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Nascimento MHS, Birindelli JLO, Fraga E, Barros MC. Exploring hidden diversity: Molecular insights into the Leporinus species of the rivers of the Brazilian states of Maranhão and Piauí. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38590289 DOI: 10.1111/jfb.15753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The present study delved into the world of hidden diversity by examining specimens identified as Leporinus piau from the river basins of the northern Brazilian states of Maranhão and Piauí. Using genetic analyses that combined data from three mitochondrial markers and one nuclear marker, the study identified two well-supported groups, reinforcing the findings of previous publications. The first group, found in samples from the Itapecuru, Mearim, Turiaçu, and Pericumã basins, in Maranhão, appears to represent a relatively ancient diversification and the possibility of concealed cryptic diversity. The second group, comprising specimens from the Parnaíba (Piauí) and Mearim (Maranhão) basins, appears to have resulted from a more recent process of diversification and has a close relationship with Leporinus friderici from the type locality. Our findings not only confirm the existence of a complex scenario of cryptic diversity in the genus Leporinus from the study basins but also underscore the taxonomic inconsistencies within this group of fish. This study offers a comprehensive analysis of the species diversity of the Maranhão and Piauí basins, which are critical regions for the conservation of Amazonian fish, providing valuable insights for the sustainable management and conservation of these fish.
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Affiliation(s)
- Maria Histelle Sousa Nascimento
- Departamento de Desenvolvimento e Ensino, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão, Caxias, Brazil
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | | | - Elmary Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | - Maria Claudene Barros
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
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2
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Dulz TA, Azambuja M, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Nascimento VD, Diniz D, de Mello Affonso PRA, Vicari MR. Repetitive DNAs and chromosome evolution in Megaleporinus obtusidens and M. reinhardti (Characiformes: Anostomidae). Genetica 2024:10.1007/s10709-024-00206-3. [PMID: 38587599 DOI: 10.1007/s10709-024-00206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
The high dynamism of repetitive DNAs is a major driver of chromosome evolution. In particular, the accumulation of repetitive DNA sequences has been reported as part of the differentiation of sex-specific chromosomes. In turn, the fish species of the genus Megaleporinus are a monophyletic clade in which the presence of differentiated ZZ/ZW sex chromosomes represents a synapomorphic condition, thus serving as a suitable model to evaluate the dynamic evolution of repetitive DNA classes. Therefore, transposable elements (TEs) and in tandem repeats were isolated and located on chromosomes of Megaleporinus obtusidens and M. reinhardti to infer their role in chromosome differentiation with emphasis on sex chromosome systems. Despite the conserved karyotype features of both species, the location of repetitive sequences - Rex 1, Rex 3, (TTAGGG)n, (GATA)n, (GA)n, (CA)n, and (A)n - varied both intra and interspecifically, being mainly accumulated in Z and W chromosomes. The physical mapping of repetitive sequences confirmed the remarkable dynamics of repetitive DNA classes on sex chromosomes that might have promoted chromosome diversification and reproductive isolation in Megaleporinus species.
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Affiliation(s)
- Thais Aparecida Dulz
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Matheus Azambuja
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Carla Andrea Lorscheider
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Rafael Bueno Noleto
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Orlando Moreira-Filho
- Department of Genetics and Evolution, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | | | - Débora Diniz
- Graduate Program in Genetics, Biodiversity and Conservation, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brazil
| | | | - Marcelo Ricardo Vicari
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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Limeira Filho D, França ERDR, Costa DKDP, Lima RC, Nascimento MHSD, Batista JDS, Barros MC, Fraga EDC. Molecular Evidence Reveals Taxonomic Uncertainties and Cryptic Diversity in the Neotropical Catfish of the Genus Pimelodus (Siluriformes: Pimelodidae). BIOLOGY 2024; 13:162. [PMID: 38534432 DOI: 10.3390/biology13030162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.
