Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding o...

研究背景：随着研究者尝试借助日益增长的数据量解决疑难演化节点，利用转录组与基因组数据集开展系统发育重建的应用愈发普遍。此类数据集规模与复杂度均较高，会给后续分析引入显著的系统发育噪声与系统发育冲突。冲突的来源可能包括杂交、不完全谱系分选（incomplete lineage sorting, ILS）或水平基因转移，且这些来源在整个系统发育树中存在差异。针对系统发育分析，学界目前针对这类噪声与冲突主要采取以下三类处理策略：一是将基因区域分箱为子集，以分离出一致的系统发育信号；二是采用基因树方法进行重建，该类方法假设冲突仅由不完全谱系分选（ILS）导致；三是采用串联拼接法，该类方法假设噪声是冲突的主要来源。本文所呈现的研究结果表明，对单个同源基因区域开展分析，能够极大地提升我们对...