陸 陸
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柒、表附錄
表一、PCR 反應試劑
試劑 濃度 劑量(µl)
Premix Blue tag Tag DNA polumerase 1.6U
dNTP 500µM 5
MgCl2 4.Mm
Primer pairs 1.5
Genomic DNA 1
dd H2o 2.5
total 10
表二、PCR 反應條件
步驟 溫度℃ 時間
1 94 5 分鐘
2 94 1 分鐘
3 視 primer 最佳反應溫度而定 30 秒鐘
4 72 1 分鐘
重複置步驟 2，持續 38 次循環
5 72 10 分鐘
6 25 End
表三、玉山杜鵑複合群台灣杜鵑的遺傳歧異度
N，樣本數量；Apriv，族群私有對偶基因的總數；AR，對偶基因豐富度平均值；PR，私有對偶基因豐富度平均值；VR，重複序列變異數平均值 HE，
異質結合期望值平均值(gene diversity)；HO，異質結合觀察值平均值；HS，Nei’s 遺傳歧異度平均值。
Population(Code) Locality
(Latitude/longitude) N Apriv AR(SD) PR(SD) VR(SD) HE(SD) HO(SD) HS(SD) P FIS
R.rubropunctatum 37 7 2.988 0.246 29.770 0.316 0.338 0.382 0.815
Tsaigongkeng(RrTGK) 121.31°/25.11° 14 2 2.866(2.16) 0.166(0.24) 27.126(103.71) 0.313(0.30) 0.355(0.35) 0.376(0.28) 0.815 -0.141*
Tsankuanliao(RrTKL) 121.51°/25.05° 23 11 3.111(2.05) 0.326(0.40) 32.414(110.45) 0.320(0.29) 0.322(0.31) 0.388(0.26) 0.815 -0.006
R.pseudochrysanthum 60 8 3.580 0.265 26.169 0.406 0.414 0.457 0.889
Dashiueshan(RpDSS) 121.07°/24.19° 20 10 3.328(2.62) 0.244(0.42) 27.513(100.30) 0.409(0.31) 0.438(0.33) 0.473(0.27) 0.889 -0.074*
Hohuanshan(RpHHS) 121.15°/24.07° 19 3 3.535(2.53) 0.212(0.32) 23.095(74.02) 0.396(0.32) 0.385(0.32) 0.459(0.29) 0.852 0.029 Lulinshan(RpLLS) 120.52°/23.27° 21 10 3.878(2.35) 0.339(0.48) 27.899(97.93) 0.413(0.27) 0.419(0.29) 0.440(0.25) 0.926 -0.017
R.morii 43 9 3.874 0.340 33.182 0.426 0.451 0.529 0.790
Alishan(RmALS) 120.48°/23.30° 19 7 3.703(2.91) 0.255(0.50) 31.879(98.85) 0.395(0.33) 0.403(0.34) 0.553(0.24) 0.704 -0.020 Dashiueshan(RmDSS) 121.07°/24.19° 9 4 3.667(2.91) 0.204(0.37) 31.254(82.42) 0.413(0.33) 0.453(0.37) 0.514(0.26) 0.778 -0.102*
Hohuanshan(RmHHS) 121.20°/24.10° 15 17 4.253(2.67) 0.562(0.65) 36.413(126.18) 0.471(0.30) 0.498(0.35) 0.520(0.25) 0.889 -0.059*
R.hyperythrum
Nanhutashan(RhNHTS) 121.26°/24.21° 45 20 3.890(2.77) 0.330(0.39) 24.491(75.57) 0.426(0.30) 0.439(0.31) 0.476(0.28) 0.889 -0.031
R.formosanum 68 11 3.277 0.381 32.264 0.395 0.406 0.447 0.874
Chilanshan(RfCLS) 121.29°/24.36° 13 8 3.265(2.12) 0.309(0.58) 33.481(126.90) 0.403(0.28) 0.385(0.27) 0.508(0.20) 0.778 0.046 Dashiueshan(RpDSS) 121.07°/24.19° 15 8 3.239(1.55) 0.317(0.43) 26.506(107.66) 0.430(0.24) 0.467(0.29) 0.438(0.23) 0.963 -0.090*
Lilungshan(RfLLS) 120.44°/22.09° 15 15 3.225(1.44) 0.532(0.54) 27.824(126.99) 0.368(0.25) 0.378(0.31) 0.375(0.24) 0.963 -0.028 Sanlinxi(RfSLX) 120.47°/23.38° 10 6 2.889(2.06) 0.249(0.52) 36.227(147.57) 0.337(0.30) 0.334(0.33) 0.466(0.24) 0.704 0.008 Szuyuan(RfSY) 121.21°/24.24° 15 16 3.769(1.92) 0.499(0.61) 37.281(111.56) 0.440(0.24) 0.467(0.29) 0.448(0.23) 0.963 -0.065*
