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Understanding Avian Diversity: a genomic approach to determine the relationships of Kingfishers and their allies McCullough, Jenna, and Michael Andersen.. University of New Mexico, 3 Oct 2016. Experiment. doi: 10.18258/7951
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.
This project has not yet shared any protocols.