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DNA barcoding and phylogeography of the Hoplias malabaricus species complex

  • Cardoso, Y. P. et al. A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias. PLoS ONE 13(8), e0202024. https://doi.org/10.1371/journal.pone.0202024 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bertollo, L. A. C., Born, G. G., Dergam, J. A., Fenocchio, A. S. & Moreira-Filho, O. A biodiversity approach in the Neotropical Erythrinidae fish, Hoplias malabaricus: Karyotypic survey, geographic distribution of karyomorphs and cytotaxonomic considerations. Chrom. Res. 8(7), 603–613 (2000).

    CAS 
    Article 

    Google Scholar 

  • Oyakawa, O. T. Family Erythrinidae (Trahiras). in Check list of the freshwater fishes of South and Central America (Reis, R. E., Kullander, S. O. & Ferraris, C.). Edipucrs 238–240 (Porto Alegre, 2003).

  • Dagosta, F. C. P. & de Pinna, M. C. C. The fishes of the Amazon: distribution and biogeographical patterns, with a comprehensive list of species. Bull. Am. Museum Nat. Hist. 431, 1–163 (2019).

    Google Scholar 

  • Da Rosa, R., Vicari, M. R., Dias, A. L. & Giuliano-Caetano, L. New insights into the biogeographic and Karyotypic Evolution of Hoplias Malabaricus. Zebrafish 11(3), 198–206. https://doi.org/10.1089/zeb.2013.0953 (2014).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Santos, U. et al. Molecular and karyotypic phylogeography in the neotropical Hoplias malabaricus (Erythrinidae) fish in eastern Brazil. J. Fish Biol. 75(9), 2326–2343. https://doi.org/10.1111/j.1095-8649.2009.02489.x (2009).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Blanco, D. R., Lui, R. L., Bertollo, L. A. C., Diniz, D. & Filho, O. M. Characterization of invasive fish species in a river transposition region: Evolutionary chromosome studies in the genus Hoplias (Characiformes, Erythrinidae). Rev. Fish Biol. Fish. 20(1), 1–8. https://doi.org/10.1007/s11160-009-9116-3 (2010).

    Article 

    Google Scholar 

  • Jacobina, U. P. et al. DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras. Genetica 146, 505. https://doi.org/10.1007/s10709-018-0043-x (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Marques, D. F., Santos, F. A., da Silva, S. S., Sampaio, I. & Rodrigues, L. R. R. Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River. Neotrop. Ichthyol. 11(2), 459–466. https://doi.org/10.1590/S1679-62252013000200015 (2013).

    Article 

    Google Scholar 

  • Paz, F. P. C., Batista, J. S. & Porto, J. I. R. DNA barcodes of rosy tetras and allied species (Characiformes: Characidae: Hyphessobrycon) from the Brazilian Amazon Basin. PLoS ONE 9(5), e98603. https://doi.org/10.1371/journal.pone.0098603 (2014).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Guimarães, K. L. A., de Sousa, M. P. A., Ribeiro, F. R. V., Porto, J. I. R. & Rodrigues, L. R. R. DNA barcoding of fish fauna from low order streams of Tapajós River basin. PLoS ONE 13(12), e0209430. https://doi.org/10.1371/journal.pone.0209430 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Machado, V. N. et al. One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognized diversity in the Amazon. Sci. Rep. 8, 8387. https://doi.org/10.1038/s41598-018-26550-x (2018).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hebert, P. D. N., Cywinska, A., Ball, S. L. & Dewaard, J. R. Biological identifications through DNA barcodes. Philos. Trans. R. Soc. B 270(1512), 313–321. https://doi.org/10.1098/rspb.2002.2218 (2003).

    CAS 
    Article 

    Google Scholar 

  • Pugedo, M. L., de Andrade Neto, F. R., Pessali, T. C., Birindelli, J. L. O. & Carvalho, D. C. Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin. Genetica 144(3), 1–9. https://doi.org/10.1007/s10709-016-9903-4 (2016).

    Article 

    Google Scholar 

  • Rosso, J. J. et al. Integrative taxonomy reveals a new species of the Hoplias malabaricus species complex (Teleostei: Erythrinidae). Ichthyol. Explor. Freshw. 1, 1–18. https://doi.org/10.23788/IEF-1076 (2018).

    Article 

    Google Scholar 

  • Azpelicueta, M. M., Benítez, M., Aichino, D. & Mendez, C. M. D. A new species of the genus Hoplias (Characiformes, Erythrinidae), a tararira from the lower Paraná River, in Missiones, Argentina. Acta Zool. Lilloana 59(1–2), 71–82 (2015).

