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Genetics of Neotropical fishes: Conservation, Management and Evolution

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

Deadline for manuscript submissions: closed (31 July 2019) | Viewed by 42061

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Special Issue Editors

Dr. Manuel Vera Rodríguez

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Guest Editor

Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Lugo, Spain
Interests: population genetics; evolution, genomics; phylogenetics; conservation of natural resources; fish evolution; mollusc evolution

Prof. Diogo Teuro Hashimoto

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Guest Editor

Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP 14884-900, Brazil
Interests: genetic diversity; population structure; management of wild resources; landscape analyses

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

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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

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Published Papers (9 papers)

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Research

27 pages, 3745 KiB

Open AccessArticle

Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region

by Néstor Ríos, Adrián Casanova, Miguel Hermida, Belén G. Pardo, Paulino Martínez, Carmen Bouza and Graciela García

Genes 2020, 11(1), 109; https://doi.org/10.3390/genes11010109 - 17 Jan 2020

Cited by 8 | Viewed by 4328

Abstract

Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region. Full article

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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12 pages, 1970 KiB

Open AccessArticle

Differential Expression of Genes Related to Sexual Determination Can Modify the Reproductive Cycle of Astyanax scabripinnis (Characiformes: Characidae) in B Chromosome Carrier Individuals

by Jonathan Pena Castro, Ricardo Shohei Hattori, Túlio Teruo Yoshinaga, Duílio Mazzoni Zerbinato de Andrade Silva, Francisco J. Ruiz-Ruano, Fausto Foresti, Mateus Henrique Santos, Mara Cristina de Almeida, Orlando Moreira-Filho and Roberto Ferreira Artoni

Genes 2019, 10(11), 909; https://doi.org/10.3390/genes10110909 - 8 Nov 2019

Cited by 5 | Viewed by 2808

Abstract

The species complex Astyanax scabripinnis is one of the most studied with respect to origin, distribution, and frequency of B chromosomes, and is considered a model organism for evolutionary studies. Research using population inferences about the occurrence and frequency of the B chromosome shows seasonal variation between sexes, which is associated with the presence of this supernumerary element. We hypothesized that the B chromosome could influence the sex ratio of these animals. Based on this assumption, the present work aimed to investigate if differences exist among levels of gene expression with qRT-PCR of the amh (associated with testicular differentiation) and foxl2a (associated with ovarian differentiation) genes between B-carrier and non-B-carrier individuals. The results showed that for the amh gene, the difference in expression between animals with B chromosomes was not accentuated compared to that in animals without this chromosome. Expression of foxl2a in B-carrier females, however, was reduced by 73.56% compared to females that lacked the B chromosome. Males had no difference in expression of the amh and foxl2a genes between carriers and non-carriers of the B chromosome. Results indicate that the presence of B chromosomes is correlated with the differential expression of sex-associated genes. An analysis of these results integrated with data from other studies on the reproductive cycle in the same species reveals that this difference in expression may be expanding the reproductive cycle of the species. Full article

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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21 pages, 2396 KiB

Open AccessArticle

Transcriptome-Based SNP Discovery and Validation in the Hybrid Zone of the Neotropical Annual Fish Genus Austrolebias

by Graciela García, Néstor Ríos, Verónica Gutiérrez, Sebastián Serra and Marcelo Loureiro

Genes 2019, 10(10), 789; https://doi.org/10.3390/genes10100789 - 11 Oct 2019

Cited by 8 | Viewed by 3657

Abstract

The genus Austrolebias (Cyprinodontiformes: Rivulidae) represents a specious group of taxa following annual life cycles in the neotropical ichthyofauna. They live in temporary ponds and each generation must be completed in a few months, depending on environmental stochasticity. Annual fish survive the dry season through diapausing eggs buried in the substrate of these ponds. 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 on genetics and morphological analyses. However, hundreds of additional nuclear molecular markers should be used to strongly support this hypothesized bimodal pattern. In the 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 (single nucleotide polymorphism) markers, representing presumably fixed allelic differences among the two species. The present study provided the first panel of 106 SNP markers as a single diagnostic multiplex assay and validated their capacity to reconstruct the patterns of the hybrid zone between both taxa. These nuclear markers combined with Cytb gene and morphological analyses detected a population structure in which some groups among the hybrid swarms showed different level of introgression towards one or the other parental species according to their geographic distribution. High-quality transcriptomes and a large set of gene-linked SNPs should greatly facilitate functional and population genomics studies in the hybrid zone of these endangered species. Full article

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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18 pages, 3439 KiB

Open AccessArticle

Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum)

by Fernando Henrique Santos de Souza, Manolo Fernandez Perez, Luiz Antônio Carlos Bertollo, Ezequiel Aguiar de Oliveira, Sebastien Lavoué, Carla Cristina Gestich, Petr Ráb, Tariq Ezaz, Thomas Liehr, Patrik Ferreira Viana, Eliana Feldberg and Marcelo de Bello Cioffi

