State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
Mol Phylogenet Evol. 2022 Oct;175:107581. doi: 10.1016/j.ympev.2022.107581. Epub 2022 Jul 8.
Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.
松红梅族是一个多样化的野牡丹科谱系，包含约 1000 种，分为 44 属，其中超过 70%的属和种分布在亚洲。亚洲松红梅族在分类上具有棘手性，其属的界限模糊不清。该类群的骨干系统发育仍然没有得到很好的解决，这可能是由于早中和中新世快速物种辐射引起的复杂性所致，这阻碍了进一步的系统研究。在这里，我们使用基因组重测序数据来重建亚洲松红梅族的系统发育。为此，我们从 205 种物种的基因组重测序数据中组装了三个平行数据集，即单拷贝直系同源物（SCO）、基因组 SNP 和全质体。基于这些基因组规模的数据，我们提供了第一个亚洲松红梅族的良好分辨率的系统发育，确定了 34 个主要分支，74%的分支间关系通过 SCO 和基因组数据一致解决。同时，在 SCO 基因树以及使用不同树估计方法（连接/基于位点的合并方法/总结方法）或不同数据集（SCO/基因组/质体）重建的物种树中，检测到广泛的系统发育分歧。我们使用多种方法探索了分歧的来源，并发现观察到的亚洲松红梅族的分歧主要是由缺失数据的偏分布、无信息基因的随机噪声、不完全谱系分选以及杂交/基因渗入的组合引起的。对这些来源的探索可以使我们为未来的测试生成假设，这是理解亚洲松红梅族进化的第一步。我们还检测到一些传统用于分类的特征具有高度的同形性，这解释了当前混乱的属界限。本研究揭示的亚洲松红梅族的骨干系统发育为未来在属级别的分类修订提供了坚实的基础。
