既有遺傳變異對局域適應的重要性 - 探尋台灣粉紅鸚嘴對海拔適應的遺傳基礎

Abstract

近期人類活動正快速地改變全球地貌及氣候型態，促使生物面臨新的選汰壓力。因此，瞭解生物如何因應快速的環境改變，不但是演化生物學的基本問題，也成為生物多樣性保育的重要議題。本研究以海拔適應做為檢測局域適應遺傳基礎的研究系統，並以近期與亞洲大陸族群分化（約四萬年前）且廣泛分布於台灣不同海拔的粉紅鸚嘴（Sinosuthora webbianus bulomachus）作為實驗物種。我先建立一隻雄性粉紅鸚嘴的基因組草圖，再自東西部高（> 2000公尺）與低（< 100公尺）海拔族群中，選取四十隻個體進行基因組重定序（平均定序深度約六倍），利用基因組掃描的方式找尋高低海拔族群局域適應的證據。我們發現107個可能與海拔適應相關的候選區域（candidate regions），且有79個基因落於這些候選區域中或附近，其中有九個基因與供氧階梯（oxygen cascade）、溫度調控（thermoregulation）及防止UV侵害（UV protection）相關。我們在這107個候選區域中，分別於台灣東西邊找到了199個及187個與海拔適應相關的SNP位點，且這些位點大部分與亞洲大陸族群共有（約91%）；此外，這些位點皆落於非編碼區。這些結果顯示，相對於編碼區改變而導致功能上的變化，調控區的改變對於局域適應可能佔有更重要的地位；而既有變異可能是海拔適應的過程中，供應有利遺傳變異的主要來源。本研究除了提供局域適應背後可能的遺傳機制外，也提供我們推測物種能否克服環境變遷的依據。Anthropogenic activities are reconfiguring the global landscape and altering climate in an unprecedented rate. Whether organisms could cope with such rapid environmental changes is largely dependent on the nature of genetic basis of local adaptation. Here, I used altitudinal adaptation of vinous-throated parrotbills (Sinosuthora webbianus bulomachus) in Taiwan to investigate the relative role of novel and standing genetic variation in local adaptation. I firstly sequenced a male parrotbill genome (1.06GB) as the reference and re-sequenced other 40 individuals from two pairs of high- (over than 2000 m)/low-altitude (lower than 100 m) populations from both sides of Taiwan (~6X mean coverage), and 40 individuals from Asian mainland (~12X mean coverage). After calling SNP, I found that 60% of SNPs in Taiwan population are shared with the mainland conspecific population. Results of whole genome scan revealed that 107 10 kb genomic regions spanning entire genome that could be responsible to altitudinal adaptation. I found 79 candidate genes were harbored within these or nearby regions. Among these 79 candidate genes, nine were presumably related to oxygen cascade (N = 6), thermoregulation (N = 1), and UV protection (N = 2). In addition, I identified 199 and 187 causal SNPs, which might be corresponding to altitudinal adaption, in the east and west Taiwan population pairs separately. I found that 91% of the causal SNPs for altitudinal adaptation were shared with the mainland population. It implies that standing genetic variation should be the major source to supply advantage alleles in altitudinal adaptation. In addition, I surprisingly found that none of these causal SNPs located within coding regions of the candidate genes. It suggests that modifications of gene regulation, instead of functional changes, are critical to altitudinal adaptation. My results not only illuminate the genetic mechanism of altitudinal adaptation, but also provide a new insight into how organisms could respond to a changing environment.