Sesli M, Yegenoglu E D
Celal Bayar University, Akhisar, Manisa, Turkey.
Genet Mol Res. 2010 Nov 16;9(4):2248-53. doi: 10.4238/vol9-4gmr966.
Five different similarity coefficients (Jaccard, Sorensen-Dice, simple matching, Rogers and Tanimoto, and Russel and Rao) were evaluated and 10 wild olives analyzed with RAPD markers. The influence of the similarity coefficients on wild olives clustering was investigated. Forty-five primers were used on samples from 10 wild olives (Wild 1 and 2 obtained from Mugla province; Wild 3, 4, 5, 6, 7, and 8 from Manisa province and Wild 9 and 10 from Izmir province of Turkey). The similarity matrices obtained from RAPD markers were compared by the Mantel test. Cluster analysis was made with UPGMA dendrograms, and the consensus fork indexes between all pairs of dendrograms were calculated. The Jaccard and Sorensen-Dice coefficients gave the same results, due to the fact that both exclude negative co-occurrences. The dendrograms using the simple matching and Rogers and Tanimoto coefficients were similar; Wild 4 (Akhisar, Manisa) and Wild 9 (Bornova, Izmir) olives had the closest genetic similarities. This occurred because these coefficients include negative co-occurrences. The Russel and Rao coefficients produced different results, because they include negative co-occurrences in the denominator. We concluded that the coefficients that do not include negative co-occurrences are more efficient for studies of wild olives clustering based on RAPD markers.
评估了五种不同的相似性系数（杰卡德系数、索伦森-戴斯系数、简单匹配系数、罗杰斯和谷本系数以及拉塞尔和饶系数），并用随机扩增多态性DNA（RAPD）标记对10种野生橄榄进行了分析。研究了相似性系数对野生橄榄聚类的影响。对来自10种野生橄榄（从穆拉省获得的野生1号和2号；从马尼萨省获得的野生3号、4号、5号、6号、7号和8号；以及从土耳其伊兹密尔省获得的野生9号和10号）的样本使用了45个引物。通过曼特尔检验比较了从RAPD标记获得的相似性矩阵。用非加权组平均法（UPGMA）树形图进行聚类分析，并计算了所有树形图对之间的一致叉指数。杰卡德系数和索伦森-戴斯系数给出了相同的结果，因为两者都排除了负共现情况。使用简单匹配系数以及罗杰斯和谷本系数的树形图相似；野生4号（马尼萨省阿希萨尔）和野生9号（伊兹密尔省博尔诺瓦）橄榄具有最接近的遗传相似性。出现这种情况是因为这些系数包括负共现情况。拉塞尔和饶系数产生了不同的结果，因为它们在分母中包括了负共现情况。我们得出结论，对于基于RAPD标记的野生橄榄聚类研究，不包括负共现情况的系数更有效。
