José Gregorio Martínez

Extensions for interactivity and retargeting in X3D

This paper presents X3D extensions that support complex virtual reality (VR) applications, in which novel interaction techniques and devices can be used and easily replaced. It is based on previous work on the Interaction Techniques Markup Language (In Tml) and some immersive VR applications we have developed. The main objectives of this proposal are to facilitate changes in VR applications among different VR setups, and to ease the development of highly interactive VR applications. X3D applications in our scheme explicitly describe all its devices, navigation, and interaction techniques, in order to facilitate changes. We ease the development of VR applications with a platform-independent set of reusable components, and a framework that describes where to locate new extensions. We describe here such extensions and the integration mechanisms to the current X3D specification.

De novo SNP markers development for the Neotropical gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing-based genotyping

We generated for the first time nuclear SNP loci for the commercially exploited gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing. We implemented double-digest-Restriction-Associated-DNA-based de novo SNP genotyping for 30 individuals (Orinoco and Amazon basins) using the IonTorrent PGM. It was analyzed the sequence reads using the Stacks pipeline. We detected 18,772 tags with 6170 polymorphic sites and 91 SNPs recovered for both basins. A significant divergence in the allele frequencies was observed between basins for some of those SNPs. Information about diversity and other statistics index are presented for these SNPs. Some of them (23) could be useful for population and conservation genetics of this species using traditional PCR-based genotyping methods.

SNPs markers for the heavily overfished tambaqui Colossoma macropomum , a Neotropical fish, using next-generation sequencing-based de novo genotyping

We developed nuclear SNPs for the heavily overfished tambaqui/cachama negra Colossoma macropomum using next-generation sequencing-based genotyping. We created a reduced-representation library for 30 individuals from Orinoco and Amazon basins following the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the software Stacks. We detected 22,476 tags characterized by 7,181 polymorphic sites, recovering 177 loci (268 SNPs) shared between both basins. A significant difference in the allelic frequencies was observed between basins for a subset of these SNPs. Thirty-nine SNPs could be useful for conservation/population genetics using traditional PCR-based genotyping methods.

Development of microsatellite markers for the near threatened eagles Harpia harpyja and Morphnus guianensis using next-generation sequencing

We isolated and characterized 11 microsatellite loci for Harpia harpyja using the IonTorrent PGM. The loci were validated in 22 Harpia harpyja and 16 Morphnus guianensis individuals. Ten of the loci were variable in H. harpyja, ranging from two to six alleles per locus. Seven of the loci were variable in M. guianensis ranging from two to six alleles per locus. Genotypes did not deviate from Hardy–Weinberg equilibrium expectation, and no linkage disequilibrium was observed. These markers have a promise to provide an important resource for genetic population studies, conservation and monitoring of these two near threatened accipitrid species.

Giving IDs to turtles: SNP markers for assignment of individuals to lineages of the geographically structured Phrynops geoffroanus (Chelidae: Testudines)

We developed forensic nuclear SNPs for the side-necked turtle, Phrynops geoffroanus, using next-generation sequencing-based genotyping. We created a reduced-representation library for 23 individuals representing four previously identified lineages of P. geoffroanus using the ddRAD methodology for sequencing on the IonTorrent PGM. We analyzed the sequence data using the Stacks pipeline. We found 811 loci containing 1380 private SNPs. Of these, 473 were fixed in lineages 1, 2 and 3, or with frequency >0.91 in lineage 4. Seventy-three SNPs could be useful for forensics purpose (assignment of individuals to lineage of origin) using traditional PCR-based genotyping methods.

Using DNA barcodes to confirm new records of Amazon longfin herrings Pellona castelnaeana Valenciennes, 1847 and Pellona flavipinnis (Valenciennes, 1837) (Clupeiformes: Pristigasteridae) in the Branco River sub-basin

This note demonstrates the use of a DNA barcoding methodology in confirming new occurrence records of Pellona castelnaeana and Pellona flavipinnis in the Branco River sub-basin. The DNA barcode result was verified by identification based on morphological characters of both species. Thus, these records increase the species’ ranges by more than 600 km in the Amazon and show evidence of high genetic variability in P. flavipinnis.