Department of Biology and Center for Molecular Biosciences, Middle Tennessee State University, Murfreesboro, Tennessee.
Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee.
Mol Ecol. 2018 May;27(10):2317-2333. doi: 10.1111/mec.14695.
Plant studies comprise a relatively small proportion of the phylogeographic literature, likely as a consequence of the fundamental challenges posed by the complex genomic structures and life history strategies of these organisms. Comparative plastomics (i.e., comparisons of mutation rates within and among regions of the chloroplast genome) across plant lineages has led to an increased understanding of which markers are likely to provide the most information at low taxonomic levels. However, the extent to which the results of such work have influenced the literature has not been fully assessed, nor has the extent to which plant phylogeographers explicitly analyse markers in time and space, both of which are integral components of the field. Here, we reviewed more than 400 publications from the last decade of plant phylogeography to specifically address the following questions: (i) What is the phylogenetic breadth of studies to date? (ii) What molecular markers have been used, and why were they chosen? (iii) What kinds of markers are most frequently used and in what combinations? (iv) How frequently are divergence time estimation and ecological niche modelling used in plant phylogeography? Our results indicate that chloroplast DNA sequence data remain the primary tool of choice, followed distantly by nuclear DNA sequences and microsatellites. Less than half (42%) of all studies use divergence time estimation, while even fewer use ecological niche modelling (14%). We discuss the implications of our findings, as well as the need for community standards on data reporting.
植物研究在系统地理学文献中所占比例相对较小，这可能是由于这些生物体具有复杂的基因组结构和生活史策略，因此带来了一些基本挑战。对植物谱系进行比较质体基因组学（即比较叶绿体基因组区域内和区域间的突变率）研究，提高了人们对哪些标记在低分类水平上可能提供最多信息的认识。然而，这种工作的结果在多大程度上影响了文献尚未得到充分评估，植物系统地理学家在时间和空间上明确分析标记的程度也尚未得到评估，而这两者都是该领域的组成部分。在这里，我们回顾了过去十年中植物系统地理学的 400 多篇出版物，专门回答以下问题：（i）迄今为止的研究在系统发育上有多广泛？（ii）使用了哪些分子标记，为什么选择它们？（iii）哪些类型的标记最常使用，以及它们的组合方式是什么？（iv）植物系统地理学中经常使用分歧时间估计和生态位模型吗？我们的研究结果表明，质体 DNA 序列数据仍然是首选工具，其次是核 DNA 序列和微卫星。只有不到一半（42%）的研究使用分歧时间估计，而使用生态位模型的研究更少（14%）。我们讨论了我们研究结果的意义，以及对数据报告社区标准的需求。