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Affiliation(s)
- Daniel Limeira Filho
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
| | - Elidy Rayane de Rezende França
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
| | - Dalton Kaynnan de Prado Costa
- Graduate Program in Biodiversity, Environment, and Health-PPGBAS, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
| | - Renato Correia Lima
- Graduate Program in Genetics, Conservation, and Evolutionary Biology (PPG-GCBEv), National Amazonian Research Institute-INPA, Av. André Araújo, 2936, Aleixo, Manaus 69060-001, AM, Brazil
| | - Maria Histelle Sousa do Nascimento
- Graduate Program in Biodiversity and Biotechnology-BIONORTE Network, Maranhão State University-UEMA, Cidade Universitária Paulo VI-Avenida Lourenço Vieira da Silva, n° 1.000, Jardim São Cristóvão, São Luís 665055-310, MA, Brazil
| | - Jacqueline da Silva Batista
- Graduate Program in Genetics, Conservation, and Evolutionary Biology (PPG-GCBEv), National Amazonian Research Institute-INPA, Av. André Araújo, 2936, Aleixo, Manaus 69060-001, AM, Brazil
- Molecular Biology Thematic Laboratory-LTBM, Coordination of Biodiversity-COBIO, National Amazonian Research Institute-INPA, Av. André Araújo, 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Maria Claudene Barros
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
- Graduate Program in Biodiversity, Environment, and Health-PPGBAS, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
- Graduate Program in Biodiversity and Biotechnology-BIONORTE Network, Maranhão State University-UEMA, Cidade Universitária Paulo VI-Avenida Lourenço Vieira da Silva, n° 1.000, Jardim São Cristóvão, São Luís 665055-310, MA, Brazil
- Laboratory of Molecular Biology-LABMOL, Department of Chemistry and Biology, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
| | - Elmary da Costa Fraga
- Graduate Program in Animal Science-PPGCA, Center of Agrarian Sciences-CCA, Maranhão State University-UEMA, São Luís 65055-310, MA, Brazil
- Graduate Program in Biodiversity, Environment, and Health-PPGBAS, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
- Laboratory of Genetics-LABGEN, Department of Chemistry and Biology, Caxias Center of Higher Education-CESC, Maranhão State University-UEMA, Praça Duque de Caxias, s/n-Morro do Alecrim, Centro, Caxias 65604-380, MA, Brazil
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4
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Ramirez JL, Valdivia P, Rosas-Puchuri U, Valdivia NL. SPdel: A pipeline to compare and visualize species delimitation methods for single-locus datasets. Mol Ecol Resour 2023; 23:1959-1965. [PMID: 37702121 DOI: 10.1111/1755-0998.13864] [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: 05/24/2023] [Revised: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with species delimitation methods would help to a rapid and accurate biodiversity assessment. The species delimitation methods cluster data sets of orthologous sequences in molecular operational taxonomic units (MOTU). In particular, the methods based on a single gene are easily integrated with the widely used DNA barcoding approach. We developed SPdel a user-friendly pipeline to integrate different single-gene species delimitation methods. SPdel is designed to calculate and compare MOTUs obtained by different species delimitation approaches. SPdel also outputs diverse ready-to-publish quality figures, that facilitate the interpretation of results. SPdel aims to help researchers use species delimitation methods that would improve biodiversity studies.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Paola Valdivia
- Department of Biology, The University of Oklahoma, Norman, Oklahoma, USA
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Ramirez JL, Machado CB, de Mello Affonso PRA, Galetti PM. Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data. Syst Biol 2023; 72:973-983. [PMID: 37260367 PMCID: PMC10627554 DOI: 10.1093/sysbio/syad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carolina B Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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Marajó L, Viana PF, Ferreira AMV, Py-Daniel LHR, Cioffi MDB, Sember A, Feldberg E. Chromosomal rearrangements and the first indication of an ♀X 1 X 1 X 2 X 2 /♂X 1 X 2 Y sex chromosome system in Rineloricaria fishes (Teleostei: Siluriformes). JOURNAL OF FISH BIOLOGY 2023; 102:443-454. [PMID: 36427042 DOI: 10.1111/jfb.15275] [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: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Rineloricaria is the most diverse genus within the freshwater fish subfamily Loricariinae, and it is widely distributed in the Neotropical region. Despite limited cytogenetic data, records from southern and south-eastern Brazil suggest a high rate of chromosomal rearrangements in this genus, mirrored in remarkable inter- and intraspecific karyotype variability. In the present work, we investigated the karyotype features of Rineloricaria teffeana, an endemic representative from northern Brazil, using both conventional and molecular cytogenetic techniques. We revealed different diploid chromosome numbers (2n) between sexes (33♂/34♀), which suggests the presence of an ♀X1 X1 X2 X2 /♂X1 X2 Y multiple sex chromosome system. The male-limited Y chromosome was the largest and the only biarmed element in the karyotype, implying Y-autosome fusion as the most probable mechanism behind its origination. C-banding revealed low amounts of constitutive heterochromatin, mostly confined to the (peri)centromeric regions of most chromosomes (including the X2 and the Y) but also occupying the distal regions of a few chromosomal pairs. The chromosomal localization of the 18S ribosomal DNA (rDNA) clusters revealed a single site on chromosome pair 4, which was adjacent to the 5S rDNA cluster. Additional 5S rDNA loci were present on the autosome pair 8, X1 chromosome, and in the presumed fusion point on the Y chromosome. The probe for telomeric repeat motif (TTAGGG)n revealed signals of variable intensities at the ends of all chromosomes except for the Y chromosome, where no detectable signals were evidenced. Male-to-female comparative genomic hybridization revealed no sex-specific or sex-biased repetitive DNA accumulations, suggesting a presumably low level of neo-Y chromosome differentiation. We provide evidence that rDNA sites might have played a role in the formation of this putative multiple sex chromosome system and that chromosome fusions originate through different mechanisms among different Rineloricaria species.
