基因组规模数据的越来越多的使用极大地促进了系统发育分析,有助于解剖形成系统发育不一致的潜在进化机制,如不完全谱系分类(ILS)和杂交。Lilieae,百合科的杰出成员,包括四个属和大约260种,占百合科所有物种的43%。它们具有很高的观赏性,药用和食用价值。然而,没有研究探索该部落内各种基因组尺度数据在系统发育分析中的有效性,也没有研究其系统发育不一致的潜在进化机制。这里,转录组,血管精子353,质体和线粒体数据,从50到93个Lilieae样本中收集,涵盖所有四个公认的属。创建了多个数据集,并将其用于基于级联和基于合并的方法的系统发育分析。计算了不同数据集的进化率,并估计了发散时间。各种方法,包括聚结模拟,四方采样(QS),协调系数(gCF和sCF)的计算,以及MSCquartets和网状网络推理,进行了推断系统发育不一致,并使用减少的33分类单元数据集分析其潜在机制。尽管基因树之间存在广泛的系统发育不一致,与线粒体数据相比,从核和质体数据推断了稳健的系统发育,在线粒体基因中检测到的同义替换比核和质体基因低。在百列的系统发育中检测到显著的ILS,有明确的网状进化证据。发散时间估计表明,百列中的大多数谱系在狭窄的时间范围内(范围从5.0Ma到10.0Ma)发散,与快速辐射演化的概念一致。我们的结果表明,整合转录组和质体数据可以作为Lilieae系统进化推断和进化分析的成本有效和有效的工具,Angiosperms353数据也是一个有利的选择。线粒体数据由于其更强的保守性和更低的同义替代率,更适合在更高的分类学水平下进行系统发育分析。在百合中检测到的显着系统发育不一致是由不完整的谱系分类(ILS)和网状进化引起的,杂交和“幽灵渗入”可能在百列物种的进化中普遍存在。我们的发现为百列的系统发育提供了新的见解,加强我们对这个部落物种进化的理解。
The increasing use of genome-scale data has significantly facilitated phylogenetic analyses, contributing to the dissection of the underlying evolutionary mechanisms that shape phylogenetic incongruences, such as incomplete lineage sorting (ILS) and hybridization. Lilieae, a prominent member of the Liliaceae family, comprises four genera and approximately 260 species, representing 43% of all species within Liliaceae. They possess high ornamental, medicinal and edible values. Yet, no study has explored the validity of various genome-scale data in phylogenetic analyses within this tribe, nor have potential evolutionary mechanisms underlying its phylogenetic incongruences been investigated. Here, transcriptome, Angiosperms353, plastid and mitochondrial data, were collected from 50 to 93 samples of Lilieae, covering all four recognized genera. Multiple datasets were created and used for phylogenetic analyses based on concatenated and coalescent-based methods. Evolutionary rates of different datasets were calculated, and divergence times were estimated. Various approaches, including coalescence simulation, Quartet Sampling (QS), calculation of concordance factors (gCF and sCF), as well as MSCquartets and reticulate network inference, were carried out to infer the phylogenetic discordances and analyze their underlying mechanisms using a reduced 33-taxon dataset. Despite extensive phylogenetic discordances among gene trees, robust phylogenies were inferred from nuclear and plastid data compared to mitochondrial data, with lower synonymous substitution detected in mitochondrial genes than in nuclear and plastid genes. Significant ILS was detected across the phylogeny of Lilieae, with clear evidence of reticulate evolution identified. Divergence time estimation indicated that most of lineages in Lilieae diverged during a narrow time frame (ranging from 5.0 Ma to 10.0 Ma), consistent with the notion of rapid radiation evolution. Our results suggest that integrating transcriptomic and plastid data can serve as cost-effective and efficient tools for phylogenetic inference and evolutionary analysis within Lilieae, and Angiosperms353 data is also a favorable choice. Mitochondrial data are more suitable for phylogenetic analyses at higher taxonomic levels due to their stronger conservation and lower synonymous substitution rates. Significant phylogenetic incongruences detected in Lilieae were caused by both incomplete lineage sorting (ILS) and reticulate evolution, with hybridization and \"ghost introgression\" likely prevalent in the evolution of Lilieae species. Our findings provide new insights into the phylogeny of Lilieae, enhancing our understanding of the evolution of species in this tribe.