RESEARCH ARTICLE High gene flow in two migratory Neotropical fish species, Salminus franciscanus and Brycon orthotaenia, and implications for conservation aquaculture Maria R.M. Coimbra | Hozana L. Dantas | Manuela M.S. Luna | Maíra A. Lima | Mondrian Sales | Bruno C.N.R. da Silva | Ana P.S. Lima Departamento de Pesca e Aquicultura, Universidade Federal Rural de Pernambuco, Recife, Pernambuco, Brazil Correspondence Maria Raquel Moura Coimbra, Universidade Federal Rural de Pernambuco, Departamento de Pesca e Aquicultura, Rua Dom Manuel de Medeiros, s/n, Dois Irm~ aos, Recife-PE, 52171-900, Brazil. Email: maria.rmcoimbra2@ufrpe.br Funding information Agencia Nacional de Energia Elétrica, Grant/ Award Number: CTNI 92.2011.0520.00 Abstract 1. Two migratory and endangered freshwater fish species, Salminus franciscanus and Brycon orthotaenia, are endemic to one of the most important basins for hydro- power capacity in South America. These two fish are target species of conserva- tion aquaculture programmes along the S~ ao Francisco River system. 2. In order to implement effective strategies for the conservation of these species, microsatellite markers were developed and used to assess the genetic diversity and structure among wild groups. Fish were collected during the spawning season at four sampling sites, covering more than 1000 km. 3. Polymorphism loci were assessed, and a total of 133 and 107 alleles were found for S. franciscanus and B. orthotaenia, respectively. Despite the critical conserva- tion status, B. orthotaenia showed high levels of genetic diversity, comparable with those of other closely related species. 4. Salminus franciscanus exhibited half of the genetic diversity of its sister species in terms of allelic diversity, indicating that this species will be more prone to genetic drift and inbreeding in conservation aquaculture programmes. 5. The results of an analysis of molecular variance for microsatellite markers in these species (F ST = 0.007 for S. franciscanus and F ST = 0.003 for B. orthotaenia) and the estimated recent migration rates (>40% among sampling sites) support panmixia in both species, despite the heterogeneities of the riverscape. 6. The results of this study and the microsatellites developed will play an important role in assisting agencies in making informed decisions on conservation aquacul- ture programmes. KEYWORDS genetic diversity, microsatellites, potamodromous fish, restocking, river fragmentation, threatened species 1 | INTRODUCTION Hydroelectricity is one of the most effective alternative energy pro- duction methods to help counteract climate change because it is renewable. Brazil is the third largest hydroelectricity producer in the world, behind China and Canada (International Energy Agency (IEA), 2015). Hydroelectric dams disrupt the natural flow of the river, however, changing its course and with the reservoir posing serious Received: 21 August 2019 Revised: 2 January 2020 Accepted: 11 March 2020 DOI: 10.1002/aqc.3336 Aquatic Conserv: Mar Freshw Ecosyst. 2020;1–11. wileyonlinelibrary.com/journal/aqc © 2020 John Wiley & Sons, Ltd. 1