Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes.
Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes.
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DOI：
10.3389/fpls.2021.767478
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发表时间：
2021
影响因子：
5.6
通讯作者：
Drew BT
中科院分区：
文献类型：
--
作者：
Rose JP;Kriebel R;Kahan L;DiNicola A;González-Gallegos JG;Celep F;Lemmon EM;Lemmon AR;Sytsma KJ;Drew BT
下一代测序技术促进了新的基因组学方法，以帮助澄清以前棘手的关系，同时突出了基因组内和基因组之间普遍存在的不一致性，这可能会使明确的分类结论复杂化。鼠尾草属，有1,000种，占薄荷科物种多样性的近15%，引起了跨学科生物学家的极大兴趣。尽管已经取得了很大的进展，在辨别放置鼠尾草唇形科，并通过质体，核核糖体和核单拷贝基因澄清其属下的关系，不完整的决议留下了开放的主要问题之间和亚属内的系统发育关系，以及在何种程度上的属下关系不同的基因组。我们扩大了以前发表的锚定杂交富集数据集的35个样本的鼠尾草179终端。我们还从脱靶读段重建了这些样品的几乎完整的塑性体。我们用这些数据来研究核位点之间的一致性和不一致性，核和质体基因组之间的详细说明，阐明了广泛的规模和物种水平的关系内鼠尾草。我们发现，尽管广泛的基因树不一致，使用级联，合并和基于网络的方法重建的核同源性恢复一个共同的骨干拓扑结构。此外，所有的亚属，除了Audibertia，强烈支持在所有的分析单系。质体谱系在很大程度上是解析的，并且与核骨架一致。然而，多项分析表明，不完整的谱系排序并不能完全解释基因树的不一致性。相反，水平基因流在鼠尾草的深层和更近的历史中都很重要。我们的研究结果提供了一个强大的物种树鼠尾草跨越系统发育尺度和基因组。未来的比较分析属将需要考虑的影响，杂交/渐渗和不完整的谱系排序的拓扑结构和分歧的时间估计。
Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.
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影响因子：
2.8
作者：
Jenks, Aaron A.;Walker, Jay B.;Kim, Seung-Chul
通讯作者：
Kim, Seung-Chul
影响因子：
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作者：
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Freudenstein, John V.
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Hejase HA;Liu KJ
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Fragoso-Martinez, Itzi;Salazar, Gerardo A.;Granados Mendoza, Carolina
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