Jin Ze-Tao, Lin Xiao-Hua, Ma Dai-Kun, Xie Si-Yu, Huang Jia-Xin, Ren Chen, Zhao Liang, Duan Lei, Xu Chao, Hodel Richard G J, Wu Jun, Liu Bin-Bin
College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China.
Key Laboratory of Systematic and Evolutionary Botany/State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
Mol Ecol Resour. 2025 Aug 12:e70029. doi: 10.1111/1755-0998.70029.
The traditional Tree of Life (ToL) model is increasingly challenged by the Web of Life (WoL) paradigm, which offers a more accurate depiction of organismal phylogeny, particularly in light of the incongruences often observed between gene and species trees. However, the absence of a standardised method for resolving evolutionary mechanisms - such as Incomplete Lineage Sorting (ILS), hybridisation, introgression, polyploidisation, and whole-genome duplication - remains a significant obstacle in defining the WoL. Characterised by extensive hybridisation events, the pear genus Pyrus provides an ideal model for exploring these complexities. In this study, we present a Step-by-Step Exclusion (SSE) approach for investigating the evolutionary pathways of Pyrus, based on Whole Genome Sequencing (WGS) and Deep Genome Skimming (DGS) data, and our results demonstrate that: (1) ILS, rather than polyploidisation, plays a dominant role in the origination of Pyrus; (2) the two subgenera of Pyrus followed independent evolutionary paths, influenced by geographical barriers formed through the uplift of the Tibetan Plateau and increased aridity in Central Asia; (3) both ILS and hybridisation have driven the diversification of subg. Pashia, while hybridisation alone has shaped the reticulate evolution of subg. Pyrus; (4) the establishment of the Silk Road during the Han Dynasty facilitated genetic exchange between subg. Pyrus and subg. Pashia. The SSE approach offers a versatile framework for studying the evolutionary mechanisms underlying the WoL paradigm.
传统的生命之树（ToL）模型正日益受到生命之网（WoL）范式的挑战，后者能更准确地描绘生物系统发育，特别是考虑到基因树和物种树之间经常观察到的不一致性。然而，缺乏一种标准化的方法来解析进化机制，如不完全谱系分选（ILS）、杂交、基因渗入、多倍体化和全基因组复制，仍然是定义生命之网的一个重大障碍。梨属（Pyrus）以广泛的杂交事件为特征，为探索这些复杂性提供了一个理想的模型。在本研究中，我们基于全基因组测序（WGS）和深度基因组重测序（DGS）数据，提出了一种逐步排除（SSE）方法来研究梨属的进化途径，我们的结果表明：（1）ILS而非多倍体化在梨属的起源中起主导作用；（2）梨属的两个亚属遵循独立的进化路径，受到青藏高原隆升和中亚干旱加剧形成的地理障碍的影响；（3）ILS和杂交都推动了梨亚属（Pashia）的多样化，而仅杂交塑造了梨亚属（Pyrus）的网状进化；（4）汉代丝绸之路的建立促进了梨亚属和梨亚属之间的基因交流。SSE方法为研究生命之网范式背后的进化机制提供了一个通用框架。