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Affiliation(s)
- Leandro Marajó
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Alex Matheus Viana Ferreira
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Lúcia Helena Rapp Py-Daniel
- Coleção de Peixes, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | - Eliana Feldberg
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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7
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Crepaldi C, Martí E, Gonçalves ÉM, Martí DA, Parise-Maltempi PP. Genomic Differences Between the Sexes in a Fish Species Seen Through Satellite DNAs. Front Genet 2021; 12:728670. [PMID: 34659353 PMCID: PMC8514694 DOI: 10.3389/fgene.2021.728670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 11/14/2022] Open
Abstract
Neotropical fishes have highly diversified karyotypic and genomic characteristics and present many diverse sex chromosome systems, with various degrees of sex chromosome differentiation. Knowledge on their sex-specific composition and evolution, however, is still limited. Satellite DNAs (satDNAs) are tandemly repeated sequences with pervasive genomic distribution and distinctive evolutionary pathways, and investigating satDNA content might shed light into how genome architecture is organized in fishes and in their sex chromosomes. The present study investigated the satellitome of Megaleporinus elongatus, a freshwater fish with a proposed Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosome system that encompasses a highly heterochromatic and differentiated W1 chromosome. The species satellitome comprises of 140 different satDNA families, including previously isolated sequences and new families found in this study. This diversity is remarkable considering the relatively low proportion that satDNAs generally account for the M. elongatus genome (around only 5%). Differences between the sexes in regards of satDNA content were also evidenced, as these sequences are 14% more abundant in the female genome. The occurrence of sex-biased signatures of satDNA evolution in the species is tightly linked to satellite enrichment associated with W1 in females. Although both sexes share practically all satDNAs, the overall massive amplification of only a few of them accompanied the W1 differentiation. We also investigated the expansion and diversification of the two most abundant satDNAs of M. elongatus, MelSat01-36 and MelSat02-26, both highly amplified sequences in W1 and, in MelSat02-26’s case, also harbored by Z2 and W2 chromosomes. We compared their occurrences in M. elongatus and the sister species M. macrocephalus (with a standard ZW sex chromosome system) and concluded that both satDNAs have led to the formation of highly amplified arrays in both species; however, they formed species-specific organization on female-restricted sex chromosomes. Our results show how satDNA composition is highly diversified in M. elongatus, in which their accumulation is significantly contributing to W1 differentiation and not satDNA diversity per se. Also, the evolutionary behavior of these repeats may be associated with genome plasticity and satDNA variability between the sexes and between closely related species, influencing how seemingly homeologous heteromorphic sex chromosomes undergo independent satDNA evolution.
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Affiliation(s)
- Carolina Crepaldi
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Évelin Mariani Gonçalves
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Dardo Andrea Martí
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS), Universidad Nacional de Misiones (UNaM), CONICET, Posadas, Argentina
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Muster C, Spelda J, Rulik B, Thormann J, von der Mark L, Astrin JJ. The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions. Ecol Evol 2021; 11:13815-13829. [PMID: 34707820 PMCID: PMC8525104 DOI: 10.1002/ece3.8088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.
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Affiliation(s)
- Christoph Muster
- Zoologisches Institut und MuseumUniversität GreifswaldGreifswaldGermany
| | - Jörg Spelda
- SNSB‐Zoologische Staatssammlung MünchenMunichGermany
| | - Björn Rulik
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | - Jana Thormann
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
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de Santana CD, Parenti LR, Dillman CB, Coddington JA, Bastos DA, Baldwin CC, Zuanon J, Torrente-Vilara G, Covain R, Menezes NA, Datovo A, Sado T, Miya M. The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes. Sci Rep 2021; 11:18159. [PMID: 34518574 PMCID: PMC8438044 DOI: 10.1038/s41598-021-97128-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.
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Affiliation(s)
- C David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.
| | - Lynne R Parenti
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Casey B Dillman
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Douglas A Bastos
- Programa de Pós-Graduação em Ciências Biológicas (BADPI), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Carole C Baldwin
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Gislene Torrente-Vilara
- Instituto do Mar, Universidade Federal de São Paulo, Campus Baixada Santista, Santos, São Paulo, Brazil
| | - Raphaël Covain
- Museum of Natural History, Department of Herpetology and Ichthyology, route de Malagnou 1, PO Box 6434, 1211, Geneva 6, Switzerland
| | - Naércio A Menezes
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - Aléssio Datovo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - T Sado
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
| | - M Miya
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
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10
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Ribolli J, Zaniboni Filho E, Scaranto BMS, Shibatta OA, Machado CB. Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding. Genet Mol Biol 2021; 44:e20200470. [PMID: 34254973 PMCID: PMC8276235 DOI: 10.1590/1678-4685-gmb-2020-0470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America’s hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.
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Affiliation(s)
- Josiane Ribolli
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Evoy Zaniboni Filho
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Bianca Maria Soares Scaranto
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Oscar Akio Shibatta
- Universidade Estadual de Londrina, Departamento de Biologia Animal e Vegetal, Centro de Ciências Biológicas, Londrina, PR, Brazil
| | - Carolina Barros Machado
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
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11
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Santos RP, Melo BF, Yazbeck GM, Oliveira RS, Hilário HO, Prosdocimi F, Carvalho DC. Diversification of
Prochilodus
in the eastern Brazilian Shield: Evidence from complete mitochondrial genomes (Teleostei, Prochilodontidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Rosiane P. Santos
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
- Laboratório de Recursos Genéticos Programa de Pós‐Graduação em Ecologia Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Bruno F. Melo
- Departamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Gabriel M. Yazbeck
- Laboratório de Recursos Genéticos Programa de Pós‐Graduação em Ecologia Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Rafael S. Oliveira
- Programa de Pós‐Graduação em Ciência da Computação Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Heron O. Hilário
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade Instituto de Bioquímica Médica Leopoldo de MeisUniversidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Daniel C. Carvalho
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
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12
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Garavello JC, Ramirez JL, Oliveira AKD, Britski HA, Birindelli JLO, Galetti Jr PM. Integrative taxonomy reveals a new species of Neotropical headstanding fish in genus Schizodon (Characiformes: Anostomidae). NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Schizodon encompasses approximately 15 species of Neotropical headstanding fishes. Integrative taxonomy, combining molecular and morphometric analyses with traditional taxonomic methods, was used to investigate Schizodon vittatus and its potential new sister species. Molecular differences between the two species in the barcode are greater than intra-specific variation recovered in species of Schizodon, and the two species represent distinct lineages for approximately one million years. The two species are morphologically very similar, and the meristic data showed great overlap. Morphometric analyses also showed overlap among the putative species but indicated differences in caudal-peduncle depth, orbital diameter, and length of anal-fin rays. Color pattern seems to provide a clear diagnostic feature for the two species. Schizodon vittatus usually has four dark brown transversal bars on body, and its sister species has three conspicuous bars, with the fourth, if present, inconspicuous and dorsal to the lateral line. Schizodon vittatus is redescribed based on the type and recently collected specimens, its type locality is revisited, and its known distribution restricted to the Araguaia and Tocantins drainages. The new species, sister to S. vittatus, distributed in the Xingu and Tapajós drainages, is described. A key for the identification of the Amazon clade species of Schizodon is provided.
