探討台灣特有種台灣鉤嘴鹛近期適應的遺傳基礎

Genetic bases of recent adaptation in an island endemic babbler Taiwan Scimitar Babbler, Pomatorhinus musicus

傅雨辰(Fu Yuchen)

指導教授 ： 李壽先

國立臺灣師範大學/理學院/生命科學系/碩士(2022年)

https://doi.org/10.6345/NTNU202200445

摘要

適應是指族群中的變異性狀受到選擇，因而提升生物生存概率和繁殖能力的過程。表型性狀變異的遺傳來源包括三種不同類型：新突變、既有變異、與漸滲。然而，它們在基因組中組成佔比如何，及對物種適應產生的相對貢獻仍然不為人知。本研究中，我以廣泛分佈于中國大陸南部、東南部、東部和海南島的棕頸鉤嘴鹛（Pomatorhinus ruficollis, Timaliidae, Aves）和它在台灣島的姐妹種，特有種台灣鉤嘴鹛（Pomatorhinus musicus）作為評估不同遺傳變異對近期適應相對貢獻的生物系統。為了評估台灣鉤嘴鹛的適應性遺傳變異的組成和來源，首先組裝了棕頸鉤嘴鹛高質量的染色體水平參考基因組。接著，我將台灣鉤嘴鹛基因組內遺傳變異分為三類：兩種鉤嘴鹛分化以來出現的新突變（5,431,390个SNPs，占總基因组SNPs的8. 87%），保持在台灣鉤嘴鹛內的既有變異（55,769,269个SNPs，占總基因组SNPs的91.04%），以及從棕頸鉤嘴鹛漸滲引入的變異（59,126个ABBA-BABA计数的SNPs，占總基因组SNPs的0.096%）。然後，我使用nSL test檢測台灣鉤嘴鹛支系中受到近期正向選擇的基因組區域。在受到正向選擇的基因組區域內，既有變異是台灣鉤嘴鹛近期適應的主要遺傳來源（642,823个SNPs，占既有變異總數的1.15%）。從棕頸鉤嘴鹛而來的漸滲基因占全部基因組的0.096%，漸滲基因中沒有顯著受到高比例的正向選擇（79個基因中有2個受到正向選擇）。儘管漸滲基因對台灣鉤嘴鹛基因組貢獻不大，但這些與生物基礎功能相關的基因可能仍對物種適應有重要作用。

關鍵字

適應性基因漸滲 ； 既有變異 ； 新突變 ； 正向選擇 ； 台灣鉤嘴鹛

並列摘要

Adaptation is the process that trait variations of a population was selected to enhance its survival and reproduction probabilities. Three types of genetic sources underpin the phenotypic variations of a population, namely novel mutation, standing variation, and introgression. However, their relative contributions to genomic variation and adaptation are still poorly understood. In this thesis, I used the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis, Timaliidae, Aves) that is widely resides in south, southeast, and eastern China mainland and Hainan Island, and its sister species Taiwan Scimitar Babbler (Pomatorhinus musicus), an endemic to Taiwan Island, as a system to evaluate how different sources of genetic variants contributed to recent adaptation. To evaluate sources of adaptive genetic variants in the Taiwan Scimitar Babbler lineage, high quality chromosome-level reference genomes for the Streak-breasted Simitar Babbler was assembled at the first. Then, I categorized the genetic variants in the Taiwan Scimitar Babbler to three classes: the novel mutations arose since the split of the two scimitar babbler species (5,431,390 SNPs, 8.87% of total genomic SNPs), the standing genetic variation maintained in the Taiwan Scimitar Babbler and outgroup species (55,769,269 SNPs, 91.04% of total genomic SNPs), and the genetic variants introgressed from the Steak-breasted Scimitar Babbler (59,126 ABBA-BABA counts SNPs, accounting for 0.096% of total genome SNPs). Then I used the nSL test to detect signatures of genomic region under recent positively selection in the Taiwan Scimitar Babbler lineage. Among these SNPs, the standing genetic variant is the dominant sources for recent adaptation in the Taiwan Scimitar Babbler genomes (642,823 SNPs, 1.15% of total standing variation SNPs). Although the introgressed variation only contribute 0.096% to genomic variations of the Taiwan Scimitar Babbler, I detected the signature of recent positive selection for two of 79 introgressed genes. My results suggest that different genetic sources contribute differently to genomic configuration. Although introgressed variants only have minor contributions to the extant Taiwan Scimitar Babbler genome, it could play a role to introduce beneficial genetic variants into a lineage.

並列關鍵字

adaptive introgression ； standing variation ； novel mutation ； positive selection ； Taiwan Scimitar Babbler

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