Ohio State University Herbarium, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd., Columbus, Ohio 43212 USA;
Am J Bot. 2004 Jan;91(1):149-57. doi: 10.3732/ajb.91.1.149.
An expanded plastid DNA phylogeny for Orchidaceae was generated from sequences of rbcL and matK for representatives of all five subfamilies. The data were analyzed using equally weighted parsimony, and branch support was assessed with jackknifing. The analysis supports recognition of five subfamilies with the following relationships: (Apostasioideae (Vanilloideae (Cypripedioideae (Orchidoideae (Epidendroideae))))). Support for many tribal-level groups within Epidendroideae is evident, but relationships among these groups remain uncertain, probably due to a rapid radiation in the subfamily that resulted in short branches along the spine of the tree. A series of experiments examined jackknife parameters and strategies to determine a reasonable balance between computational effort and results. We found that support values plateau rapidly with increased search effort. Tree bisection-reconnection swapping in a single search replicate per jackknife replicate and saving only two trees resulted in values that were close to those obtained in the most extensive searches. Although this approach uses considerably more computational effort than less extensive (or no) swapping, the results were also distinctly better. The effect of saving a maximal number of trees in each jackknife replicate can also be pronounced and is important for representing support accurately.
利用 rbcL 和 matK 序列对五个亚科的代表进行了扩展的质体 DNA 系统发育分析。使用等权重简约法进行数据分析，并通过 Jackknifing 评估分支支持。分析支持识别五个亚科，其关系如下：（Apostasioideae（Vanilloideae（Cypripedioideae（Orchidoideae（Epidendroideae））））。Epidendroideae 内许多部落级群的支持是明显的，但这些群之间的关系仍然不确定，可能是由于亚科的快速辐射导致了树的脊柱上的短分支。一系列实验检验了 Jackknifing 参数和策略，以确定在计算工作量和结果之间取得合理平衡。我们发现，随着搜索工作量的增加，支持值迅速达到峰值。在每个 Jackknifing 重复的单个搜索复制中进行树二分连接交换，并仅保存两棵树，得到的值与最广泛搜索获得的值非常接近。尽管这种方法比不广泛（或不）交换使用更多的计算资源，但结果也明显更好。在每个 Jackknifing 重复中保存最大数量的树的效果也可能很明显，对于准确表示支持非常重要。