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13
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Puillandre N, Brouillet S, Achaz G. ASAP: assemble species by automatic partitioning. Mol Ecol Resour 2020; 21:609-620. [PMID: 33058550 DOI: 10.1111/1755-0998.13281] [Citation(s) in RCA: 359] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
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Affiliation(s)
- Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sophie Brouillet
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,SMILE Group, CIRB, UMR 7241, Collège de France, CNRS, INSERM, Paris, France.,Éco-anthropologie, Muséum National d'Histoire Naturelle, CNRS UMR 7206, Université de Paris, Paris, France
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14
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DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau. BMC Evol Biol 2020; 20:151. [PMID: 33183225 PMCID: PMC7663858 DOI: 10.1186/s12862-020-01718-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/04/2020] [Indexed: 01/12/2023] Open
Abstract
Background The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions. Conclusions The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.
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15
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Recent Apareiodon species evolutionary divergence (Characiformes: Parodontidae) evidenced by chromosomal and molecular inference. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Milan DT, Mendes IS, Damasceno JS, Teixeira DF, Sales NG, Carvalho DC. New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment. Sci Rep 2020; 10:17966. [PMID: 33087755 PMCID: PMC7578065 DOI: 10.1038/s41598-020-74902-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.
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Affiliation(s)
- David T Milan
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil
| | - Izabela S Mendes
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil.,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Júnio S Damasceno
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil
| | - Daniel F Teixeira
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil.,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Naiara G Sales
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK.,CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Daniel C Carvalho
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifical Catholic University of Minas Gerais, PUC Minas, Belo Horizonte, Brazil. .,Postgraduate Program in Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.
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17
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Sassi FDMC, Deon GA, Moreira-Filho O, Vicari MR, Bertollo LAC, Liehr T, de Oliveira EA, Cioffi MB. Multiple Sex Chromosomes and Evolutionary Relationships in Amazonian Catfishes: The Outstanding Model of the Genus Harttia (Siluriformes: Loricariidae). Genes (Basel) 2020; 11:genes11101179. [PMID: 33050411 PMCID: PMC7600804 DOI: 10.3390/genes11101179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
The armored Harttia catfishes present great species diversity and remarkable cytogenetic variation, including different sex chromosome systems. Here we analyzed three new species, H. duriventris, H. villasboas and H. rondoni, using both conventional and molecular cytogenetic techniques (Giemsa-staining and C-banding), including the mapping of repetitive DNAs using fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) experiments. Both H. duriventris and H. villasboas have 2n = ♀56/♂55 chromosomes, and an X1X1X2X2 /X1X2Y sex chromosome system, while a proto or neo-XY system is proposed for H. rondoni (2n = 54♀♂). Single motifs of 5S and 18S rDNA occur in all three species, with the latter being also mapped in the sex chromosomes. The results confirm the general evolutionary trend that has been noticed for the genus: an extensive variation on their chromosome number, single sites of rDNA sequences and the occurrence of multiple sex chromosomes. Comparative genomic analyses with another congeneric species, H. punctata, reveal that the X1X2Y sex chromosomes of these species share the genomic contents, indicating a probable common origin. The remarkable karyotypic variation, including sex chromosomes systems, makes Harttia a suitable model for evolutionary studies focusing on karyotype differentiation and sex chromosome evolution among lower vertebrates.
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Affiliation(s)
- Francisco de M. C. Sassi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
| | - Geize A. Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84010-330, Brazil;
| | - Orlando Moreira-Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84010-330, Brazil;
| | - Marcelo R. Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84010-330, Brazil;
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena 07747, Germany
- Correspondence: ; Tel.: +49-3641-9396850; Fax: +49-3641-9396852
| | | | - Marcelo B. Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São, Carlos, São Carlos, SP 13565-905, Brazil; (F.d.M.C.S.); (G.A.D.); (O.M.-F.); (L.A.C.B.); (M.B.C.)
