Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.
PLoS Biol. 2024 May 24;22(5):e3002633. doi: 10.1371/journal.pbio.3002633. eCollection 2024 May.
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons evoke evolutionary histories, as depicted by phylogenetic trees, that define relationships between species, genes, and cells. This Essay considers each of these in turn, laying out challenges and solutions derived from a phylogenetic comparative approach and relating these solutions to previously proposed methods for the pairwise alignment of cellular dimensional maps. This Essay contends that species trees, gene trees, cell phylogenies, and cell lineages can all be reconciled as descriptions of the same concept-the tree of cellular life. By integrating phylogenetic approaches into scRNA-seq analyses, challenges for building informed comparisons across species can be overcome, and hypotheses about gene and cell evolution can be robustly tested.
单细胞 RNA 测序 (scRNA-seq) 数据在物种间的比较可以揭示细胞基因表达与细胞功能、特征和表型进化之间的联系。这些比较唤起了进化历史，正如系统发育树所描绘的那样，这些进化历史定义了物种、基因和细胞之间的关系。本文依次考虑了这三个方面，阐述了从系统发育比较方法中得出的挑战和解决方案，并将这些解决方案与之前提出的细胞维度图谱两两比对的方法联系起来。本文认为，物种树、基因树、细胞系统发育树和细胞谱系都可以被协调为对同一概念——细胞生命之树——的描述。通过将系统发育方法整合到 scRNA-seq 分析中，可以克服在物种间进行有意义比较的挑战，并可以稳健地检验关于基因和细胞进化的假设。
