a The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA.
b Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA.
Genome. 2017 Sep;60(9):720-732. doi: 10.1139/gen-2016-0191. Epub 2017 Apr 26.
Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%-21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%-41% of plastome variation, geography 3%-41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.
由于高度的渐渗杂交，质体基因组不适用于橡木属（栎属，壳斗科）的精细 DNA 条形码和系统发育研究。在橡木质体系统发育的末端，最近的基因迁移和网状结构通常导致拓扑结构反映地理结构，而更深的分支反映谱系分化。在这项研究中，我们量化了地理接近度和核推断的系统发育历史对不同进化尺度上橡木质体系统发育的简单和部分影响。我们的研究比较了基于完整质体序列的成对系统发育距离、基于核限制位点相关 DNA 序列（RADseq）的成对系统发育距离，以及代表 24 种北美和欧亚物种的 34 个白橡木类群的成对地理距离。仅在北美白橡木类群中，系统发育历史对质体变异几乎没有影响，而地理解释了 11%-21%的质体系统发育方差。然而，在多个大陆和类群中，系统发育预测了 30%-41%的质体变异，地理解释了 3%-41%。在质体中，分支点上的系统发育信息量衰减意味着在实际应用中，质体数据在解决系统发育问题方面几乎没有用处，但仍然可以作为解决主要类群之间问题的有用条形码或系统发育标记。