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18
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Molecular phylogeny and species delimitation of the genus Schizodon (Characiformes, Anostomidae). Mol Phylogenet Evol 2020; 153:106959. [PMID: 32920128 DOI: 10.1016/j.ympev.2020.106959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 07/16/2020] [Accepted: 08/13/2020] [Indexed: 11/23/2022]
Abstract
The genus Schizodon is part of a group of headstanders and relatives (Family Anostomidae) that are widespread and ecologically important fishes in South American rivers. Schizodon includes 15 nominal species but their taxonomy has been challenging due to paucity of decisive characters to diagnose species. We present new molecular data to assess species boundaries or molecular operational taxonomic units (MOTUs), and to infer phylogenetic relationships among species. Evidence from two mitochondrial and three nuclear genes was used in these analyses. Mitochondrial DNA data for 112 specimens (from 11 nominal species) supported 13 consensus MOTUs, six of which matched valid nominal species (Schizodon borellii, S. fasciatus, S. intermedius, S. isognathus, S. knerii and S. scotorhabdotus). The nominal species Schizodon vittatus, S. nasutus, and S. dissimilis were subdivided into two MOTUs each, revealing either cryptic species or strong population structuring. In contrast, S. platae and S. jacuiensis constituted a single MOTU, indicating a possible case of synonymy. Our phylogenetic analysis subdivided the genus Schizodon into two large clades that are compatible with observed color patterns and biogeographic distribution. The first clade includes species with three to four conspicuous dark vertical bars on the flanks that originated in the Amazonas region (S. borellii, S. dissimilis, S. intermedius, S. fasciatus, S. scotorhabdotus, S. vittatus, and a cryptic species, Schizodon aff. vittatus). The second clade includes species with a conspicuous dark caudal blotch on the caudal peduncle, with vertical bars absent or inconspicuous, with a biogeographic origin in the La Plata drainage (S. isognathus, S. jacuiensis, S. knerii, S. nasutus and S. platae). Our results reinforce the importance of using molecular analyses to accelerate the study of diversity, particularly in groups with a wide distribution, few variable meristic characters, and high morphological plasticity, which may hide still unknown or underestimated diversity.
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19
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Birindelli JLO, Britski HA, Ramirez JL. A new endangered species of Megaleporinus (Characiformes: Anostomidae) from the Rio de Contas basin, eastern Brazil. JOURNAL OF FISH BIOLOGY 2020; 96:1349-1359. [PMID: 32096231 DOI: 10.1111/jfb.14299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/18/2020] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
A new species of Megaleporinus is described from the Rio de Contas, a coastal drainage of eastern Brazil, and its phylogenetic relationships are studied using molecular data. The new species is unique among Anostomidae by possessing two exclusive features: an irregular dark longitudinal stripe from supracleithrum to second midlateral blotch and anterior cranial fontanel partially closed. In addition, the new species is diagnosed by having three premaxillary teeth, three dentary teeth, 37 or 38 scales in lateral line, 16 scale rows around caudal peduncle, three dark midlateral blotches on body, and red fins in life. The new species is closely related to M. obtusidens from the São Francisco basin, corroborating previous studies that indicated that the latter represents a species complex as currently defined. The new species exhibits the first rib enlarged in mature males, a feature described for some congeners. The new species is herein considered to be Endangered under the IUCN criteria.
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Affiliation(s)
- José L O Birindelli
- Museu de Zoologia, Departamento de Biologia Animal e Vegetal, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Ciudad Universitaria, Lima, Peru
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20
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Sember A, de Oliveira EA, Ráb P, Bertollo LAC, de Freitas NL, Viana PF, Yano CF, Hatanaka T, Marinho MMF, de Moraes RLR, Feldberg E, Cioffi MDB. Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective. Genes (Basel) 2020; 11:genes11010091. [PMID: 31941136 PMCID: PMC7017317 DOI: 10.3390/genes11010091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability in the diploid chromosome number (2n), which is pronounced in the speciose genus Nannostomus, a popular taxon in ornamental fish trade due to its remarkable body coloration. Aiming to more deeply examine the karyotype diversification in Nannostomus, we combined conventional cytogenetics (Giemsa-staining and C-banding) with the chromosomal mapping of tandemly repeated 5S and 18S rDNA clusters and with interspecific comparative genomic hybridization (CGH) to investigate genomes of four representative Nannostomus species: N. beckfordi, N. eques, N. marginatus, and N. unifasciatus. Our data showed a remarkable variability in 2n, ranging from 2n = 22 in N. unifasciatus (karyotype composed exclusively of metacentrics/submetacentrics) to 2n = 44 in N. beckfordi (karyotype composed entirely of acrocentrics). On the other hand, patterns of 18S and 5S rDNA distribution in the analyzed karyotypes remained rather conservative, with only two 18S and two to four 5S rDNA sites. In view of the mostly unchanged number of chromosome arms (FN = 44) in all but one species (N. eques; FN = 36), and with respect to the current phylogenetic hypothesis, we propose Robertsonian translocations to be a significant contributor to the karyotype differentiation in (at least herein studied) Nannostomus species. Interspecific comparative genome hybridization (CGH) using whole genomic DNAs mapped against the chromosome background of N. beckfordi found a moderate divergence in the repetitive DNA content among the species’ genomes. Collectively, our data suggest that the karyotype differentiation in Nannostomus has been largely driven by major structural rearrangements, accompanied by only low to moderate dynamics of repetitive DNA at the sub-chromosomal level. Possible mechanisms and factors behind the elevated tolerance to such a rate of karyotype change in Nannostomus are discussed.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic; (A.S.); (P.R.)
