American pika (Ochotona princeps) are small winter-active mammals inhabiting alpine environments. As the American pika occupies a niche characterized by hypoxia, these animals are an excellent system to use for detecting genetic changes associated with adaptation to these conditions. American pika populations were located at lower elevations during glacials, and shifted upslope during interglacials. In this scenario, pikas would have experienced increased selective pressure to develop adaptations to hypoxia. Here, I use a candidate gene approach to identify molecular signals of adaptation in the American pika genome. I first examined the sequences of 54 candidate genes for adaptation in two subspecies of O. princeps using draft genomes available from public databases. I constructed phylogenies using the two O. princeps alleles and homologs from other mammal species, and then used the CODEML module of PAML to detect evidence of selection along branches in the phylogeny. Four genes (EHHADH, IGF-1, TGF-β1, and NOS2) showed evidence of adaptation in these analyses. I then resequenced portions of these four genes in 25 individuals from across the species’ range, and analyzed the resulting data using frequency-based tests of non-neutral evolution. These tests have provided additional support for positive selection in the EHHADH, IGF-1, and TGF-β1 loci. These loci represent strong candidates for further study of adaptation in this system, including examination of their functional role in the response to hypoxia.
","abstract_html":"<p>American pika (<em>Ochotona princeps</em>) are small winter-active mammals inhabiting alpine environments. As the American pika occupies a niche characterized by hypoxia, these animals are an excellent system to use for detecting genetic changes associated with adaptation to these conditions. American pika populations were located at lower elevations during glacials, and shifted upslope during interglacials. In this scenario, pikas would have experienced increased selective pressure to develop adaptations to hypoxia. Here, I use a candidate gene approach to identify molecular signals of adaptation in the American pika genome. I first examined the sequences of 54 candidate genes for adaptation in two subspecies of <em>O. princeps</em> using draft genomes available from public databases. I constructed phylogenies using the two <em>O. princeps </em>alleles and homologs from other mammal species, and then used the CODEML module of PAML to detect evidence of selection along branches in the phylogeny. Four genes (<em>EHHADH</em>, <em>IGF-1</em>, <em>TGF-β1</em>, and <em>NOS2</em>) showed evidence of adaptation in these analyses. I then resequenced portions of these four genes in 25 individuals from across the species’ range, and analyzed the resulting data using frequency-based tests of non-neutral evolution. These tests have provided additional support for positive selection in the <em>EHHADH</em>, <em>IGF-1</em>, and <em>TGF-β1 </em>loci. These loci represent strong candidates for further study of adaptation in this system, including examination of their functional role in the response to hypoxia.</p>","abstract_has_math":false,"creators":["Rankin, Andrew Michael"],"institution":null,"degree_name":"Master of Science","degree_level":"Thesis","degree_discipline":"Biology","degree_department":null,"school":null,"contributors":["Katherine Teeter"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-05-01T07:00:00Z","date_published":"2016-05-01T07:00:00Z","updated_at":"2026-07-24T03:23:34Z","subjects":["nucleotide substitution","genetic drift","natural selection","Genetics and Genomics"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://commons.nmu.edu/theses/89","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Katherine Teeter"]},{"key":"dc:creator","label":"Author","values":["Rankin, Andrew Michael"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2016-03-29T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["nucleotide substitution","genetic drift","natural selection","Genetics and Genomics"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://commons.nmu.edu/theses/89"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["American pika (Ochotona princeps) are small winter-active mammals inhabiting alpine environments. As the American pika occupies a niche characterized by hypoxia, these animals are an excellent system to use for detecting genetic changes associated with adaptation to these conditions. American pika populations were located at lower elevations during glacials, and shifted upslope during interglacials. In this scenario, pikas would have experienced increased selective pressure to develop adaptations to hypoxia. Here, I use a candidate gene approach to identify molecular signals of adaptation in the American pika genome. I first examined the sequences of 54 candidate genes for adaptation in two subspecies of O. princeps using draft genomes available from public databases. I constructed phylogenies using the two O. princeps alleles and homologs from other mammal species, and then used the CODEML module of PAML to detect evidence of selection along branches in the phylogeny. Four genes (EHHADH, IGF-1, TGF-β1, and NOS2) showed evidence of adaptation in these analyses. I then resequenced portions of these four genes in 25 individuals from across the species’ range, and analyzed the resulting data using frequency-based tests of non-neutral evolution. These tests have provided additional support for positive selection in the EHHADH, IGF-1, and TGF-β1 loci. These loci represent strong candidates for further study of adaptation in this system, including examination of their functional role in the response to hypoxia.
"]},{"key":"dc:title","label":"Title","values":["Molecular evolutionary analysis of the American pika (Ochotona princeps)"]}]}],"canonical_facts":{"dc:contributor":["Katherine Teeter"],"dc:creator":["Rankin, Andrew Michael"],"dc:date.available":["2016-03-29T07:00:00Z"],"dc:description.abstract":["American pika (Ochotona princeps) are small winter-active mammals inhabiting alpine environments. As the American pika occupies a niche characterized by hypoxia, these animals are an excellent system to use for detecting genetic changes associated with adaptation to these conditions. American pika populations were located at lower elevations during glacials, and shifted upslope during interglacials. In this scenario, pikas would have experienced increased selective pressure to develop adaptations to hypoxia. Here, I use a candidate gene approach to identify molecular signals of adaptation in the American pika genome. I first examined the sequences of 54 candidate genes for adaptation in two subspecies of O. princeps using draft genomes available from public databases. I constructed phylogenies using the two O. princeps alleles and homologs from other mammal species, and then used the CODEML module of PAML to detect evidence of selection along branches in the phylogeny. Four genes (EHHADH, IGF-1, TGF-β1, and NOS2) showed evidence of adaptation in these analyses. I then resequenced portions of these four genes in 25 individuals from across the species’ range, and analyzed the resulting data using frequency-based tests of non-neutral evolution. These tests have provided additional support for positive selection in the EHHADH, IGF-1, and TGF-β1 loci. These loci represent strong candidates for further study of adaptation in this system, including examination of their functional role in the response to hypoxia.
"],"dc:identifier":["https://commons.nmu.edu/theses/89"],"dc:subject":["nucleotide substitution","genetic drift","natural selection","Genetics and Genomics"],"dc:title":["Molecular evolutionary analysis of the American pika (Ochotona princeps)"],"thesis:degree_discipline":["Biology"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Master of Science"]},"updated_at":"2026-07-24T03:23:34Z"}