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Pires WMM, Barros MC, Fraga EC. DNA Barcoding unveils cryptic lineages of Hoplias malabaricus from Northeastern Brazil. BRAZ J BIOL 2021; 81:917-927. [PMID: 33053129 DOI: 10.1590/1519-6984.231598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/29/2020] [Indexed: 11/22/2022] Open
Abstract
The trahira or wolf fish - Hoplias malabaricus- is a valid species, although recent cytogenetic and molecular studies have indicated the existence of a species complex. In this context, the present study analyzed the mitochondrial COI marker to determine the levels of genetic diversity of specimens from the Brazilian state of Maranhão, and verify the occurrence of distinct lineages within the study area. Samples were collected from the basins of the Turiaçu, Pindaré, Mearim, Itapecuru, and Parnaíba rivers. A 630-bp fragment was obtained from 211 specimens, with 484 conserved and 108 variable sites, and 60 haplotypes (Hd = 0,947; π = 0,033). The phylogenetic analyses indicated the existence of three distinct lineages of H. malabaricus from Maranhão. Genetic distances of 1.5-8.2% were found between all the populations analyzed, while the variation between haplogroups ranged from 2.1% to 7.7%. The AMOVA indicated that most of the molecular variation was found among groups, with high FST values. The high levels of genetic variability found in the present study are supported by the available cytogenetic data. These findings reinforce the need for the development of effective programs of conservation and management independently for each river basin, in order to preserve the genetic variability found in this taxon.
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Affiliation(s)
- W M M Pires
- Universidade Estadual do Maranhão - UEMA, Programa de Pós- Graduação em Biodiversidade Ambiente e Saúde, Laboratório de Genética e Biologia Molecular, Caxias, MA, Brasil.,Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil
| | - M C Barros
- Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil.,Universidade Estadual do Maranhão - UEMA, Departamento de Química e Biologia, Caxias, MA, Brasil
| | - E C Fraga
- Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil.,Universidade Estadual do Maranhão - UEMA, Departamento de Química e Biologia, Caxias, MA, Brasil
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2
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Delomas TA, Willis SC, Parker BL, Miller D, Anders P, Schreier A, Narum S. Genotyping single nucleotide polymorphisms and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms. Mol Ecol Resour 2021; 21:2288-2298. [PMID: 34008918 DOI: 10.1111/1755-0998.13431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Whole genome duplication is hypothesized to have played a critical role in the evolution of several major taxa, including vertebrates, and while many lineages have rediploidized, some retain polyploid genomes. Additionally, variation in ploidy can occur naturally or be artificially induced within select plant and animal species. Modern genetic techniques have not been widely applied to polyploid or ploidy-variable species, in part due to the difficulty of obtaining genotype data from polyploids. In this study, we demonstrate a strategy for developing an amplicon sequencing panel of single nucleotide polymorphisms for high-throughput genotyping of polyploid organisms. We then develop a method to infer ploidy of individuals from amplicon sequencing data that is generalized to apply to any ploidy and does not require prior identification of heterozygous genotypes. Combining these two techniques will allow researchers to both infer ploidy and generate ploidy-aware genotypes with the same amplicon sequencing panel. We demonstrate this approach with white sturgeon Acipenser transmontanus, a ploidy-variable (octoploid, decaploid and dodecaploid) imperiled species under conservation management in the Pacific Northwest and obtained a panel of 325 loci. These loci were validated by examining inheritance in known-cross families, and the ploidy inference method was validated with known ploidy samples. We provide scripts that adapt existing pipelines to genotype polyploids and an R package for application of the ploidy inference method. We expect that these techniques will empower studies of genetic variation and inheritance in polyploid organisms that vary in ploidy level, either naturally or as a result of artificial propagation practices.
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Affiliation(s)
- Thomas A Delomas
- Pacific States Marine Fisheries Commission/Idaho Department of Fish and Game, Eagle Fish Genetics Laboratory, Eagle, ID, USA
| | - Stuart C Willis
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Blaine L Parker
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | | | | | - Andrea Schreier
- Genomic Variation Laboratory, Department of Animal Science, University of California Davis, Davis, CA, USA
| | - Shawn Narum
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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3
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Heat-induced triploids in Brycon amazonicus: a strategic fish species for aquaculture and conservation. ZYGOTE 2021; 29:372-376. [PMID: 33818341 DOI: 10.1017/s0967199421000125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Triploidization plays an important role in aquaculture and surrogate technologies. In this study, we induced triploidy in the matrinxã fish (Brycon amazonicus) using a heat-shock technique. Embryos at 2 min post fertilization (mpf) were heat shocked at 38°C, 40°C, or 42°C for 2 min. Untreated, intact embryos were used as a control. Survival rates during early development were monitored and ploidy status was confirmed using flow cytometry and nuclear diameter analysis of erythrocytes. The hatching rate reduced with heat-shock treatment, and heat-shock treatments at 42°C resulted in no hatching events. Optimal results were obtained at 40°C with 95% of larvae exhibiting triploidy. Therefore, we report that heat-shock treatments of embryos (2 mpf) at 40°C for 2 min is an effective way to induce triploid individuals in B. amazonicus.
