本研究利用同功異構電泳法與粒線體去氧核糖核酸序列分析，探討台灣與琉球地區褐吻虎複合種之分子系統分類及族群遺傳變異。兩個資料組架構出不同的系譜圖，二者皆無證據支持產於台灣地區之褐吻虎複合種內大部分物種以及琉球地區不同色型之褐吻虎為有效種。所有採自琉球地區之樣本為一單系群。台灣與琉球皆有分布之名古屋吻虎（Rhinogobius nagoyae formosanus）（褐吻虎橫斑型, Rhinogobius sp. CB），二地間族群之遺傳距離遠大於相同地區之不同物種或不同色型之族群。僅台灣特有之短吻紅斑吻虎（R. rubromaculatus）與斑帶吻虎（R. maculafasciatus）應為有效種。以分子變異分析（AMOVA）檢視27個族群，二組不同的設定，分別顯示大部分的變異發生在不同島嶼之間（52.10%），及同種或同色型之不同族群之間（70.95%）。此結果顯示褐吻虎複合種之親緣關係與色型之關聯性相當微弱，較可能歸因於過去地貌變化作用所產生的結果。因此，褐吻虎複合種之物種命名有必要重整。
在探討短吻紅斑吻虎之形態與遺傳變異的研究中，於台灣南部之林邊溪發現一個全新紀錄的色型，經由同功異構與粒線體DNA序列的比較分析，證明其應屬於短吻紅斑虎。此色型具有較小之體型與卵徑，不同地區之短吻紅斑虎之卵徑與溫度呈負相關。新色型與其他短吻紅斑吻虎族群間無特有之對偶基因，種內之同功異構之遺傳距離為0.001至0.078，遠低於與明潭吻虎（0.532 ~ 0.687）及琉球地區之陸封型虎（0.326 ~ 0.464）之遺傳距離。粒線體DNA序列包含cytochrom b，2 tRNA及D-loop，顯示種內有207鹼基發生置換，種間則有363個鹼基。族群內序列之遺傳距離為0.000 ~ 0.004，種內族群間序列之距離為0.005 ~ 0.074，遠小於種間之歧異度 （0.094~0.113）。二標誌皆顯示短吻紅斑虎樣本間有顯著分化之現象（同功異構之FST = 0.404，mtDNA之ΦST = 0.986）。利用同功異構與粒線體DNA序列所架構之樹型圖顯示台灣中部與南部之族群比北部較為近緣。個別的表型並非由遺傳變異所造成，可能是表型可塑性之結果。
檢視台灣特有種斑帶吻虎分布於三個不同流域其族群內與族群間之遺傳歧異度，粒線體DNA序列包含cytochrom b，2 tRNA及D-loop，共2124~2126鹼基，由60個個體定序出41個單系型（haplotype），序列分析顯示有二個分別的演化分枝存在於台灣南部的高屏溪流域。分布於蘭陽溪之斑帶吻虎可能起源於中國大陸東部沿岸，與台灣西南部族群的基因交流可能是藉由台灣西部沿岸流而產生。以分子變異分析檢視三個流域之6個族群，發現主要之遺傳分化來自於同一流域間之不同族群（68.37%），大部分的變異來自於高屏溪流域族群之分化。此結果支持族群基因結構強烈地受到河道改變之影響，歸因於晚近地貌發生改變的作用。

Molecular systematic studies and population genetics of Rhinogobius brunneus species complex were carried out by allozyme electrophoresis and mtDNA sequences analysis. The phylogenetic trees derived from these two data sets were indicated different topologies. Both allozyme and mtDNA data provided no evidence to support that the most species of R. brunneus species complex in Taiwan and the different color types in Ryukyu Islands were valid. The specimens from Ryukyu Islands form a monophyletic group within the species complex. The genetic distance of R. nagoyae formosanus (Rhinogobius sp. CB) between Taiwan and Ryukyu Islands was larger than that between different species and color types in the same area. Only the endemic R. rubromaculatus and R. maculafasciatus in Taiwan were valid species. Two hierarchical examinations of 27 populations using analysis of molecular variance (AMOVA) indicate high genetic differentiation among different islands (52.10%) and different populations (70.95%). The results support the hypothesis that the genetic relationship of R. brunneus species complex is weak contingency with color patterns and is otherwise possibly caused by geomorphological processes that occurred in the past. Therefore, the species nominated for the R. brunneus species complex should be reorganized.
An additional color type discovered from the Linbian River in southern Taiwan is morphologically and genetically closely related to Rhinogobius rubromaculatus with little variation. Specimens from the Linbian River characterized by a smaller body size and egg size, are negatively correlated with thermal gradient. There is no fixed alleles between the new color type from Linbian River and R. rubromaculatus, with extremely lower genetic distance of 0.001 to 0.078, when compared to R. candidianus (0.523~0.687) and two other undetermined Rhinogobius species from the Ryukyu Islands (0.326~0.464). The complete sequences of the cytochrome b gene, tRNA genes, and the control region of mtDNA revealed substitution differences within R. rubromaculatus at 207 base pairs (bp) and among the three species (R. candidianus, Rhinogobius sp. BB, and Rhinogobius sp. YB) at 363 bp. The sequence diversity within the population of R. rubromaculatus ranged 0.000-0.004. Among local populations of R. rubromaculatus, the mean sequence distance diversities ranged 0.005-0.074, is far lower than that between R. rubromaculatus and other Rhinogobius species (0.094~0.113). The results from both genetic markers revealed the same significant differences between local populations of R. rubromaculatus (global FST = 0.404 for the allozyme and ΦST = 0.986 for the mitochondrial DNA data). The molecular trees constructed for R. rubromaculatus based on both allozyme and mtDNA data revealed a higher similarity between central and southern populations than to northern population. The phenotypic differences could have been produced by phenotypic plasticity.
The genetic diversity within and among populations of the endemic spot-banded goby, Rhinogobius maculafasciatus, from three drainage basins in Taiwan was derived from a sequence length of 2124-2126 bp, including the complete cytochrome b gene, two tRNA genes, and the control region of mtDNA. Forty-one haplotypes obtained from sequence analysis of 60 specimens indicated two distinct clades in the samples from Kaoping River, southwestern Taiwan. The populations inhabiting the Lanyang River in northern Taiwan is allied to that in southwestern Taiwan, and both are probably originated from the east coast of Mainland China via Current Taiwan Striat by aide of the Coastal Current on along the western coast of Taiwan. A hierarchical examination of six populations of R. maculafasciatus from three drainage basins using analysis of molecular variance (AMOVA) indicates high genetic differentiation among populations within basins (68.37%). Most of the variation deduced from the population differentiations in Kaoping River. The results support the hypothesis that the current genetic structure of R. maculafasciatus is strongly affected by changes in drainage patterns due to geomorphological processes that occurred in the recent past.

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