使用全基因組單核苷酸多型性探討台灣白線斑蚊的地景基因體學

Abstract

白線斑蚊（Aedes albopictus）為全球重要病媒蚊種之一，具高度擴散潛能與生態可塑性，其在台灣的遺傳結構與基因流動模式對疾病傳播風險與防治策略具有關鍵意義。本研究運用雙限制酶切位點關聯DNA定序技術（ddRAD-seq），結合兩階段系統性採樣設計，針對台灣本島共416筆白線斑蚊樣本進行族群遺傳分析，以全面描繪其遺傳組成、親緣關係與環境因子影響。 運用ddRAD-seq獲得數萬個高品質單核苷酸多態性（SNP）位點，針對台灣白線斑蚊進行族群遺傳結構與基因流動分析。第一階段於南部都市地區密集採樣，第二階段則以10平方公里網格於全島範圍內系統性取樣，建立涵蓋多樣棲地的代表性樣本集。分析結果顯示，白線斑蚊整體遺傳多樣性中等，族群間遺傳組成相對均質，未呈現明確地理分化；但在部分樣本中，意外發現與地形高度相關的微弱分化現象，顯示中央山脈與西部都市區間可能潛藏山區族群與平地都市族群之遺傳結構差異。親緣分析亦發現部分近親樣本對相隔數十至百公里，反映該物種具有長距離基因交流潛力，可能受交通或人為因素促進。 遺傳與地理距離相關性分析顯示，地理距離對白線斑蚊遺傳差異的解釋力有限，整體未呈現明顯的距離隔離現象。進一步的空間分析顯示，山區與都市平地族群間存在潛在的基因交流阻力邊界，顯示地形與棲地環境可能對遺傳連通性造成干擾。為進一步探討此現象與環境因子之間的關聯性，本研究分析八項地景與氣候因子對基因流動的影響，結果顯示無單一因子具主導性作用，推測多重環境因子共同調控基因交流模式。另針對山區與都市族群間顯著分化的基因進行功能富集分析，結果顯示相關基因主要涉及神經發育、行為調控與細胞訊號傳導等功能，可能與族群對不同環境條件的適應差異有關。 綜上所述，本研究建立白線斑蚊於台灣之高解析度族群遺傳圖譜，揭示其高度基因流動特性與環境交互作用下的遺傳結構樣態，拓展對其族群動態與演化潛力之理解，亦為病媒生物相關研究與風險評估提供參考依據。

Aedes albopictus is one of the most important vector mosquito species worldwide, characterized by high dispersal potential and ecological plasticity. Understanding its genetic structure and gene flow patterns is critical for assessing disease transmission risk and informing control strategies. In this study, we applied double-digest restriction-site associated DNA sequencing (ddRAD-seq), combined with a two-phase systematic sampling strategy, to analyze 416 individuals of Ae. albopictus collected across Taiwan. Our aim was to comprehensively characterize genetic composition, kinship relationships, and the influence of environmental factors on population genetic variation. Using ddRAD-seq, we obtained tens of thousands of high-quality single nucleotide polymorphisms (SNPs) for downstream population genomic analyses. The first phase involved intensive sampling in urban areas of southern Taiwan, while the second phase employed a 10 km² grid-based sampling scheme covering a wide range of habitats across the island. Results revealed moderate genetic diversity and largely homogeneous genetic composition across populations, with no strong geographic differentiation. However, subtle genetic structuring associated with elevation was detected, suggesting potential differentiation between mountain and lowland urban populations, possibly influenced by the Central Mountain Range. Kinship analysis identified closely related individuals separated by tens to over one hundred kilometers, implying the potential for long-distance gene flow, possibly facilitated by human transportation. Analyses of genetic and geographic distances indicated limited isolation by distance, with gene flow exhibiting spatial heterogeneity. Further landscape analyses identified potential gene flow barriers between mountainous and urban lowland populations, likely shaped by topography and habitat differences. No single environmental factor was found to dominate gene flow dynamics, suggesting a complex interplay of multiple landscape and climatic factors. Functional enrichment analysis of highly differentiated genes between mountain and lowland groups indicated significant associations with neurodevelopment, behavioral regulation, and signal transduction, potentially reflecting local adaptation to contrasting environments. In summary, this study provides a high-resolution genetic landscape of Ae. albopictus populations in Taiwan, revealing extensive gene flow and spatially variable genetic structuring influenced by environmental heterogeneity. These findings offer new insights into the species’ population dynamics and have important implications for vector surveillance and disease risk assessment.