Genes 2019, 10(9), 693; https://doi.org/10.3390/genes10090693 - 9 Sep 2019

Cited by 10 | Viewed by 4064

Abstract

The South American arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum) are emblematic species widely distributed in the Amazon and surrounding basins. Arowana species are under strong anthropogenic pressure as they are extensively exploited for ornamental and food purposes. Until now, limited genetic and cytogenetic information has been available, with only a few studies reporting to their genetic diversity and population structure. In the present study, cytogenetic and DArTseq-derived single nucleotide polymorphism (SNP) data were used to investigate the genetic diversity of the two Osteoglossum species, the silver arowana O. bicirrhosum, and the black arowana O. ferreirai. Both species differ in their 2n (with 2n = 54 and 56 for O. ferreirai and O. bicirrhosum, respectively) and in the composition and distribution of their repetitive DNA content, consistent with their taxonomic status as different species. Our genetic dataset was coupled with contemporary and paleogeographic niche modeling, to develop concurrent demographic models that were tested against each other with a deep learning approach in O. bicirrhosum. Our genetic results reveal that O. bicirrhosum colonized the Tocantins-Araguaia basin from the Amazon basin about one million years ago. In addition, we highlighted a higher genetic diversity of O. bicirrhosum in the Amazon populations in comparison to those from the Tocantins-Araguaia basin. Full article

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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10 pages, 1867 KiB

Open AccessArticle

The Duplicated Y-specific amhy Gene Is Conserved and Linked to Maleness in Silversides of the Genus Odontesthes

by Ricardo S. Hattori, Gustavo M. Somoza, Juan I. Fernandino, Dario C. Colautti, Kaho Miyoshi, Zhuang Gong, Yoji Yamamoto and Carlos A. Strüssmann

Genes 2019, 10(9), 679; https://doi.org/10.3390/genes10090679 - 5 Sep 2019

Cited by 26 | Viewed by 3578

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. Full article

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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13 pages, 844 KiB

Open AccessArticle

Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs

by 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

Genes 2019, 10(9), 668; https://doi.org/10.3390/genes10090668 - 31 Aug 2019

Cited by 22 | Viewed by 4469

Abstract

The pacu (Piaractus mesopotamicus) is a Neotropical fish with remarkable productive performance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for their 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 basis for a broodstock foundation for coming breeding programs in Brazil. Analysis of one wild population (Paraná River) was used as a reference to compare genetic parameters in the farmed populations. The analyses were performed using 32 single-nucleotide polymorphisms (SNP) and 8 simple sequence repeat (SSR) markers. No significant differences in genetic diversity between populations estimated through the number of alleles and allelic richness, observed heterozygosity, expected heterozygosity, and minimum allele frequency were detected (p > 0.05). Low genetic diversity was observed in all farmed stocks and the wild population. Moreover, we detected low genetic structure when comparing farmed and wild populations for SNPs (F_ST = 0.07; K = 3) and SSRs (F_ST = 0.08; K = 2). Analysis of molecular variance (AMOVA) demonstrated that genetic variation was mostly within populations. Kinship analysis showed that most fish farms included related individuals at a proportion of at least 25%. Our results suggest that the basal broodstock for pacu breeding programs should be founded with individuals from different fish farms for higher genetic diversity and to avoid inbreeding risks. Full article

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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12 pages, 1506 KiB

Open AccessArticle

DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae)

by Pábila S. S. Arruda, Daniela C. Ferreira, Claudio Oliveira and Paulo C. Venere

Genes 2019, 10(9), 639; https://doi.org/10.3390/genes10090639 - 23 Aug 2019

Cited by 15 | Viewed by 3771

Abstract

Brycon is an important group of Neotropical fish and the principal genus of the family Bryconidae, with 44 valid species that are found in some Central American rivers and practically all the major hydrographic basins of South America. These fish are medium to large in size, migratory, omnivorous, important seed dispersers for riparian forests, and bioindicators of environmental quality, given that they are found preferentially in rivers with clean, well oxygenated water. Many Brycon species are important fishery resources and some are farmed. Morphological and molecular studies have nevertheless indicated that the group is not monophyletic and has a number of unresolved taxonomic problems. Given this, the present study aimed to identify the Molecular Operational Taxonomic Units (MOTUs) of the genus using the mitochondrial cytochrome c oxidase I (COI) gene, with analyses of genetics distance (NJ), maximum likelihood (ML), and Bayesian Inference (BI), combined with two different species delimitation approaches (GMYC and ABGD). The results indicate that at least 31 MOTUs exist within the 18 species identified a priori based on their morphology. Many of these lineages require further investigation for a more definitive classification. Full article

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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18 pages, 1820 KiB

Open AccessArticle

Molecular Data Reveal Multiple Lineages in Piranhas of the Genus Pygocentrus (Teleostei, Characiformes)

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

Genes 2019, 10(5), 371; https://doi.org/10.3390/genes10050371 - 15 May 2019

Cited by 11 | Viewed by 6394

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, 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

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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15 pages, 1375 KiB

Open AccessArticle

DNA Barcode Reveals the Bycatch of Endangered Batoids Species in the Southwest Atlantic: Implications for Sustainable Fisheries Management and Conservation Efforts

by Bruno Lopes da Silva Ferrette, Rodrigo Rodrigues Domingues, Matheus Marcos Rotundo, Marina Provetti Miranda, Ingrid Vasconcellos Bunholi, Juliana Beltramin De Biasi, Claudio Oliveira, Fausto Foresti and Fernando Fernandes Mendonça

Genes 2019, 10(4), 304; https://doi.org/10.3390/genes10040304 - 18 Apr 2019

Cited by 26 | Viewed by 7891

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 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

(This article belongs to the Special Issue Genetics of Neotropical fishes: Conservation, Management and Evolution)

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