Field Museum, Science and Education, Chicago, 60605, USA.
University of Illinois at Chicago, Biological Sciences, Chicago, 60607, USA.
Sci Rep. 2019 Jun 20;9(1):8968. doi: 10.1038/s41598-019-45455-x.
In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
在新一代测序时代，可用于系统发育分析的基因座数量呈数量级增加。但尽管数据量有了显著增加，一些基因组学研究仍揭示了猖獗的基因树分歧，这种分歧可能是由许多历史过程引起的，如快速多样化、基因复制或网状进化。我们使用目标富集方法对 13 个地衣形成家族 Lobariaceae 属的 400 个单拷贝核基因进行采样，以解决数据类型（核苷酸和氨基酸）和系统发育重建方法（连接和种系树方法）的影响。此外，我们检查了数据集，以寻找快速多样化和网状进化等历史过程的证据。我们发现，与序列数据类型（核苷酸与氨基酸序列）和不同的系统发育重建方法（种系树与连接）相关的不一致性。由此产生的系统发育树为快速和网状进化提供了证据，这是基于系统发育树主干中极短的分支。观察到的快速和网状多样化可能解释了基因树之间的冲突以及解决进化关系的挑战。根据分化时间，主干的多样化发生在白垩纪-古近纪（K-Pg）边界（6500 万年前）附近，这与生命之树中的其他快速多样化相一致。尽管 Lobariaceae 家族内的一些系统发育关系仍然支持率较低，即使我们使用多达 376 个基因的强大基因组数据集，我们对目标捕获数据的使用也允许对系统发育和系统发育不一致的机制进行新的探索。
