Understanding Avian Diversity: a genomic approach to determine the relationships of Kingfishers and their allies

Methods

Summary

I will extract DNA from tissues via museum loans using the Qiagen DNeasy extraction kit. To prepare libraries, I will shear DNA with a Covaris sonicator, and use the Kapa Biosystems Hyper Prep kit to perform DNA end repair, A-tailing, adapter ligation, and limited-cycle PCR amplification. I will follow established protocols by Faircloth et al. (2012) for sequence capture using the MYcroarray MYbaits Tetrapod 5k v1 probe kit from www.ultraconserved.org to target 5,060 UCE loci. I will sequence UCE-enriched libraries on an Illumina HiSeq 3000 sequencer with a PE-150 flow cell at the University of Oklahoma Clinical Genomics Center.

I will process sequence data with the phyluce bioinformatics pipeline to clean and assemble raw reads into contigs and assemble them into UCE alignments for phylogenetic analysis. I will employ multiple statistical frameworks to analyze the data, including concatenation and species tree methods under the multi species coalescent model. I will use fossil calibrations from todies (Mayr and Knopf 2007) and secondary calibrations from recent phylogenomic studies (Jarvis et al. 2014, Prum et al. 2015) to produce a time-calibrated phylogeny.