Date of Award

12-2015

Degree Type

Thesis

Degree Name

Master of Science

Department

Biology

Program

Biology

First Advisor/Chairperson

Dr. Alec Lindsay

Second Advisor

Dr. Katherine Teeter

Third Advisor

Dr. Kurt Galbreath

Fourth Advisor

Dr. Jeff Horn

Abstract

With rapid advances in Next-Generation Sequencing technology, comparative genomics has become a viable method for studying the adaptation of species to their environment at the genome level. I investigated this in common loons (Gavia immer)—for which molecular adaptation has not been characterized—by finding signatures of positive selection as evidence for genomic adaptation.

I used Illumina short read sequencing data from a single female common loon to produce a fragmented assembly of the common loon (Gavia immer) genome. The resulting assembly had a contig N50 of 814 bp, a total length of 767,326,331 bp, and 45.7 % GC content. I identified fragments of 13,821 common loon genes with known function and another 348 coding sequences of unknown function, for a total of 14,169 common loon genes. Based on estimates from well-resolved avian genomes, this figure represents 80.7% of common loon genes. I calculated dN/dS ratios between common loon and chicken (Gallus gallus) for a high confidence set of 10,106 gene fragments to find genes under positive selection. I found 490 positively selected genes in the common loon that were enriched for a number of protein classes, including those involved in muscle tissue development, immunoglobulin function, hemoglobin iron binding, nervous system development, G-protein receptors, and ATP metabolic process.

The signature of positive selection in these key areas suggests common loons may have adapted for underwater diving by (1) compensations of the cardiovascular system and oxygen respiration, (2) low-light visual acuity, (3) and improved metabolism. Genes relating to immune system and neural development were also positively selected in concordance with prior research.

This work represents the first effort to understand the genomic adaptations of the common loon and genus Gavia and may have implications for scholars seeking to find genes of interest for population genetic, ecological or conservation studies of the common loon.

Thesis_Supplemental_file1_Identified_Genes .xlsx (5169 kB)
Common Loon Genes Identified

Thesis_Supplemental_file_2_GO_TERMS.xlsx (313 kB)
Gene Ontology Summary

Supplemental file 3_COLO_COMBINED_P-VALUES.xlsx (2913 kB)
Evolutionary Analyses

GAYK MS THESIS FINAL.docx (2112 kB)

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