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. 2019 Mar 22;7:e6580.
doi: 10.7717/peerj.6580. eCollection 2019.

Evidence of Cryptic Lineages Within a Small South American Crocodilian: The Schneider's Dwarf Caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

Free PMC article

Evidence of Cryptic Lineages Within a Small South American Crocodilian: The Schneider's Dwarf Caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

Pedro Senna Bittencourt et al. PeerJ. .
Free PMC article


Schneider's dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus-an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.

Keywords: Amazonian crocodilians; Biogeography; Conservation genetics; Diversification; Jacaré-coroa; Population genetics.

Conflict of interest statement

Tomas Hrbek is an Academic Editor for PeerJ. All other authors declare that there are no competing interests.


Figure 1
Figure 1. Map showing all the sites sampled in this study, results of the BAPS analysis and haplotype network based on the mitochondrial cyt b gene.
The colors represent the cluster to which the analyzed individuals belong based on BAPS assignments. The points with two colors on the map indicate sites where haplotypes assigned to different groups were found. Each cluster is also highlighted in the haplotype network, indicating the Amazonia lineage (red and green) and the Guiana lineage (purple and blue). Shaded area represents the species geographic range currently accepted by IUCN (Crocodile Specialist Group, 1996). The orange highlighted area in Branco River comprises relicts of the paleodivisor Amazon/Proto-Berbice (Parima, Demini, Apiaú, Mucajaí, Mocidade, Grande, Lua, Anauá, and Acaraí mountain ranges). White boundaries to the north and south of the Amazon River represents the Guiana and Brazilian shields, respectively. The map was constructed in QGIS and the final graphic in Inkscape.
Figure 2
Figure 2. Maximum clade credibility chronogram generated using BEAST.
Maximum clade credibility chronogram from 9,000 posterior trees generated using BEAST. Dataset comprised 36 unique haplotypes of P. trigonatus, and 22 unique haplotypes of P. palpebrosus (Muniz et al., 2018) cytb sequences (1020 aligned base pairs). Bayesian posterior probabilities above 0.95 are shown as dark nodes. MPTP and bGMYC single locus species discovery methods resulted in the discovery of five lineages, two of P. trigonatus and three of P. palpebrosus (see also Muniz et al., 2018). GMYC resulted in the discovery of six lineages, representing population structuring identified by other analyses carried out in this study.
Figure 3
Figure 3. BEAST cytochrome b chronogram for P. trigonatus using the CladeAge calibration method.
Numbers below nodes correspond to time in millions of years and bars represent 95% HPD intervals, where red bars indicates fossil constraints. The colors boxes represents the cluster to which the analyzed individuals belong based on species discovery assignments, indicating Amazonia lineage (red and green) and Guiana lineage (purple).
Figure 4
Figure 4. River basin dissimilarity scatter plot based on a pairwise ΦST genetic distance matrix between populations of P. trigonatus using a non-metric multidimensional scaling analysis (MDS).
Stress value indicates goodness-of-fit. The analysis was made utilizing the isoMDS function of the MASS package (Venables & Ripley, 2002) and the scatter plot was made using scatterplot3d (Ligges & Mächler, 2003) in the software R (R Development Core Team, 2011). The colors represents the cluster to which the analyzed individuals belong based on BAPS assignments, indicating the Amazonia lineage (red and green) and the Guiana lineage (purple and blue).

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Grant support

This study was financed by the following grants: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq grant no. 575603/2008-9) and CNPq/SISBIOTA- BioPHAM (CNPq grant no. 563348/2010) awarded to Izeni Pires Farias, CNPq grant no. 400813/2012-2 and 482662/2013-1 to Tomas Hrbek, and grant no. 470383/2007-0 and 479179/2014 to Zilca Campos. Additional financial and logistical support were also financed by Empresa Brasileira de Pesquisa Agropecuaria Pantanal (Macroprograma 3), Instituto Nacional de Pesquisas da Amazônia (INPA), Parque Nacional Viruá, Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado do Mato Grosso do Sul (Fundect/CNPq grant PRONEX 006/2015), Norte Energia, Tractebel Energia, O Boticário Foundation, Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) and Santo Antônio Energia. Pedro Senna Bittencourt was supported by a Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM), and Izeni Pires Farias and Tomas Hrbek by a grant from CNPq. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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