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Secretaria de Estado de Educação de Mato Grosso–SEDUC-MT, Cuiabá 78049-909, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic; (A.S.); (P.R.)
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Natália Lourenço de Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Manoela Maria Ferreira Marinho
- Universidade Federal da Paraíba (UFPB), Departamento de Sistemática e Ecologia (DSE), Laboratório de Sistemática e Morfologia de Peixes, João Pessoa 58051-090, Brazil;
| | - Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Correspondence: ; Tel.: +55-16-3351-8431; Fax: +55-16-3351-8377
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Toma GA, de Moraes RLR, Sassi FDMC, Bertollo LAC, de Oliveira EA, Rab P, Sember A, Liehr T, Hatanaka T, Viana PF, Marinho MMF, Feldberg E, Cioffi MDB. Cytogenetics of the small-sized fish, Copeina guttata (Characiformes, Lebiasinidae): Novel insights into the karyotype differentiation of the family. PLoS One 2019; 14:e0226746. [PMID: 31856256 PMCID: PMC6922430 DOI: 10.1371/journal.pone.0226746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 11/19/2022] Open
Abstract
Lebiasinidae is a small fish family composed by miniature to small-sized fishes with few cytogenetic data (most of them limited to descriptions of diploid chromosome numbers), thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing, the first cytogenetic data for the red spotted tetra, Copeina guttata, including the standard karyotype, C-banding, repetitive DNA mapping by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH), providing chromosomal patterns and novel insights into the karyotype differentiation of the family. Males and females share diploid chromosome number 2n = 42 and karyotype composed of 2 metacentric (m), 4 submetacentric (sm) and 36 subtelocentric to acrocentric (st-a) chromosomes. Blocks of constitutive heterochromatin were observed in the centromeric and interstitial regions of several chromosomes, in addition to a remarkably large distal block, heteromorphic in size, which fully corresponded with the 18S rDNA sites in the fourth chromosomal pair. This overlap was confirmed by 5S/18S rDNA dual-color FISH. On the other hand, 5S rDNA clusters were situated in the long and short arms of the 2nd and 15th pairs, respectively. No sex-linked karyotype differences were revealed by male/female CGH experiments. The genomic probes from other two lebiasinid species, Lebiasina melanoguttata and Pyrrhulina brevis, showed positive hybridization signals only in the NOR region in the genome of C. guttata. We demonstrated that karyotype diversification in lebiasinids was accompanied by a series of structural and numeric chromosome rearrangements of different types, including particularly fusions and fissions.
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Affiliation(s)
- Gustavo Akira Toma
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Renata Luiza Rosa de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Ezequiel Aguiar de Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Secretaria de Estado de Educação de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
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22
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Santos EOD, Deon GA, Almeida RBD, Oliveira EAD, Nogaroto V, Silva HPD, Pavanelli CS, Cestari MM, Bertollo LAC, Moreira-Filho O, Vicari MR. Cytogenetics and DNA barcode reveal an undescribed Apareiodon species (Characiformes: Parodontidae). Genet Mol Biol 2019; 42:365-373. [PMID: 31259363 PMCID: PMC6726146 DOI: 10.1590/1678-4685-gmb-2018-0066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/01/2018] [Indexed: 11/22/2022] Open
Abstract
Parodontidae is a small group of fish and some species are particularly difficult
to identify due to the lack of sufficiently consistent morphological traits.
Cytogenetically, the species possess 2n = 54 chromosomes and are either
sex-homomorphic or sex-heteromorphic (regarding its chromosomes). We evaluated
data on color, tooth morphology, cytogenetics, and mitochondrial markers (COI)
in Apareiodon specimens from the Aripuanã River (Amazon basin)
and the results were compared to other congeneric taxa. Morphological results
show an overlap of body color and tooth morphology to other known
Apareiodon. The cytogenetics data showed that the 2n = 54
chromosomes, 50 m/sm + 4 st and, a ZZ/ZW sex chromosome system in
Apareiodon sp. are common to other species of the genus.
However, the number and chromosomal localization of the 45S ribosomal and
pPh2004 satellite DNA sites, in addition to W chromosome
localization of the pPh2004 appear to be exclusive cytogenetic
features in Apareiodon sp. Our phylogenetic tree revealed
well-supported clades and confirmed, by barcode species delimitation analysis, a
new Molecular Operational Taxonomic Unit (MOTU) for Apareiodon
sp. (Aripuanã River). As a whole, the above features support the occurrence of a
new species of the Apareiodon, thus far unknown for the
Parodontidae.