表四、檢測玉山杜鵑複合群與台灣杜鵑每個基因座符合哈溫平衡
表五、檢測玉山杜鵑複合群與台灣杜鵑 27 個 EST-SSR 基因座連鎖平衡
經由 Bonferroni 校正(α = 0.05)，P‐values 顯著連鎖不平衡的值以*表示。
表六、對偶基因大小對於估算遺傳結構是否有效率之檢測 Global R-statistics
All loci
Rit Ris Rst
95%CI(lower) 0.0860 -0.1245 0.1620
95%CI(upper) 0.3130 0.0400 0.3127
P(1-sided test, H1: obs<exp) 0.3204 0.0288 0.8345 P(1-sided test, H1: obs>exp) 0.6797 0.9713 0.1656 P(2-sided test, H1: obs<>exp) 0.6407 0.0575 0.3311
此分析為檢測對偶基因大小估計遺傳結構是否與 FST 估計的遺傳結構相似(H0：
RST=FSTT)。
表七、玉山杜鵑複合群與台灣杜鵑族群間兩兩比較 FST 值
Population RrTGK RrTKL RpDSS RpHHS RpLLS RmALS RmDSS RmHHS RhNHTS RfCLS RfDSS RfLLS RfSLX RfSY
RrTGK 0
RrTKL 0.0734 0
RpDSS 0.1981 0.2131 0
RpHHS 0.1588 0.2132 0.0458 0
RpLLS 0.1538 0.2157 0.0768 0.0285 0
RmALS 0.1531 0.2136 0.0931 0.0418 0.0335 0
RmDSS 0.1755 0.2240 0.0678 0.0178* 0.0589 0.0454 0
RmHHS 0.1606 0.2024 0.0538 0.0205* 0.0440 0.0389 0.0417 0
RhNHTS 0.1805 0.2068 0.0471 0.0388 0.0818 0.0700 0.0409 0.0493 0
RfCLS 0.5482 0.5481 0.4568 0.4717 0.4701 0.4766 0.4607 0.4168 0.4476 0
RfDSS 0.5214 0.5244 0.4306 0.4505 0.4437 0.4557 0.4429 0.3979 0.4337 0.1821 0
RfLLS 0.5813 0.5753 0.4933 0.5093 0.5044 0.5208 0.5091 0.4659 0.4832 0.1800 0.1798 0
RfSLX 0.5936 0.5890 0.4950 0.5133 0.5076 0.5230 0.5129 0.4616 0.4836 0.1190 0.1325 0.1593 0
RfSY 0.5225 0.5250 0.4252 0.4467 0.4394 0.4499 0.4358 0.3909 0.4292 0.0999 0.0970 0.1081 0.1171 0 FST 值旁邊的*，代表 P value 不顯著的 FST 值。
玉山杜鵑複合群與台灣杜鵑族群 FST 值的 P value 表
Population RrTGK RrTKL RpDSS RpHHS RpLLS RmALS RmDSS RmHHS RhNHTS RfCLS RfDSS RfLLS RfSLX RfSY
RrTGK *
RrTKL 0 *
RpDSS 0 0 *
RpHHS 0 0 0 *
RpLLS 0 0 0 0.0005 *
RmALS 0 0 0 0.0001 0 *
RmDSS 0 0 0 0.0299* 0 0.0005 *
RmHHS 0 0 0 0.0049* 0 0 0 *
RhNHTS 0 0 0 0 0 0 0 0 *
RfCLS 0 0 0 0 0 0 0 0 0 *
RfDSS 0 0 0 0 0 0 0 0 0 0 *
RfLLS 0 0 0 0 0 0 0 0 0 0 0 *
RfSLX 0 0 0 0 0 0 0 0 0 0 0 0 *
RfSY 0 0 0 0 0 0 0 0 0 0 0 0 0 *
Bonferroni 校正(α = 0.05)後，顯著標準 P = 0.00055。*代表 P > 0.00055，P value 不顯著。
表九、玉山杜鵑複合群與台灣杜鵑的 AMOVA 分析結果
Source of variation d.f. Sum of squares Variance components Percentage of variation φ‐Statistics P‐value R.f. and R.p.complex two groups
Among groups 1 857.033 4.16412 41.01 φCT = 0.41013 < 0.001
Four species groups in Rp.complex
Among groups 3 173.495 0.41697 6.96 φCT = 0.06956 < 0.001
表十、檢測玉山杜鵑複合群與台灣杜鵑族群 heterozygosity excess
