A SURVEY OF THE COMMON LOON (Gavia immer) GENOME REVEALS PATTERNS OF NATURAL SELECTION

<p>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 (<em>Gavia immer</em>)—for which molecular adaptation has not been characterized—by finding signatures of positive selection as evidence for genomic adaptation.</p> <p>I used Illumina short read sequencing data from a single female common loon to produce a fragmented assembly of the common loon (<em>Gavia immer</em>) 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 (<em>Gallus gallus</em>) 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.</p> <p>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.</p> <p>This work represents the first effort to understand the genomic adaptations of the common loon and genus <em>Gavia </em>and may have implications for scholars seeking to find genes of interest for population genetic, ecological or conservation studies of the common loon.</p>

Name thesis:degree_name

Master of Science

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Biology

Year dc:date.available

2015

Author dc:creator

• Gayk, Zach G

Contributors dc:contributor

• Dr. Alec Lindsay

• Gavia immer
• evolutionary genomics
• natural selection
• adaptation
• Bioinformatics
• Computational Biology
• Evolution
• Genomics

Repository record dc:identifier

https://commons.nmu.edu/theses/71

OAI identifier oai:identifier

oai:commons.nmu.edu:theses-1075