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Ibagón N, Maldonado-Ocampo JA, Cioffi MDB, Dergam JA. Chromosomal Diversity of Hoplias malabaricus (Characiformes, Erythrinidae) Along the Magdalena River (Colombia—Northern South America) and Its Significance for the Neotropical Region. Zebrafish 2020. [DOI: 10.1089/zeb.2019.1827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Nicole Ibagón
- Departamento de Biologia Geral, Universidad Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Programa de Ecología, Fundación Universitaria de Popayán, Popayán, Cauca, Colombia
| | - Javier A. Maldonado-Ocampo
- Laboratorio de Ictiologia, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Jorge A. Dergam
- Departamento de Biologia Animal, Universidad Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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5
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Nirchio M, Gaviria JI, Siccha-Ramirez ZR, Oliveira C, Foresti F, Milana V, Rossi AR. Chromosomal polymorphism and molecular variability in the pearly razorfish Xyrichtys novacula (Labriformes, Labridae): taxonomic and biogeographic implications. Genetica 2019; 147:47-56. [PMID: 30673915 DOI: 10.1007/s10709-019-00051-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/09/2019] [Indexed: 01/28/2023]
Abstract
The pearly razorfish Xyrichtys novacula (Linnaeus, 1758) is a sedentary benthic species distributed in both sides of the Atlantic Ocean and in the Mediterranean Sea. Previous cytogenetic analysis reported different diploid numbers in samples from Italy, Venezuela and Brazil. This research aims to test the hypothesis that samples from American Atlantic coast and Mediterranean Sea belong to the same single evolutionary lineage, characterized by intra-specific chromosome polymorphism. To this purpose a cytogenetic and molecular (mitochondrial COI sequences) survey was undertaken. Results revealed the existence of three different pearly razorfish molecular lineages: one present in Mediterranean Sea and two in the central and south American area, which are characterized by different karyotypes. One of these lineages shows substantial intra-population chromosomal polymorphism (2n = 45-48) determined by Robertsonian fusions that produce large metacentric chromosomes. On the whole data suggest that specimens morphologically identified as X. novacula correspond to three cryptic species.
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Affiliation(s)
- Mauro Nirchio
- Escuela de Ciencias Aplicadas del Mar, Núcleo de Nueva Esparta, Universidad de Oriente, Apartado 174, Porlamar, Isla de Margarita, Venezuela.,Universidad Técnica de Machala, Av. Panamericana km 5½, Via Pasaje, Machala, El Oro, Ecuador
| | - Juan Ignacio Gaviria
- Escuela de Ciencias Aplicadas del Mar, Núcleo de Nueva Esparta, Universidad de Oriente, Apartado 174, Porlamar, Isla de Margarita, Venezuela
| | | | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu, São Paulo, 18618-970, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu, São Paulo, 18618-970, Brazil
| | - Valentina Milana
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Via Alfonso Borelli 50, 00161, Rome, Italy
| | - Anna Rita Rossi
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Via Alfonso Borelli 50, 00161, Rome, Italy.
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Cardoso YP, Rosso JJ, Mabragaña E, González-Castro M, Delpiani M, Avigliano E, Bogan S, Covain R, Schenone NF, Díaz de Astarloa JM. A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias. PLoS One 2018; 13:e0202024. [PMID: 30102742 PMCID: PMC6089427 DOI: 10.1371/journal.pone.0202024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/26/2018] [Indexed: 01/26/2023] Open
Abstract
With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently "masked" within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.