TPM (% step variance/% SMM) Population I.A.M. S.M.M. 族群在 infinite allele model (IAM)、stepwise mutation model (SMM)與 two phase model (TPM)呈現的 P-values 如上。TPM 30/40 表示變異數為 30 並基因座 40%為 SMM。
表十一、玉山杜鵑複合群族群變動的結論統計值(Summary statistics)
Log(r) Log(tf) r=N0/N1 tf=ta/N0
Population LHPD MODE UHPD LHPD MODE UHPD LHPD MODE MODE LHPD MODE MODE
RrTGK -3.330 -2.780 -2.216 1.510 2.173 2.794 0.00047 0.00166 0.00608 32.4 149.0 621.6 RrTKL -3.543 -2.947 -2.283 1.388 1.980 2.590 0.00029 0.00113 0.00522 24.4 95.6 388.8
RpDSS -3.516 -2.651 -2.051 0.881 1.946 2.643 0.00030 0.00224 0.00890 7.6 88.4 439.5
RpHHS -3.015 -2.362 -1.738 1.130 1.837 2.497 0.00097 0.00435 0.01827 13.5 68.6 314.4
RpLLS -2.413 -1.774 -1.143 0.935 1.607 2.214 0.00386 0.01684 0.07190 8.6 40.5 163.7
RmALS -2.909 -2.253 -1.601 1.160 2.002 2.748 0.00123 0.00558 0.02508 14.5 100.5 560.1 RmDSS -2.945 -2.395 -1.856 1.614 2.213 2.807 0.00114 0.00402 0.01394 41.1 163.2 641.3
RmHHS -2.566 -1.955 -1.314 0.914 1.625 2.292 0.00272 0.01109 0.04854 8.2 42.2 195.8
RhNHTS -2.429 -1.873 -1.317 1.175 1.753 2.387 0.00373 0.01339 0.04816 15.0 56.6 243.8
RfCLS -3.122 -2.095 -1.470 0.662 1.839 2.649 0.00076 0.00804 0.03386 4.6 69.0 445.7
RfDSS -2.777 -2.152 -1.609 1.170 1.843 2.407 0.00167 0.00705 0.02458 14.8 69.6 255.2 RfLLS -2.608 -2.062 -1.557 1.195 1.762 2.292 0.00247 0.00868 0.02773 15.7 57.8 196.1 RfSLX -3.294 -2.747 -2.245 1.618 2.265 2.917 0.00051 0.00179 0.00569 41.5 184.3 825.5 RfSY -2.655 -2.045 -1.477 0.961 1.614 2.221 0.00221 0.00902 0.03332 9.1 41.1 166.4 上表所列為 MSVAR 1.3 所估算的早期有效除群數量(N1)、當代有效族群數量(N0)、族群變動的起始時間(t)，期眾數與高達 90%機率的區間。各參數是 從對數轉換而來。N0/N1 是當代有效族群數量與早期有效除群數量的比例，意義為族群的改變率。(t/N0)是族群變動的起始時間與當代有效族群數量的 比例，意義為族群變動開始的代數。LHPD，90%機率區間的最低限；UHPD，90% 率區間的最高限。
表十二、玉山杜鵑複合群的早期有效族群數量與族群變動時間
N1 N0 t
Population LHPD MODE UHPD LHPD MODE UHPD LHPD MODE UHPD
RrTGK 14488 74994 277987 35 125 456 4032 18552 77393
RrTKL 34493 107805 324994 31 122 562 2971 11631 47322
RpDSS 16342 71483 236475 22 160 636 1216 14123 70244
RpHHS 11657 44185 154522 43 192 807 2590 13179 60359
RpLLS 8683 32819 118831 127 553 2360 4754 22380 90456
RmALS 10514 53624 219716 66 299 1345 4333 30099 167729
RmDSS 29572 109682 385691 125 441 1529 18133 72008 283024
RmHHS 11618 40908 139900 111 454 1986 3724 19155 88848
RhNHTS 16968 70043 265960 261 938 3373 14036 53072 228589
RfCLS 5296 27870 142612 21 224 943 1029 15450 99862
RfDSS 11984 44575 158410 74 314 1095 4649 21877 80245
RfLLS 11126 36195 119319 89 314 1003 4927 18148 61583