    Google Scholar 

  • Rosso, J. J. et al. A new species of the Hoplias malabaricus species complex (Characiformes: Erythrinidae) from the La Plata River basin. Cybium 40(3), 199–208 (2016).

    Google Scholar 

  • Cardoso, Y. P. & Montoya-Burgos, J. I. Unexpected diversity in the catfish Pseudancistrus brevispinis reveals dispersal routes in a Neotropical center of endemism: The Guyanas Region. Mol. Ecol. 18(5), 947–964. https://doi.org/10.1111/j.1365-294X.2008.04068.x (2009).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Hoorn, C., Wesselingh, F. P., Hovikoski, J. & Guerrero, J. The development of the Amazonian mega-wetland (Miocene; Brazil, Colombia, Peru, Bolivia). Amazon. Landsc. Species Evol. https://doi.org/10.1002/9781444306408.ch8 (2010).

    Article 

    Google Scholar 

  • Albert, J. S. & Reis, R. E. Introduction to neotropical freshwaters. In Historical Biogeography of Neotropical Freshwater Fishes (eds Albert, J. S. & Reis, R. E.) 3–19 (University of California Press, 2011).

    Google Scholar 

  • Leys, M., Keller, I., Räsänen, K., Gattolliat, J.-L. & Robinson, C. T. Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps. BMC Evol. Biol. https://doi.org/10.1186/s12862-016-0643-y (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Aljanabi, S. M. & Martinez, I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25(22), 4692–4693 (1997).

    CAS 
    Article 

    Google Scholar 

  • Vitorino, C. A., Oliveira, R. C. C., Margarido, V. P. & Venere, P. C. Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker. Neotrop. Ichthyol. 13, 557–568. https://doi.org/10.1590/1982-0224-20150037 (2015).

    Article 

    Google Scholar 

  • Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. DNA barcoding Australia’s fish species. Philos. Trans. R. Soc. B 359, 1847–1857. https://doi.org/10.1098/srtb.2005.1716 (2005).

    Article 

    Google Scholar 

  • Dunn, I. S. & Blattner, F. R. Sharons 36 to 40: Multienzyme, high capacity, recombination deficient replacement vectors with polylinkers and polystuffers. Nucleic Acids Res. 15, 2677–2698 (1987).

    CAS 
    Article 

    Google Scholar 

  • Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22), 4673–4680 (1994).

    CAS 
    Article 

    Google Scholar 

  • Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334 (2000).

    CAS 
    Article 

    Google Scholar 

  • Ratnasingham, S. & Hebert, P. D. N. DNA-Based registry for all animal species: The Barcode Index Number (BIN) system. PLoS ONE 8(7), e66213. https://doi.org/10.1371/journal.pone.0066213 (2013).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pons, J. et al. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55(4), 595–609. https://doi.org/10.1080/10635150600852011 (2006).

    Article 
    PubMed 

    Google Scholar 

  • Fujisawa, T. & Barraclough, T. G. Delimiting species using single-locus data and the generalized mixed yule coalescent approach: A revised method and evaluation on simulated data sets. Syst. Biol. 62(5), 707–724. https://doi.org/10.1093/sysbio/syt033 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. ABGD, automatic barcode gap discovery for primary species delimitation. Mol. Ecol. 21(8), 1864–1877. https://doi.org/10.1111/j.1365-294X.2011.05239.x (2012).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Drummond, A. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. https://doi.org/10.1186/1471-2148-7-214 (2007).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Posada, D. jModelTest: Phylogenetic model averaging. Mol. Biol. Evol. 25, 1253–1256. https://doi.org/10.1093/molbev/msn083 (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • R Core Team. R: A Language and Environment for Statistical Computing. https://www.R-project.org/ (2017).

  • Ezard, T., Fujisawa, T. & Barraclough, T. splits: Species Limits by Threshold Statistics. R package version 1.0–19/r52. https://R-Forge.R-project.org/projects/splits/ (2017).

  • Paradis, E. & Schliep, K. ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2018).

    Article 

    Google Scholar 

  • Bermingham, E., McCafferty, S. S. & Martin, A. P. Fish biogeography and molecular clocks: Perspectives from the Panamanian Isthmus. In Molecular Systematics of Fishes (eds Kocher, T. D. & Stepien, C. A.) 113–128 (Academic Press, 1997).

    Chapter 

    Google Scholar 

  • Thomaz, A. T., Malabarba, L. R., Bonatto, S. L. & Knowles, L. L. Testing the effect of palaeodrainages versus habitat stability on genetic divergence in riverine systems: Study of a Neotropical fish of the Brazilian coastal Atlantic Forest. J. Biogeogr. 42, 2389–2401. https://doi.org/10.1111/jbi.12597 (2015).

