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. 2025 Aug 12:e70029.
doi: 10.1111/1755-0998.70029. Online ahead of print.

Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species

Ze-Tao Jin  1   2   3 , Xiao-Hua Lin  2   3   4 , Dai-Kun Ma  2   3   5 , Si-Yu Xie  2   3   4 , Jia-Xin Huang  2   3   6 , Chen Ren  2   7 , Liang Zhao  4 , Lei Duan  2   7 , Chao Xu  2   3 , Richard G J Hodel  8 , Jun Wu  1 , Bin-Bin Liu  2   3
Affiliations

Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species

Ze-Tao Jin et al. Mol Ecol Resour. .

Abstract

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.

Keywords: Pyrus; Rosaceae; diversification; reticulation; step‐by‐step exclusion approach.

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