Phylogeography, genetic diversity and population structure of the freshwater stingray, Paratrygon aiereba (Müller & Henle, 1841) (Myliobatiformes: Potamotrygonidae) in the Colombian Amazon and Orinoco basins.

The freshwater stingray Paratrygon aiereba have coloration, osteological and morphometric variations that could suggest the existence of more than one species in Colombia. In order to evaluate the phylogeography, population structure and genetic diversity for P. aiereba distributed in the Amazon and Orinoco basins, we amplified Cytochrome oxidase subunit 1 (COI) partial region of mitochondrial DNA (mtDNA) in 50 samples from eight different sub-basins. Our results suggest three phylogroups and a vicariance event occurred 43 million years ago proposing how Paratrygon diverged into the basins. A high population structure (ΦST = 0.692; p < 0.005) and a value of (K) of 3 were defined. A high genetic diversity within phylogroups was found: Phylogroup A (h = 0.64; π% = 2.48), Phylogroup B (h = 0.552; π% = 1.67), and Phylogroup C (h = 0.49; π% = 0.73). These results should be considered in local management plans, conservation programs and reclassification in at least Amazon and Orinoco.

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

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 in Colombia and Venezuela. However, neither the extent of the harvest nor its impact are known. Hence, it is crucial to gather more information and to assess its exploitation throughout its distribution range to obtain a better understanding of its conservation status and to design appropriate conservation and management procedures. RESUMEN: La matamata es una de las tortugas más carismáticas del mundo, ampliamente distribuida en el norte de Sudamérica. Debido a su variación morfológica geográfica, se debate sobre el reconocimiento de dos subespecies o especies. A pesar de que la matamata es universalmente conocida, su historia natural, estado de conservación y biogeografía han sido muy poco estudiados. En este estudio examinamos la diferenciación filogeográfica de las matamatas en base ​​a tres fragmentos de ADN mitocondrial (2168 pb de la región de control, la subunidad I del citocromo oxidasa y el gen del citocromo b), un fragmento de ADN genómico nuclear (1068 pb del intrón R35) y 1661 polimorfismos de nucleótido único (SNPs). Nuestros análisis moleculares y morfológicos revelaron la existencia de dos linajes evolutivos distintos de matamatas, genéticamente divergentes que se separaron en el Mioceno tardio (hace aproximadamente 12.7 millones de años), correspondiendo al tiempo en que se estableció la cuenca del Orinoco. Como resultado de nuestros análisis, describimos las genéticamente y morfológicamente distintas matamatas de las cuencas del Orinoco, Río Negro y Essequibo como una especie nueva para la ciencia (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto se distribuye en la cuenca del Amazonas y en el drenaje del Mahury. Adicionalmente, los análisis revelaron que cada especie muestra diferenciación filogeográfica. Para C. orinocensis, hay una moderada diferenciación mitocondrial entre el Orinoco y el Río Negro. Para C. fimbriata, hay una diferenciación más pronunciada, concordando con los diferentes sistemas fluviales. Se identificó un clado de los ríos Amazonas, Ucayali y Mahury y otro de los ríos Madeira y Jaci Paraná. Las C. orinocensis de los ríos Essequibo y Branco tienen haplotipos que constituyen un tercer clado que se agrupa con C. fimbriata. Los análisis filogenéticos del intrón R35 y los datos de SNP asocian las matamatas de Essequibo y Branco con la nueva especie, sugiriendo flujo de genes pasado ​​e introgresión mitocondrial antigua. Chelus orinocensis se colecta para el comercio de mascotas en Colombia y Venezuela. Sin embargo, ni se conoce el alcance de las colectas ni su impacto. Por lo tanto, es crucial recopilar más información y evaluar su explotación en todo su rango de distribución, comprender mejor su estado de conservación y para diseñar acciones apropiadas de conservación y manejo.

Mitochondrial DNA diversity and population structure of the ocellate freshwater stingray Potamotrygon motoro (Müller & Henle, 1841) (Myliobatiformes: Potamotrygonidae) in the Colombian Amazon and Orinoco Basins.

The lack of clarity regarding the taxonomy of the ocellate river stingray (Potamotrygon motoro) and the absence of previous studies regarding its genetic diversity and population structure makes this species vulnerable to overexploitation, being now the second species of freshwater ray most extracted and exported for ornamental purposes in Colombia. The aim of this work was to determine the population genetic structure and genetic diversity of P. motoro in the Colombian Amazon and Orinoco basins. A total of 110 samples collected from six sub-basins of the Orinoco and in two sub-basins of the Amazon, were analyzed by amplification and sequencing of two fragments of the mitochondrial genes, Cytochrome oxidase subunit I (COI) (532 bp), and Cytochrome b (Cytb) (429 bp). Haplotype networks were constructed, followed by an analysis of molecular variance (AMOVA). The most probable number of genetic groups (K) was evaluated by means of Bayesian inference using BAPS. One shared haplotype was found between the Colombian Amazon and Orinoco basins for COI but no shared haplotypes were found for Cytb. A K of 4 was found, differentiating three of the four units by sub-basins. A high and significant FST was found when comparing the two basins, suggesting significant genetic differentiation between basins for both mitochondrial gene fragments. These results suggest that P. motoro populations in Colombia should be managed as independent units in each basin for conservation and extraction purposes.

Conservation status and regional habitat priorities for the Orinoco crocodile: Past, present, and future.

Conservation of large predator species has historically been a challenge because they often overlap in resource utilization with humans; furthermore, there is a general lack of in-depth knowledge of their ecology and natural history. We assessed the conservation status of the Orinoco crocodile (Crocodylus intermedius), defining regional habitat priorities/crocodile conservation units (RHP/CCU) and regional research priorities (RRP) for this species. We also estimated a species distribution model (SDM) to define current suitable areas where the species might inhabit and/or that might be successfully colonized. The SDM area obtained with a suitable habitat probability ≥ 0.5 was 23,621 km2. Out of 2,562 km2 are included within protected areas in both Colombia (1,643 km2) and Venezuela (919 km2), which represents only 10.8% of C. intermedius' potential range. Areas such as Laguna de Chigüichigüe (flood plain lagoon) exhibited an increase in population abundance. In contrast, localities such as the Cojedes and Manapire Rivers reported a significant reduction in relative abundance values. In Colombia, disparity in previous survey methods prevented accurate estimation of population trends. Only one study in this country described an increase over a 13 years span in the Ele, Lipa, and Cravo Norte River populations based on nest surveys. We defined 34 critical areas (16 in Colombia, 17 in Venezuela, and one covering both countries) where we need to preserve/research/monitor and/or generate management actions, 10 RHP/CCU (six from Venezuela and four from Colombia) and 24 RRP (11 from Venezuela, 12 from Colombia, and one in both countries). Caño Guaritico (Creek) and the Capanaparo River in Venezuela and the Ele, Lipa, Cravo Norte River System and the Guayabero River in Colombia were defined as areas with the most optimal conditions for long-term preservation and maintenance of C. intermedius populations. We conclude that the conservation status of this species is still critical, which implies the necessity to increase efforts to recover the species, especially in Colombia, to guarantee its survival as a structural and functional component of the ecosystems it inhabits.