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The parallel altitudinal adaptation of rufous-capped babblers (Cyanoderma ruficeps) in Taiwan based on whole genome sequencing data
whole genome sequence
|Abstract:||適應是一種因選汰壓力使得族群更適合環境的過程，期間往往伴隨著族群遺傳變異的改變。然而，適應演化的可預測性充滿爭議。本研究以山紅頭作為研究材料，探討適應的重複性；在這研究當中，我以基因差異指數FST為基礎的族群遺傳統計方法分析了來自台灣西部的集集與玉山塔塔加、東部的花蓮崇德與合歡山大禹嶺四個地點各十隻山紅頭的全基因體定序資料，共一千六百多萬個單核甘酸多態性（Single Nucleotide Polymorphism，簡稱SNP）位點，來尋找在高低海拔分布的山紅頭基因組中高度分化的區域。這些高分化的基因組區域可能包含造成山紅頭分別在東部與西部台灣海拔適應的基因，將有助於了解對生物如何產生重複性海拔適應（parallel altitudinal adaptation）。分析結果發現，東部與西部的山紅頭族群在各自高度分化的基因當中，共享了約3%的受選擇基因，顯示台灣的山紅頭在海拔適應上，具有基因層面的重複性不高。而在這些基因當中，含有與血管新生有關的基因，可以解釋的山紅頭海拔適應的部分生理機制。|
Adaptation is a process, through which populations improve their survivorship or production in a given environment due to genetic changes shaped by selection. However, the predictability of adaptation is controversial. In this study, I used the altitudinal adaptation of the rufous-capped babbler (Cyanoderma ruficeps) as our research system to examine the predictability of adaptation. I examined the genomic bases of physiological adaptation in the rufous-capped babbler. Ten babblers were collected from each of the Jiji (lowland) and the Tataka (montane) populations in western Taiwan and the Chongde (lowland) and the Dayuling (montane) populations in eastern Taiwan. I analyzed more than 16 million single nucleotide polymorphism (SNP) sites across the whole genomes of these babblers to search highly differentiation genomic regions between high and low altitudinal populations using FST- and Da-based population genetic approaches. The differentiated regions likely contained genes contributing to the altitudinal adaptation of this bird in eastern and western Taiwan, respectively. Based on the results, I examined the repeatability of altitudinal adaptation of this bird at the genomic level. I found that around 3% of altitudinally divergent genes were shared between eastern and western groups, suggesting a low level of genetic repeatability in the parallel altitudinal adaptation of rufous-capped babblers. Some of these common outlier genes were related to angiogenesis, which can partially explain the physiological mechanism of their altitudinal adaptation.
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