Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)
Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)
复制标题
DOI：
10.1111/syen.12540
复制
发表时间：
2022-02-18
影响因子：
4.8
通讯作者：
Dmitriev, Dmitry A.
中科院分区：
文献类型：
--
作者：
Cao, Yanghui;Dietrich, Christopher H.;Dmitriev, Dmitry A.
我们分析了一个包含730个末端分类群和> 160，000个核苷酸位置的基因组数据集，该数据集是使用三角头叶蝉和外群样本的基因组DNA的锚定杂交富集获得的。连接的核苷酸和氨基酸序列的最大似然分析，以及结合基因树分析，得到了很好的解决系统发育的估计是高度一致的最大支持的分支。一些拓扑不一致发生在不同的分析，主要分布在很短的分支中间水平的进化树，有关的一些部落和多部落血统之间的关系限制在特定的大陆。合并基因树分析显示，在这些节点广泛的基因树冲突，这表明某些关系可能仍然难以解决一致，即使与基因组规模的数据集和密集的分类单元采样。祖先的特征状态重建的摄食偏好表明，草专业化已获得三次或更少的时间，在一些高度多样化，但相对衍生的谱系。分子分歧的时间估计表明，最早的分歧在亚科发生在白垩纪，但大多数现代部落没有出现，直到之后的白垩纪-古近纪边界和草专业谱系一般多样化和传播的同时，草原正在成为全球广泛。这些分析还显示了高水平的全球性的地理结构，主要是树栖三角脑动物的几个大的谱系局限于特定的地区或大陆和大陆之间的长距离传播主要发生在草专业谱系。结果代表了一个重大的改进，比以前的分析，这是基于152个或更少的分类群和数据的形态和部分序列的两个基因。
We analysed a phylogenomic dataset comprising 730 terminal taxa and >160,000 nucleotide positions obtained using anchored hybrid enrichment of genomic DNA for a sample of deltocephaline leafhoppers and outgroups. Maximum likelihood analyses of concatenated nucleotide and amino acid sequences as well as coalescent gene tree analysis, yielded well-resolved phylogenetic estimates that were highly congruent with most branches receiving maximum support. Some topological incongruence occurs among the trees resulting from different analyses, mainly distributed among very short branches at intermediate levels in the phylogeny, pertaining to relationships among some tribes and multi-tribe lineages restricted to particular continents. Coalescent gene tree analysis revealed extensive gene tree conflict at these nodes, suggesting that certain relationships may remain difficult to resolve consistently even with genome-scale datasets and dense taxon sampling. Ancestral character state reconstruction of feeding preference indicates that grass specialization has been acquired three or fewer times in some highly diverse but relatively derived lineages. Molecular divergence time estimation suggests that the earliest divergences in the subfamily occurred during the Cretaceous but that most modern tribes did not appear until after the Cretaceous-Palaeogene boundary and that grass specialist lineages generally diversified and spread at the same time as grasslands were becoming widespread globally. These analyses also show a high level of global biogeographic structure, with several large lineages of primarily arboreal deltocephalines restricted to particular regions or continents and long-distance dispersal among continents occurring primarily among grass-specialist lineages. The results represent a major improvement over previous analyses of this diverse subfamily, which were based on 152 or fewer taxa and data from morphology and partial sequences of two genes.