Genomic analyses reveal two species of the matamata (Testudines: Chelidae: Chelus spp.) and clarify their phylogeography

• Published in: Molecular phylogenetics and evolution 2020-07, Vol.148, p.106823-106823, Article 106823
• Main Authors: Vargas-Ramírez, Mario, Caballero, Susana, Morales-Betancourt, Mónica A., Lasso, Carlos A., Amaya, Laura, Martínez, José Gregorio, das Neves Silva Viana, Maria, Vogt, Richard C., Farias, Izeni Pires, Hrbek, Tomas, Campbell, Patrick D., Fritz, Uwe
• Format: Article
• Language: English
• Subjects: Amazonas; Chelus orinocensis sp. nov; mtDNA, nDNA; Orinoco; South America; Taxonomy
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2020.106823

[Display omitted] •Another matamata species is described as new to science.•Chelus orinocensis is genetically and morphologically significantly different.•Chelus orinocensis and C. fimbriata diverged approximately 13 million years ago.•Chelus orinocensis lives in the Orinoco, Río Negro, and Essequibo drainages.•Chelus fimbriata sensu stricto occurs in the Amazon and Mahury drainages. The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeography are largely unexplored. In this study we examined the phylogeographic differentiation of the matamata based on three mitochondrial DNA fragments (2168 bp of the control region, cytochrome oxidase subunit I, and the cytochrome b gene), one nuclear genomic DNA fragment (1068 bp of the R35 intron) and 1661 Single Nucleotide Polymorphisms (SNPs). Our molecular and morphological analyses revealed the existence of two distinct, genetically deeply divergent evolutionary lineages of matamatas that separated in the late Miocene (approximately 12.7 million years ago), corresponding well to the time when the Orinoco Basin was established. As a result of our analyses, we describe the genetically and morphologically highly distinct matamata from the Orinoco and Río Negro Basins and the Essequibo drainage as a species new to science (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto is distributed in the Amazon Basin and the Mahury drainage. Additionally, the analyses revealed that each species displays phylogeographic differentiation. For C. orinocensis, there is moderate mitochondrial differentiation between the Orinoco and the Río Negro. For C. fimbriata, there is more pronounced differentiation matching different river systems. One mitochondrial clade was identified from the Amazon, Ucayali, and Mahury Rivers, and another one from the Madeira and Jaci Paraná Rivers. The C. orinocensis in the Essequibo and Branco Rivers have haplotypes that constitute a third clade clustering with C. fimbriata. Phylogenetic analyses of the R35 intron and SNP data link the matamatas from the Essequibo and Branco with the new species, suggesting past gene flow and old mitochondrial introgression. Chelus orinocensis is collected for the pet trade i