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Affiliation(s)
- Emanoel Oliveira Dos Santos
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Geize Aparecida Deon
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Rafael Bonfim de Almeida
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Hugmar Pains da Silva
- Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Carla Simone Pavanelli
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Marta Margarete Cestari
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, SP, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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23
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Wang X, Liu F, Yu D, Liu H. Mitochondrial divergence suggests unexpected high species diversity in the opsariichthine fishes (Teleostei: Cyprinidae) and the revalidation of Opsariichthys macrolepis. Ecol Evol 2019; 9:2664-2677. [PMID: 30891207 PMCID: PMC6405531 DOI: 10.1002/ece3.4933] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/16/2018] [Accepted: 12/28/2018] [Indexed: 01/04/2023] Open
Abstract
Opsariichthine (sensu Oceanologi Et Limnologia Sinica, 1982, 13, 293-298) is a cyprinid group consisting of five genera and endemic to East Asia. Previous studies suggested that there may be many possible cryptic species in this group, but this has not been confirmed. In this study, using mitochondrial cyt b sequences on 1,388 samples and 739 haplotypes, we showed very high species diversity within this group. The results showed that phylogenetic relationships of the opsariichthine group were as ([Nipponocypris-Parazacco-Candidia] + [Zacco + Opsariichthys]), and there were multiple deep lineages within several species, flagging putative cryptic species. When a 3% genetic distance was used as a threshold for species delimitation, 35 haplogroups were found, nine haplogroups in Candidia-Parazacco-Nipponocypris group, six haplogroups in the Zacco group, and 20 haplogroups in the Opsariichthys group. We consider all of them to be putative until determination of distinct species based on the tree topology, geographic distributions, or a combination of both. In addition, two kinds of species delimitation tools, ABGD and PTP, were applied to construct molecular operational taxonomic units (MOTUs). The ABGD method revealed nine MOTUs in Candidia-Parazacco-Nipponocypris group, two MOTUs in the Zacco group, and 17 MOTUs in the Opsariichthys group. And the PTP method revealed 10 MOTUs in Candidia-Parazacco-Nipponocypris group, 10 MOTUs in the Zacco group, and 29 MOTUs in the Opsariichthys group. Therefore, there should be more species in the opsariichthine group than presently described. Based on the molecular data and morphological characteristics, we proposed Opsariichthys macrolepis as a valid species and described its morphological diagnostic characters.
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Affiliation(s)
- Xue Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fei Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Huanzhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
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24
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Hofmann EP, Nicholson KE, Luque-Montes IR, Köhler G, Cerrato-Mendoza CA, Medina-Flores M, Wilson LD, Townsend JH. Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America. Front Genet 2019; 10:11. [PMID: 30804976 PMCID: PMC6378269 DOI: 10.3389/fgene.2019.00011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/11/2019] [Indexed: 01/10/2023] Open
Abstract
Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
- Department of Biological Sciences, Clemson University, Clemson, SC, United States
| | - Kirsten E. Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | | | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt, Germany
| | - César A. Cerrato-Mendoza
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Melissa Medina-Flores
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Larry David Wilson
- Centro Zamorano de Biodiversidad, Escuela Agrícola Panamericana Zamorano, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
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25
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Conventional Cytogenetic Approaches—Useful and Indispensable Tools in Discovering Fish Biodiversity. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0148-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Berbel-Filho WM, Ramos TPA, Jacobina UP, Maia DJG, Torres RA, Lima SMQ. Updated checklist and DNA barcode-based species delimitations reveal taxonomic uncertainties among freshwater fishes from the mid-north-eastern Caatinga ecoregion, north-eastern Brazil. JOURNAL OF FISH BIOLOGY 2018; 93:311-323. [PMID: 30047136 DOI: 10.1111/jfb.13758] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The mid-north-eastern Caatinga is a semiarid freshwater ecoregion in North-eastern Brazil that is dominated by temporary rivers and is currently classified as one of the least ichthyologically-known ecoregions in the world. The present study aimed to provide an updated checklist of mid-north-eastern Caatinga ecoregion (MNCE) freshwater fish species and evaluate their taxonomic identity using morphology, DNA barcoding and multiple species delimitation approaches. After reviewing published studies and ichthyological collections, 119 species were identified. Among these were 94 putatively valid native and 14 non-native species, five undescribed native species, four new records for the MNCE, 11 potential cases of misidentification and 14 species listed as inquirenda. Additionally, 252 individuals from 49 species were barcoded, revealing three potential taxonomic synonyms. The combined molecular approaches estimated a total of 91 native species, although a finalized species list for the MNCE awaits additional taxonomic revisions and field surveys. This study provides the most up-to-date species checklist for the MNCE and a molecular reference database for identifying MNCE fishes with DNA barcodes. Results highlight the need to integrate traditional taxonomy with molecular approaches to correctly identify species, especially in taxonomically problematic ecoregions such as the MNCE.
