Local Genome Diversity Studies
- Using a geographically representative sample of the Puerto Rican population from the previous NSF-funded study (Award #DUE-1044714) as a resource, identify geographic patterns of distribution of genetic markers related to disease, environment, or other adaptations
- Evaluate this distribution in relation to the history of the Puerto Rican population in the context of genome-wide patterns of European, African and Amerindian (Taino) admixture across different parts of the island
- Generate an online resource (map) of genome diversity across Puerto Rico
Parrots of the Caribbean
- Re-sequence the genome of the Puerto Rican parrot (Amazona vittata) using a combination of IIlumina reads and various size mate-pairs (DNA from blood samples is extracted following routine veterinary procedures at the Rio Abajo Aviary of the U.S. Fish and Wildlife Service (FWS) to enable a high coverage assembly of the draft reference genome
- Shotgun-sequence expressed DNA transcripts from various tissues of vittata (collaboration with Rio Abajo Aviary of US FWS) to provide gene models for genome annotation
- Assemble drafts of related species ventralis and A. leucocephala from Hispaniola nd Cube respectfully, in order to develop a comparative stury of genome evolution on islands of the Caribbean
- Annotate the genome draft using the known gene models and repetitive sequences from other species (Gallus gallus, Taeniopygia guttata, Homo sapiens), as well as from the species-specific gene discovery
- Describe population diversity of the captive vittata population using (1) complete mitochondrial sequences, and (2) repetitive markers discovered from next-generation sequencing in samples of birds provided by Rio Abajo Aviary of US FWS
- Develop a genome browser to communicate the complete and annotated draft of the A. vittata genome, and make it available for the subsequent manual annotation by undergraduate students.
- Develop a core graduate/undergraduate course in the discipline directly related to the research component of the career plan: Biology of Genomes.
- Incorporate and institutionalize training activities that incorporate hands-on experience with next generation sequencing and data analysis within the scope of an actual research project
- Develop collaborative class projects based on the geographically representative sample of the Puerto Rican population from the previous NSF-funded study (Award #DUE-1044714)
- Develop undergraduate projects based on sequencing, assembly, annotation of genomes of local species and characterization of genome variation in the local population across the island
- Develop an online presentation system to show progress of the undergraduate project – a student reviewed online journal
- Develop critical thinking, independence, assertiveness, awareness of contemporary issues, and confidence in students at a predominately Hispanic institution
- Develop recommendations that will allow this course to be adopted by undergraduate programs at other institutions, and create student-oriented outreach efforts at local high schools
- Continue developing Caribbean Genome Center to become a major research and educational center and a collaboration hub in Puerto Rico
- Establish a functional genetics laboratory at the Puerto Rico Zoo Juan A Rivero
- Organize a successful Annual Meeting of the Society of Molecular Biology and Evolution (SMBE 2014) in San Juan, Puerto Rico
- Organize a successful International School in Recent Advances in Conservation Genetics (ConGen 2015) in Rincon PR.