Molecular Biology Reports

, Volume 46, Issue 2, pp 2473–2484 | Cite as

Detecting population structure of Paleosuchus trigonatus (Alligatoridae: Caimaninae) through microsatellites markers developed by next generation sequencing

  • F. L. MunizEmail author
  • A. M. Ximenes
  • P. S. Bittencourt
  • S. M. Hernández-Rangel
  • Z. Campos
  • T. Hrbek
  • I. P. Farias
Original Article


We isolated and characterized 10 new microsatellites loci for Paleosuchus trigonatus using ION TORRENT Sequencing Technology. We tested the transferability of these loci to three related species of the subfamily Caimaninae, and used these bi-parental markers to test population structure and genetic diversity of two populations of P. trigonatus impacted by hydroelectric dam construction on the Madeira (N = 16) and Xingu (N = 16) rivers. We also investigated the transferability of these markers to three related species: Paleosuchus palpebrosus (N = 5), Caiman crocodilus (N = 6) and Melanosuchus niger (N = 6). The genetic diversity of P. trigonatus was low in both the Madeira (He: 0.535 ± 0.148) and Xingu (He: 0.381 ± 0.222) populations, but the loci were sufficiently polymorphic to be used in system of mating and kinship studies in P. trigonatus. DAPC analysis with our set of microsatellites loci was able to separate the four species of Caimaninae studied and to detect a shallow genetic structure between Madeira and Xingu populations of P. trigonatus. AMOVA and STRUCTURE analyses using locprior model corroborate this shallow genetic structure. These novel molecular markers will be also useful in conservation genetics and phylogeographic studies of P. trigonatus, since they improve our ability to monitor the putative effects of dams on the loss of genetic diversity and allow us to investigate population dynamics and microevolutionary processes that occurred in the species.


Cross-amplification Species identification Dwarf caiman Madeira River Xingu River Ion Torrent 



This study was financed by the following Grants: CNPq/CT-Amazon Project no. 575603/2008-9 awarded to IPF, CNPq Project no. 482662/2013-1 to TH, and CNPq Project no. 470383/2007-0 and 479179/2014 to ZC. FM and PSB were supported by Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM), doctoral and master fellowship respectively. SMHR was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). AMX was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) masters fellowship, financial code 001, and a research fellowship from FAPEAM. We are also grateful for the additional financial and logistical support from Embrapa Pantanal (Macroprogram 3), Instituto Nacional de Pesquisas da Amazônia (INPA), Fundect, Norte Energia, Tractebel, O Boticário Foundation, Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) and Santo Antônio Energia.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no financial or non-financial conflict of interest.

Ethical approval

This study was approved by Embrapa ethics committee under the Permit no. 009/2016, Mato Grosso do Sul, Brazil. All tissue samples of the caimans were colected under the license no. 13048-1, granted by the Brazilian Institute of Environment and Renewable Natural Resources (IBAMA), and deposited in the CTGA (Coleção de Tecidos de Genética Animal) tissue collection at Universidade Federal do Amazonas (UFAM), Amazonas, Brazil.

Supplementary material

11033_2019_4709_MOESM1_ESM.docx (36 kb)
Supplementary material 1 (DOCX 35 KB)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Laboratory of Animal Genetics and Evolution (LEGAL), Department of GeneticsFederal University of Amazonas (UFAM)ManausBrazil
  2. 2.Graduate Program in Genetics, Conservation and Evolutionary BiologyNational Institute for Amazonian Research (INPA)ManausBrazil
  3. 3.Wildlife LaboratoryBrazilian Agricultural Research Corporation (EMBRAPA) PantanalCorumbáBrazil

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