Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.
Genome Biol Evol. 2010;2:504-17. doi: 10.1093/gbe/evq036. Epub 2010 Jul 2.
As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.
作为最大和最基础的松柏目家族，松科为松柏目植物的进化历史提供了关键的见解。我们展示了比较叶绿体基因组学和对 19 种裸子植物共有的 49 个叶绿体蛋白编码基因的串联分析，包括 8 个松科属中的 15 个物种，以解决松科植物系统发育的长期争议。报告了银杉和雪松（冷杉亚科）的完整 cpDNA 和落叶松、白云杉和湿地松的 cpDNA 草案。我们在同属物种和不同松科物种的种群中发现了 21-和 42-kb 倒位，这表明结构多态性在松科中可能是常见和古老的。我们的系统发育分析表明，雪松与冷杉-铁杉属聚类，而不是最基础的松科属，银杉与松属比与云杉属或落叶松-黄杉属更接近。拓扑结构和结构变化测试以及插入缺失分布比较为我们的系统发育发现提供了进一步的证据。我们的分子定年表明，松科在早侏罗世首次进化，松科亚科和属的多样化分别发生在中侏罗世和下白垩世。使用不同的最大似然分歧作为阈值，我们得出结论，2 个（冷杉亚科和落叶松-黄杉-银杉-松属）、4 个（雪松、非雪松冷杉亚科、落叶松-黄杉和松属）或 5 个（雪松、非雪松冷杉亚科、落叶松-黄杉、云杉和银杉-松属）组/亚科更合理地限定了松科。具体而言，我们对亚科分类的看法与之前的研究在雪松的等级和识别两个以上的亚科方面有所不同。
