台灣油杉族群基因組分歧以及與環境因子關連之在地適應性演化

Abstract

台灣油杉(Keteleeria davidiana var. formosana)族群於過去AFLP (amplified fragment length polymorphisms)研究中發現，因為分歧天擇作用而發生在地適應性演化。本研究透過ddRADseq (double digest Restriction Associated DNA sequencing)以檢測天擇作用如何造成台灣油杉族群基因組的分歧。收集台灣油杉五個族群共62株樣本及10株與其同屬的近源種鐵堅油杉(Keteleeria davidiana)。ddRADseq獲得15,094個單一核甘酸多形性(single nucleotide polymorphism, SNP)。BayeScan的結果找到61個FST outliers。LFMM及BayEnv則分別發現288跟221個與溫度、降水、地貌、植被豐富度具關連性的基因座。其中包含57個FST outliers，顯示台灣油杉族群受到與棲地環境差異有關的分歧天擇作用。然而台灣油杉兩兩族群間L形的FST頻率分布圖，顯示大部分基因座的分歧程度低。鐵堅油杉與台灣油杉的FST頻率分布則有右移的趨勢。此外TreeMix及f3 statixtic發現台灣油杉存在由南部往北部族群的基因交流。然而台灣油杉與鐵堅油杉並沒有發現基因交流，加上分歧的時間較長，遺傳漂變可能才是造成兩個近緣物種遺傳分歧的主因。In a previous study, divergent selection and local adaptation in populations of Keteleeria davidiana var. formosana has been identified based on survey of genetic variation using AFLP. In the present study, we aimed to investigate how population genomic divergence can be shaped by natural selection in the populations of K. davidiana var. formosana using method of ddRADseq. We collected 62 samples from five populations K. davidiana var. formosana and 10 from its closely related species Keteleeria davidiana. ddRADseq generated 15,094 SNPs. Sixty-one FST outliers were identified by BayeScan. LFMM and BayEnv identified 288 and 221 loci potentially under selection, respectively. Of these 57 were found to be associated with temperature, precipitation, topography and vegetation abundance, indicating ecological divergent in K. davidiana var. formosana populations. However , many loci showed low levels of divergence between K. davidiana var. formosana populations, resulting in L shape pairwise FST distributions. Pairwise FST distributions shifted to right when compared populations of K. davidiana var. formosana to K. davidiana. Results of TreeMix and f3 statistic suggest significant gene flow was mainly from south to north populations between K. davidiana var. formosana. However, no significant gene flow was found between K. davidiana var. formosana and K. davidiana, probably because they have been diverged for a long time, and genetic drift is most probably responsible for the genetic divergence between these two closely related species.