Local Genome Diversity Studies

  1. 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
  2. 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
  3. 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.

Educational activities

  1. Develop a core graduate/undergraduate course in the discipline directly related to the research component of the career plan: Biology of Genomes.
  2. 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
  3. Develop collaborative class projects based on the geographically representative sample of the Puerto Rican population from the previous NSF-funded study (Award #DUE-1044714)
  4. 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
  5. Develop an online presentation system to show progress of the undergraduate project – a student reviewed online journal
  6. Develop critical thinking, independence, assertiveness, awareness of contemporary issues, and confidence in students at a predominately Hispanic institution
  7. 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

Organizational activities:

  1. Continue developing Caribbean Genome Center to become a major research and educational center and a collaboration hub in Puerto Rico
  2. Establish a functional genetics laboratory at the Puerto Rico Zoo Juan A Rivero
  3. Organize a successful Annual Meeting of the Society of Molecular Biology and Evolution (SMBE 2014) in San Juan, Puerto Rico
  4. Organize a successful International School in Recent Advances in Conservation Genetics (ConGen 2015) in Rincon PR.

Laboratory of Genomic Diversity