本研究探討台灣石魚賓主要組織相容性複合體(MHC)分子演化所受的天擇效應與模式以及其它內在的演化力量的影響，根據族群具有低核苷酸歧異度及高基因型歧異度，中性假說測驗在MHC第二型基因DAB基因座exon 2到exon 3部分片段中非同義和同義鹼基替代位置皆呈現負值，且利用異質性檢測也指出台灣石魚賓MHC第二型基因DAB基因座的演化是受到基因同質化力量的作用，顯示台灣石魚賓曾經為一個小族群，族群內僅見少數單型及低的核苷酸歧異度，伴隨後續因棲地擴張之族群快速擴張。根據分化指數與相對應地理距離對數值相關性分析，台灣石魚賓族群分佈呈現隔離分化(isolation by distance)，但相關係數低(R2=0.1199)。在親緣演化樹狀圖中未顯示地理區系分群分化的現象，可能因MHC基因受到制衡性天擇的影響，導至多型性在族群中長時間保存，加長了譜系排序(lineage sorting)所需的時間，而族群中高比例的異型合子(H=0.95)也進一步支持制衡性天擇的存在。屬於中部及苗栗台地的單型分佈在親緣網狀圖中心位置，因此中部及苗栗台地的族群應為較古老的族群，與粒線體DNA所得的結果相符。而位於親緣網狀圖外部，即新產生的單型與最近緣單型間之dN/dS值大部分大於1，也暗示著台灣石魚賓的MHC第二型基因DAB基因座在近代台灣石魚賓進入台灣及擴張後正受到正向天擇力量的作用以增加族群內MHC基因型的變異，利用PAML來檢測各胺基酸位置所受到的天擇影響，顯示此片段在每個胺基酸位置是受到不同天擇力量作用的。

Sequence variation of the partial exons 2 and 3 of MHC class II DAB locus of Acrossocheilus paradoxus populations was examined to determine the mode of natural selection and effects of the intrinsic evolutionary forces. Based on the existence of low levels of nucleotide diversity and high levels of haplotype diversity among populations, significantly negative Tajima’s D statistics for both nonsynonymous and synonymous sites in A. paradoxus, and Hahn et al.’s heterogeneity test supporting demographic (homogeneous) process, a phylogeographical hypothesis of range expansion after the settlement of the surviving founder population from Asian continent was generated. According to the regression statistics of FST value and logarithmic scales of geographical distance between population, the geographical distributions of genetic diversity is consistent with an “isolation by distance” model (R2=0.1199). Geographical structuring was not detected in the NJ tree. Trans-region polymorphisms indicate effects of balancing selection. Accordingly, polymorphisms can persist much longer than in the neutral case and prolong the time of lineage sorting, leading to paraphyly of geographical regions and populations. High level of heterozygosity in population also suggests the effect of balancing selection. Most haplotypes distributed in the nested in the minimum spanning network as interior nodes were central subzoogeographical district and Miao-li plateau, a pattern consists with mtDNA genealogy indicating ancestry of central subzoogeographical district and Miao-li plateau. Based on pairwise comparisons of the dN/dS ratio, lineages of closely related haplotypes of the species located at tips of minimum spanning network representing newly evolved haplotype appear to be under positive selection. PAML analysis detected different modes of natural selection along each amino acid sites.

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