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Affiliation(s)
- Yamila P. Cardoso
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Juan J. Rosso
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
- Fundación Bosques Nativos Argentinos para la Biodiversidad, Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
- Fundación Bosques Nativos Argentinos para la Biodiversidad, Buenos Aires, Argentina
| | - Mariano González-Castro
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Matías Delpiani
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Esteban Avigliano
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Fundación Bosques Nativos Argentinos para la Biodiversidad, Buenos Aires, Argentina
- Instituto de Investigaciones en Producción Animal, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sergio Bogan
- Fundación de Historia Natural “Félix de Azara”, Departamento de Ciencias Naturales y Antropología, Universidad Maimónides, Buenos Aires, Argentina
| | - Raphael Covain
- Department of Herpetology and Ichthyology, Museum of Natural History, Geneva, Switzerland
| | - Nahuel F. Schenone
- Centro de Investigaciones Antonia Ramos, Villa Bonita, Campo Ramón, Misiones, Argentina
| | - Juan M. Díaz de Astarloa
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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7
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Sember A, Bertollo LAC, Ráb P, Yano CF, Hatanaka T, de Oliveira EA, Cioffi MDB. Sex Chromosome Evolution and Genomic Divergence in the Fish Hoplias malabaricus (Characiformes, Erythrinidae). Front Genet 2018; 9:71. [PMID: 29556249 PMCID: PMC5845122 DOI: 10.3389/fgene.2018.00071] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/16/2018] [Indexed: 11/13/2022] Open
Abstract
The Erythrinidae family (Teleostei: Characiformes) is a small Neotropical fish group with a wide distribution throughout South America, where Hoplias malabaricus corresponds to the most widespread and cytogenetically studied taxon. This species possesses significant genetic variation, as well as huge karyotype diversity among populations, as reflected by its seven major karyotype forms (i.e., karyomorphs A-G) identified up to now. Although morphological differences in their bodies are not outstanding, H. malabaricus karyomorphs are easily identified by differences in 2n, morphology and size of chromosomes, as well as by distinct evolutionary steps of sex chromosomes development. Here, we performed comparative genomic hybridization (CGH) to analyse both the intra- and inter-genomic status in terms of repetitive DNA divergence among all but one (E) H. malabaricus karyomorphs. Our results indicated that they have close relationships, but with evolutionary divergences among their genomes, yielding a range of non-overlapping karyomorph-specific signals. Besides, male-specific regions were uncovered on the sex chromosomes, confirming their differential evolutionary trajectories. In conclusion, the hypothesis that H. malabaricus karyomorphs are result of speciation events was strengthened.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Luiz A. C. Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Cassia F. Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Ezequiel A. de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Secretaria de Estado de Educação de Mato Grosso (SEDUC-MT), Cuiabá, Brazil
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8
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Carvalho ML, Costa Silva GJD, Melo S, Ashikaga FY, Shimabukuro-Dias CK, Scacchetti PC, Devidé R, Foresti F, Oliveira C. The non-monotypic status of the neotropical fish genus Hemiodontichthys (Siluriformes, Loricariidae) evidenced by genetic approaches. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1224-1230. [DOI: 10.1080/24701394.2018.1431230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Margarida Lima Carvalho
- Laboratório de Citogenética e Genética Molecular – LABGENE, Universidade Federal do Acre, Rio Branco, Acre, Brazil
| | - Guilherme José da Costa Silva
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
- Departamento de Biologia, Universidade Santo Amaro São Paulo, Brazil
| | - Silvana Melo
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Fernando Yuldi Ashikaga
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Cristiane Kioko Shimabukuro-Dias
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Priscilla Cardim Scacchetti
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Renato Devidé
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Fausto Foresti
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Instituto de Biociências de Botucatu, Laboratório de Biologia e Genética de Peixes – LBGP, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
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9
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da Costa-Silva GJ, Yuldi Ashikaga F, Kioko Shimabukuro Dias C, Garcia Pereira LH, Foresti F, Oliveira C. DNA barcoding techniques used to identify the shared ichthyofauna between the Pantanal floodplain and Upper Parana River. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1063-1072. [PMID: 29157062 DOI: 10.1080/24701394.2017.1404046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The biological invasion process is widely debated topic, as the population depletion of some species and the extinction of others are related to this process. To accelerate the identification of species and to detect non-native forms, new tools are being developed, such as those based on genetic markers. This study aimed to use Barcode DNA methodology to identify fish species that had translocated between the Parana and Paraguay River Basins. Based on a database of two studies that were conducted in these regions, 289 sequences of Cytochrome Oxidase C subunit 1 (COI) were used for General Mixed Youle Coalecent (GMYC) analysis, including 29 morphospecies that were sampled in both river basins. As a result, we observed that while some morphospecies have low variation, demonstrating a recent occupation of the basins, other morphospecies probably represent species complexes. A third of the morphospecies had well-defined lineages but not enough to be treated as different Molecular Operational Taxonomic Units (MOTUs). These results demonstrate that human interventions possibly participated in the distribution of some lineages. However, biogeographical historical processes are also important for the morphospecies distribution. The data suggest that the number of species that are present in these two basins is underestimated and that human actions can irreversibly affect the natural history of the species in these regions.
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Affiliation(s)
- Guilherme J da Costa-Silva
- a Departamento de Morfologia, Instituto de Biociências , Universidade Estadual Paulista (UNESP) , Botucatu , São Paulo , Brazil
| | - Fernando Yuldi Ashikaga
- a Departamento de Morfologia, Instituto de Biociências , Universidade Estadual Paulista (UNESP) , Botucatu , São Paulo , Brazil
| | | | - Luiz Henrique Garcia Pereira
- b Instituto de Ciências da Vida e da Natureza , Universidade Federal da Integração Latino-Americana (UNILA) , Foz do Iguaçu , Paraná , Brazil
| | - Fausto Foresti
- a Departamento de Morfologia, Instituto de Biociências , Universidade Estadual Paulista (UNESP) , Botucatu , São Paulo , Brazil
| | - Claudio Oliveira
- a Departamento de Morfologia, Instituto de Biociências , Universidade Estadual Paulista (UNESP) , Botucatu , São Paulo , Brazil
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