RfSLX 19929 105525 411618 54 189 601 7829 34786 155832
RfSY 10201 33299 110567 74 300 1109 2743 12345 49980
上表所列為 MSVAR 1.3 所估算的早期有效除群數量(N1)、當代有效族群數量(N0)、族群變動的起始時間(t)，期眾數與高達 90%機率的區間。各參數是 從對數轉換而來。LHPD，90%機率區間的最低限；UHPD，90% 率區間的最高限。
表十三、Maximum-likelihood 估算玉山杜鵑複合群的 θ、有效族群數量(Ne)與每代遷移個體數 Source
Recipient
θ Ne(0.05-0.95) RrTGK RrTKL RpDSS RpHHS RpLLS RmALS RmDSS RmHHS RhNHTS
RrTGK 0.909 2273(2140-2416) * 0.260 0.174 0.245 0.290 0.269 0.243 0.175 0.213 RrTKL 0.941 2352(2236-2469) 0.212 * 0.211 0.230 0.263 0.299 0.187 0.209 0.256 RpDSS 1.011 2528(2401-2660) 0.246 0.282 * 0.270 0.222 0.261 0.195 0.229 0.299 RpHHS 0.970 2424(2304-2554) 0.260 0.183 0.220 * 0.289 0.238 0.275 0.241 0.319 RpLLS 0.969 2423(2305~2550) 0.211 0.233 0.190 0.305 * 0.242 0.161 0.285 0.355 RmALS 1.005 2512(2385~2649) 0.218 0.251 0.269 0.245 0.276 * 0.271 0.264 0.309 RmDSS 0.951 2377(2225~2542) 0.168 0.209 0.209 0.258 0.195 0.193 * 0.269 0.220 RmHHS 1.071 2676(2520~2846) 0.215 0.279 0.347 0.322 0.255 0.368 0.236 * 0.316 RhNHTS 1.064 2661(2568~2758) 0.288 0.327 0.320 0.230 0.244 0.284 0.204 0.233 * Source 是來源的族群，Recipient 是接受族群。每代遷移個體數是從公式計算而來，Nem(i→j)=θj *M(i→j)/4, M 是遷移率。
表十四、使用 Arlequin、Fdist2、與 lnθ 檢測玉山杜鵑複合群偏離中性演化基因座
Locus names
Outlier detection method
Selection mode 1655 1723 1804 1812 1915 5362 5416 5557 5571 5685 5727 6007 6170 6228 6455 6477 6487 6515 6637
Fdist2 (SMM) Positive O O O O O
Balancing O O
Fdist2 (IAM) Positive O O O O O
Balancing O O O O O O O
Arlequin HIS FCT† Positive O O
Balancing O O
Arlequin HIS FST Positive O O
Balancing O
lnRV RrTKL RmDSS RrTKL
lnRH
†：分群為兩群，紅星一群，其他杜鵑一群。
O 代表顯著偏離中性演化的基因座(P-value < 0.025)，HIS, hierarchical island model; SMM, stepwise mutation model; IAM,infinite allele model.。
表十五、DETSEL 檢測紅星杜鵑分群與玉山、森氏、南湖杜鵑分群的偏離中性演化基因座的分析結果 Pairwise
comparison Locus names 165
表十六、玉山杜鵑複合群 EST-SSR 對偶基因顯著相關的環境因子 Locus name Allele size Environmental variable
1655 306 WND
捌、圖附錄
圖一、本研究中玉山杜鵑複合群之採樣族群地理位置。選用的玉山杜鵑複合群總 共有 9 個族群。
圖二(1)、玉山杜鵑複合群個體之間的遺傳關係。每一個點代表一個個體，這些個體並不指定屬於任何一個族群。
圖二(2)、玉山杜鵑複合群族群之間的遺傳關係，一個點代表一個族群。
(a)
(b)
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0 1 2 3 4 5 6 7 8 9 10
K
∆k
圖三(1)、(a)玉山杜鵑複合群個體的分群結果(k=2)，使用 no admixture model。(b)∆k 值是根據 Evanno (2005)提出的分群機率校正值，K 代表分群的數目。
(a)
(b)
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0 1 2 3 4 5 6 7 8 9 10
K
∆K
圖三(2)、(a)玉山杜鵑複合群個體的分群結果(k=2)，使用 admixture model。(b)∆k 值是根據 Evanno (2005)提出的分群機率校正值，K 代表分群的數目。
0.00 0.05 0.10 0.15 0.20 0.25
0 50 100 150 200 250