了解物種分化的歷史為現今演化生物學的重要議題，為了探討此議題，分類界線模糊或分化年代相對近的複合群便成為一個合適的研究對象。然而此類研究被認為需要大量基因資料，而使用傳統的定序方法可能無法有效率地取得足夠數量的基因座。近年，次世代定序技術可在短期之內取得大量的基因座與單核苷酸多型性，使我們能更深入地進行更縝密的運算，並執行理論的檢測。滑蜥屬 (Scincella) 是一群外觀極為相似的小型石龍子，物種的界定一直都處於爭議的狀態。例如分布於東亞的寧波滑蜥複合群 (S. modesta complex)，成員包含分布於日本的先島滑蜥 (S. boettgeri)、台灣的台灣滑蜥 (S. formosensis) 與中國的寧波滑蜥 (S. modesta)；另外尚有數個其他的隱蔽種 (Scincella spp.) 分布於台灣與中國，加深了滑蜥屬物種界定的必要性。我們採用限制酶位點標定定序 (RADseq) 之中的multiplexed shotgun genotyping (MSG) 方法來取得大量的基因座，檢測此複合群的物種界線並重塑其分化歷史。本研究共定序並使用56隻滑蜥做分析，共取得約兩億條短片段序列，並以pyRAD軟體進行序列的分析。隨後使用了367至4188個基因座進行親緣關係、Structure、DAPC與BFD*之物種界定檢測。結果顯示寧波滑蜥複合群包含了六個獨立的支系，其中三個為未被發表過的隱蔽種。另一方面，使用G-PhoCS進行分化歷史的重建，顯示寧波滑蜥複合群主要在上新世晚期至更新世早期分化，且在分化的過程中大部分的物種都有族群數縮減的趨勢。在基因交流檢測方面，我們檢測到了非姊妹種間歷史的基因滲入，顯示了複雜的基因交流歷史。

Understanding the process and mechanism of speciation has long been a major issue in evolutionary biology. Young species complexes provide excellent opportunities to study the model and process of species diversification. However, the power of evolutionary analyses was limited by the number of available loci. Recently, next-generation sequencing techniques can easily generate numerous loci for testing complex models on how species diverged. In this study, I aim to study the species delimitation of the ground skinks (genus Scincella), a group of small-sized skinks widely distributed throughout North America and Oriental Asia. Due to their morphological similarity, the taxonomic status of Scincella in East Asia is always a controversial issue. Previous studies have shown insufficient diagnosis among S. modesta complex, which comprises S. modesta, S. formosensis, and S. boettgeri. Furthermore, there are several other cryptic taxa (Scincella spp.) recently found in Taiwan and China, which led to taxonomic confusion. In this study, I applied multiplexed shotgun genotyping (MSG) to obtain genome-wide loci. By incorporating coalescent-based methods, I clarified the taxonomic status of members in this species complex and inferred their speciation history. Sequences from 56 individuals were included in analyses, with two hundred million reads reported from 2 reaction lanes. Sequences were assembled and called for single nucleotide polymorphic (SNP) sites using pyRAD. Several analyses (included phylogenetic reconstruction, Structure, DAPC, BFD*) were conducted on 367–4188 RAD loci to show that there are six lineages within S. modesta complex, where 3 of them have not been described before and should be treated as new species. On the other hand, a coalescence-based model, G-PhoCS, revealed that S. modesta complex diverged mainly between middle to late Pleistocene, and most of the taxa experienced population shrinkage. Although there is no evidence of gene flow between sister taxa, historical introgression was detected between non-sister taxa during the process of diversification. The results suggested the complicated history of gene flow among these taxa.

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