Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caimanPaleosuchus trigonatus(Alligatoridae: Caimaninae)

• DOI: 10.7717/peerj.6580
• Publication Date: 2019-03-22T09:33:12Z
• Authors: Pedro Senna Bitte...; Zilca Campos; Fábio de Lima Muniz; Boris Marioni; Bruno Campos Souza; Ronis Da Silveira; Benoit de Thoisy; Tomas Hrbek; Izeni Pires Farias
• Keywords: Gene Flow; 0301 basic medicine; Gene Sequence; Maximum Likelihood Method; Amazonian crocodilians; Population genetics; QH301-705.5; Genomic Dna; Structure Analysis; Crocodilian; Polymerase Chain Reaction; Phylogenetic Tree; 03 medical and health sciences; Population Genetic Structure; Alligatoridae; Dna Extraction; Haplotype; Cluster Analysis; Biology (General); Population Growth; Phylogeny; Population Structure; Cryptic (era); Whole Genome Sequencing; Cytochrome B; R; Fossil; Biodiversity; South America; 15. Life on land; Nonhuman; Jacaré-coroa; Phylogeography; Genetic Variability; Biogeography; Diversification; Medicine; Genetic Parameters; Gene Structures; Conservation genetics; Principal Coordinate Analysis

Schneider’s dwarf caimanPaleosuchus trigonatusis 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 thatP. trigonatusis 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 withinP. 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 ofP. trigonatusand these lineages.