Sul, Santa Catarina, Paraná, São Paulo and Rio de Janeiro). Haplotype diversity in populations of North Argentina and Rio Grande do Sul was higher (h=0.87708) and diversity nucleotide more high for São Paulo and Rio de Janeiro (π =0.00493). The AMOVA test identified a ΦST value ranging from 0.20989 to 0.56202 in different structure scenarios, being detected three distinct populations for P. horkelii. Our results detected high indices of genetic diversity, occurring mostly in the region of Rio Grande do Sul, where actions prohibiting indiscriminate fishing of this species already act effectively. In P. percellens 72 specimens were analyzed in six localities in Brazil, distributed in the states Santa Catarina, Paraná and São Paulo. Diversity indices were higher for individuals of São Paulo (h =0.30868 and π =0.00493). Hypothetic groups for running AMOVA test ranging from ΦST = -0.04856 to 0.0794, identifying three distinct populations. The levels of genetic diversity in P. percellens are the lowest reported for rays, which would be alarming for the species. In view of these results, we believe that P. percellens currently classified as near threatened should be re-evaluated.

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Species delimitation in piranhas of the genus Pygocentrus reveals multiple sibling species in P. nattereri (Teleostei, Characiformes)

Nadayca T. B. Mateussi, Bruno F. Melo, Fausto Foresti, Claudio Oliveira

Carnivorous piranhas are distributed in four serrasalmid genera including Pygocentrus, the largest species that inhabit major river basins of South America. While P. cariba and P. piraya are endemics of the Orinoco and São Francisco basins, respectively, P. nattereri is widely distributed across the Amazon, Essequibo, Paraná-Paraguai, and coastal rivers of northeastern Brazil, with recent records of introductions in Asia. A few studies have focused on the genetic diversity and systematics of Pygocentrus but the putative presence of additional species within P. nattereri has never been the subject of a detailed molecular study. Here we aimed to delimit species of Pygocentrus, test the phylogeographic structure of P. nattereri, and access the origin of introduced specimens of P. nattereri in Asia. Phylogenetic analyses based on a mitochondrial dataset including maximum-likelihood tree reconstruction, genetic distances, and three delimitation approaches indicate three well-defined species and thus corroborating a prior morphological hypothesis. Results also evidence that P. nattereri contains at least four sibling species in the Amazon, Araguaia, Itapecuru and Paraguai river basins supplemented by specimens closer to the type locality in the Rio Guaporé, indicating that future taxonomic studies should compare specimens from those five distinct riverine systems. We finally found evidence that the introduced specimens in Asia descend from the lineage of P. nattereri from the main Amazon basin.

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Evaluation of the genetic diversity for pre-breeding program in Piaractus mesopotamicus by SNPs and SSRs

Vito Antonio Mastrochirico-Filho, Felipe del Pazo, Milene Elissa Hata, Gabriela Vanina Villanova, Fausto Foresti, Manuel Vera, Paulino Martínez, Fábio Porto-Foresti, and Diogo Teruo Hashimoto

Pacu (Piaractus mesopotamicus) is a Neotropical fish species with high productive performance in aquaculture. Evaluation of the genetic structure in Neotropical species is still insufficient, mainly for applications in breeding programs. The aim of this study was to characterize the genetic diversity of seven farmed populations of pacu which will constitute the population basis for future breeding programs in Brazil. The analyses were performed using 32 SNPs and 8 SSRs. The comparative analysis of all populations did not demonstrate significant differences between allele number and allelic richness (SSRs), observed heterozygosity (Hobs), expected heterozygosity (Hexp) and minimum allele frequency (MAF) of SNPs (P < 0.05). High genetic diversity in farmed stocks and wild population was detected. However, we detected moderate genetic structure between farmed and wild populations for SNPs (FST = 0.064; K=3) and SSRs (FST = 0.080; K=2). AMOVA demonstrated that genetic variation was within populations. Kinship analysis showed that most of fish farms had at least 40% of related individuals. Our results suggest that the population basis in pacu must be constituted of individuals from fish farms of distinct genetic groups, by selective mating program and without inbreeding risks to maintain the current genetic variability.

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Transcriptome-based SNP discovery and validation in the reconstruction of the genomic architecture in the hybrid zone of the Neotropical annual fish genus Austrolebias

Graciela García, Néstor Ríos, Verónica Gutiérrez, Sebastián Serra, Marcelo Loureiro.

Austrolebias genus (Cyprinodontiformes: Rivulidae) represents a specious group of taxa with annual life cycle among Neotropical ichthyofauna, in South America. They live in temporary ponds and each generation should be completed in few months, depending on environmental stochasticity. Annual fish survive the dry season through diapausing eggs buried in the substrate of these temporary ponds. Spectacular species radiation has been reported for Austrolebias from the Pampas, where high morphological diversity and extensive karyotype divergence have been recorded in this. Additionally, the burst speciation process in this genus included an unusually large genome size increase within the aplocheilids, associated to the explosive expansion of the transposable elements (TEs) representing more than 45% of the diploid Austrolebias genomes. A hypothesized bimodal hybrid zone between two taxa of the genus, A. charrua and A. reicherti from Dos Patos Merin lagoon system was recently proposed based in genetics and morphological analyses. However, because of the relatively small number of microsatellite loci used in that study, the hypothetic bimodal pattern must be contrasted by including hundreds of nuclear molecular markers to strongly support it. In present paper, we conducted RNA-seq-based sequencing of the transcriptomes from pools of individuals of A. charrua, A. reicherti and their putative natural hybrids from the previously characterized hybrid zone. As a result, we identified a set of 111,725 SNP markers presumably fixed-allelic differences among the two species. These markers belong to a total of 22,490 contig transcripts. We then developed a subset of 130 SNPs into a single diagnostic multiplex assay and validated their capacity to reconstruct the patterns of the hybrid zone and levels of introgression between both taxa. The availability of this resource, high-quality transcriptomes and a large set of gene-linked SNPs, should greatly facilitate the functional and population genomics studies in these endangered species and will allow the identification of traits and processes under selection during introgressive hybridization.

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