Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient

Abstract

Species are shifting their ranges due to climate change, many moving to cooler and higher locations. However, with elevation increase comes oxygen decline, potentially limiting a species’ ability to track its environment depending on what mechanisms it has available to compensate for hypoxic stress. Pikas (Family Ochotonidae), cold-specialist small mammal species, are already undergoing elevational range shifts. We collected RNA samples from one population of Ochotona roylei in the western Himalaya at three sites– 3,600, 4,000, and 5,000 meters–and found no evidence of significant population genetic structure nor positive selection among sites. However, out of over 10,000 expressed transcripts, 26 were significantly upregulated at the 5,000 m site and were significantly enriched for pathways consistent with physiological compensation for limited oxygen. These results suggest that differences in gene expression may play a key role in enabling hypoxia tolerance on this local scale, indicating elevational flexibility that may facilitate successful range shifts in response to climate change.

Experimental study of hypoxia-induced changes in gene expression in an Asian pika, Ochotona dauurica

“…Up to 61-80% of protein-coding genes have been found to be expressed in the blood transcriptome [37,40,41]. Indeed, previous studies have used the blood transcriptome to asses responses to high-altitude hypoxic stress in humans [42], the Tibetan Plateau saker falcon (Falco cherrug) [43], and a species of Himalayan pika (Ochotona roylei) [30]. These studies have generated meaningful results and confirm that the blood transcriptome is a promising indicator of hypoxic stress.…”

“…In our previous O. roylei field study [30], the up-regulation of the six gene sets used in this study were driven by the significant up-regulation of six nuclear genes (ATP5I, UQCRQ, NDUFA11, NDUFB7, NDUFS8, and NDUFS7) and two mitochondrial genes (CYTB and ND4). Five of these six nuclear genes also showed core enrichment in this study.…”

“…We drew candidate GO categories and KEGG pathways from previous studies that have explored changes in gene expression related to hypoxia in two other small mammal species, O. roylei (a Himalayan pika species) and Peromyscus maniculatus (deer mouse), the most closely related species for which any gene expression work related to hypoxia has been conducted. We used six gene sets that were up-regulated in high-elevation individuals of O. roylei when compared to lower-elevation individuals using blood samples [30]. We drew 11 gene sets from the four studies assessing changes in gene expression due to hypoxia in high and low-elevation deer mice using skeletal muscle and brown adipose tissue samples [57][58][59][60].…”

“…Oxidative phosphorylation (KEGG) Pika and deer mouse [30,57,58] Mitochondrial inner membrane (GO:0005743) Pika [30] Mitochondrial respiratory chain complex I assembly (GO:0032981)…”

“…Pika [30] Mitochondrial respiratory chain complex I (GO:0005747) Pika [30] NADH dehydrogenase (ubiquinone) activity (GO:0008137) Pika [30] respectively, leaving 0.7-6 (average 2.7) million reads per sample that successfully mapped to the reference transcriptome.…”