How much do duplicated genomic regions skew our analyses?

Advisor:
Elizabeth Mandeville (IB)

Duplication of some or all of the genome is common in the evolutionary history of animal and plant species, including for species that are of conservation concern or are important to agriculture and aquaculture (e.g. salmonid fish and some crop plants). Genome duplication produces genomic regions that are quite similar but are located in different places in the genome and are evolving relatively independently. Identifying these paralogous regions in empirical datasets has been the subject of much angst and hand-wringing among evolutionary biologists. In this project, we will test methods for identifying paralogs in empirical genomic data from two species-rich groups of fish with a history of genome duplication (already collected by Dr. Mandeville for other projects), and attempt to identify to what extent population genetic analyses are negatively impacted by the presence of paralogs. This project will include opportunity for authorship on a peer reviewed paper.