    Article 

    Google Scholar 

  • Kimura, M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120 (1980).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Guillot, G., Renaud, S., Ledevin, R., Michaux, J. & Claude, J. A unifying model for the analysis of phenotypic, genetic and geograhic data. Syst. Biol. 61(6), 897–911. https://doi.org/10.1093/sysbio/sys038 (2012).

    Article 
    PubMed 

    Google Scholar 

  • Excoffier, L., Laval, G. & Schneider, S. Arlequin: A Software for Population Data Analysis. Version 3.1. http://cmpg.unibe.ch/software/arlequin3 (2007).

  • Wright, S. Evolution and the genetics of populations: Variability within and among natural populations. Univ. Chicago 4, 580 (1978).

    Google Scholar 

  • Rozas, J. et al. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol. Biol. Evol. 34, 3299–3302. https://doi.org/10.1093/molbev/msx248 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Bandelt, H. J., Forster, P. & Röhl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16(1), 37–48 (1999).

    CAS 
    Article 

    Google Scholar 

  • Leigh, J. W. & Bryant, D. POPART: Full-feature software for haplotype network construction. Methods Ecol. Evol. 6, 1110–1116. https://doi.org/10.1111/2041-210X.12410 (2015).

    Article 

    Google Scholar 

  • Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595 (1989).

    CAS 
    Article 

    Google Scholar 

  • Fu, Y. X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925 (1997).

    CAS 
    Article 

    Google Scholar 

  • Austin, M. P. Continuum concept, ordination methods, and niche theory. Annu. Rev. Ecol. Syst. 16(1), 39–61. https://doi.org/10.1146/annurev.es.16.110185.000351 (1985).

    MathSciNet 
    Article 

    Google Scholar 

  • Graham, A., Atkinson, P. & Danson, F. Spatial analysis for epidemiology. Acta Trop. 91(3), 219–225. https://doi.org/10.1016/j.actatropica.2004.05.001 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol. Model. 190(3–4), 231–259. https://doi.org/10.1016/j.ecolmodel.2005.03.026 (2006).

    Article 

    Google Scholar 

  • Guimarães, K. L. A., Rosso, J. J., Souza, M. F. B., de Astarloa, J. M. D. & Rodrigues, L. R. R. Integrative taxonomy reveals disjunct distribution and first record of Hoplias misionera (Characiformes: Erythrinidae) in the Amazon River basin: Morphological, DNA barcoding and cytogenetic considerations. Neotrop. Ichthyol. 19(2), e200110. https://doi.org/10.1590/1982-0224-2020-0110 (2021).

    Article 

    Google Scholar 

  • Queiroz, L. J. et al. Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus. Mol. Phylogenet. Evol. 145, 106711. https://doi.org/10.1016/j.ympev.2019.106711 (2020).

    Article 

    Google Scholar 

  • Phillips, J. D., Gillis, D. J. & Hanner, R. H. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol. Evol. https://doi.org/10.1002/ece3.4757 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Blaxter, M. L. The promise of a DNA taxonomy. Philos. Trans. R. Soc. B. 359(1444), 669–679. https://doi.org/10.1098/rstb.2003.1447 (2004).

    CAS 
    Article 

    Google Scholar 

  • Nwani, C. D. et al. DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species. Mitochondrial DNA 22(1), 43–51. https://doi.org/10.3109/19401736.2010.536537 (2011).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Aguirre, W. E., Shervette, V. R., Navarrete, R., Calle, P. & Agorastos, S. Morphological and genetic divergence of Hoplias microlepis (Characiformes: Erythrinidae) in rivers and artificial impoundments of Western Ecuador. Copeia 2013(2), 312–323. https://doi.org/10.1643/ci-12-083 (2013).

    Article 

    Google Scholar 

  • Pires, W. M. M., Barros, M. C. & Fraga, E. C. DNA Barcoding unveils cryptic lineages of Hoplias malabaricus from Northeastern Brazil. Braz. J. Biol. 81(4), 917–927. https://doi.org/10.1590/1519-6984.231598 (2020).

    Article 

    Google Scholar 

  • Souza, F. H. S. et al. interspecific genetic differences and historical demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum). Genes 10(9), 693. https://doi.org/10.3390/genes10090693 (2019).

    CAS 
    Article 
    PubMed Central 

    Google Scholar 

  • Torati, L. S. et al. Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins. BMC Genet. https://doi.org/10.1186/s12863-018-0711-y (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lovejoy, N. R. & Araujo, M. L. G. Molecular systematics, biogeography and population structure of Neotropical freshwater needlefishes of the genus Potamorrhaphis. Mol. Ecol. 9(3), 259–268. https://doi.org/10.1046/j.1365-294x.2000.00845.x (2000).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Mabesoone, J. M. Sedimentary Basins of Northeast Brazil (Federal University of Pernambuco, 1994).

    Google Scholar 

  • Haffer, J. & Prance, G. T. Impulsos climáticos da evolução na Amazônia durante o Cenozóico: Sobre a teoria dos Refúgios da diferenciação biótica. Estudos Avançados USP 46, 175–208. https://doi.org/10.1590/S0103-40142002000300014 (2002).

    Article 

    Google Scholar 

  • Riker, S. R. L., Lima, F. J. C., Motta, M. B. Evidências de glaciação Pleistocênica na Amazônia Brasileira. Anais do 14° Simpósio de Geologia da Amazônia, Sociedade Brasileira de Geologia 15–18 (2015).

  • Albert, J. S., Val, P. & Hoorn, C. The changing course of the Amazon River in the Neogene: Center stage for Neotropical diversification. Neotrop. Ichthyol. 16(3), e180033. https://doi.org/10.1590/1982-0224-20180033 (2018).

    Article 

    Google Scholar 

  • Lundberg, J. G. et al. The stage for Neotropical fish diversification: a history of tropical South American rivers. (eds. Malabarba, L. R., Reis, R. E., Vari, R. P., Lucena, Z. M., Lucena, C. A. S. Phylogeny and classification of Neotropical fishes). Edipucrs 13–48 (1998).

  • Hubert, N. & Renno, J. F. Historical biogeography of South American freshwater fishes. J. Biogeogr. 33(8), 1414–1436. https://doi.org/10.1111/j.1365-2699.2006.01518.x (2006).

    Article 

    Google Scholar 

  • Farias, I. P. & Hrbek, T. Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin. Mol. Phylogenet. Evol. 49, 32–43. https://doi.org/10.1016/j.ympev.2008.05.033 (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Tagliacollo, V. A., Bernt, M. J., Craig, J. M., Oliveira, C. & Albert, J. S. Model-based total evidence phylogeny of Neotropical electric knifefishes (Teleostei, Gymnoti-formes). Mol. Phylogenet. Evol. 95, 20–33. https://doi.org/10.1016/j.ympev.2015.11.007 (2015).

    Article 
    PubMed 

    Google Scholar 

  • Hutchinson, G. E. Concluding remarks. Cold Spring Harbor Symposium. Quant. Biol. 22, 415–427 (1957).

    Article 

    Google Scholar 

  • Wiens, J. J. & Graham, C. H. Niche conservatism: Inte-grating evolution, ecology, and conservation biology. Annu. Rev. Ecol. Evol. Syst. 36, 519–539 (2005).

    Article 

    Google Scholar 

  • McNyset, K. M. Ecological niche conservatism in North American freshwater fishes. Biol. J. Lin. Soc. 96, 282–295 (2009).

    Article 

    Google Scholar 

  • Silva, W. C., Marceniuk, A. P., Sales, J. B. L. & Araripe, J. Early pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species. Neotrop. Ichthyol. https://doi.org/10.1590/1982-0224-20150184 (2016).

    Article 

    Google Scholar 

  • Lemopoulos, A. & Covain, R. Biogeography of the freshwater fishes of the Guianas using a partitioned parsimony analysis of endemicity with reappraisal of ecoregional boundaries. Cladistics 35(2019), 106–124. https://doi.org/10.1111/cla.12341 (2018).

    Article 
    PubMed 

    Google Scholar 

  • Hoorn, C. Marine incursions and the influence of Andean tectonics on the Miocene depositional history of northwestern Amazonia: Results of a palynostratigraphic study. Palaeogeogr. Palaeoclimatol. Palaeoecol. 105, 267–309. https://doi.org/10.1016/0031-0182(93)90087-Y (1993).

    Article 

    Google Scholar 

  • Hoorn, C., Guerreiro, J. & Sarmiento, G. Andean tectonics as a cause for changing drainage patterns in Miocene Northern South America. Geology 23(3), 237–240. https://doi.org/10.1130/0091-7613(1995)023%3c0237:ATAACF%3e2.3.CO;2 (1995).

    ADS 
    Article 

    Google Scholar 

  • Ribeiro, A. C. Tectonic history and the biogeography of the freshwater fishes from the coastal drainages of eastern Brazil: An example of faunal evolution associated with a divergent continental margin. Neotrop. Ichthyol. 4(2), 225–246. https://doi.org/10.1590/S1679-62252006000200009 (2006).

    Article 

    Google Scholar 

  • Lovejoy, N. R., Albert, J. S. & Crampton, W. G. R. Miocene marine incursions and marine/freshwater transitions: Evidence from Neotropical fishes. J. S. Am. Earth Sci. 21(1–2), 5–13. https://doi.org/10.1016/j.jsames.2005.07.009 (2006).

    Article 

    Google Scholar 


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