Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
复制标题
DOI：
10.1016/j.ympev.2018.07.014
复制
发表时间：
2018-12-01
影响因子：
4.1
通讯作者：
Gravendeel, Barbara
中科院分区：
文献类型：
--
作者：
Bogarin, Diego;Perez-Escobar, Oscar Alejandro;Gravendeel, Barbara
在物种复合体和谱系的系统发育关系来自快速多样化往往是具有挑战性的，以解决使用形态或标准的DNA条形码标记。来自新热带区云雾林的超多样性属Lepanthes包括超过1200种和许多最近的爆炸性多样化，导致支持节点和跨分支的形态趋同。在这里，我们评估了446个核-质体-线粒体标记物的性能，这些标记物来自锚定杂交富集方法（AHE），再加上基于聚结和基于物种网络的推断，以解决系统发育关系并提高Lepanthes horrida种群中的物种识别。除了使用拟南芥特异性探针来提高富集效率之外，我们还通过将标准被子植物靶标延伸到相邻外显子来提高基因树分辨率。我们发现高拓扑不一致的个别基因树，表明杂交/多倍体可能促进物种形成的谱系通过形成新的杂交类群。此外，我们从这些基因组中确定了10个具有最高系统发育信息价值的基因座。大多数以前的系统发育采样在Pleurothallidinae依赖于两个区域（ITS和matK），因此，其他标记，如这里所示的评价可能是有用的，在未来的系统发育研究中的兰科。基于聚类分析的种树估计方法解决了L. horrida种组。系统发育估计的分辨率随着扩展的锚靶标的加入而提高。这种方法产生了更长的位点，具有更高的区分能力。这些分析还揭示了两个未描述的物种，L。amicitiae和L. genetoapophantica，这里正式描述，这也是由形态学支持。我们的研究表明，结合基因组证据的效用，解开系统发育关系在很浅的层次上的生命树，并在分支显示收敛性状进化。有了一个完全解决的同源性，是否有可能将这些兰花谱系中平行或趋同进化的性状（如花朵的颜色和大小）与诊断性状（如花瓣和唇的形状和方向）分开。
Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip.