Theory: Principles of restriction-associated DNA (RAD) sequencing and its uses: population genomics, genetic connectivity, genome mapping, association and QTL mapping, identifying loci under selection. Comparison of RAD methods (standard RAD-seq, ddRAD, ezRAD, and 2bRAD).
Wet lab: DNA isolation using the universal and exceedingly low cost phenol-chlorophorm method from coral holobiont (Davies et al., 2013); preparation of 2bRAD libraries; precise mixing of barcoded samples based on qPCR quantification.
Dry lab: UNIX environment and work of high-performance computing (HPC) clusters; sequence pre-processing, genotype calling using de novo and reference-based (GATK) pipelines; filtering of genotype calls based on replicates; assessing the quality of genotyping; basic statistics (heterozygosity, Fst, Tajima’s D, relatedness, linkage disequilibrium), population genetic analysis using ADMIXTURE, detecting outlier loci with Lositan and BayeScan.
Project: Only a fraction of coral recruits reach large size and sexual maturity; is this mortality completely indiscriminate or are some regions in the coral genome being selected for? Does this genomic pattern of selection vary between reefs? Answering these questions would greatly inform us about corals’ capacity to adapt to local conditions and elucidate the molecular mechanisms involved. We will use 2bRAD to genotype juveniles and adults of the same coral species collected from two reef environments and look for genomic regions experiencing age-dependent selection.  
Instructor: Mikhail V. Matz; Teaching Assistants: Groves Dixon and Marie Strader
cost: US $2000
Whole-genome genotyping with 2bRAD
June 30 - July 7