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Lectures by Dr. Taras Oleksyk, professor at the University of Puerto Rico

Our guest next week is Dr. Taras Oleksyk from the University of Puerto Rico. He will give three talks and spend the week at the Center learning about our work and sharing his experience and expertise. See the three topics and a brief abstract for each one below (if you are interested but not on our seminar announcement list, please write to Valentina so we could inform you if there are any changes).

Lecture 1 – Monday, 26 August. 3 PM

A simple guide to discovering signatures of selection in the genome data
Detecting recent selected ‘genomic footprints’ applies directly to the discovery of disease genes and in the imputation of the formative events that molded modern population genetic structure. The imprints of historic selection/adaptation episodes left in human and animal genomes allow one to interpret modern and ancestral gene origins and modifications. Current approaches to reveal selected regions applied in genome-wide selection scans (GWSSs) fall into eight principal categories: (I) phylogenetic footprinting, (II) detecting increased rates of functional mutations, (III) evaluating divergence versus polymorphism, (IV) detecting extended segments of linkage disequilibrium, (V) evaluating local reduction in genetic variation, (VI) detecting changes in the shape of the frequency distribution (spectrum) of genetic variation, (VII) assessing differentiating between populations (FST), and (VIII) detecting excess or decrease in admixture contribution from one population. Here, we review and compare these approaches using available human genome-wide datasets to provide independent verification (or not) of regions found by different methods and using different populations. The lessons learned from GWSSs will be applied to identify genome signatures of historic selective pressures on genes and gene regions in other species with emerging genome sequences. This would offer considerable potential for genome annotation in functional, developmental and evolutionary contexts.

Lecture 2 – Tuesday, 27 August. 3 PM

Genetic history of Puerto Rico: origins, people and diseases
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand how current inhabitants relate genetically to earlier populations of origin. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays. We participated in the 1000 Genomes Project that provided a unique opportunity for improving our understanding of population genetic history sequencing genomes and exomes from Puerto Rican (PUR) populations we collected. Genomic contributions of Native American ancestry to PUR population are estimated to be 13% appear most closely related to Equatorial-Tucanoan-speaking populations, supporting a Southern America ancestry of the Taino people of the Caribbean. To develop our success, we implemented a new instructional strategy in the form of a research-oriented educational cycle: Local Genome Diversity Studies (LGDS), involving > 50 undergraduate students per semester that carried out sample collection, DNA extraction and genotyping in a series of individual projects within the educational LGDS cycle comprised of two research-based classes: Local Genome Diversity Studies and Monogenic Population Studies. As a result, a geographically representative sample of DNA from > 5,000 individuals across 78 municipalities of Puerto Rico have been collected and purified so far. Using our sample set, we are in the process identifying patterns of European, African and Amerindian admixture proportions across different parts of the island using a panel of Ancestry Informative Markers to develop a map of the local genome diversity and interpreted to uncover the complexity of the islands’ rich genetic history.
Related article in TheScientist:

Lecture 3 – Wednesday, 28 August. 5 PM

Parrots of the Caribbean: from one genome to an evolutionary model of island evolution
To achieve the first community-sponsored genome of an endangered species, we organized an outreach campaign resulting in a publication of the sequence of the critically endangered Puerto Rican parrot. We continue to engage students and promote issues in conservation and evolutionary genomics to the local public, while creating opportunities for scientific research for dozens of young researchers. Our early efforts have proven a success, and subsequent research has been reinforced by hundreds of small individual donations. Our research objective is to use a local model of island speciation centered on the endemic Caribbean group of parrots, starting with Puerto Rico’s own critically endangered Amazona vittata. Inferences about genome variation and population structure of this species are used to help decisions in the captive breeding programs. Crowdfunding has allowed for addition sequence data from the closely related A. ventralis, and various transcriptomes to annotate genes and to evaluate expression differences. In the next step, genomes of closely related parrot species from the Caribbean islands are assembled using the genome draft of A. vittata, and cross-examined for differences and conservation patterns to find genes, regulatory and structural elements. The genome alignments are further interrogated for similarities and differences in the evolutionary context examining past migration, colonization and adaptation events. Our hypothesis is that observed differences are rare, and point to the evolutionary adaptations and stepwise migration events from island to island.