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Affiliation(s)
- Waldir M Berbel-Filho
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Telton P A Ramos
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Uedson P Jacobina
- Laboratório de Genômica Evolutiva e Ambiental, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
- Laboratório de Ictiologia e Conservação, Universidade Federal de Alagoas, Penedo, Brazil
| | - Danielle J G Maia
- Laboratório de Genômica Evolutiva e Ambiental, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Rodrigo A Torres
- Laboratório de Genômica Evolutiva e Ambiental, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio M Q Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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27
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Sales NG, Mariani S, Salvador GN, Pessali TC, Carvalho DC. Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System. Front Genet 2018; 9:271. [PMID: 30087693 PMCID: PMC6066647 DOI: 10.3389/fgene.2018.00271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Neotropical Rivers host a highly diverse ichthyofauna, but taxonomic uncertainty prevents appropriate conservation measures. The Doce River Basin (DRB), lying within two Brazilian threatened hotspots (Atlantic Forest and Brazilian Savanna) in south-east Brazil, faced the worst ever environmental accident reported for South American catchments, due to a dam collapse that spread toxic mining tailings along the course of its main river. Its ichthyofauna was known to comprise 71 native freshwater fish species, of which 13 endemic. Here, we build a DNA barcode library for the DRB ichthyofauna, using samples obtained before the 2015 mining disaster, in order to provide a more robust biodiversity record for this basin, as a baseline for future management actions. Throughout the whole DRB, we obtained a total of 306 barcodes, assigned to 69 putative species (with a mean of 4.54 barcodes per species), belonging to 45 genera, 18 families, and 5 orders. Average genetic distances within species, genus, and families were 2.59, 11.4, and 20.5%, respectively. The 69 species identified represent over 76% of the known DRB ichthyofauna, comprising 43 native (five endemic, of which three threatened by extinction), 13 already known introduced species, and 13 unknown species (such as Characidium sp., Neoplecostomus sp., and specimens identified only at the sub-family level Neoplecostominae, according to morphological identification provided by the museum collections). Over one fifth of all analyzed species (N = 16) had a mean intraspecific genetic divergence higher than 2%. An integrative approach, combining NND (nearest neighbor distance), BIN (barcode index number), ABGD (automatic barcode gap discovery), and bPTP (Bayesian Poisson Tree Processes model) analyses, suggested the occurrence of potential cryptic species, species complex, or historical errors in morphological identification. The evidence presented calls for a more robust, DNA-assisted cataloging of biodiversity-rich ecosystems, in order to enable effective monitoring and informed actions to preserve and restore these delicate habitats.
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Affiliation(s)
- Naiara G Sales
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Gilberto N Salvador
- Laboratório de Ecologia e Conservação, Universidade Federal do Pará, Belém, Brazil
| | - Tiago C Pessali
- Museu de Ciências Naturais PUC Minas, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel C Carvalho
- Programa de Pós-graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
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28
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Melo BF, Dorini BF, Foresti F, Oliveira C. Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes). Front Genet 2018; 9:107. [PMID: 29670644 PMCID: PMC5893770 DOI: 10.3389/fgene.2018.00107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.
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Affiliation(s)
- Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Beatriz F. Dorini
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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29
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Silva-Santos R, Ramirez JL, Galetti PM, Freitas PD. Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici. Front Genet 2018; 9:47. [PMID: 29497440 PMCID: PMC5818402 DOI: 10.3389/fgene.2018.00047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/31/2018] [Indexed: 12/11/2022] Open
Abstract
The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity. In this study, we performed phylogenetic analyses, based on three nuclear (recombination activating gene 1, RAG1, recombination activating gene 2, RAG2, and myosin heavy chain 6 cardiac muscle alpha gene, Myh6) and two mitochondrial (COI and Cytochrome b, Cytb) markers, in specimens morphologically similar to L. friderici and related species from different hydrographic basins in South America. Our phylogenetic tree identified four well-supported clades, which point out to the existence of taxonomic inconsistencies within this fish group. A clade named L. cf. friderici sensu stricto included eight Molecular Operational Taxonomic Units recently diversified in the Brazilian Shield basins. These results were also confirmed by a single-gene species delimitation analysis. It is suggested that this clade includes a species complex, characterizing taxonomic uncertainties. Another clade recovered only L. friderici from the Suriname rivers, validating this nominal species in its type locality. A third no-named clade, characterized by deeper species divergence, recovered five different nominal species interleaved with other undescribed forms previously also recognized as L. cf. friderici, indicating taxonomic errors. The fourth clade only included L. taeniatus. Our results showed a complex scenario involving the morphotype L. cf. friderici and allowed us to address aspects related to evolutionary diversification of this fish group and historical processes involved with, highlighting the importance of revealing hidden biodiversity for the taxonomy and conservationist action plans of these fish.
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Affiliation(s)
- Rosane Silva-Santos
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Jorge L Ramirez
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Pedro M Galetti
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Patrícia D Freitas
- Laboratório de Biodiversidade Molecular e Conservação, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
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30
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Nirchio M, Paim FG, Milana V, Rossi AR, Oliveira C. Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes). Front Genet 2018; 9:17. [PMID: 29459882 PMCID: PMC5807406 DOI: 10.3389/fgene.2018.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 01/15/2018] [Indexed: 11/13/2022] Open
Abstract
Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.
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Affiliation(s)
- Mauro Nirchio
- Facultad de Ciencias Agropecuarias, Universidad Técnica de Machala, Machala, Ecuador
| | - Fabilene G. Paim
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São Paulo, Brazil
| | - Valentina Milana
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Anna R. Rossi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São Paulo, Brazil
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Birindelli JLO, Sidlauskas BL. Preface: How far has Neotropical Ichthyology progressed in twenty years? NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Studies on the diversity, taxonomy, phylogeny, and biogeography of Neotropical Fishes have thrived over the twenty years that have elapsed since the first symposium on their phylogeny and classification in Porto Alegre, Brazil. Here, we review recent advances in the study of Neotropical fishes and assess the known diversity of freshwater species in that region. 6,255 valid freshwater species have been discovered in the Neotropics so far, and we estimate that over 9,000 species will be known when the inventory is complete. We also summarize the events of the second Symposium on Phylogeny and Classification of Neotropical Fishes that took place last year in Londrina, Brazil. Along with invited talks on the biodiversity of all major groups of Neotropical fishes, a series of presentations on the development of fish collections, and numerous contributed talks, the meeting included a special session to honor Dr. Richard Vari, who was one of the most prolific and beloved members of our community.
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