Abstract
High elevation adaptation offers an excellent study system to understand the genetic basis of adaptive evolution. We acquired transcriptome sequences of two closely related lizards, Phrynocephalus przewalskii from low elevations and P. vlangalii from high elevations. Within a phylogenetic framework, we compared their genomic data along with green anole, chicken and Chinese softshell turtle, and identified candidate genes and functional categories that are potentially linked to adaptation to high elevation environments. More than 100 million sequence reads were generated for each species via Illumina sequencing. A de novo assembly produced 70,919 and 62,118 transcripts for P. przewalskii and P. vlangalii, respectively. Based on a well-established reptile phylogeny, we detected 143 positively selected genes (PSGs) along the P. vlangalii lineage from the 7,012 putative orthologs using a branch-site model. Furthermore, ten GO categories and one KEGG pathway that are over-represented by PSGs were recognized. In addition, 58 GO categories were revealed to have elevated evolutionary rates along the P. vlangalii lineage relative to P. przewalskii. These functional analyses further filter out PSGs that are most likely involved in the adaptation process to high elevations. Among them, ADAM17, MD, and HSP90B1 likely contributed to response to hypoxia, and POLK likely contributed to DNA repair. Many other candidate genes involved in gene expression and metabolism were also identified. Genome-wide scan for candidate genes may serve as the first step to explore the genetic basis of high elevation adaptation. Detailed comparative study and functional verification are needed to solidify any conclusions. High elevation adaptation requires coordinated changes in multiple genes that involve various physiological and biochemical pathways; we hope that our genetic studies will provide useful directions for future physiological or molecular studies in reptiles as well as other poikilothermic species.
Highlights
Understanding the genetic basis of adaptive changes is one of the central goals in evolutionary biology [1], and organisms living in extreme environments often provide the best study systems [2]
Genes associated with response to hypoxia appeae to play a key role in the adaptation process
Yang et al [10] compared the transcriptomes of the plateau (frog ((Ranakukunoris) and its low elevation relative R. chensinensis, and found that genes related to oxygen binding may have been involved in high elevation adaptation, but there was no evidence of involvement among the HIF pathway genes
Summary
Understanding the genetic basis of adaptive changes is one of the central goals in evolutionary biology [1], and organisms living in extreme environments often provide the best study systems [2]. In order to survive these extreme stressors, high elevation adaptation may require coordinated structural and transcriptional changes in multiple genes that interact at different levels and involve various physiological and biochemical pathways [3]. Elucidating how animals cope with high elevation environments provides unique insights in the process of adaptive evolution, especially its intertwined genetic and regulatory basis. A. A number of studies have revealed aspects of the genetic mechanisms for high elevation adaptation, for endothermic species [4]. Several studies of Tibetan human populations reported that genes EGLN1, PPARA, and EPAS1, all part of the hypoxia-inducible factor (HIF) pathway, were involved in high elevation adaptation [5,6,7]. Yang et al [10] compared the transcriptomes of the plateau (frog ((Ranakukunoris) and its low elevation relative R. chensinensis, and found that genes related to oxygen binding may have been involved in high elevation adaptation, but there was no evidence of involvement among the HIF pathway genes
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