物種的界定，是生物學界中最基本的議題之一。隨著遺傳分析技術的進步，我們可以容易地取得非模式生物的完整基因組序列，進而結合形態、生態棲位等資訊，以綜合性的方法找到過去未被辨識的物種，以正確評估生物多樣性。遺傳數據顯示動物界中許多生物擁有形態上難以辨識，但族群間經歷獨立演化的歷史，應被視為獨立的物種，這些物種可稱為隱密種(cryptic species)。隱密種在寄生蟲、線蟲類及節肢動物最具有代表性，也常見有脊椎動物的案例，但其形成機制仍然罕為深入探究。在此，我透過灰胸竹雞了解隱密種種化過程及可能機制，並找出物種形成(speciation)的候選基因(candidate genes)。過去發現在單型種的灰胸竹雞有分屬兩個不同演化支系的地理族群：以四川陝西為主的西部族群，以及由貴州、湖南和湖北以東的中東部族群。本研究使用全基因組重定序序列，得到灰胸竹雞西部族群、中東部族群以及作為外群的台灣竹雞完整族群基因組數據。分析結果顯示，西部族群與中東部族群已經分化40萬年之久，並且期間沒有基因流。以模型檢測在中東部族群與西部族群之間的物種界定，也顯示灰胸竹雞的東西部族群該分為兩個物種。而在兩個潛在隱密種之間基因組高度分化區域內，共找到19個粒線體功能相關基因，5個與聲音感知或鳴唱學習有關的基因，5個與營養代謝及生長相關的基因，2個與性腺發育及精子生成有關的基因以及2個和羽色有關的基因。除此之外，在性染色體(Z)上兩處長度大約2 Mb大片段區域顯著的高度分化，暗示性染色體在灰胸竹雞種化的重要性。本研究第一次描述雞型目中的隱密種，填補了對於生物多樣性描述上缺失的一塊，並且有助於對隱密種種化機制與過程的了解。

Species delineation is one of the fundamental issues in biology. Technological advances have made accessing complete genomic information for non-model organisms feasible. It allows us to combine genetic data with morphological and ecological characteristics to identify previously undetected species. It has been observed that many animals exhibit similar morphological traits but have independent evolutionary histories among populations, leading to the recognition of cryptic species that are hard to distinguish morphologically. Cryptic species are often found in parasites and nematodes while also being commonly encountered among vertebrates. Furthermore, the mechanism and process of cryptic species formation is still poorly studied. So, I used the Chinese bamboo partridge, a monotypic species, as an avian system to study how cryptic species might arise. Previous studies have revealed two distinct evolutionary lineages within the Chinese bamboo partridge: the Western lineage, mainly distributed from Sichuan and Shaanxi, and the Central-Eastern lineage, spanning from Guizhou and Hunan to eastern China. Here, I used the whole-genome sequences to infer the divergence history of the two lineages, with the Taiwan bamboo partridge serving as an outgroup. I demonstrate that the two lineages of Chinese Bamboo partridges diverged around 400,000 years ago, with no gene flow during their diversification process. Model-based species delimitation suggests that the Chinese bamboo partridge should be subdivided into two species. In a highly differentiated region between two potential cryptic species, 19 genes related to mitochondrial function, 5 genes associated with sound perception or song learning, 5 genes involved in nutrient metabolism and growth, 2 genes linked to gonad development and spermatogenesis, and 2 genes related to feather coloration were identified. Additionally, two large segments on the sex chromosome (Z), each approximately 2 Mb in length, showed significant differentiation. This suggests that sex chromosome differentiation plays a crucial role in the speciation events of the Chinese bamboo partridge. This study is the first to describe cryptic species within the Galliformes, filling a gap in understanding biodiversity and shedding light on cryptic species speciation.

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